From a2324a6dcbb04f847fdffb595b9cc1fda4062c8f Mon Sep 17 00:00:00 2001 From: bvarner-ebi <95643797+bvarner-ebi@users.noreply.github.com> Date: Thu, 21 Sep 2023 10:14:17 +0100 Subject: [PATCH] CL release 2023-09-21 --- cl-base.owl | 1281 +- cl.obo | 1182 +- patterns/definitions.owl | 4 +- src/ontology/diffs/cl-diff.md | 14322 +++------------- .../reports/cl-edit.owl-obo-report.tsv | 85 +- .../subsets/blood_and_immune_upper_slim.json | 822 +- .../subsets/blood_and_immune_upper_slim.obo | 177 +- .../subsets/blood_and_immune_upper_slim.owl | 1034 +- .../subsets/blood_and_immune_upper_slim.tsv | 806 +- src/ontology/subsets/eye_upper_slim.json | 927 +- src/ontology/subsets/eye_upper_slim.obo | 209 +- src/ontology/subsets/eye_upper_slim.owl | 1654 +- src/ontology/subsets/eye_upper_slim.tsv | 660 +- .../general_cell_types_upper_slim.json | 879 +- .../subsets/general_cell_types_upper_slim.obo | 193 +- .../subsets/general_cell_types_upper_slim.owl | 1061 +- .../subsets/general_cell_types_upper_slim.tsv | 574 +- subsets/blood_and_immune_upper_slim.json | 822 +- subsets/blood_and_immune_upper_slim.obo | 177 +- subsets/blood_and_immune_upper_slim.owl | 1034 +- subsets/blood_and_immune_upper_slim.tsv | 806 +- subsets/eye_upper_slim.json | 927 +- subsets/eye_upper_slim.obo | 209 +- subsets/eye_upper_slim.owl | 1654 +- subsets/eye_upper_slim.tsv | 660 +- subsets/general_cell_types_upper_slim.json | 879 +- subsets/general_cell_types_upper_slim.obo | 193 +- subsets/general_cell_types_upper_slim.owl | 1061 +- subsets/general_cell_types_upper_slim.tsv | 574 +- 29 files changed, 14377 insertions(+), 20489 deletions(-) diff --git a/cl-base.owl b/cl-base.owl index cc6c6a1d8..00ed838d4 100644 --- a/cl-base.owl +++ b/cl-base.owl @@ -17,7 +17,7 @@ xmlns:ubprop="http://purl.obolibrary.org/obo/ubprop#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + An ontology of cell types. Cell Ontology @@ -33,7 +33,7 @@ See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, University at Buffalo. - 2023-08-24 + 2023-09-21 @@ -852,18 +852,19 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). + OBSOLETE. A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). + CARO:0000013 cell in vivo - To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). - native cell + https://github.com/obophenotype/cell-ontology/issues/2124 + obsolete native cell + true - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). + OBSOLETE. A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). CARO:mah @@ -1069,7 +1070,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A stem cell that is the precursor of gametes. FBbt:00004861 germline stem cell @@ -1081,12 +1081,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u true - - - - - true - @@ -1162,8 +1156,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - @@ -1179,12 +1171,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u FBbt:00004936 spermatocyte - - - - - true - @@ -1221,8 +1207,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - @@ -1239,12 +1223,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u nematoblast spermatid - - - - - true - @@ -1258,7 +1236,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -1311,7 +1288,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - An euploid male germ cell of an early stage of spermatogenesis. BTO:0000958 CALOHA:TS-2193 @@ -1467,7 +1443,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -1497,7 +1472,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -1544,7 +1518,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -1665,7 +1638,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -1731,7 +1703,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - An exocrine cell characterized by loss of part of the cytoplasm during the process of secretion. The secreted substance is accumulated at the apical end and is either budded off through the plasma membrane producing secreted vesicles or dissolved in the cytoplasm that is lost during secretion. @@ -1754,7 +1725,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -1762,7 +1733,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -1801,7 +1771,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -2010,14 +1980,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + - A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring. @@ -2434,7 +2403,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -2710,7 +2679,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -2736,7 +2705,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair. BTO:0000222 @@ -3021,7 +2989,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -3075,7 +3043,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -3150,7 +3118,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - An epithelial cell that is part of a duct. duct epithelial cell @@ -3197,7 +3164,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -3244,7 +3210,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - barrier epithelial cell @@ -3272,7 +3237,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube. @@ -3330,7 +3294,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - peridermal cell @@ -3340,7 +3303,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -3358,7 +3320,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -3465,8 +3427,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - @@ -3479,12 +3439,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u pancreatic epithelial cell epithelial cell of pancreas - - - - - true - @@ -4152,9 +4106,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells. neuroepithelial cell BTO:0004301 @@ -4814,7 +4766,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u macroglia doi:10.1152/physrev.2001.81.2.871 - + @@ -5008,7 +4960,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u microglia doi:10.1038/s41598-020-66092-9 - + @@ -5053,7 +5005,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -5180,20 +5131,20 @@ Covers cells actively being cultured or stored in a quiescent state for future u mesenchymal progenitor cells MESH:D044982 - + mesenchymal stromal cells - + stem cells, mesenchymal MESH:D044982 - + @@ -5562,9 +5513,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance. BTO:0000847 @@ -5577,12 +5525,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u melanocyte - - - - - true - @@ -5596,7 +5538,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - pigment cell visual pigment cell @@ -5608,7 +5549,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -5635,7 +5575,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -5675,7 +5615,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct. FMA:16014 @@ -5921,7 +5860,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -5939,7 +5878,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -6411,6 +6349,7 @@ The modern definition of neurosecretion has evolved to include the release of an BTO:0003939 FMA:18688 + corpus luteum cell lutein cell luteal cell @@ -6421,6 +6360,12 @@ The modern definition of neurosecretion has evolved to include the release of an A progesterone secreting cell in the corpus luteum. The large luteal cells develop from the granulosa cells. The small luteal cells develop from the theca cells. MESH:D008184 + + + + corpus luteum cell + PMID:16790079 + @@ -6466,7 +6411,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -6568,7 +6512,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -6624,7 +6567,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + A cell whose primary function is to shorten. contractile cell @@ -6652,7 +6595,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -6681,8 +6623,6 @@ The modern definition of neurosecretion has evolved to include the release of an - - @@ -6721,8 +6661,6 @@ The modern definition of neurosecretion has evolved to include the release of an - - @@ -6756,7 +6694,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -6764,7 +6702,6 @@ The modern definition of neurosecretion has evolved to include the release of an - A somatic cell located in skeletal muscle. BTO:0004392 @@ -6994,7 +6931,6 @@ The modern definition of neurosecretion has evolved to include the release of an - A cell that is capable of detection of a stimulus involved in sensory perception. MESH:D011984 receptor cell @@ -7317,7 +7253,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + A cell whose function is determined by the generation or the reception of an electric signal. electrically active cell @@ -7333,7 +7269,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + A cell that takes up and metabolizes substances. @@ -7393,7 +7329,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + A cell whose primary function is to prevent the transport of stuff across compartments. barrier cell @@ -7497,7 +7433,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -7630,7 +7566,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -7659,7 +7595,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -7686,7 +7622,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -7705,7 +7641,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -7905,7 +7841,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -7916,7 +7852,6 @@ The modern definition of neurosecretion has evolved to include the release of an - Any cell capable of ingesting particulate matter via phagocytosis. BTO:0001044 FMA:83806 @@ -8168,7 +8103,6 @@ The modern definition of neurosecretion has evolved to include the release of an - A cell characteristically found lining hollow organs that are subject to great mechanical change due to contraction and distention; originally thought to represent a transition between stratified squamous and columnar epithelium. FMA:66778 @@ -8270,7 +8204,6 @@ The modern definition of neurosecretion has evolved to include the release of an - hatching gland cell @@ -8352,7 +8285,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -8382,7 +8315,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -8892,7 +8825,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism. structural cell @@ -9520,7 +9453,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + A cell that is specialised to accumulate a particular substance(s). stuff accumulating cell @@ -9570,7 +9503,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -9638,7 +9571,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -9675,7 +9608,6 @@ The modern definition of neurosecretion has evolved to include the release of an - A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors. mesenchyme condensation cell @@ -9828,7 +9760,6 @@ The modern definition of neurosecretion has evolved to include the release of an - pigment cell (sensu Nematoda and Protostomia) @@ -9905,7 +9836,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -9988,7 +9918,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -10022,7 +9951,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -10048,7 +9976,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -10056,7 +9984,6 @@ The modern definition of neurosecretion has evolved to include the release of an - extraembryonic cell @@ -10344,7 +10271,6 @@ The modern definition of neurosecretion has evolved to include the release of an - An epithelial cell of the integument (the outer layer of an organism). BTO:0001470 CALOHA:TS-0283 @@ -10464,7 +10390,6 @@ The modern definition of neurosecretion has evolved to include the release of an - glial cell (sensu Nematoda) sheath cell (sensu Nematoda) @@ -10653,7 +10578,6 @@ The modern definition of neurosecretion has evolved to include the release of an - The support cell that makes the thecogen dendritic cap - a cuticle-like matrix around the tip of the eo-dendrite and which encloses the soma of the eo-neuron. FBbt:00005173 fly sheath cell @@ -10684,7 +10608,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -10730,7 +10653,6 @@ The modern definition of neurosecretion has evolved to include the release of an - ligament cell @@ -11122,7 +11044,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -11163,7 +11084,6 @@ The modern definition of neurosecretion has evolved to include the release of an - BTO:0001277 CALOHA:TS-0949 male gamete @@ -11208,7 +11128,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -11234,15 +11153,27 @@ The modern definition of neurosecretion has evolved to include the release of an - - A cell whose nucleus, or nuclei, each contain more than two haploid genomes. + + + + + + + + + + + + A cell that contains more than two haploid sets of chromosomes. polyploid cell - A cell whose nucleus, or nuclei, each contain more than two haploid genomes. + A cell that contains more than two haploid sets of chromosomes. FB:ma + PMID:32646579 + https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy @@ -11253,7 +11184,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -11299,7 +11230,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + A cell whose nucleus has two haploid genomes. FMA:72300 diploid cell @@ -11335,7 +11266,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -11379,7 +11309,6 @@ The modern definition of neurosecretion has evolved to include the release of an - syncytial epithelial cell @@ -11390,7 +11319,6 @@ The modern definition of neurosecretion has evolved to include the release of an - A free floating cell, including amebocytes and eleocytes, in the coelom of certain animals, especially annelids. BTO:0002856 WBbt:0005751 @@ -11409,7 +11337,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + A cell whose primary function is to cause growth by stimulating cell division in its immediate cellular environment. mitogenic signaling cell @@ -11426,7 +11354,6 @@ The modern definition of neurosecretion has evolved to include the release of an - tip cell @@ -11561,7 +11488,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -11814,7 +11740,6 @@ The modern definition of neurosecretion has evolved to include the release of an - A cell with extensive dendritic processes found in the B cell areas (primary follicles and germinal centers) of lymphoid tissue. They are unrelated to the dendritic cell associated with T cells. Follicular dendritic cells have Fc receptors and C3b receptors, but unlike other dendritic cells, they do not process or present antigen in a way that allows recognition by T cells. Instead, they hold antigen in the form of immune complexes on their surfaces for long periods and can present antigen to B cells during an immune response. BTO:0004267 @@ -11887,7 +11812,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + apoptosis fated cell @@ -11948,7 +11873,6 @@ The modern definition of neurosecretion has evolved to include the release of an CALOHA:TS-1119 FMA:83434 white adipose cell - white fat cell white adipocyte white fat cell @@ -12092,7 +12016,6 @@ The modern definition of neurosecretion has evolved to include the release of an - thyroid hormone secreting cell @@ -12329,7 +12252,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -12409,7 +12331,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -12512,7 +12433,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -12566,7 +12486,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + A cell whose primary function is to protect the organism. defensive cell @@ -12919,7 +12839,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -13201,7 +13120,6 @@ The modern definition of neurosecretion has evolved to include the release of an - An epithelial somatic cell associated with a maturing oocyte. follicular epithelial cell @@ -13457,7 +13375,6 @@ The modern definition of neurosecretion has evolved to include the release of an - A paracrine cell is a secretory cell that secretes an agonist into intercellular spaces in which it diffuses to a target cell other than that which produced it. paracrine cell @@ -13526,20 +13443,12 @@ The modern definition of neurosecretion has evolved to include the release of an - - A precursor cell destined to differentiate into smooth muscle myocytes. FMA:84798 myoblast, smooth muscle satellite cell smooth muscle myoblast - - - - - true - @@ -13570,8 +13479,6 @@ The modern definition of neurosecretion has evolved to include the release of an - - @@ -13583,12 +13490,6 @@ The modern definition of neurosecretion has evolved to include the release of an skeletal myoblast skeletal muscle myoblast - - - - - true - @@ -13675,7 +13576,6 @@ The modern definition of neurosecretion has evolved to include the release of an - A phagocyte from organisms in the Nematoda or Protostomia clades. phagocyte (sensu Nematoda and Protostomia) @@ -13692,7 +13592,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + MESH:D011387 prokaryotic cell @@ -13706,7 +13606,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -13715,7 +13615,6 @@ The modern definition of neurosecretion has evolved to include the release of an - fungal cell @@ -13895,18 +13794,18 @@ The modern definition of neurosecretion has evolved to include the release of an - + A neuron that develops during the early segmentation stages in teleosts, before the neural tube is formed. primary neuron (sensu Teleostei) - + - + https://github.com/obophenotype/cell-ontology/pull/1950 @@ -13989,18 +13888,18 @@ The modern definition of neurosecretion has evolved to include the release of an - + A neuron of teleosts that develops later than a primary neuron, typically during the larval stages. secondary neuron (sensu Teleostei) - + - + https://github.com/obophenotype/cell-ontology/pull/1950 @@ -14127,8 +14026,6 @@ The modern definition of neurosecretion has evolved to include the release of an - - @@ -14513,28 +14410,13 @@ The modern definition of neurosecretion has evolved to include the release of an - - - - - - - - - - - - - - - - - - - A native cell that is part of some Metazoa. + OBSOLETE. A native cell that is part of some Metazoa. + metazoan cell - animal cell + https://github.com/obophenotype/cell-ontology/issues/2124 + obsolete animal cell + true https://www.swissbiopics.org/api/image/Animal_cells.svg @@ -15417,8 +15299,8 @@ The modern definition of neurosecretion has evolved to include the release of an ACs doi:10.1038/s41598-020-66092-9 + - @@ -15560,7 +15442,6 @@ The modern definition of neurosecretion has evolved to include the release of an - A cell found in fat bodies whose primary function is intermediary metabolism. fat body cell @@ -15784,7 +15665,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -15851,7 +15731,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -15885,7 +15764,6 @@ The modern definition of neurosecretion has evolved to include the release of an - An epithelial cell of the cornea. BTO:0004298 @@ -16668,7 +16546,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -16801,7 +16678,6 @@ The modern definition of neurosecretion has evolved to include the release of an NIFSTD:sao862606388 projection neuron pyramidal cell - pyramidal neuron pyramidal neuron @@ -17555,7 +17431,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -17832,7 +17707,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + A cell involved in transporting nutrients, minerals, water, gases and other chemicals between cells for a variety of purposes including conveying nutrition to other tissues, removing waste products from the tissues, conveying gases for respiration, distributing heat and repelling invasion of foreign substances. transporting cell @@ -17848,7 +17723,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -17887,7 +17762,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + A cell whose primary function is to support other cell types. BTO:0002315 supportive cell @@ -17906,7 +17781,6 @@ The modern definition of neurosecretion has evolved to include the release of an - Cells forming a framework supporting the organ of Corti. Specific cells are those of Claudius, Deiters and Hensen. labyrinth supporting cell @@ -18197,7 +18071,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -18758,20 +18631,12 @@ The modern definition of neurosecretion has evolved to include the release of an - - A diploid cell that has derived from a spermatogonium and can subsequently begin meiosis and divide into two haploid secondary spermatocytes. BTO:0001115 CALOHA:TS-2194 FMA:72292 primary spermatocyte - - - - - true - @@ -18800,8 +18665,6 @@ The modern definition of neurosecretion has evolved to include the release of an - - @@ -18815,12 +18678,6 @@ The modern definition of neurosecretion has evolved to include the release of an FBbt:00004941 secondary spermatocyte - - - - - true - @@ -18836,7 +18693,6 @@ The modern definition of neurosecretion has evolved to include the release of an - An epithelial cell that secretes cuticle. cuticle secreting cell @@ -18886,7 +18742,6 @@ The modern definition of neurosecretion has evolved to include the release of an - distal tip cell (sensu Nematoda) @@ -18939,7 +18794,6 @@ The modern definition of neurosecretion has evolved to include the release of an - window cell fenestrated cell @@ -19043,7 +18897,6 @@ The modern definition of neurosecretion has evolved to include the release of an - A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells. FMA:70567 gonocyte @@ -19178,7 +19031,6 @@ The modern definition of neurosecretion has evolved to include the release of an - BTO:0001033 cap cell @@ -19188,7 +19040,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -19256,8 +19108,6 @@ The modern definition of neurosecretion has evolved to include the release of an - - @@ -19307,7 +19157,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -19358,7 +19207,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -19464,7 +19312,6 @@ radial glial cells acting as neural progenitors throughout life. - A cell with both myofibrils and secretory granules. myoendocrine cell @@ -19742,7 +19589,6 @@ radial glial cells acting as neural progenitors throughout life. - Supports paraganglial type 1 cell. paraganglia type 2 cell @@ -20078,7 +19924,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -20111,7 +19956,6 @@ radial glial cells acting as neural progenitors throughout life. - posterior cone cell (sensu Endopterygota) @@ -20121,7 +19965,6 @@ radial glial cells acting as neural progenitors throughout life. - anterior cone cell (sensu Endopterygota) @@ -20131,7 +19974,6 @@ radial glial cells acting as neural progenitors throughout life. - equatorial cone cell (sensu Endopterygota) @@ -20167,20 +20009,12 @@ radial glial cells acting as neural progenitors throughout life. - - A stem cell that can give rise to cell types of the body other than those of the germ-line. CALOHA:TS-2086 FMA:63368 MESH:D053687 somatic stem cell - - - - - true - @@ -20214,7 +20048,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -20222,7 +20056,6 @@ radial glial cells acting as neural progenitors throughout life. - nitrogen fixing cell @@ -20283,7 +20116,6 @@ radial glial cells acting as neural progenitors throughout life. - A cell at the front of a migrating epithelial sheet. leading edge cell @@ -20310,18 +20142,11 @@ radial glial cells acting as neural progenitors throughout life. - A cell of a layer of transitional epithelium in the wall of the proximal urethra, bladder, ureter or renal pelvis, external to the lamina propria. FMA:84127 urinary tract transitional epithelial cell urothelial cell - - - - - true - @@ -20337,7 +20162,6 @@ radial glial cells acting as neural progenitors throughout life. - amoeboid cell @@ -20547,8 +20371,8 @@ radial glial cells acting as neural progenitors throughout life. RGCs doi:10.1038/s41598-020-66092-9 + - @@ -20670,8 +20494,8 @@ radial glial cells acting as neural progenitors throughout life. HCs doi:10.1038/s41598-020-66092-9 + - @@ -20748,7 +20572,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -20832,16 +20655,16 @@ radial glial cells acting as neural progenitors throughout life. BCs doi:10.1038/s41598-020-66092-9 + - BPs GSE137537 + - @@ -20985,7 +20808,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -21003,7 +20826,7 @@ radial glial cells acting as neural progenitors throughout life. FMB cone bipolar cell type 2 cone bipolar cell (sensu Mus) - + @@ -21023,7 +20846,7 @@ radial glial cells acting as neural progenitors throughout life. - + PMID:27565351 @@ -25768,7 +25591,6 @@ radial glial cells acting as neural progenitors throughout life. - An epithelial cell of the vestibular sensory organ that is characterized by intense enzymatic activities and numerous basal membrane infoldings. vestibular dark cell @@ -25883,7 +25705,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -26043,7 +25864,6 @@ radial glial cells acting as neural progenitors throughout life. - A skeletal muscle myoblast that differentiates into slow muscle fibers. slow muscle myoblast @@ -26070,7 +25890,6 @@ radial glial cells acting as neural progenitors throughout life. - A skeletal muscle myoblast that differentiates into fast muscle fibers. fast muscle myoblast @@ -27512,7 +27331,7 @@ radial glial cells acting as neural progenitors throughout life. - + A type of cell containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions. BTO:0003872 FMA:83586 @@ -32627,8 +32446,7 @@ radial glial cells acting as neural progenitors throughout life. - - + A cell of a hematopoietic lineage. BTO:0000574 CALOHA:TS-2017 @@ -35005,7 +34823,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -35013,7 +34831,6 @@ radial glial cells acting as neural progenitors throughout life. - A connective tissue cell found in bone. @@ -35022,12 +34839,6 @@ radial glial cells acting as neural progenitors throughout life. bone cell - - - - - true - @@ -37304,7 +37115,6 @@ radial glial cells acting as neural progenitors throughout life. - FBbt:00004230 visual pigment cell (sensu Nematoda and Protostomia) @@ -41318,7 +41128,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -41355,7 +41164,6 @@ radial glial cells acting as neural progenitors throughout life. - An epithelial cell derived from ectoderm. 2010-06-29T03:38:22Z @@ -41386,7 +41194,6 @@ radial glial cells acting as neural progenitors throughout life. - Epithelial cell derived from mesoderm or mesenchyme. 2010-06-29T03:49:14Z @@ -41859,7 +41666,6 @@ radial glial cells acting as neural progenitors throughout life. - One of two small cells formed by the first and second meiotic division of oocytes. 2010-08-23T09:49:53Z @@ -41884,7 +41690,6 @@ radial glial cells acting as neural progenitors throughout life. - A small cell formed by the first meiotic division of oocytes. @@ -41962,7 +41767,6 @@ radial glial cells acting as neural progenitors throughout life. - A small cell formed by the second meiotic division of oocytes. In mammals, the second polar body may fail to form unless the ovum has been penetrated by a sperm cell. @@ -44070,7 +43874,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -45243,7 +45046,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -45980,7 +45782,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -46487,7 +46288,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -46608,7 +46408,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -46682,7 +46482,6 @@ radial glial cells acting as neural progenitors throughout life. - A nonstratified squamous cell located in the ectocervix. 2010-09-08T09:12:23Z @@ -47920,7 +47719,6 @@ radial glial cells acting as neural progenitors throughout life. - A sperm bearing a Y chromosome. Chromosomal and genetic sex is established at fertilization in mammals and depends upon whether an X-bearing sperm or a Y-bearing sperm fertilizes the X-bearing ovum. 2010-09-13T11:35:24Z @@ -47943,7 +47741,6 @@ radial glial cells acting as neural progenitors throughout life. - A sperm bearing an X chromosome. Chromosomal and genetic sex is established at fertilization in mammals and depends upon whether an X-bearing sperm or a Y-bearing sperm fertilizes the X-bearing ovum. 2010-09-13T11:35:26Z @@ -48035,7 +47832,7 @@ radial glial cells acting as neural progenitors throughout life. 2010-09-13T02:37:23Z FMA:72209 - subcapsular thymic epithelial cell + subcapsular thymic epithelial cell type-1 epithelial cell of thymus @@ -48045,6 +47842,13 @@ radial glial cells acting as neural progenitors throughout life. GOC:tfm PMID:9264335 + + + + subcapsular thymic epithelial cell + PMID:18194204 + PMID:2694455 + @@ -48257,7 +48061,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -48272,14 +48076,14 @@ radial glial cells acting as neural progenitors throughout life. Type A cells are usually round and located in the upper part of the synovial intima. type A synovial cell - + - + PMID:10770586 @@ -48800,7 +48604,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -48808,8 +48612,6 @@ radial glial cells acting as neural progenitors throughout life. - - A cell that is part of the nervous system. 2010-09-15T01:34:57Z @@ -48833,7 +48635,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -48841,8 +48643,6 @@ radial glial cells acting as neural progenitors throughout life. - - A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. @@ -48853,12 +48653,6 @@ radial glial cells acting as neural progenitors throughout life. connective tissue cell - - - - - true - @@ -48872,7 +48666,7 @@ radial glial cells acting as neural progenitors throughout life. - + A cell of the embryo. 2010-09-15T03:39:21Z @@ -49089,7 +48883,6 @@ radial glial cells acting as neural progenitors throughout life. - An epithelial cell of the mammary gland. 2010-09-20T01:49:37Z @@ -49876,7 +49669,6 @@ radial glial cells acting as neural progenitors throughout life. - A progenitor cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1. @@ -50671,21 +50463,22 @@ radial glial cells acting as neural progenitors throughout life. - - - A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). + OBSOLETE. A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). + 2010-09-24T09:44:42Z BTO:0001268 FMA:72300 WBbt:0008378 - somatic cell + https://github.com/obophenotype/cell-ontology/issues/1150 + obsolete somatic cell + true - A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). + OBSOLETE. A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). GOC:tfm ISBN:0721662544 @@ -50790,7 +50583,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -54640,19 +54432,11 @@ radial glial cells acting as neural progenitors throughout life. - - A melanocyte that produces pigment in the dermis. 2010-12-03T03:17:05Z dermal melanocyte - - - - - true - @@ -54679,7 +54463,6 @@ radial glial cells acting as neural progenitors throughout life. - A melanocyte that produces pigment within the hair follicle. 2010-12-03T03:17:09Z @@ -54716,7 +54499,6 @@ radial glial cells acting as neural progenitors throughout life. - A melanocyte that produces pigment in the epithelium. 2010-12-03T03:17:14Z @@ -54753,20 +54535,12 @@ radial glial cells acting as neural progenitors throughout life. - - A melanocyte of the retina. This cell type is distinct from pigmented retinal epithelium. 2010-12-03T03:25:32Z retinal melanocyte - - - - - true - @@ -55027,7 +54801,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -55035,8 +54809,6 @@ radial glial cells acting as neural progenitors throughout life. - - A cell located in the heart, including both muscle and non muscle cells. 2010-12-07T09:37:22Z @@ -55048,12 +54820,6 @@ radial glial cells acting as neural progenitors throughout life. From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cardiocyte - - - - - true - @@ -56442,8 +56208,6 @@ radial glial cells acting as neural progenitors throughout life. - - @@ -56466,12 +56230,6 @@ radial glial cells acting as neural progenitors throughout life. uterine cervix epithelial cell epithelial cell of cervix - - - - - true - @@ -56561,8 +56319,6 @@ radial glial cells acting as neural progenitors throughout life. - - An epithelial cell that is part of the amnion. @@ -56571,18 +56327,6 @@ radial glial cells acting as neural progenitors throughout life. epithelial cell of amnion - - - - - true - - - - - - true - @@ -56868,7 +56612,6 @@ radial glial cells acting as neural progenitors throughout life. - An endothelial progenitor cell that participates in angiogenesis during development. 2011-02-28T04:20:39Z @@ -57291,7 +57034,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -57299,19 +57042,11 @@ radial glial cells acting as neural progenitors throughout life. - - An animal cell that is part of a hair follicle. 2011-03-01T04:11:01Z hair follicle cell - - - - - true - @@ -57336,19 +57071,12 @@ radial glial cells acting as neural progenitors throughout life. - An epithelial cell that resides in the inner root sheath of the hair follicle. 2011-03-01T04:27:51Z inner root sheath cell - - - - - true - @@ -57378,26 +57106,12 @@ radial glial cells acting as neural progenitors throughout life. - - An epithelial cell that is part of the outer root sheath. 2011-03-01T04:29:47Z outer root sheath cell - - - - - true - - - - - - true - @@ -57555,7 +57269,6 @@ radial glial cells acting as neural progenitors throughout life. - A melanocyte that appears darker due to content or amount of melanin granules. 2011-03-01T05:57:11Z @@ -57588,7 +57301,6 @@ radial glial cells acting as neural progenitors throughout life. - A melanocyte that appears lighter in color. 2011-03-01T05:58:23Z @@ -57932,7 +57644,6 @@ radial glial cells acting as neural progenitors throughout life. - An epithelial cell of the placenta. 2011-03-02T03:21:30Z @@ -57944,12 +57655,6 @@ radial glial cells acting as neural progenitors throughout life. true - - - - - true - @@ -58231,9 +57936,7 @@ radial glial cells acting as neural progenitors throughout life. - - @@ -58250,12 +57953,6 @@ radial glial cells acting as neural progenitors throughout life. retinal pigment epithelial cell - - - - - true - @@ -59409,24 +59106,10 @@ radial glial cells acting as neural progenitors throughout life. - - 2011-03-14T12:46:28Z gingival epithelial cell - - - - - true - - - - - - true - @@ -59831,25 +59514,11 @@ radial glial cells acting as neural progenitors throughout life. - - An epithelial cell of the anal column. 2011-07-08T12:11:38Z epithelial cell of anal column - - - - - true - - - - - - true - @@ -63246,7 +62915,8 @@ radial glial cells acting as neural progenitors throughout life. - + + @@ -63265,7 +62935,7 @@ radial glial cells acting as neural progenitors throughout life. - A bistratifed retinal amacrine cell with a small dendritic field, dendrite stratification in S1-S2, and a second dendrite stratification in S5. + A bistratifed retinal amacrine cell with a small dendritic field, dendrite stratification in S1-S2, and a second dendrite stratification in S5. This cell type releases the neurotransmitter glycine. https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315 @@ -63277,7 +62947,8 @@ radial glial cells acting as neural progenitors throughout life. - A bistratifed retinal amacrine cell with a small dendritic field, dendrite stratification in S1-S2, and a second dendrite stratification in S5. + A bistratifed retinal amacrine cell with a small dendritic field, dendrite stratification in S1-S2, and a second dendrite stratification in S5. This cell type releases the neurotransmitter glycine. + PMID:24246263 PMID:9620701 @@ -63286,7 +62957,7 @@ radial glial cells acting as neural progenitors throughout life. - + An amacrine cell with a small, asymteric dendritic field. https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315 @@ -63307,6 +62978,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -63319,7 +62991,7 @@ radial glial cells acting as neural progenitors throughout life. - A flag amacrine cell with post-synaptic terminals in S2 and S3. + A flag amacrine cell with post-synaptic terminals in S2 and S3. This cell type releases the neurotransmitter glycine. https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315 cell @@ -63329,7 +63001,8 @@ radial glial cells acting as neural progenitors throughout life. - A flag amacrine cell with post-synaptic terminals in S2 and S3. + A flag amacrine cell with post-synaptic terminals in S2 and S3. This cell type releases the neurotransmitter glycine. + PMID:24246263 PMID:9620701 @@ -63339,6 +63012,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -63357,7 +63031,7 @@ radial glial cells acting as neural progenitors throughout life. - A flag amacrine cell with post-synaptic terminals in S3, S4, and S5. + A flag amacrine cell with post-synaptic terminals in S3, S4, and S5. This cell type releases the neurotransmitter glycine. https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315 cell @@ -63367,7 +63041,8 @@ radial glial cells acting as neural progenitors throughout life. - A flag amacrine cell with post-synaptic terminals in S3, S4, and S5. + A flag amacrine cell with post-synaptic terminals in S3, S4, and S5. This cell type releases the neurotransmitter glycine. + PMID:24246263 PMID:9620701 @@ -63376,7 +63051,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -63420,7 +63095,8 @@ radial glial cells acting as neural progenitors throughout life. - + + @@ -63433,7 +63109,7 @@ radial glial cells acting as neural progenitors throughout life. - A broadly stratifying amacrine cell that has a small dendritic field and post-synaptic terminals in S2 and S3. + A broadly stratifying amacrine cell that has a small dendritic field and post-synaptic terminals in S2 and S3. This cell type releases the neurotransmitter glycine. https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315 cell @@ -63443,7 +63119,8 @@ radial glial cells acting as neural progenitors throughout life. - A broadly stratifying amacrine cell that has a small dendritic field and post-synaptic terminals in S2 and S3. + A broadly stratifying amacrine cell that has a small dendritic field and post-synaptic terminals in S2 and S3. This cell type releases the neurotransmitter glycine. + PMID:32032773 PMID:9620701 @@ -63452,7 +63129,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -63493,7 +63170,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -63532,7 +63209,8 @@ radial glial cells acting as neural progenitors throughout life. - + + @@ -63551,7 +63229,7 @@ radial glial cells acting as neural progenitors throughout life. - A bistratified amacrine cell with a small dendritic field. Flat bistratified amacrine cells have post-synaptic terminals both on the border of S1 and S2, and on the border of S3 and S4. + A bistratified amacrine cell with a small dendritic field. Flat bistratified amacrine cells have post-synaptic terminals both on the border of S1 and S2, and on the border of S3 and S4. This cell type releases the neurotransmitter glycine. https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315 cell @@ -63561,7 +63239,8 @@ radial glial cells acting as neural progenitors throughout life. - A bistratified amacrine cell with a small dendritic field. Flat bistratified amacrine cells have post-synaptic terminals both on the border of S1 and S2, and on the border of S3 and S4. + A bistratified amacrine cell with a small dendritic field. Flat bistratified amacrine cells have post-synaptic terminals both on the border of S1 and S2, and on the border of S3 and S4. This cell type releases the neurotransmitter glycine. + PMID:25630271 PMID:9620701 @@ -63570,7 +63249,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -63614,7 +63293,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -63652,7 +63331,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -63702,7 +63381,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -63741,13 +63420,20 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + - An amacrine cell with a flat dendritic arbor and a medium dendritic field. Starburst amacrine cells have post-synaptic terminals in S2. + An amacrine cell with a flat dendritic arbor and a medium dendritic field. Starburst amacrine cells have post-synaptic terminals in S2. This cell type releases the neurotransmitters gamma-aminobutyric acid (GABA) and acetylcholine. https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315 @@ -63759,7 +63445,8 @@ radial glial cells acting as neural progenitors throughout life. - An amacrine cell with a flat dendritic arbor and a medium dendritic field. Starburst amacrine cells have post-synaptic terminals in S2. + An amacrine cell with a flat dendritic arbor and a medium dendritic field. Starburst amacrine cells have post-synaptic terminals in S2. This cell type releases the neurotransmitters gamma-aminobutyric acid (GABA) and acetylcholine. + PMID:32032773 PMID:9620701 @@ -63768,7 +63455,8 @@ radial glial cells acting as neural progenitors throughout life. - + + @@ -63787,20 +63475,26 @@ radial glial cells acting as neural progenitors throughout life. - An amacrine cell with a medium dendritic field and post-synaptic terminals that stratify at S2, with a second stratification that occurs in S3 and S4. + An amacrine cell with a medium dendritic field and post-synaptic terminals that stratify at S2, with a second stratification that occurs in S3 and S4. This cell type releases the neurotransmitter glycine. https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315 cell CL:0004233 DAPI-3 amacrine cell + + + + An amacrine cell with a medium dendritic field and post-synaptic terminals that stratify at S2, with a second stratification that occurs in S3 and S4. This cell type releases the neurotransmitter glycine. + PMID:9194315 + - + @@ -63832,7 +63526,8 @@ radial glial cells acting as neural progenitors throughout life. - + + @@ -63845,7 +63540,7 @@ radial glial cells acting as neural progenitors throughout life. - An amacrine cell with a medium dendritic field and post-synaptic terminals in S2 and S3. + An amacrine cell with a medium dendritic field and post-synaptic terminals in S2 and S3. This cell type releases the neurotransmitter gamma-aminobutyric acid (GABA). https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315 cell @@ -63855,7 +63550,8 @@ radial glial cells acting as neural progenitors throughout life. - An amacrine cell with a medium dendritic field and post-synaptic terminals in S2 and S3. + An amacrine cell with a medium dendritic field and post-synaptic terminals in S2 and S3. This cell type releases the neurotransmitter gamma-aminobutyric acid (GABA). + PMID:32032773 PMID:9620701 @@ -63864,7 +63560,8 @@ radial glial cells acting as neural progenitors throughout life. - + + @@ -63883,7 +63580,7 @@ radial glial cells acting as neural progenitors throughout life. - An amacrine cell with a medium dendritic field and post-synaptic terminals in S2, S3, and S4. + An amacrine cell with a medium dendritic field and post-synaptic terminals in S2, S3, and S4. This cell type releases the neurotransmitter gamma-aminobutyric acid (GABA). https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315 cell @@ -63893,7 +63590,8 @@ radial glial cells acting as neural progenitors throughout life. - An amacrine cell with a medium dendritic field and post-synaptic terminals in S2, S3, and S4. + An amacrine cell with a medium dendritic field and post-synaptic terminals in S2, S3, and S4. This cell type releases the neurotransmitter gamma-aminobutyric acid (GABA). + PMID:32032773 PMID:9620701 @@ -63902,7 +63600,8 @@ radial glial cells acting as neural progenitors throughout life. - + + @@ -63927,7 +63626,7 @@ radial glial cells acting as neural progenitors throughout life. - A retinal amacrine cell with a medium dendritic field and post-synaptic terminals in S1, S2, S3, and S4. + A retinal amacrine cell with a medium dendritic field and post-synaptic terminals in S1, S2, S3, and S4. This cell type releases the neurotransmitter gamma-aminobutyric acid (GABA). https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315 cell @@ -63937,7 +63636,8 @@ radial glial cells acting as neural progenitors throughout life. - A retinal amacrine cell with a medium dendritic field and post-synaptic terminals in S1, S2, S3, and S4. + A retinal amacrine cell with a medium dendritic field and post-synaptic terminals in S1, S2, S3, and S4. This cell type releases the neurotransmitter gamma-aminobutyric acid (GABA). + PMID:10614594 PMID:9620701 @@ -63946,7 +63646,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -63984,7 +63684,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -64028,7 +63728,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -64054,7 +63754,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -64080,7 +63780,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -64106,7 +63806,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -64132,7 +63832,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -64158,14 +63858,21 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + - An amacrine cell with a wide dendritic field and post-synaptic terminals in S5. + An amacrine cell with a wide dendritic field and post-synaptic terminals in S5. This cell type releases the neurotransmitters gamma-aminobutyric acid (GABA) and serotonin. https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315 cell @@ -64175,7 +63882,8 @@ radial glial cells acting as neural progenitors throughout life. - An amacrine cell with a wide dendritic field and post-synaptic terminals in S5. + An amacrine cell with a wide dendritic field and post-synaptic terminals in S5. This cell type releases the neurotransmitters gamma-aminobutyric acid (GABA) and serotonin. + PMID:12486181 PMID:9620701 @@ -64377,7 +64085,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -64401,7 +64108,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -64424,7 +64130,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -64447,7 +64152,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -64470,7 +64174,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -64493,7 +64196,6 @@ radial glial cells acting as neural progenitors throughout life. - Specialized epithelial cells involved in the maintenance of osmotic homeostasis. They are characterized by abundant mitochondria and ion transporters. In amniotes, they are present in the renal system. In freshwater fish, ionocytes in the skin and gills help maintain osmotic homeostasis by absorbing salt from the external environment. ionocyte @@ -64519,12 +64221,6 @@ radial glial cells acting as neural progenitors throughout life. Kolmer-Agduhr cell Kolmer-Agduhr neuron - - - - Kolmer-Agduhr neurons are ciliated GABAergic neurons that contact the central canal of the spinal cord and have ipsilateral ascending axons. - PMID:18680739 - @@ -64537,6 +64233,12 @@ radial glial cells acting as neural progenitors throughout life. KA neuron PMID:9634146 + + + + Kolmer-Agduhr neurons are ciliated GABAergic neurons that contact the central canal of the spinal cord and have ipsilateral ascending axons. + PMID:18680739 + @@ -64826,7 +64528,6 @@ radial glial cells acting as neural progenitors throughout life. - Ghrelin secreting cells found in the endocrine pancreas. @@ -65047,7 +64748,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -65085,7 +64785,7 @@ radial glial cells acting as neural progenitors throughout life. - + Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized). 2012-06-15T02:51:27Z @@ -65112,7 +64812,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -65137,7 +64836,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -65197,8 +64895,7 @@ radial glial cells acting as neural progenitors throughout life. - - + @@ -65254,7 +64951,6 @@ radial glial cells acting as neural progenitors throughout life. - Notochordal cell that is part of the outer epithelium of the notochord and surrounds the vacuolated notochord cells. @@ -65273,7 +64969,6 @@ radial glial cells acting as neural progenitors throughout life. - Notochordal cell that is inner portion of the notochord and becomes vacuolated as development proceeds. @@ -65307,7 +65002,6 @@ radial glial cells acting as neural progenitors throughout life. - Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells. 2012-06-27T10:44:01Z @@ -65326,7 +65020,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -65484,7 +65177,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -65599,7 +65291,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -65644,7 +65335,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -65669,8 +65360,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - + @@ -65861,7 +65551,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -66035,7 +65724,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A skeletal muscle satellite cell that is mitotically quiescent. These cells are wedge shaped and have a large nuclear to cytoplasmic ratio with few organelles, a small nucleus and condensed interphase chromatin. Satellite cells typically remain in this state until activated following muscle damage. quiescent skeletal muscle satellite cell @@ -66103,20 +65791,19 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - + A skeletal muscle satellite cell that has become mitotically active - typically following muscle damage. activated skeletal muscle satellite cell - + - + More accurately - transformation_of ? @@ -66147,7 +65834,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A skeletal muscle myoblast that is part of a skeletal mucle. These cells are formed following acivation and division of skeletal muscle satellite cells. They form a transient population that is lost when they fuse to form skeletal muscle fibers. myogenic precursor cell The vast majority of these cells develop from skeletal muscle satellite cells, although there are some reports of other origins. @@ -66182,8 +65868,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - A myoblast that is commited to developing into a somatic muscle. somatic muscle myoblast @@ -66193,8 +65877,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - + @@ -66217,7 +65900,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -66309,7 +65991,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - An endocrine cell that is part of the pancreas. @@ -66550,8 +66231,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of the microcirculation. @@ -66905,8 +66584,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - Any cell in the compound eye, a light sensing organ composed of ommatidia. GOC:pr PMID:12021768 @@ -66918,7 +66595,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -66936,8 +66613,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - + @@ -66997,8 +66673,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - + @@ -67140,7 +66815,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -67187,7 +66862,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -67231,7 +66905,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -67261,7 +66934,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -67338,7 +67010,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A follicular dendritic cell located in the Peyer's patch. These cells from a meshwork in which Peyer's patch B cells reside. @@ -67701,7 +67372,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -68599,7 +68269,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A transit amplifying cell that is located in the anorectum. anorectum transit amplifying cell @@ -69828,7 +69497,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A progenitor cell that is a tissue-resident mesenchymal cell, important for skeletal muscle regeneration, and able to differentiate into both adipocytes or fibroblasts. @@ -70352,7 +70020,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -70496,7 +70163,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -70504,7 +70171,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A specialized cardiomyocyte that transmit signals from the AV node to the cardiac Purkinje fibers. AV bundle cell atrioventricular bundle cell @@ -70543,7 +70209,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -70551,7 +70217,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - His-Purkinje system cell @@ -70718,7 +70383,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -70740,7 +70405,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + A zygote in a plant or an animal. MESH:D015053 zygote @@ -70782,7 +70447,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - MESH:D032386 cardiac myoblast @@ -71148,8 +70812,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - A sperm cell that is cabaple of motion (motility). motile sperm cell @@ -71167,7 +70829,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A sperm cell that is not cabaple of motion (motility). non-motile sperm cell @@ -71184,7 +70845,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A motile sperm cell that contain no F-actin, and their motility is powered by a dynamic filament system. @@ -71213,7 +70873,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A motile sperm cell that contains a slender threadlike microscopic appendage that enables motion. @@ -71302,7 +70961,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - An undifferentiated cell that originates from a neural stem cell and has the capacity to generate multiple types of lineage-restricted progenitors but not to self-renew. neural progenitor cell @@ -71378,7 +71036,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A mast cell that is CD25+. @@ -71520,7 +71177,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -72043,7 +71699,7 @@ plexiform layer using GABA. - + @@ -72051,7 +71707,6 @@ plexiform layer using GABA. - A cell that, by division or terminal differentiation, can give rise to other cell types. Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. precursor cell @@ -72734,7 +72389,6 @@ plexiform layer using GABA. - Any serous secreting cell that is part of the tracheobronchial epithelium. 2020-05-07T16:03:27Z @@ -73470,7 +73124,7 @@ plexiform layer using GABA. - + @@ -73478,7 +73132,6 @@ plexiform layer using GABA. - A cell that is part of a cardiac valve. heart valve cell cardiac valve cell @@ -73502,7 +73155,6 @@ plexiform layer using GABA. - @@ -73543,7 +73195,6 @@ plexiform layer using GABA. - malpighian tubule tip cell @@ -73744,7 +73395,6 @@ plexiform layer using GABA. - @@ -73767,7 +73417,6 @@ plexiform layer using GABA. - lung secretory cell @@ -74418,18 +74067,10 @@ plexiform layer using GABA. - - An epithelial cell that is part of the urethra. FMA:256165 epithelial cell of urethra - - - - - true - @@ -74463,19 +74104,11 @@ plexiform layer using GABA. - - A mesothelial cell that is part of the dura mater. FMA:256516 squamous mesothelial cell of dura mater mesothelial cell of dura mater - - - - - true - @@ -75603,20 +75236,12 @@ plexiform layer using GABA. - - A serous secreting cell that is part of the epithelium of trachea. FMA:263078 serous cell of epithelium of trachea - - - - - true - @@ -75640,7 +75265,6 @@ plexiform layer using GABA. - A serous secreting cell that is part of the epithelium of bronchus. FMA:263080 @@ -75670,7 +75294,6 @@ plexiform layer using GABA. - A serous secreting cell that is part of the epithelium of terminal bronchiole. FMA:263082 serous cell of epithelium of terminal bronchiole @@ -75698,7 +75321,6 @@ plexiform layer using GABA. - A serous secreting cell that is part of the epithelium of bronchiole. FMA:263084 serous cell of epithelium of lobular bronchiole @@ -77201,7 +76823,6 @@ plexiform layer using GABA. - A melanocyte that is part of the eyelid. FMA:59175 eyelid melanocyte @@ -77437,26 +77058,12 @@ plexiform layer using GABA. - - An epithelial cell that is part of the appendix. FMA:63602 columnar epitheliocyte of appendix epithelial cell of vermiform appendix epithelial cell of appendix - - - - - true - - - - - - true - @@ -77527,7 +77134,6 @@ plexiform layer using GABA. FMA:67102 SA nodal myocyte SA node cardiac muscle cell - myocyte of sinoatrial node sinoatrial node cell sinoatrial node myocyte sinuatrial node myocyte @@ -77552,12 +77158,6 @@ plexiform layer using GABA. SA node cardiac muscle cell GOC:pr - - - - myocyte of sinoatrial node - FMA:67102 - @@ -77797,18 +77397,10 @@ plexiform layer using GABA. - - An epithelial cell that is part of the gallbladder. FMA:67780 epithelial cell of gallbladder - - - - - true - @@ -78240,7 +77832,6 @@ plexiform layer using GABA. - An epithelial cell that is part of the conjunctiva. FMA:70552 epithelial cell of conjunctiva @@ -78282,18 +77873,10 @@ plexiform layer using GABA. - - An epithelial cell that is part of the lacrimal canaliculus. FMA:70553 epithelial cell of lacrimal canaliculus - - - - - true - @@ -78317,18 +77900,10 @@ plexiform layer using GABA. - - An epithelial cell that is part of the external acoustic meatus. FMA:70555 epithelial cell of external acoustic meatus - - - - - true - @@ -78386,18 +77961,10 @@ plexiform layer using GABA. - - An epithelial cell that is part of the lacrimal sac. FMA:70560 epithelial cell of lacrimal sac - - - - - true - @@ -78482,7 +78049,6 @@ plexiform layer using GABA. - An epithelial cell that is part of the viscerocranial mucosa. FMA:70583 epithelial cell of viscerocranial mucosa @@ -78596,18 +78162,10 @@ plexiform layer using GABA. - - A mesothelial cell that is part of the anterior chamber of eyeball. FMA:70615 mesothelial cell of anterior chamber of eye - - - - - true - @@ -78716,24 +78274,10 @@ plexiform layer using GABA. - - An epithelial cell that is part of the sweat gland. FMA:70952 epithelial cell of sweat gland - - - - - true - - - - - - true - @@ -78757,24 +78301,10 @@ plexiform layer using GABA. - - An epithelial cell that is part of the nephron. FMA:70965 epithelial cell of nephron - - - - - true - - - - - - true - @@ -78798,8 +78328,6 @@ plexiform layer using GABA. - - An epithelial cell that is part of the glomerular capsule. @@ -78809,18 +78337,6 @@ plexiform layer using GABA. epithelial cell of Bowman's capsule epithelial cell of glomerular capsule - - - - - true - - - - - - true - @@ -78910,24 +78426,10 @@ plexiform layer using GABA. - - An epithelial cell that is part of the intermediate tubule. FMA:70980 epithelial cell of intermediate tubule - - - - - true - - - - - - true - @@ -79009,24 +78511,10 @@ plexiform layer using GABA. - - A mesothelial cell that is part of the parietal peritoneum. FMA:72142 mesothelial cell of parietal peritoneum - - - - - true - - - - - - true - @@ -79050,26 +78538,12 @@ plexiform layer using GABA. - - A mesothelial cell that is part of the visceral peritoneum. FMA:72143 mesothelial cell of visceral peritoneum - - - - - true - - - - - - true - @@ -79094,7 +78568,6 @@ plexiform layer using GABA. - A melanocyte that is part of the skin of body. CALOHA:TS-2374 @@ -79896,19 +79369,11 @@ plexiform layer using GABA. - - A mesothelial cell that is part of the peritoneum. FMA:86736 peritoneal mesothelial cell mesothelial cell of peritoneum - - - - - true - @@ -79938,19 +79403,11 @@ plexiform layer using GABA. - - A mesothelial cell that is part of the pleura. FMA:86737 pleural mesothelial cell mesothelial cell of pleura - - - - - true - @@ -79980,24 +79437,10 @@ plexiform layer using GABA. - - A mesothelial cell that is part of the parietal pleura. FMA:86738 mesothelial cell of parietal pleura - - - - - true - - - - - - true - @@ -80021,17 +79464,10 @@ plexiform layer using GABA. - A mesothelial cell that is part of the visceral pleura. FMA:86739 mesothelial cell of visceral pleura - - - - - true - @@ -80119,7 +79555,7 @@ plexiform layer using GABA. - + @@ -80127,23 +79563,9 @@ plexiform layer using GABA. - - - - - - - - KUPO:0001010 kidney cell - - - - - true - @@ -80553,7 +79975,7 @@ plexiform layer using GABA. - + @@ -80561,7 +79983,6 @@ plexiform layer using GABA. - @@ -80571,12 +79992,6 @@ plexiform layer using GABA. KUPO:0001115 lower urinary tract cell - - - - - true - @@ -80586,7 +80001,7 @@ plexiform layer using GABA. - + @@ -80594,7 +80009,6 @@ plexiform layer using GABA. - @@ -80604,12 +80018,6 @@ plexiform layer using GABA. KUPO:0001116 ureteral cell - - - - - true - @@ -83633,7 +83041,7 @@ plexiform layer using GABA. - + @@ -83641,7 +83049,6 @@ plexiform layer using GABA. - @@ -83653,12 +83060,6 @@ plexiform layer using GABA. bladder cell - - - - - true - @@ -83668,7 +83069,7 @@ plexiform layer using GABA. - + @@ -83676,7 +83077,6 @@ plexiform layer using GABA. - @@ -83686,12 +83086,6 @@ plexiform layer using GABA. KUPO:0001123 urethra cell - - - - - true - @@ -83921,7 +83315,6 @@ plexiform layer using GABA. olfactory bulb glomerular layer cell olfactory bulb glomerularal cell olfactory bulb periglomerular cell - periglomerular cell periglomerular cell @@ -83954,12 +83347,6 @@ plexiform layer using GABA. olfactory bulb glomerularal cell MP:0009943 - - - - periglomerular cell - NIFEXT:122 - @@ -84474,7 +83861,7 @@ plexiform layer using GABA. colon endothelial cells CALOHA:TS-2397 - + @@ -85992,7 +85379,6 @@ plexiform layer using GABA. - Any melanocyte that is part of a epidermis. 2014-02-03T23:03:09Z @@ -86098,7 +85484,7 @@ plexiform layer using GABA. - + @@ -86106,7 +85492,6 @@ plexiform layer using GABA. - Any cell that is part of a pituitary gland. 2014-03-26T22:14:56Z @@ -86556,7 +85941,7 @@ plexiform layer using GABA. - + @@ -86585,7 +85970,7 @@ plexiform layer using GABA. - + @@ -86593,7 +85978,6 @@ plexiform layer using GABA. - Any native cell that is part of a sebaceous gland. 2014-06-24T23:17:00Z @@ -86615,7 +85999,7 @@ plexiform layer using GABA. - + @@ -86623,7 +86007,6 @@ plexiform layer using GABA. - Any native cell that is part of a cardiac septum. 2014-06-24T23:17:07Z @@ -86838,7 +86221,7 @@ plexiform layer using GABA. - + @@ -86846,7 +86229,6 @@ plexiform layer using GABA. - Any native cell that is part of a hypothalamus. 2014-06-25T01:17:50Z @@ -86996,7 +86378,6 @@ plexiform layer using GABA. - Any neuromast mantle cell that is part of an anterior lateral line. 2014-06-25T03:44:44Z @@ -87085,7 +86466,6 @@ plexiform layer using GABA. - Any neuromast mantle cell that is part of a posterior lateral line. 2014-06-25T03:45:04Z @@ -87115,7 +86495,6 @@ plexiform layer using GABA. - Any neuromast support cell that is part of a posterior lateral line. 2014-06-25T03:45:11Z @@ -87293,7 +86672,6 @@ plexiform layer using GABA. - Any melanocyte that is part of a prepuce of penis. 2014-07-09T00:45:07Z @@ -88373,7 +87751,6 @@ plexiform layer using GABA. - Any melanocyte of skin that is part of a skin of face. 2014-12-02T19:10:40Z @@ -88403,7 +87780,6 @@ plexiform layer using GABA. - Any melanocyte of skin that is part of a skin of prepuce of penis. 2014-12-02T19:10:45Z @@ -89237,7 +88613,7 @@ plexiform layer using GABA. L2/3 bipolar Vip (Mus musculus) - L2/3 bipolar vip GABAergic cortical interneuron (Mmus) + L2/3 bipolar vip GABAergic interneuron (Mmus) @@ -89518,7 +88894,7 @@ plexiform layer using GABA. L5 VIP (Mus musculus) - L5 vip cortical GABAergic interneuron (Mmus) + L5 vip GABAergic interneuron (Mmus) @@ -89700,7 +89076,7 @@ plexiform layer using GABA. L5/6 CCK Vip (Mus musculus) - L5/6 cck, vip cortical GABAergic interneuron (Mmus) + L5/6 cck, vip GABAergic interneuron (Mmus) @@ -89843,7 +89219,7 @@ plexiform layer using GABA. L5,6 NGC Lamp5 (Mus musculus) - L5,6 neurogliaform lamp5 GABAergic cortical interneuron (Mmus) + L5,6 neurogliaform lamp5 GABAergic interneuron (Mmus) @@ -90039,7 +89415,7 @@ plexiform layer using GABA. L5 T Martinotti SST (Mus musculus) - L5 T-Martinotti sst GABAergic cortical interneuron (Mmus) + L5 sst T-Martinotti interneuron (Mmus) @@ -90084,7 +89460,7 @@ plexiform layer using GABA. L5 non-Martinotti SST (Mus musculus) - L5 non-Martinotti sst GABAergic cortical interneuron (Mmus) + L5 non-Martinotti sst GABAergic interneuron (Mmus) @@ -90183,7 +89559,7 @@ plexiform layer using GABA. L2/3/5 fan Martinotti SST (Mus musculus) L2/3/5 fan Martionotti SST cells have an adapting firing pattern and non-zero afterdepolarization (ADP). - L2/3/5 fan Martinotti sst GABAergic cortical interneuron (Mmus) + L2/3/5 fan Martinotti sst GABAergic interneuron (Mmus) @@ -90242,7 +89618,7 @@ plexiform layer using GABA. L4 SST (Mus musculus) - L4 sst GABAergic cortical interneuron (Mmus) + L4 sst Martinotti interneuron (Mmus) @@ -90432,7 +89808,7 @@ plexiform layer using GABA. L2/3-6 IT projecting neuron - L2/3-6 intratelencephalic projecting glutamatergic cortical neuron + L2/3-6 intratelencephalic projecting glutamatergic neuron @@ -90679,8 +90055,9 @@ plexiform layer using GABA. L6b subplate glut An excitatory glutamatergic neuron transcriptomically related to the CT subclass, with a soma preferentially located in the bottom of L6 of the primary motor cortex. + L6b subplate glutamatergic neuron of the primary motor cortex - L6b subplate glutamatergic neuron of the primary motor cortex + L6b glutamatergic neuron of the primary motor cortex @@ -90710,7 +90087,7 @@ plexiform layer using GABA. L2/3 IT glut MOp - An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2/3. + An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2/3 of the primary motor cortex. L2/3 IT M1 L2/3 IT MOp @@ -90720,7 +90097,7 @@ plexiform layer using GABA. - An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2/3. + An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2/3 of the primary motor cortex. DOI:10.1101/2020.10.19.343129 @@ -90971,6 +90348,7 @@ plexiform layer using GABA. CT VAL/VM M1 CT VAL/VM MOp + The assertion of this cell type under L6 CT is due to the ambiguity of lower L5 and L6. corticothalamic VAL/VM projecting glutamatergic neuron of the primary motor cortex @@ -90993,43 +90371,43 @@ plexiform layer using GABA. - - - + + + A type of mouse mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain. VLMC (Mus musculus) vascular leptomeningeal cell (Mmus) - + - + - + - + PMID:30096314 - + PMID:30096314 - + PMID:30096314 @@ -91480,7 +90858,7 @@ plexiform layer using GABA. L5/6 CCK (Mus musculus) - L5/6 cck cortical GABAergic interneuron (Mmus) + L5/6 cck GABAergic interneuron (Mmus) @@ -91497,7 +90875,7 @@ plexiform layer using GABA. - + @@ -91610,7 +90988,7 @@ plexiform layer using GABA. L6 Th+ SST (Mus musculus) L6 tyrosine hydroxylase positive sst expressing GABAergic cortical interneuron (Mus musculus) - L6 tyrosine hydroxylase sst GABAergic cortical interneuron (Mmus) + L6 th sst GABAergic interneuron (Mmus) @@ -92690,7 +92068,7 @@ plexiform layer using GABA. L5/6 non-Martinotti morphology sst expressing GABAergic cortical interneuron (Mus musculus) L5/6 non-Martinotti SST cells have strongly facilitating excitatory inputs and moderately depressing outputs. They have faster action potential than Martinotti morphology SST cells and slightly slower than PV basket cells. - L5/6 non-Martinotti sst GABAergic cortical interneuron (Mmus) + L5/6 non-Martinotti sst GABAergic interneuron (Mmus) @@ -93832,7 +93210,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + A cell that supports the development of a gamete by providing it cytoplasmic material (including entire organelles) by direct cross-membrane channels (del Pino, 2021). 2022-06-08T15:29:54Z @@ -93853,7 +93231,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - A gamete-nursing cell that derives from a germline cell (del Pino, 2021). @@ -93880,8 +93257,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - A gamete-nursing cell that derives from the somatic tissues of the gonad (del Pino, 2021). @@ -93919,7 +93294,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - A melanocyte located in the vascular uvea and involved in photoprotection, regulation of oxidative damage and immune responses. 2022-01-20T12:59:06Z @@ -94931,7 +94305,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + @@ -96706,8 +96080,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances retinal astroglia - PMID:33796062 + @@ -96772,8 +96146,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances SCMFs PMID:25448080 + - @@ -96879,8 +96253,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances lung MKs PMID:33351116 + - @@ -97842,8 +97216,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances lung mDCs PMID:34516781 + - @@ -98230,7 +97604,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + @@ -98253,6 +97627,40 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + + + + + + + + A ciliated cell that is part of a ciliated duct of an airway submucosal gland. + + + 2023-09-08T10:32:27Z + airway submucosal gland duct ciliated cell + + + + + A ciliated cell that is part of a ciliated duct of an airway submucosal gland. + PMID:17707699 + PMID:30864819 + + + + @@ -98380,8 +97788,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances enteric glia - PMID:11169131 + @@ -98426,6 +97834,55 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + + + + Any mesenchymal stem cell of adipose tissue that is part of an orbital region. + + 2023-09-18T10:43:00Z + OAMSC + Orbital ASCs + orbital adipose-derived mesenchymal stem cell + mesenchymal stem cell of orbital adipose tissue + + + + + Any mesenchymal stem cell of adipose tissue that is part of an orbital region. + + + + + + OAMSC + PMID:31377878 + + + + + Orbital ASCs + PMID:30210548 + + + + + orbital adipose-derived mesenchymal stem cell + PMID:31377878 + + + + @@ -100366,6 +99823,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -104722,6 +104185,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -106264,6 +105733,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + definition + + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition + definition @@ -85,12 +111,18 @@ + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> IAO:0000116 uberon editor_note true editor_note editor note + editor note @@ -115,7 +147,13 @@ - + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + @@ -128,6 +166,12 @@ + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg IAO:0000233 external uberon @@ -135,15 +179,31 @@ true true term_tracker_item + The 'tracker item' can associate a tracker with a specific ontology term. term tracker item + term tracker item + + + + + + + expand expression to + ObjectProperty: RO_0002104 +Label: has plasma membrane part +Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones + Chris Mungall expand expression to + expand expression to @@ -175,6 +235,9 @@ + has ontology root term + Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. + Nicolas Matentzoglu IAO:0000700 external uberon @@ -183,6 +246,7 @@ true has_ontology_root_term has ontology root term + has ontology root term preferred_root @@ -197,7 +261,14 @@ + term replaced by + + Use on obsolete terms, relating the term to another term that can be used as a substitute + Person:Alan Ruttenberg + Person:Alan Ruttenberg + Add as annotation triples in the granting ontology term replaced by + term replaced by @@ -216,7 +287,44 @@ - + + 'part disjoint with' 'defined by construct' """ + PREFIX owl: <http://www.w3.org/2002/07/owl#> + PREFIX : <http://example.org/ + CONSTRUCT { + [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?a ; + owl:disjointWith [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?b + ] + ] + } + WHERE { + ?a :part_disjoint_with ?b . + } + Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. + + + + defined by construct + + + + + + + + CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) + A synonym type for describing pluralization synonyms + + + 2023-03-03 + plural form + @@ -1102,7 +1210,6 @@ WHERE { - plural term @@ -1396,6 +1503,12 @@ WHERE { + + + + + + @@ -1589,7 +1702,12 @@ WHERE { + An alternative label for a class or property which has a more general meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + has broad synonym has_broad_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 @@ -1605,7 +1723,12 @@ WHERE { + An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + has exact synonym has_exact_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 @@ -1613,7 +1736,12 @@ WHERE { + An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + has narrow synonym has_narrow_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 @@ -1629,7 +1757,12 @@ WHERE { + An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + has related synonym has_related_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 @@ -1894,12 +2027,35 @@ WHERE { + + + + + + + + + + + + + + + + + - - - contains - RO:0001019 - uberon - contains - contains - contains - obsolete contains - - true - - - - @@ -8177,26 +8317,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - CARO:0000013 - cell in vivo - - To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). - native cell - - - - - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - CARO:mah - - - - @@ -8219,7 +8339,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -8227,7 +8347,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -8603,7 +8722,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -8616,7 +8735,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -8959,7 +9077,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9057,7 +9175,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9065,7 +9183,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9772,20 +9890,20 @@ MH: sexual subtypes should probably be logically defined based on sexual process mesenchymal progenitor cells MESH:D044982 - + mesenchymal stromal cells - + stem cells, mesenchymal MESH:D044982 - + @@ -9839,7 +9957,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9847,7 +9965,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9874,7 +9992,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose primary function is to shorten. contractile cell @@ -9892,7 +10010,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -9923,7 +10040,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose function is determined by the generation or the reception of an electric signal. electrically active cell @@ -9956,7 +10073,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose primary function is to prevent the transport of stuff across compartments. barrier cell @@ -9975,7 +10092,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9983,7 +10100,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10081,7 +10198,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10089,7 +10206,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10117,7 +10234,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10151,7 +10268,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10335,7 +10452,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10346,7 +10463,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -10499,7 +10615,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10507,7 +10623,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10523,7 +10639,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell that is specialised to accumulate a particular substance(s). stuff accumulating cell @@ -10543,7 +10659,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10551,7 +10667,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10637,7 +10753,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process + + + + + + + Diploid cell produced by the fusion of sperm cell nucleus and egg cell. zygote BTO:0000854 @@ -10862,7 +10985,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose primary function is to protect the organism. defensive cell @@ -11189,36 +11312,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - - - - - - - - - - - - - - - - - A native cell that is part of some Metazoa. - metazoan cell - - animal cell - https://www.swissbiopics.org/api/image/Animal_cells.svg - - - - @@ -12450,7 +12543,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -12490,7 +12582,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -12503,12 +12594,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process MESH:D053687 somatic stem cell - - - - - true - @@ -12537,6 +12622,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process + @@ -15081,7 +15167,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell of a hematopoietic lineage. BTO:0000574 CALOHA:TS-2017 @@ -15170,7 +15256,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -15178,7 +15264,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -15193,12 +15279,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process bone cell - - - - - true - @@ -15810,7 +15890,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -15848,7 +15927,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -16078,7 +16156,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -16086,7 +16164,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -16149,7 +16227,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -16157,7 +16235,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -16187,7 +16265,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -16195,7 +16273,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -16212,12 +16290,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process connective tissue cell - - - - - true - @@ -16231,7 +16303,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell of the embryo. 2010-09-15T03:39:21Z @@ -16250,29 +16322,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). - - 2010-09-24T09:44:42Z - BTO:0001268 - FMA:72300 - WBbt:0008378 - - somatic cell - - - - - A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). - GOC:tfm - ISBN:0721662544 - - - - @@ -16324,7 +16373,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -16332,7 +16381,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -16350,12 +16399,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cardiocyte - - - - - true - @@ -16369,7 +16412,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - An endothelial progenitor cell that participates in angiogenesis during development. 2011-02-28T04:20:39Z @@ -16521,7 +16563,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized). 2012-06-15T02:51:27Z @@ -16594,7 +16636,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -16617,7 +16658,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A zygote in a plant or an animal. MESH:D015053 zygote @@ -16685,7 +16726,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -16693,7 +16734,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -20259,32 +20300,32 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -32471,6 +32512,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process GC_ID:1 + PMID:30365038 + PMID:32761142 ncbi_taxonomy all NCBITaxon:1 @@ -38802,7 +38845,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -38838,14 +38881,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process gastrula stage - + - + BILS @@ -39066,7 +39109,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -39139,7 +39182,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process https://github.com/obophenotype/uberon/issues/661 http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg - + @@ -39152,7 +39195,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + exceptions in some taxa @@ -39277,15 +39320,15 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + - - + + A fluid that is composed of blood plasma and erythrocytes. This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. @@ -39327,34 +39370,34 @@ MH: sexual subtypes should probably be logically defined based on sexual process blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -39658,7 +39701,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -39700,14 +39743,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process organism substance - + - + this relationship may be too strong and may be weakened in future @@ -40937,7 +40980,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] @@ -40975,14 +41018,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -41035,7 +41078,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] endodermal @@ -41072,14 +41115,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -41124,7 +41167,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The middle germ layer of the embryo, between the endoderm and ectoderm. Primary germ layer that is the middle of the embryonic germ layers.[AAO] @@ -41169,7 +41212,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + @@ -41182,7 +41225,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Bgee:AN @@ -41389,7 +41432,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -41462,15 +41505,18 @@ MH: sexual subtypes should probably be logically defined based on sexual process Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706 heart + https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + MA @@ -41748,6 +41794,11 @@ MH: sexual subtypes should probably be logically defined based on sexual process respiratory system http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg + https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb @@ -42126,7 +42177,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -42179,14 +42230,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -42274,7 +42325,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. Part of the nervous system which includes the brain and spinal cord.[AAO] @@ -42321,7 +42372,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process central nervous system - + @@ -42335,7 +42386,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Bgee:AN @@ -42829,7 +42880,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Skeletal element that is composed of bone tissue. @@ -42879,14 +42930,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process bone element - + - + VSAO-modified @@ -42997,7 +43048,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A tube extending from the mouth to the anus. @@ -43037,14 +43088,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process digestive tract - + - + NCBIBook:NBK10107 @@ -43321,8 +43372,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + @@ -43335,7 +43386,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -43350,7 +43401,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process A vessel through which blood circulates in the body. consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus - Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] Any of the vessels through which blood circulates in the body.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] @@ -43387,41 +43437,40 @@ MH: sexual subtypes should probably be logically defined based on sexual process vas sanguineum UBERON:0001981 - blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -44144,7 +44193,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -44178,14 +44227,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process musculoskeletal system - + - + check ctenophore @@ -44314,7 +44363,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -44355,14 +44404,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process coelemic cavity lumen - + - + definitional @@ -44470,9 +44519,9 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - + + + @@ -44527,15 +44576,15 @@ MH: sexual subtypes should probably be logically defined based on sexual process notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -44554,19 +44603,19 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -44651,8 +44700,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk @@ -44698,11 +44747,11 @@ MH: sexual subtypes should probably be logically defined based on sexual process somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -44715,13 +44764,13 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + GOTAX:0000352 - + ZFA @@ -44834,12 +44883,12 @@ MH: sexual subtypes should probably be logically defined based on sexual process + + + + + - - - - - A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). @@ -44879,66 +44928,66 @@ MH: sexual subtypes should probably be logically defined based on sexual process http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells ISBN:0073040584 - + BTO - + PMID:11523831 - + pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest - + PMID:11523831 @@ -45126,7 +45175,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -45184,14 +45233,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -45462,14 +45511,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + - + Anatomical system that is involved in the production of hematopoietic cells. Anatomical system that consists of the blood and blood forming tissues.[AAO] @@ -45512,24 +45561,24 @@ MH: sexual subtypes should probably be logically defined based on sexual process hematopoietic system - + - + - + FMA - + definitional @@ -45900,7 +45949,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] @@ -45925,14 +45974,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process presomitic mesoderm - + - + Bgee:AN @@ -46162,9 +46211,9 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] @@ -46196,34 +46245,34 @@ MH: sexual subtypes should probably be logically defined based on sexual process neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -46288,7 +46337,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] @@ -46317,7 +46366,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -46330,7 +46379,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Bgee:AN @@ -46402,7 +46451,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -46446,7 +46495,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -46459,7 +46508,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + EHDAA2 VHOG @@ -46543,15 +46592,15 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] @@ -46571,15 +46620,15 @@ MH: sexual subtypes should probably be logically defined based on sexual process heart primordium - + - + - + @@ -46592,19 +46641,19 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + ZFA - + ZFA - + XAO @@ -46659,8 +46708,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. Skeletogenic portion of somites.[AAO] The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] @@ -46687,11 +46736,11 @@ MH: sexual subtypes should probably be logically defined based on sexual process sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -46710,13 +46759,13 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + VHOG:0000680 - + ZFA @@ -46982,7 +47031,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] @@ -46998,14 +47047,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process intraembryonic coelom - + - + Wikipedia @@ -47324,8 +47373,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] XAO:0004185 @@ -47338,24 +47387,24 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -47414,7 +47463,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + An epithelial tube that will give rise to the mature heart. the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. AAO:0010411 @@ -47434,14 +47483,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process heart tube - + - + ZFA-modified @@ -47775,6 +47824,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0004537 blood vasculature + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb @@ -48056,7 +48107,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]. A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] EMAPA:37744 @@ -48070,7 +48121,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from skeletal tissue - + @@ -48083,7 +48134,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + 2012-08-14 VSAO:0000015 VSAO @@ -48122,7 +48173,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] @@ -48138,14 +48189,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process skeletal element - + - + VSAO @@ -48190,7 +48241,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -48229,14 +48280,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0004770 articular system - + - + FMA @@ -48994,7 +49045,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -49010,14 +49061,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process trunk mesenchyme - + - + EHDAA2 @@ -49128,7 +49179,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -49146,14 +49197,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process primitive heart tube - + - + ZFA @@ -49321,7 +49372,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -49331,7 +49382,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0005856 developing mesenchymal condensation - + @@ -49350,7 +49401,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + AEO-modified-relation @@ -49455,7 +49506,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] @@ -49470,7 +49521,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process notochordal plate - + @@ -49483,7 +49534,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + EHDAA2 @@ -49520,7 +49571,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -49537,14 +49588,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -50287,7 +50338,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis SPD:0000130 @@ -50302,14 +50353,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process Gene notes: Bmp, Nkx, Gata primary circulatory organ - + - + GO uses blood circulation generically to include the haemolymphatic fluid of arthropods @@ -50399,7 +50450,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -50416,14 +50467,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process presumptive segmental plate - + - + https://github.com/obophenotype/uberon/wiki/The-neural-crest EDHAA2 @@ -50522,7 +50573,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -50548,7 +50599,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process presumptive paraxial mesoderm - + @@ -50564,7 +50615,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + https://github.com/obophenotype/uberon/issues/1277 @@ -50640,7 +50691,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -50648,7 +50699,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0007524 dense mesenchyme tissue - + @@ -50661,7 +50712,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + AEO @@ -50758,7 +50809,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. @@ -50775,14 +50826,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process vascular system - + - + MA @@ -50915,7 +50966,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -50932,14 +50983,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -50995,7 +51046,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -51003,14 +51054,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -51032,7 +51083,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -51042,14 +51093,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process anterior lateral plate mesoderm - + - + ZFA @@ -51183,7 +51234,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -51203,14 +51254,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0010210 blood clot - + - + BTO @@ -51332,8 +51383,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] FMA:23879 @@ -51346,11 +51397,11 @@ MH: sexual subtypes should probably be logically defined based on sexual process subdivision of skeleton - + - + @@ -51363,13 +51414,13 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + UBERONREF:0000003 - + VSAO @@ -51446,7 +51497,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -51456,7 +51507,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -51469,7 +51520,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + cjm @@ -51734,7 +51785,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -51756,7 +51807,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0012429 hematopoietic tissue - + @@ -51769,7 +51820,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + defitional @@ -52339,7 +52390,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -52362,7 +52413,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0016887 entire extraembryonic component - + @@ -52375,7 +52426,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + AEO @@ -52600,6 +52651,209 @@ MH: sexual subtypes should probably be logically defined based on sexual process + + + + + + + + + example to be eventually removed + example to be eventually removed + + + + + + + + failed exploratory term + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + + + + + + metadata complete + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + organizational term + Term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + ready for release + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + metadata incomplete + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + uncurated + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + pending final vetting + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + placeholder removed + placeholder removed + + + + + + + + terms merged + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + + + + + + term imported + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + + + + + + term split + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + + + + + + universal + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + + + + + + defined class + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + + + + + + named class expression + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + + + + + + to be replaced with external ontology term + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + requires discussion + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. + This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/77 + https://orcid.org/0000-0001-5208-3432 + out of scope + + + + + definition + + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition + definition @@ -85,12 +111,18 @@ + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> IAO:0000116 uberon editor_note true editor_note editor note + editor note @@ -115,7 +147,13 @@ - + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + @@ -128,6 +166,12 @@ + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg IAO:0000233 external uberon @@ -135,15 +179,31 @@ true true term_tracker_item + The 'tracker item' can associate a tracker with a specific ontology term. term tracker item + term tracker item + + + + + + + expand expression to + ObjectProperty: RO_0002104 +Label: has plasma membrane part +Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones + Chris Mungall expand expression to + expand expression to @@ -175,6 +235,9 @@ + has ontology root term + Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. + Nicolas Matentzoglu IAO:0000700 external uberon @@ -183,6 +246,7 @@ true has_ontology_root_term has ontology root term + has ontology root term preferred_root @@ -197,7 +261,14 @@ + term replaced by + + Use on obsolete terms, relating the term to another term that can be used as a substitute + Person:Alan Ruttenberg + Person:Alan Ruttenberg + Add as annotation triples in the granting ontology term replaced by + term replaced by @@ -216,7 +287,44 @@ - + + 'part disjoint with' 'defined by construct' """ + PREFIX owl: <http://www.w3.org/2002/07/owl#> + PREFIX : <http://example.org/ + CONSTRUCT { + [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?a ; + owl:disjointWith [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?b + ] + ] + } + WHERE { + ?a :part_disjoint_with ?b . + } + Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. + + + + defined by construct + + + + + + + + CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) + A synonym type for describing pluralization synonyms + + + 2023-03-03 + plural form + @@ -1102,7 +1210,6 @@ WHERE { - plural term @@ -1396,6 +1503,12 @@ WHERE { + + + + + + @@ -1589,7 +1702,12 @@ WHERE { + An alternative label for a class or property which has a more general meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + has broad synonym has_broad_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 @@ -1605,7 +1723,12 @@ WHERE { + An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + has exact synonym has_exact_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 @@ -1613,7 +1736,12 @@ WHERE { + An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + has narrow synonym has_narrow_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 @@ -1629,7 +1757,12 @@ WHERE { + An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + has related synonym has_related_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 @@ -1894,12 +2027,35 @@ WHERE { + + + + + + + + + + + + + + + + + - - - contains - RO:0001019 - uberon - contains - contains - contains - obsolete contains - - true - - - - @@ -8220,26 +8360,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - CARO:0000013 - cell in vivo - - To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). - native cell - - - - - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - CARO:mah - - - - @@ -8333,7 +8453,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -8349,7 +8468,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -8378,7 +8497,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -8386,7 +8505,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -8665,7 +8783,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -8678,7 +8796,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -8949,7 +9066,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9034,7 +9151,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube. @@ -9291,6 +9407,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process + @@ -9362,7 +9479,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process macroglia doi:10.1152/physrev.2001.81.2.871 - + @@ -9528,20 +9645,20 @@ MH: sexual subtypes should probably be logically defined based on sexual process mesenchymal progenitor cells MESH:D044982 - + mesenchymal stromal cells - + stem cells, mesenchymal MESH:D044982 - + @@ -9584,7 +9701,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -9609,12 +9725,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process melanocyte - - - - - true - @@ -9628,7 +9738,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - pigment cell visual pigment cell @@ -9641,7 +9750,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9649,7 +9758,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9676,7 +9785,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose primary function is to shorten. contractile cell @@ -9694,7 +9803,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -9787,7 +9895,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9854,7 +9962,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose function is determined by the generation or the reception of an electric signal. electrically active cell @@ -9887,7 +9995,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose primary function is to prevent the transport of stuff across compartments. barrier cell @@ -9906,7 +10014,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9914,7 +10022,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10096,7 +10204,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10104,7 +10212,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10149,7 +10257,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism. structural cell @@ -10176,7 +10284,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell that is specialised to accumulate a particular substance(s). stuff accumulating cell @@ -10196,7 +10304,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10204,7 +10312,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10283,7 +10391,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10318,7 +10426,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -10359,7 +10466,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -10417,7 +10523,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process + + + + + + + Diploid cell produced by the fusion of sperm cell nucleus and egg cell. zygote BTO:0000854 @@ -10524,12 +10637,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process satellite cell smooth muscle myoblast - - - - - true - @@ -10617,7 +10724,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -10843,36 +10949,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - - - - - - - - - - - - - - - - - A native cell that is part of some Metazoa. - metazoan cell - - animal cell - https://www.swissbiopics.org/api/image/Animal_cells.svg - - - - @@ -11652,8 +11728,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process ACs doi:10.1038/s41598-020-66092-9 + - @@ -11932,7 +12008,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -12035,7 +12110,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -12048,12 +12122,6 @@ radial glial cells acting as neural progenitors throughout life. MESH:D053687 somatic stem cell - - - - - true - @@ -12104,8 +12172,8 @@ radial glial cells acting as neural progenitors throughout life. RGCs doi:10.1038/s41598-020-66092-9 + - @@ -12148,8 +12216,8 @@ radial glial cells acting as neural progenitors throughout life. HCs doi:10.1038/s41598-020-66092-9 + - @@ -12221,16 +12289,16 @@ radial glial cells acting as neural progenitors throughout life. BCs doi:10.1038/s41598-020-66092-9 + - BPs GSE137537 + - @@ -12726,7 +12794,7 @@ radial glial cells acting as neural progenitors throughout life. - + A cell of a hematopoietic lineage. BTO:0000574 CALOHA:TS-2017 @@ -12851,7 +12919,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -12889,7 +12956,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -12963,7 +13029,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -12993,7 +13058,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -13001,7 +13066,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -13121,7 +13186,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -13129,7 +13194,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -13159,7 +13224,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -13167,7 +13232,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -13184,12 +13249,6 @@ radial glial cells acting as neural progenitors throughout life. connective tissue cell - - - - - true - @@ -13203,7 +13262,7 @@ radial glial cells acting as neural progenitors throughout life. - + A cell of the embryo. 2010-09-15T03:39:21Z @@ -13263,29 +13322,6 @@ radial glial cells acting as neural progenitors throughout life. - - - - - A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). - - 2010-09-24T09:44:42Z - BTO:0001268 - FMA:72300 - WBbt:0008378 - - somatic cell - - - - - A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). - GOC:tfm - ISBN:0721662544 - - - - @@ -13314,12 +13350,6 @@ radial glial cells acting as neural progenitors throughout life. retinal melanocyte - - - - - true - @@ -13336,7 +13366,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -13344,7 +13374,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -13362,12 +13392,6 @@ radial glial cells acting as neural progenitors throughout life. From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cardiocyte - - - - - true - @@ -13381,7 +13405,6 @@ radial glial cells acting as neural progenitors throughout life. - An endothelial progenitor cell that participates in angiogenesis during development. 2011-02-28T04:20:39Z @@ -13526,12 +13549,6 @@ radial glial cells acting as neural progenitors throughout life. retinal pigment epithelial cell - - - - - true - @@ -13709,7 +13726,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -13822,7 +13838,7 @@ radial glial cells acting as neural progenitors throughout life. - + A zygote in a plant or an animal. MESH:D015053 zygote @@ -13920,7 +13936,7 @@ plexiform layer. - + @@ -13928,7 +13944,7 @@ plexiform layer. - + @@ -14104,7 +14120,6 @@ plexiform layer. - @@ -14295,8 +14310,8 @@ plexiform layer. retinal astroglia - PMID:33796062 + @@ -15229,32 +15244,32 @@ plexiform layer. - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -23903,6 +23918,8 @@ plexiform layer. GC_ID:1 + PMID:30365038 + PMID:32761142 ncbi_taxonomy all NCBITaxon:1 @@ -27283,7 +27300,7 @@ plexiform layer. - + @@ -27324,14 +27341,14 @@ plexiform layer. camera-type eye - + - + definitional @@ -28432,7 +28449,7 @@ plexiform layer. - + The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube) @@ -28457,7 +28474,7 @@ plexiform layer. external ectoderm http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png - + @@ -28470,7 +28487,7 @@ plexiform layer. - + EHDAA2 @@ -28839,7 +28856,7 @@ plexiform layer. - + @@ -28875,14 +28892,14 @@ plexiform layer. gastrula stage - + - + BILS @@ -29148,7 +29165,7 @@ plexiform layer. - + @@ -29221,7 +29238,7 @@ plexiform layer. https://github.com/obophenotype/uberon/issues/661 http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg - + @@ -29234,7 +29251,7 @@ plexiform layer. - + exceptions in some taxa @@ -29359,15 +29376,15 @@ plexiform layer. - + - - + + A fluid that is composed of blood plasma and erythrocytes. This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. @@ -29409,34 +29426,34 @@ plexiform layer. blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -29740,7 +29757,7 @@ plexiform layer. - + @@ -29782,14 +29799,14 @@ plexiform layer. organism substance - + - + this relationship may be too strong and may be weakened in future @@ -31122,7 +31139,7 @@ plexiform layer. - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] @@ -31160,14 +31177,14 @@ plexiform layer. ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -31220,7 +31237,7 @@ plexiform layer. - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] endodermal @@ -31257,14 +31274,14 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -31309,7 +31326,7 @@ plexiform layer. - + The middle germ layer of the embryo, between the endoderm and ectoderm. Primary germ layer that is the middle of the embryonic germ layers.[AAO] @@ -31354,7 +31371,7 @@ plexiform layer. mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + @@ -31367,7 +31384,7 @@ plexiform layer. - + Bgee:AN @@ -31589,7 +31606,7 @@ plexiform layer. - + @@ -31655,14 +31672,14 @@ plexiform layer. cranial nerve II - + - + EHDAA2 @@ -31806,7 +31823,7 @@ plexiform layer. - + @@ -31879,15 +31896,18 @@ plexiform layer. Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706 heart + https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + MA @@ -31965,7 +31985,7 @@ plexiform layer. - + @@ -31990,7 +32010,7 @@ plexiform layer. - + The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. requires review for applicability to invertebrate structures, e.g. synganglion @@ -32050,12 +32070,14 @@ plexiform layer. brain + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb - + - + @@ -32068,13 +32090,13 @@ plexiform layer. - + FMA - + Bgee:AN @@ -32375,9 +32397,9 @@ plexiform layer. - - - + + + @@ -32402,7 +32424,7 @@ plexiform layer. - + @@ -32458,44 +32480,44 @@ plexiform layer. cornea http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - + - + MA - + MA - + FMA-isa - + definitional @@ -32684,10 +32706,10 @@ plexiform layer. - - - - + + + + The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. @@ -32738,44 +32760,44 @@ plexiform layer. retina http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png - + - + - + - + - + FMA - + FMA - + FMA - + EHDAA2 @@ -32849,8 +32871,8 @@ plexiform layer. - - + + @@ -32886,24 +32908,24 @@ plexiform layer. eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -33125,6 +33147,11 @@ plexiform layer. respiratory system http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg + https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb @@ -33503,7 +33530,7 @@ plexiform layer. - + @@ -33556,14 +33583,14 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -33651,7 +33678,7 @@ plexiform layer. - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. Part of the nervous system which includes the brain and spinal cord.[AAO] @@ -33698,7 +33725,7 @@ plexiform layer. central nervous system - + @@ -33712,7 +33739,7 @@ plexiform layer. - + Bgee:AN @@ -34459,7 +34486,7 @@ plexiform layer. - + Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). AEO:0000111 BTO:0002422 @@ -34484,14 +34511,14 @@ plexiform layer. mesothelium http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg - + - + FMA @@ -34864,7 +34891,7 @@ plexiform layer. - + A tube extending from the mouth to the anus. @@ -34904,14 +34931,14 @@ plexiform layer. digestive tract - + - + NCBIBook:NBK10107 @@ -34991,7 +35018,7 @@ plexiform layer. - + The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. BTO:0000654 @@ -35014,7 +35041,7 @@ plexiform layer. ciliary muscle http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png - + @@ -35033,7 +35060,7 @@ plexiform layer. - + FMA @@ -35174,7 +35201,7 @@ plexiform layer. - + @@ -35226,14 +35253,14 @@ plexiform layer. eyelid https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg - + - + multiple @@ -35528,7 +35555,7 @@ plexiform layer. - + @@ -35571,14 +35598,14 @@ plexiform layer. iris - + - + XAO @@ -35650,7 +35677,7 @@ plexiform layer. - + @@ -35702,14 +35729,14 @@ plexiform layer. corneal epithelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png - + - + ISBN:0781772214 @@ -35805,16 +35832,16 @@ plexiform layer. - - + + - - + + @@ -35856,44 +35883,44 @@ plexiform layer. sclera http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - + - + FMA - + ZFA - + ISBN:0781772214 - + cjm ISBN:0781772214 Wikipedia @@ -35953,7 +35980,7 @@ plexiform layer. - + @@ -35992,14 +36019,14 @@ plexiform layer. ciliary body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + ISBN:0781772214 @@ -36047,14 +36074,14 @@ plexiform layer. - + - + @@ -36117,24 +36144,24 @@ plexiform layer. optic choroid http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + MA - + Wikipedia @@ -36234,7 +36261,7 @@ plexiform layer. - + @@ -36283,14 +36310,14 @@ plexiform layer. substantia propria of cornea http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png - + - + cjm ISBN:0781772214 Wikipedia @@ -36367,9 +36394,9 @@ plexiform layer. - - - + + + A double layer covering the ciliary body that produces aqueous humor. BTO:0001770 @@ -36389,15 +36416,15 @@ plexiform layer. ciliary epithelium - + - + - + @@ -36410,19 +36437,19 @@ plexiform layer. - + MA - + MP - + Wikipedia @@ -36545,7 +36572,7 @@ plexiform layer. - + @@ -36606,14 +36633,14 @@ plexiform layer. pigmented layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + Wikipedia @@ -36717,7 +36744,7 @@ plexiform layer. - + @@ -36751,14 +36778,14 @@ plexiform layer. photoreceptor layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + ZFA @@ -36931,7 +36958,7 @@ plexiform layer. - + @@ -36978,14 +37005,14 @@ plexiform layer. outer nuclear layer of retina - + - + soma ZFA @@ -37323,7 +37350,7 @@ plexiform layer. - + @@ -37382,7 +37409,7 @@ plexiform layer. ganglionic layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + @@ -37395,7 +37422,7 @@ plexiform layer. - + FMA @@ -37471,7 +37498,7 @@ plexiform layer. - + @@ -37527,14 +37554,14 @@ plexiform layer. nerve fiber layer of retina - + - + FMA @@ -37912,7 +37939,7 @@ plexiform layer. - + @@ -37948,14 +37975,14 @@ plexiform layer. aqueous humor of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + FMA def states A and P located_in in EHDAA2 VHOG @@ -38137,7 +38164,7 @@ plexiform layer. - + @@ -38161,7 +38188,7 @@ plexiform layer. vitreous body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + @@ -38174,7 +38201,7 @@ plexiform layer. - + neural ectoderm of optic cup ISBN:0781772214 @@ -38309,8 +38336,8 @@ plexiform layer. - - + + @@ -38343,24 +38370,24 @@ plexiform layer. anterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png - + - + - + FMA - + cjm @@ -38411,8 +38438,8 @@ plexiform layer. - - + + @@ -38442,24 +38469,24 @@ plexiform layer. posterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + FMA - + cjm @@ -38495,9 +38522,9 @@ plexiform layer. - - - + + + @@ -38547,15 +38574,15 @@ plexiform layer. conjunctiva http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png - + - + - + @@ -38568,19 +38595,19 @@ plexiform layer. - + cjm - + MA - + ISBN:0781772214 @@ -38644,7 +38671,7 @@ plexiform layer. - + The most anterior region of the brain including both the telencephalon and diencephalon. @@ -38691,14 +38718,14 @@ plexiform layer. forebrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + - + definitional @@ -38774,14 +38801,14 @@ plexiform layer. - + - + The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. developmental relationships need revised @@ -38834,24 +38861,24 @@ plexiform layer. midbrain http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG - + - + - + definitional - + Bgee:AN @@ -38954,14 +38981,14 @@ plexiform layer. - + - + The division of the forebrain that develops from the foremost primary cerebral vesicle. @@ -39024,24 +39051,24 @@ plexiform layer. diencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + - + - + definitional - + definitional @@ -39409,6 +39436,8 @@ plexiform layer. optic tract http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb @@ -39477,7 +39506,7 @@ plexiform layer. - + Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] @@ -39517,14 +39546,14 @@ plexiform layer. midbrain tegmentum http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png - + - + ZFA @@ -39703,8 +39732,8 @@ plexiform layer. - - + + @@ -39717,7 +39746,7 @@ plexiform layer. - + @@ -39732,7 +39761,6 @@ plexiform layer. A vessel through which blood circulates in the body. consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus - Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] Any of the vessels through which blood circulates in the body.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] @@ -39769,41 +39797,40 @@ plexiform layer. vas sanguineum UBERON:0001981 - blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -40162,7 +40189,7 @@ plexiform layer. - + @@ -40175,7 +40202,7 @@ plexiform layer. - + The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. @@ -40226,25 +40253,25 @@ plexiform layer. hindbrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + - + - + modified-source-relation ABA - + Bgee:AN @@ -41063,7 +41090,7 @@ plexiform layer. - + Vasculature that is part of the eye region. not part of the eye in ZFA. Note this changed to a blood vessel in ZFA @@ -41083,15 +41110,17 @@ plexiform layer. vasculature of eye + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb - + - + ISBN:0781772214 @@ -41150,7 +41179,7 @@ plexiform layer. - + @@ -41184,14 +41213,14 @@ plexiform layer. musculoskeletal system - + - + check ctenophore @@ -41329,15 +41358,15 @@ plexiform layer. - + - - + + Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO). TODO - add superclass to unify with VNC? @@ -41393,35 +41422,37 @@ plexiform layer. spinal cord http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb - + - + - + - + ZFA - + definitional - + definitional @@ -41863,7 +41894,7 @@ plexiform layer. - + @@ -41904,14 +41935,14 @@ plexiform layer. coelemic cavity lumen - + - + definitional @@ -42019,9 +42050,9 @@ plexiform layer. - - - + + + @@ -42076,15 +42107,15 @@ plexiform layer. notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -42103,19 +42134,19 @@ plexiform layer. - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -42200,8 +42231,8 @@ plexiform layer. - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk @@ -42247,11 +42278,11 @@ plexiform layer. somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -42264,13 +42295,13 @@ plexiform layer. - + GOTAX:0000352 - + ZFA @@ -42383,12 +42414,12 @@ plexiform layer. - - - - - - + + + + + + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). @@ -42428,66 +42459,66 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells ISBN:0073040584 - + BTO - + PMID:11523831 - + pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest - + PMID:11523831 @@ -42870,14 +42901,14 @@ plexiform layer. - + - + Anatomical system that is involved in the production of hematopoietic cells. Anatomical system that consists of the blood and blood forming tissues.[AAO] @@ -42920,24 +42951,24 @@ plexiform layer. hematopoietic system - + - + - + FMA - + definitional @@ -43002,8 +43033,8 @@ plexiform layer. - - + + @@ -43029,11 +43060,11 @@ plexiform layer. iris epithelium - + - + @@ -43046,13 +43077,13 @@ plexiform layer. - + MA - + MP @@ -43202,7 +43233,7 @@ plexiform layer. - + Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. Do not merge with neurogenic placode Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons @@ -43222,7 +43253,7 @@ plexiform layer. cranial placode - + @@ -43235,7 +43266,7 @@ plexiform layer. - + PMID:11523831 PMID:22512454 @@ -43440,7 +43471,7 @@ plexiform layer. - + @@ -43453,7 +43484,7 @@ plexiform layer. - + The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. consider adding class for organizer. Consider adding separate class for isthmus as a structure Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] @@ -43483,11 +43514,11 @@ plexiform layer. midbrain-hindbrain boundary - + - + @@ -43501,13 +43532,13 @@ plexiform layer. - + ZFA - + ZFA @@ -43672,7 +43703,7 @@ plexiform layer. - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] @@ -43697,14 +43728,14 @@ plexiform layer. presomitic mesoderm - + - + Bgee:AN @@ -43946,7 +43977,7 @@ plexiform layer. - + @@ -43984,7 +44015,7 @@ plexiform layer. eye primordium - + @@ -43997,7 +44028,7 @@ plexiform layer. - + PMID:16496288 XAO @@ -44053,8 +44084,8 @@ plexiform layer. - - + + @@ -44083,24 +44114,24 @@ plexiform layer. optic cup - + - + - + ZFA - + ZFA @@ -44165,7 +44196,7 @@ plexiform layer. - + @@ -44206,7 +44237,7 @@ plexiform layer. lens placode http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png - + @@ -44219,7 +44250,7 @@ plexiform layer. - + ZFA @@ -44283,9 +44314,9 @@ plexiform layer. - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] @@ -44317,34 +44348,34 @@ plexiform layer. neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -44455,7 +44486,7 @@ plexiform layer. - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] @@ -44484,7 +44515,7 @@ plexiform layer. paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -44497,7 +44528,7 @@ plexiform layer. - + Bgee:AN @@ -44609,7 +44640,7 @@ plexiform layer. - + @@ -44653,7 +44684,7 @@ plexiform layer. lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -44666,7 +44697,7 @@ plexiform layer. - + EHDAA2 VHOG @@ -44750,15 +44781,15 @@ plexiform layer. - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] @@ -44778,15 +44809,15 @@ plexiform layer. heart primordium - + - + - + @@ -44799,19 +44830,19 @@ plexiform layer. - + ZFA - + ZFA - + XAO @@ -44866,8 +44897,8 @@ plexiform layer. - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. Skeletogenic portion of somites.[AAO] The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] @@ -44894,11 +44925,11 @@ plexiform layer. sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -44917,13 +44948,13 @@ plexiform layer. - + VHOG:0000680 - + ZFA @@ -45341,7 +45372,7 @@ plexiform layer. - + Mesenchyme that is part of a developing camera-type eye. TODO - change mesenchyme relationships to precursor_of EHDAA2:0000485 @@ -45353,14 +45384,14 @@ plexiform layer. UBERON:0003314 eye mesenchyme - + - + EHDAA2 @@ -46218,7 +46249,7 @@ plexiform layer. - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] @@ -46234,14 +46265,14 @@ plexiform layer. intraembryonic coelom - + - + Wikipedia @@ -46346,7 +46377,7 @@ plexiform layer. - + The part of the retina that contains neurons and photoreceptor cells[GO]. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] @@ -46378,14 +46409,14 @@ plexiform layer. retinal neural layer - + - + Bgee:AN @@ -46643,7 +46674,7 @@ plexiform layer. - + The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium. consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure The layer of undifferentiated, proliferating cells that line the neural tube lumen @@ -46661,7 +46692,7 @@ plexiform layer. neural tube ventricular layer - + @@ -46674,7 +46705,7 @@ plexiform layer. - + NCBIBook:NBK10047 @@ -46734,7 +46765,7 @@ plexiform layer. - + @@ -46758,7 +46789,7 @@ plexiform layer. neural tube mantle layer - + @@ -46771,7 +46802,7 @@ plexiform layer. - + by division NCBIBook:NBK10047 @@ -46808,7 +46839,7 @@ plexiform layer. - + @@ -46825,14 +46856,14 @@ plexiform layer. neural tube marginal layer - + - + forms from axons @@ -47107,9 +47138,9 @@ plexiform layer. - - - + + + @@ -47142,34 +47173,34 @@ plexiform layer. optic vesicle http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png - + - + - + - + ZFA - + GO-def - + ZFA @@ -47285,8 +47316,8 @@ plexiform layer. - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] XAO:0004185 @@ -47299,24 +47330,24 @@ plexiform layer. UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -47375,7 +47406,7 @@ plexiform layer. - + An epithelial tube that will give rise to the mature heart. the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. AAO:0010411 @@ -47395,14 +47426,14 @@ plexiform layer. heart tube - + - + ZFA-modified @@ -47483,7 +47514,7 @@ plexiform layer. - + @@ -47499,14 +47530,14 @@ plexiform layer. eye muscle - + - + MA @@ -47710,7 +47741,7 @@ plexiform layer. - + A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN] @@ -47740,14 +47771,14 @@ plexiform layer. Descemet's membrane https://github.com/obophenotype/uberon/issues/15 - + - + Cline et al @@ -48157,6 +48188,8 @@ plexiform layer. UBERON:0004537 blood vasculature + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb @@ -48528,7 +48561,7 @@ plexiform layer. - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] @@ -48544,14 +48577,14 @@ plexiform layer. skeletal element - + - + VSAO @@ -48596,7 +48629,7 @@ plexiform layer. - + @@ -48635,14 +48668,14 @@ plexiform layer. UBERON:0004770 articular system - + - + FMA @@ -49549,7 +49582,7 @@ plexiform layer. - + Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO] EFO:0003492 @@ -49571,14 +49604,14 @@ plexiform layer. head mesenchyme - + - + EHDAA2 @@ -49645,7 +49678,7 @@ plexiform layer. - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -49661,14 +49694,14 @@ plexiform layer. trunk mesenchyme - + - + EHDAA2 @@ -49691,7 +49724,7 @@ plexiform layer. - + The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]. The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] @@ -49716,14 +49749,14 @@ plexiform layer. myelencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + - + definitional @@ -50250,7 +50283,7 @@ plexiform layer. - + Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. TAO:0002188 ZFA:0001688 @@ -50258,7 +50291,7 @@ plexiform layer. UBERON:0005427 corneal primordium - + @@ -50277,7 +50310,7 @@ plexiform layer. - + ZFA @@ -50300,7 +50333,7 @@ plexiform layer. - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -50318,14 +50351,14 @@ plexiform layer. primitive heart tube - + - + ZFA @@ -50528,7 +50561,7 @@ plexiform layer. - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -50538,7 +50571,7 @@ plexiform layer. UBERON:0005856 developing mesenchymal condensation - + @@ -50557,7 +50590,7 @@ plexiform layer. - + AEO-modified-relation @@ -50616,9 +50649,9 @@ plexiform layer. - - - + + + A serous sac which is the aggregate of the conjunctiva plus the conjunctival space. EMAPA:18233 FMA:20291 @@ -50629,15 +50662,15 @@ plexiform layer. UBERON:0005908 conjunctival sac - + - + - + @@ -50650,19 +50683,19 @@ plexiform layer. - + FMA - + HPO:pr - + MA @@ -50917,7 +50950,7 @@ plexiform layer. - + @@ -50940,14 +50973,14 @@ plexiform layer. future diencephalon - + - + EHDAA2 @@ -51130,7 +51163,7 @@ plexiform layer. - + @@ -51154,14 +51187,14 @@ plexiform layer. future spinal cord - + - + EHDAA2 @@ -51198,7 +51231,7 @@ plexiform layer. - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] @@ -51213,7 +51246,7 @@ plexiform layer. notochordal plate - + @@ -51226,7 +51259,7 @@ plexiform layer. - + EHDAA2 @@ -51263,7 +51296,7 @@ plexiform layer. - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -51280,14 +51313,14 @@ plexiform layer. The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -52192,7 +52225,7 @@ plexiform layer. - + A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis SPD:0000130 @@ -52207,14 +52240,14 @@ plexiform layer. Gene notes: Bmp, Nkx, Gata primary circulatory organ - + - + GO uses blood circulation generically to include the haemolymphatic fluid of arthropods @@ -52369,8 +52402,8 @@ plexiform layer. - - + + @@ -52397,24 +52430,24 @@ plexiform layer. presumptive hindbrain - + - + - + XAO-abduced - + cjm @@ -52471,7 +52504,7 @@ plexiform layer. - + @@ -52490,14 +52523,14 @@ plexiform layer. presumptive midbrain hindbrain boundary - + - + ZFA @@ -52536,7 +52569,7 @@ plexiform layer. - + @@ -52553,14 +52586,14 @@ plexiform layer. presumptive segmental plate - + - + https://github.com/obophenotype/uberon/wiki/The-neural-crest EDHAA2 @@ -52659,7 +52692,7 @@ plexiform layer. - + @@ -52685,7 +52718,7 @@ plexiform layer. presumptive paraxial mesoderm - + @@ -52701,7 +52734,7 @@ plexiform layer. - + https://github.com/obophenotype/uberon/issues/1277 @@ -52783,7 +52816,7 @@ plexiform layer. - + A neural decussation that is part of a diencephalon. FMA:62446 diencephalon decussation @@ -52791,7 +52824,7 @@ plexiform layer. UBERON:0007425 decussation of diencephalon - + @@ -52804,7 +52837,7 @@ plexiform layer. - + Obol @@ -52879,7 +52912,7 @@ plexiform layer. - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -52887,7 +52920,7 @@ plexiform layer. UBERON:0007524 dense mesenchyme tissue - + @@ -52900,7 +52933,7 @@ plexiform layer. - + AEO @@ -53140,7 +53173,7 @@ plexiform layer. - + An axon tract that is part of a brain. the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts FMA:83848 @@ -53150,14 +53183,14 @@ plexiform layer. UBERON:0007702 tract of brain - + - + cjm @@ -53185,7 +53218,7 @@ plexiform layer. - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. @@ -53202,14 +53235,14 @@ plexiform layer. vascular system - + - + MA @@ -53342,7 +53375,7 @@ plexiform layer. - + @@ -53359,14 +53392,14 @@ plexiform layer. UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -53462,8 +53495,8 @@ plexiform layer. - - + + TODO - developmental relationships for lines TAO:0007044 ZFA:0007044 @@ -53473,24 +53506,24 @@ plexiform layer. UBERON:0009615 midbrain hindbrain boundary neural plate - + - + - + ZFA - + https://github.com/obophenotype/uberon/issues/438 Bgee:AN @@ -53524,14 +53557,14 @@ plexiform layer. - + - + @@ -53556,24 +53589,24 @@ plexiform layer. presumptive midbrain - + - + - + ZFA - + ZFA @@ -53619,7 +53652,7 @@ plexiform layer. - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -53627,14 +53660,14 @@ plexiform layer. UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -53656,7 +53689,7 @@ plexiform layer. - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -53666,14 +53699,14 @@ plexiform layer. anterior lateral plate mesoderm - + - + ZFA @@ -53729,14 +53762,14 @@ plexiform layer. - + EHDAA2:0001315 EHDAA:1122 uberon UBERON:0009920 optic neural crest - + @@ -53749,7 +53782,7 @@ plexiform layer. - + EHDAA2 @@ -53883,7 +53916,7 @@ plexiform layer. - + @@ -53908,14 +53941,14 @@ plexiform layer. eyeball of camera-type eye - + - + FMA @@ -53956,8 +53989,8 @@ plexiform layer. - - + + Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. DHBA:12322 EFO:0003567 @@ -53971,11 +54004,11 @@ plexiform layer. midbrain basal plate - + - + @@ -53988,13 +54021,13 @@ plexiform layer. - + EHDAA2 - + ZFA @@ -54022,7 +54055,7 @@ plexiform layer. - + Portion of neural tube that gives rise to the midbrain. we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed TAO:0007039 @@ -54031,14 +54064,14 @@ plexiform layer. UBERON:0010286 midbrain neural tube - + - + ZFA @@ -54065,7 +54098,7 @@ plexiform layer. - + @@ -54081,14 +54114,14 @@ plexiform layer. UBERON:0010312 immature eye - + - + definitional @@ -54306,6 +54339,14 @@ plexiform layer. UBERON:0010427 ciliary processes http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Eye_L.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Eye_R.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Eye_L.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Eye_R.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb @@ -54358,8 +54399,8 @@ plexiform layer. - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] FMA:23879 @@ -54372,11 +54413,11 @@ plexiform layer. subdivision of skeleton - + - + @@ -54389,13 +54430,13 @@ plexiform layer. - + UBERONREF:0000003 - + VSAO @@ -54472,7 +54513,7 @@ plexiform layer. - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -54482,7 +54523,7 @@ plexiform layer. postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -54495,7 +54536,7 @@ plexiform layer. - + cjm @@ -54607,7 +54648,7 @@ plexiform layer. - + Muscles within the eye (bulbus oculi).[AAO] AAO:0010038 EMAPA:18808 @@ -54618,14 +54659,14 @@ plexiform layer. UBERON:0011222 intra-ocular muscle - + - + EMAPA @@ -54895,7 +54936,7 @@ plexiform layer. - + @@ -54937,7 +54978,7 @@ plexiform layer. anterior uvea - + @@ -54950,7 +54991,7 @@ plexiform layer. - + MP @@ -55726,7 +55767,7 @@ plexiform layer. - + @@ -55749,7 +55790,7 @@ plexiform layer. UBERON:0016887 entire extraembryonic component - + @@ -55762,7 +55803,7 @@ plexiform layer. - + AEO @@ -56514,6 +56555,209 @@ plexiform layer. + + + + + + + + + example to be eventually removed + example to be eventually removed + + + + + + + + failed exploratory term + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + + + + + + metadata complete + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + organizational term + Term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + ready for release + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + metadata incomplete + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + uncurated + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + pending final vetting + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + placeholder removed + placeholder removed + + + + + + + + terms merged + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + + + + + + term imported + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + + + + + + term split + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + + + + + + universal + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + + + + + + defined class + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + + + + + + named class expression + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + + + + + + to be replaced with external ontology term + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + requires discussion + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. + This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/77 + https://orcid.org/0000-0001-5208-3432 + out of scope + + + + + definition + + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition + definition @@ -85,12 +111,18 @@ + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> IAO:0000116 uberon editor_note true editor_note editor note + editor note @@ -115,7 +147,13 @@ - + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + @@ -128,6 +166,12 @@ + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg IAO:0000233 external uberon @@ -135,15 +179,31 @@ true true term_tracker_item + The 'tracker item' can associate a tracker with a specific ontology term. term tracker item + term tracker item + + + + + + + expand expression to + ObjectProperty: RO_0002104 +Label: has plasma membrane part +Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones + Chris Mungall expand expression to + expand expression to @@ -175,6 +235,9 @@ + has ontology root term + Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. + Nicolas Matentzoglu IAO:0000700 external uberon @@ -183,6 +246,7 @@ true has_ontology_root_term has ontology root term + has ontology root term preferred_root @@ -197,7 +261,14 @@ + term replaced by + + Use on obsolete terms, relating the term to another term that can be used as a substitute + Person:Alan Ruttenberg + Person:Alan Ruttenberg + Add as annotation triples in the granting ontology term replaced by + term replaced by @@ -216,7 +287,44 @@ - + + 'part disjoint with' 'defined by construct' """ + PREFIX owl: <http://www.w3.org/2002/07/owl#> + PREFIX : <http://example.org/ + CONSTRUCT { + [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?a ; + owl:disjointWith [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?b + ] + ] + } + WHERE { + ?a :part_disjoint_with ?b . + } + Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. + + + + defined by construct + + + + + + + + CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) + A synonym type for describing pluralization synonyms + + + 2023-03-03 + plural form + @@ -1102,7 +1210,6 @@ WHERE { - plural term @@ -1396,6 +1503,12 @@ WHERE { + + + + + + @@ -1589,7 +1702,12 @@ WHERE { + An alternative label for a class or property which has a more general meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + has broad synonym has_broad_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 @@ -1605,7 +1723,12 @@ WHERE { + An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + has exact synonym has_exact_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 @@ -1613,7 +1736,12 @@ WHERE { + An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + has narrow synonym has_narrow_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 @@ -1629,7 +1757,12 @@ WHERE { + An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + has related synonym has_related_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 @@ -1894,12 +2027,35 @@ WHERE { + + + + + + + + + + + + + + + + + - - - contains - RO:0001019 - uberon - contains - contains - contains - obsolete contains - - true - - - - @@ -8172,26 +8312,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - CARO:0000013 - cell in vivo - - To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). - native cell - - - - - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - CARO:mah - - - - @@ -8237,7 +8357,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -8245,7 +8365,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -8471,14 +8590,13 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + - A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring. @@ -8598,7 +8716,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -8611,7 +8729,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -8885,7 +9002,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -8922,7 +9039,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube. @@ -9502,20 +9618,20 @@ MH: sexual subtypes should probably be logically defined based on sexual process mesenchymal progenitor cells MESH:D044982 - + mesenchymal stromal cells - + stem cells, mesenchymal MESH:D044982 - + @@ -9632,7 +9748,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -9657,12 +9772,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process melanocyte - - - - - true - @@ -9676,7 +9785,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - pigment cell visual pigment cell @@ -9689,7 +9797,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9697,7 +9805,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9736,7 +9844,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -9763,7 +9870,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9782,7 +9889,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -9825,7 +9931,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose primary function is to shorten. contractile cell @@ -9843,7 +9949,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -9877,7 +9982,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9885,7 +9990,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9976,7 +10081,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10043,7 +10148,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose function is determined by the generation or the reception of an electric signal. electrically active cell @@ -10062,7 +10167,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10070,7 +10175,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10168,7 +10273,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10202,7 +10307,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10240,7 +10345,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10251,7 +10356,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -10404,7 +10508,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10412,7 +10516,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10428,7 +10532,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell that is specialised to accumulate a particular substance(s). stuff accumulating cell @@ -10499,7 +10603,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10507,7 +10611,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10588,7 +10692,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process + + + + + + + Diploid cell produced by the fusion of sperm cell nucleus and egg cell. zygote BTO:0000854 @@ -10768,7 +10879,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose primary function is to protect the organism. defensive cell @@ -10878,12 +10989,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process satellite cell smooth muscle myoblast - - - - - true - @@ -10933,12 +11038,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process skeletal myoblast skeletal muscle myoblast - - - - - true - @@ -11027,7 +11126,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -11126,36 +11224,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - - - - - - - - - - - - - - - - - A native cell that is part of some Metazoa. - metazoan cell - - animal cell - https://www.swissbiopics.org/api/image/Animal_cells.svg - - - - @@ -11646,7 +11714,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -11686,7 +11753,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -11699,12 +11765,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process MESH:D053687 somatic stem cell - - - - - true - @@ -11781,6 +11841,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process + @@ -12216,6 +12277,24 @@ MH: sexual subtypes should probably be logically defined based on sexual process Most markers only described for human pro NK cells. pro-NK cell + + + + null cell + PMID:11532393 + + + + + preNK cell + PMID:11532393 + + + + + + true + @@ -12236,24 +12315,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process PMID:15032583 PMID:15766674 - - - - null cell - PMID:11532393 - - - - - preNK cell - PMID:11532393 - - - - - - true - @@ -12767,7 +12828,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell of a hematopoietic lineage. BTO:0000574 CALOHA:TS-2017 @@ -12856,7 +12917,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -12864,7 +12925,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -12879,12 +12940,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process bone cell - - - - - true - @@ -13320,7 +13375,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -13437,7 +13491,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -13445,7 +13499,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -13473,7 +13527,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -13481,7 +13535,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -13511,7 +13565,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -13519,7 +13573,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -13536,12 +13590,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process connective tissue cell - - - - - true - @@ -13555,7 +13603,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell of the embryo. 2010-09-15T03:39:21Z @@ -13574,29 +13622,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). - - 2010-09-24T09:44:42Z - BTO:0001268 - FMA:72300 - WBbt:0008378 - - somatic cell - - - - - A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). - GOC:tfm - ISBN:0721662544 - - - - @@ -13653,7 +13678,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -13661,7 +13686,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -13679,12 +13704,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cardiocyte - - - - - true - @@ -13697,7 +13716,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized). 2012-06-15T02:51:27Z @@ -13870,7 +13889,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -13928,7 +13946,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A zygote in a plant or an animal. MESH:D015053 zygote @@ -14023,7 +14041,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -14031,7 +14049,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -15723,32 +15741,32 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -21748,28 +21766,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system. - endocrine physiological process - endocrine physiology - biological_process - GO:0050886 - - - endocrine process - - - - - The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system. - ISBN:0721662544 - - - - @@ -24057,6 +24053,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process GC_ID:1 + PMID:30365038 + PMID:32761142 ncbi_taxonomy all NCBITaxon:1 @@ -28429,8 +28427,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + @@ -28481,11 +28479,11 @@ MH: sexual subtypes should probably be logically defined based on sexual process tendon http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg - + - + @@ -28498,13 +28496,13 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + OG - + AEO @@ -29495,7 +29493,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -29531,14 +29529,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process gastrula stage - + - + BILS @@ -29759,7 +29757,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -29832,7 +29830,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process https://github.com/obophenotype/uberon/issues/661 http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg - + @@ -29845,7 +29843,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + exceptions in some taxa @@ -30154,7 +30152,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -30196,14 +30194,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process organism substance - + - + this relationship may be too strong and may be weakened in future @@ -31435,7 +31433,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] @@ -31473,14 +31471,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -31533,7 +31531,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] endodermal @@ -31570,14 +31568,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -31622,7 +31620,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The middle germ layer of the embryo, between the endoderm and ectoderm. Primary germ layer that is the middle of the embryonic germ layers.[AAO] @@ -31667,7 +31665,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + @@ -31680,7 +31678,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Bgee:AN @@ -31872,17 +31870,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - - - - - - @@ -31890,12 +31877,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - @@ -32003,8 +31984,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + @@ -32040,24 +32021,24 @@ MH: sexual subtypes should probably be logically defined based on sexual process eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -32282,6 +32263,11 @@ MH: sexual subtypes should probably be logically defined based on sexual process respiratory system http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg + https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb @@ -32664,7 +32650,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -32719,14 +32705,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -32814,7 +32800,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. Part of the nervous system which includes the brain and spinal cord.[AAO] @@ -32861,7 +32847,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process central nervous system - + @@ -32875,7 +32861,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Bgee:AN @@ -33742,7 +33728,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Skeletal element that is composed of bone tissue. @@ -33792,14 +33778,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process bone element - + - + VSAO-modified @@ -33910,7 +33896,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A tube extending from the mouth to the anus. @@ -33950,14 +33936,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process digestive tract - + - + NCBIBook:NBK10107 @@ -34548,7 +34534,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -34584,14 +34570,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process musculoskeletal system - + - + check ctenophore @@ -34654,9 +34640,9 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - + + + @@ -34711,15 +34697,15 @@ MH: sexual subtypes should probably be logically defined based on sexual process notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -34738,19 +34724,19 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -34835,8 +34821,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk @@ -34882,11 +34868,11 @@ MH: sexual subtypes should probably be logically defined based on sexual process somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -34899,13 +34885,13 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + GOTAX:0000352 - + ZFA @@ -35082,12 +35068,12 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - + + + + + + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). @@ -35127,66 +35113,66 @@ MH: sexual subtypes should probably be logically defined based on sexual process http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells ISBN:0073040584 - + BTO - + PMID:11523831 - + pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest - + PMID:11523831 @@ -35541,7 +35527,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -35599,14 +35585,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -35877,14 +35863,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + - + Anatomical system that is involved in the production of hematopoietic cells. @@ -35928,24 +35914,24 @@ MH: sexual subtypes should probably be logically defined based on sexual process hematopoietic system - + - + - + FMA - + definitional @@ -36411,7 +36397,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] @@ -36436,14 +36422,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process presomitic mesoderm - + - + Bgee:AN @@ -36673,9 +36659,9 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] @@ -36707,34 +36693,34 @@ MH: sexual subtypes should probably be logically defined based on sexual process neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -36799,7 +36785,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] @@ -36828,7 +36814,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -36841,7 +36827,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Bgee:AN @@ -36913,7 +36899,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -36957,7 +36943,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -36970,7 +36956,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + EHDAA2 VHOG @@ -37054,7 +37040,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -37097,7 +37083,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process myotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + @@ -37110,7 +37096,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + EHDAA2-abduced @@ -37166,8 +37152,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. Skeletogenic portion of somites.[AAO] The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] @@ -37194,11 +37180,11 @@ MH: sexual subtypes should probably be logically defined based on sexual process sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -37217,13 +37203,13 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + VHOG:0000680 - + ZFA @@ -37432,7 +37418,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] @@ -37448,14 +37434,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process intraembryonic coelom - + - + Wikipedia @@ -37783,7 +37769,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The bilaminar epithelium formed from the myotome and dermatome. Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]. Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO] @@ -37806,7 +37792,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0004290 dermomyotome - + @@ -37825,7 +37811,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + EHDAA2 ZFA @@ -38151,7 +38137,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]. A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] EMAPA:37744 @@ -38165,7 +38151,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from skeletal tissue - + @@ -38178,7 +38164,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + 2012-08-14 VSAO:0000015 VSAO @@ -38217,7 +38203,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] @@ -38233,14 +38219,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process skeletal element - + - + VSAO @@ -38285,7 +38271,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -38324,14 +38310,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0004770 articular system - + - + FMA @@ -38798,7 +38784,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -38814,14 +38800,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process trunk mesenchyme - + - + EHDAA2 @@ -39118,7 +39104,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -39128,7 +39114,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0005856 developing mesenchymal condensation - + @@ -39147,7 +39133,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + AEO-modified-relation @@ -39252,7 +39238,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] @@ -39267,7 +39253,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process notochordal plate - + @@ -39280,7 +39266,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + EHDAA2 @@ -39317,7 +39303,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -39334,14 +39320,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -39799,7 +39785,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis SPD:0000130 @@ -39814,14 +39800,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process Gene notes: Bmp, Nkx, Gata primary circulatory organ - + - + GO uses blood circulation generically to include the haemolymphatic fluid of arthropods @@ -39911,7 +39897,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -39928,14 +39914,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process presumptive segmental plate - + - + https://github.com/obophenotype/uberon/wiki/The-neural-crest EDHAA2 @@ -40034,7 +40020,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -40060,7 +40046,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process presumptive paraxial mesoderm - + @@ -40076,7 +40062,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + https://github.com/obophenotype/uberon/issues/1277 @@ -40125,7 +40111,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -40133,7 +40119,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0007524 dense mesenchyme tissue - + @@ -40146,7 +40132,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + AEO @@ -40456,7 +40442,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -40473,14 +40459,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -40502,7 +40488,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -40510,14 +40496,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -40677,8 +40663,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] FMA:23879 @@ -40691,11 +40677,11 @@ MH: sexual subtypes should probably be logically defined based on sexual process subdivision of skeleton - + - + @@ -40708,13 +40694,13 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + UBERONREF:0000003 - + VSAO @@ -41085,7 +41071,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -41110,7 +41096,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0011899 epimysium - + @@ -41123,7 +41109,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + FMA @@ -41229,7 +41215,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -41251,7 +41237,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0012429 hematopoietic tissue - + @@ -41264,7 +41250,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + defitional @@ -41832,7 +41818,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -41855,7 +41841,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0016887 entire extraembryonic component - + @@ -41868,7 +41854,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + AEO @@ -41954,7 +41940,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -41970,14 +41956,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process skeletal musculature - + - + MA @@ -42265,6 +42251,209 @@ MH: sexual subtypes should probably be logically defined based on sexual process + + + + + + + + + example to be eventually removed + example to be eventually removed + + + + + + + + failed exploratory term + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + + + + + + metadata complete + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + organizational term + Term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + ready for release + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + metadata incomplete + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + uncurated + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + pending final vetting + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + placeholder removed + placeholder removed + + + + + + + + terms merged + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + + + + + + term imported + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + + + + + + term split + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + + + + + + universal + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + + + + + + defined class + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + + + + + + named class expression + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + + + + + + to be replaced with external ontology term + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + requires discussion + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. + This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/77 + https://orcid.org/0000-0001-5208-3432 + out of scope + + + + + definition + + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition + definition @@ -85,12 +111,18 @@ + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> IAO:0000116 uberon editor_note true editor_note editor note + editor note @@ -115,7 +147,13 @@ - + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + @@ -128,6 +166,12 @@ + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg IAO:0000233 external uberon @@ -135,15 +179,31 @@ true true term_tracker_item + The 'tracker item' can associate a tracker with a specific ontology term. term tracker item + term tracker item + + + + + + + expand expression to + ObjectProperty: RO_0002104 +Label: has plasma membrane part +Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones + Chris Mungall expand expression to + expand expression to @@ -175,6 +235,9 @@ + has ontology root term + Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. + Nicolas Matentzoglu IAO:0000700 external uberon @@ -183,6 +246,7 @@ true has_ontology_root_term has ontology root term + has ontology root term preferred_root @@ -197,7 +261,14 @@ + term replaced by + + Use on obsolete terms, relating the term to another term that can be used as a substitute + Person:Alan Ruttenberg + Person:Alan Ruttenberg + Add as annotation triples in the granting ontology term replaced by + term replaced by @@ -216,7 +287,44 @@ - + + 'part disjoint with' 'defined by construct' """ + PREFIX owl: <http://www.w3.org/2002/07/owl#> + PREFIX : <http://example.org/ + CONSTRUCT { + [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?a ; + owl:disjointWith [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?b + ] + ] + } + WHERE { + ?a :part_disjoint_with ?b . + } + Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. + + + + defined by construct + + + + + + + + CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) + A synonym type for describing pluralization synonyms + + + 2023-03-03 + plural form + @@ -1102,7 +1210,6 @@ WHERE { - plural term @@ -1396,6 +1503,12 @@ WHERE { + + + + + + @@ -1589,7 +1702,12 @@ WHERE { + An alternative label for a class or property which has a more general meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + has broad synonym has_broad_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 @@ -1605,7 +1723,12 @@ WHERE { + An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + has exact synonym has_exact_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 @@ -1613,7 +1736,12 @@ WHERE { + An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + has narrow synonym has_narrow_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 @@ -1629,7 +1757,12 @@ WHERE { + An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + has related synonym has_related_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 @@ -1894,12 +2027,35 @@ WHERE { + + + + + + + + + + + + + + + + + - - - contains - RO:0001019 - uberon - contains - contains - contains - obsolete contains - - true - - - - @@ -8177,26 +8317,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - CARO:0000013 - cell in vivo - - To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). - native cell - - - - - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - CARO:mah - - - - @@ -8219,7 +8339,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -8227,7 +8347,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -8603,7 +8722,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -8616,7 +8735,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -8959,7 +9077,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9057,7 +9175,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9065,7 +9183,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9772,20 +9890,20 @@ MH: sexual subtypes should probably be logically defined based on sexual process mesenchymal progenitor cells MESH:D044982 - + mesenchymal stromal cells - + stem cells, mesenchymal MESH:D044982 - + @@ -9839,7 +9957,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9847,7 +9965,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9874,7 +9992,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose primary function is to shorten. contractile cell @@ -9892,7 +10010,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -9923,7 +10040,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose function is determined by the generation or the reception of an electric signal. electrically active cell @@ -9956,7 +10073,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose primary function is to prevent the transport of stuff across compartments. barrier cell @@ -9975,7 +10092,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9983,7 +10100,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10081,7 +10198,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10089,7 +10206,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10117,7 +10234,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10151,7 +10268,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10335,7 +10452,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10346,7 +10463,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -10499,7 +10615,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10507,7 +10623,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10523,7 +10639,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell that is specialised to accumulate a particular substance(s). stuff accumulating cell @@ -10543,7 +10659,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10551,7 +10667,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10637,7 +10753,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process + + + + + + + Diploid cell produced by the fusion of sperm cell nucleus and egg cell. zygote BTO:0000854 @@ -10862,7 +10985,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose primary function is to protect the organism. defensive cell @@ -11189,36 +11312,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - - - - - - - - - - - - - - - - - A native cell that is part of some Metazoa. - metazoan cell - - animal cell - https://www.swissbiopics.org/api/image/Animal_cells.svg - - - - @@ -12450,7 +12543,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -12490,7 +12582,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -12503,12 +12594,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process MESH:D053687 somatic stem cell - - - - - true - @@ -12537,6 +12622,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process + @@ -15081,7 +15167,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell of a hematopoietic lineage. BTO:0000574 CALOHA:TS-2017 @@ -15170,7 +15256,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -15178,7 +15264,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -15193,12 +15279,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process bone cell - - - - - true - @@ -15810,7 +15890,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -15848,7 +15927,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -16078,7 +16156,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -16086,7 +16164,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -16149,7 +16227,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -16157,7 +16235,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -16187,7 +16265,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -16195,7 +16273,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -16212,12 +16290,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process connective tissue cell - - - - - true - @@ -16231,7 +16303,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell of the embryo. 2010-09-15T03:39:21Z @@ -16250,29 +16322,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). - - 2010-09-24T09:44:42Z - BTO:0001268 - FMA:72300 - WBbt:0008378 - - somatic cell - - - - - A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). - GOC:tfm - ISBN:0721662544 - - - - @@ -16324,7 +16373,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -16332,7 +16381,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -16350,12 +16399,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cardiocyte - - - - - true - @@ -16369,7 +16412,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - An endothelial progenitor cell that participates in angiogenesis during development. 2011-02-28T04:20:39Z @@ -16521,7 +16563,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized). 2012-06-15T02:51:27Z @@ -16594,7 +16636,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -16617,7 +16658,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A zygote in a plant or an animal. MESH:D015053 zygote @@ -16685,7 +16726,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -16693,7 +16734,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -20259,32 +20300,32 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -32471,6 +32512,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process GC_ID:1 + PMID:30365038 + PMID:32761142 ncbi_taxonomy all NCBITaxon:1 @@ -38802,7 +38845,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -38838,14 +38881,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process gastrula stage - + - + BILS @@ -39066,7 +39109,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -39139,7 +39182,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process https://github.com/obophenotype/uberon/issues/661 http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg - + @@ -39152,7 +39195,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + exceptions in some taxa @@ -39277,15 +39320,15 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + - - + + A fluid that is composed of blood plasma and erythrocytes. This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. @@ -39327,34 +39370,34 @@ MH: sexual subtypes should probably be logically defined based on sexual process blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -39658,7 +39701,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -39700,14 +39743,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process organism substance - + - + this relationship may be too strong and may be weakened in future @@ -40937,7 +40980,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] @@ -40975,14 +41018,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -41035,7 +41078,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] endodermal @@ -41072,14 +41115,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -41124,7 +41167,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The middle germ layer of the embryo, between the endoderm and ectoderm. Primary germ layer that is the middle of the embryonic germ layers.[AAO] @@ -41169,7 +41212,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + @@ -41182,7 +41225,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Bgee:AN @@ -41389,7 +41432,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -41462,15 +41505,18 @@ MH: sexual subtypes should probably be logically defined based on sexual process Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706 heart + https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + MA @@ -41748,6 +41794,11 @@ MH: sexual subtypes should probably be logically defined based on sexual process respiratory system http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg + https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb @@ -42126,7 +42177,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -42179,14 +42230,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -42274,7 +42325,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. Part of the nervous system which includes the brain and spinal cord.[AAO] @@ -42321,7 +42372,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process central nervous system - + @@ -42335,7 +42386,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Bgee:AN @@ -42829,7 +42880,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Skeletal element that is composed of bone tissue. @@ -42879,14 +42930,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process bone element - + - + VSAO-modified @@ -42997,7 +43048,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A tube extending from the mouth to the anus. @@ -43037,14 +43088,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process digestive tract - + - + NCBIBook:NBK10107 @@ -43321,8 +43372,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + @@ -43335,7 +43386,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -43350,7 +43401,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process A vessel through which blood circulates in the body. consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus - Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] Any of the vessels through which blood circulates in the body.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] @@ -43387,41 +43437,40 @@ MH: sexual subtypes should probably be logically defined based on sexual process vas sanguineum UBERON:0001981 - blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -44144,7 +44193,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -44178,14 +44227,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process musculoskeletal system - + - + check ctenophore @@ -44314,7 +44363,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -44355,14 +44404,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process coelemic cavity lumen - + - + definitional @@ -44470,9 +44519,9 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - + + + @@ -44527,15 +44576,15 @@ MH: sexual subtypes should probably be logically defined based on sexual process notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -44554,19 +44603,19 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -44651,8 +44700,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk @@ -44698,11 +44747,11 @@ MH: sexual subtypes should probably be logically defined based on sexual process somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -44715,13 +44764,13 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + GOTAX:0000352 - + ZFA @@ -44834,12 +44883,12 @@ MH: sexual subtypes should probably be logically defined based on sexual process + + + + + - - - - - A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). @@ -44879,66 +44928,66 @@ MH: sexual subtypes should probably be logically defined based on sexual process http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells ISBN:0073040584 - + BTO - + PMID:11523831 - + pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest - + PMID:11523831 @@ -45126,7 +45175,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -45184,14 +45233,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -45462,14 +45511,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + - + Anatomical system that is involved in the production of hematopoietic cells. Anatomical system that consists of the blood and blood forming tissues.[AAO] @@ -45512,24 +45561,24 @@ MH: sexual subtypes should probably be logically defined based on sexual process hematopoietic system - + - + - + FMA - + definitional @@ -45900,7 +45949,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] @@ -45925,14 +45974,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process presomitic mesoderm - + - + Bgee:AN @@ -46162,9 +46211,9 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] @@ -46196,34 +46245,34 @@ MH: sexual subtypes should probably be logically defined based on sexual process neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -46288,7 +46337,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] @@ -46317,7 +46366,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -46330,7 +46379,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Bgee:AN @@ -46402,7 +46451,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -46446,7 +46495,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -46459,7 +46508,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + EHDAA2 VHOG @@ -46543,15 +46592,15 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] @@ -46571,15 +46620,15 @@ MH: sexual subtypes should probably be logically defined based on sexual process heart primordium - + - + - + @@ -46592,19 +46641,19 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + ZFA - + ZFA - + XAO @@ -46659,8 +46708,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. Skeletogenic portion of somites.[AAO] The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] @@ -46687,11 +46736,11 @@ MH: sexual subtypes should probably be logically defined based on sexual process sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -46710,13 +46759,13 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + VHOG:0000680 - + ZFA @@ -46982,7 +47031,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] @@ -46998,14 +47047,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process intraembryonic coelom - + - + Wikipedia @@ -47324,8 +47373,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] XAO:0004185 @@ -47338,24 +47387,24 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -47414,7 +47463,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + An epithelial tube that will give rise to the mature heart. the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. AAO:0010411 @@ -47434,14 +47483,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process heart tube - + - + ZFA-modified @@ -47775,6 +47824,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0004537 blood vasculature + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb @@ -48056,7 +48107,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]. A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] EMAPA:37744 @@ -48070,7 +48121,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from skeletal tissue - + @@ -48083,7 +48134,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + 2012-08-14 VSAO:0000015 VSAO @@ -48122,7 +48173,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] @@ -48138,14 +48189,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process skeletal element - + - + VSAO @@ -48190,7 +48241,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -48229,14 +48280,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0004770 articular system - + - + FMA @@ -48994,7 +49045,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -49010,14 +49061,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process trunk mesenchyme - + - + EHDAA2 @@ -49128,7 +49179,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -49146,14 +49197,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process primitive heart tube - + - + ZFA @@ -49321,7 +49372,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -49331,7 +49382,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0005856 developing mesenchymal condensation - + @@ -49350,7 +49401,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + AEO-modified-relation @@ -49455,7 +49506,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] @@ -49470,7 +49521,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process notochordal plate - + @@ -49483,7 +49534,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + EHDAA2 @@ -49520,7 +49571,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -49537,14 +49588,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -50287,7 +50338,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis SPD:0000130 @@ -50302,14 +50353,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process Gene notes: Bmp, Nkx, Gata primary circulatory organ - + - + GO uses blood circulation generically to include the haemolymphatic fluid of arthropods @@ -50399,7 +50450,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -50416,14 +50467,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process presumptive segmental plate - + - + https://github.com/obophenotype/uberon/wiki/The-neural-crest EDHAA2 @@ -50522,7 +50573,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -50548,7 +50599,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process presumptive paraxial mesoderm - + @@ -50564,7 +50615,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + https://github.com/obophenotype/uberon/issues/1277 @@ -50640,7 +50691,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -50648,7 +50699,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0007524 dense mesenchyme tissue - + @@ -50661,7 +50712,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + AEO @@ -50758,7 +50809,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. @@ -50775,14 +50826,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process vascular system - + - + MA @@ -50915,7 +50966,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -50932,14 +50983,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -50995,7 +51046,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -51003,14 +51054,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -51032,7 +51083,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -51042,14 +51093,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process anterior lateral plate mesoderm - + - + ZFA @@ -51183,7 +51234,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -51203,14 +51254,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0010210 blood clot - + - + BTO @@ -51332,8 +51383,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] FMA:23879 @@ -51346,11 +51397,11 @@ MH: sexual subtypes should probably be logically defined based on sexual process subdivision of skeleton - + - + @@ -51363,13 +51414,13 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + UBERONREF:0000003 - + VSAO @@ -51446,7 +51497,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -51456,7 +51507,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -51469,7 +51520,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + cjm @@ -51734,7 +51785,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -51756,7 +51807,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0012429 hematopoietic tissue - + @@ -51769,7 +51820,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + defitional @@ -52339,7 +52390,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -52362,7 +52413,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0016887 entire extraembryonic component - + @@ -52375,7 +52426,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + AEO @@ -52600,6 +52651,209 @@ MH: sexual subtypes should probably be logically defined based on sexual process + + + + + + + + + example to be eventually removed + example to be eventually removed + + + + + + + + failed exploratory term + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + + + + + + metadata complete + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + organizational term + Term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + ready for release + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + metadata incomplete + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + uncurated + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + pending final vetting + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + placeholder removed + placeholder removed + + + + + + + + terms merged + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + + + + + + term imported + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + + + + + + term split + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + + + + + + universal + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + + + + + + defined class + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + + + + + + named class expression + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + + + + + + to be replaced with external ontology term + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + requires discussion + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. + This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/77 + https://orcid.org/0000-0001-5208-3432 + out of scope + + + + + definition + + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition + definition @@ -85,12 +111,18 @@ + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> IAO:0000116 uberon editor_note true editor_note editor note + editor note @@ -115,7 +147,13 @@ - + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + @@ -128,6 +166,12 @@ + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg IAO:0000233 external uberon @@ -135,15 +179,31 @@ true true term_tracker_item + The 'tracker item' can associate a tracker with a specific ontology term. term tracker item + term tracker item + + + + + + + expand expression to + ObjectProperty: RO_0002104 +Label: has plasma membrane part +Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones + Chris Mungall expand expression to + expand expression to @@ -175,6 +235,9 @@ + has ontology root term + Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. + Nicolas Matentzoglu IAO:0000700 external uberon @@ -183,6 +246,7 @@ true has_ontology_root_term has ontology root term + has ontology root term preferred_root @@ -197,7 +261,14 @@ + term replaced by + + Use on obsolete terms, relating the term to another term that can be used as a substitute + Person:Alan Ruttenberg + Person:Alan Ruttenberg + Add as annotation triples in the granting ontology term replaced by + term replaced by @@ -216,7 +287,44 @@ - + + 'part disjoint with' 'defined by construct' """ + PREFIX owl: <http://www.w3.org/2002/07/owl#> + PREFIX : <http://example.org/ + CONSTRUCT { + [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?a ; + owl:disjointWith [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?b + ] + ] + } + WHERE { + ?a :part_disjoint_with ?b . + } + Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. + + + + defined by construct + + + + + + + + CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) + A synonym type for describing pluralization synonyms + + + 2023-03-03 + plural form + @@ -1102,7 +1210,6 @@ WHERE { - plural term @@ -1396,6 +1503,12 @@ WHERE { + + + + + + @@ -1589,7 +1702,12 @@ WHERE { + An alternative label for a class or property which has a more general meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + has broad synonym has_broad_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 @@ -1605,7 +1723,12 @@ WHERE { + An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + has exact synonym has_exact_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 @@ -1613,7 +1736,12 @@ WHERE { + An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + has narrow synonym has_narrow_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 @@ -1629,7 +1757,12 @@ WHERE { + An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + has related synonym has_related_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 @@ -1894,12 +2027,35 @@ WHERE { + + + + + + + + + + + + + + + + + - - - contains - RO:0001019 - uberon - contains - contains - contains - obsolete contains - - true - - - - @@ -8220,26 +8360,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - CARO:0000013 - cell in vivo - - To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). - native cell - - - - - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - CARO:mah - - - - @@ -8333,7 +8453,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -8349,7 +8468,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -8378,7 +8497,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -8386,7 +8505,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -8665,7 +8783,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -8678,7 +8796,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -8949,7 +9066,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9034,7 +9151,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube. @@ -9291,6 +9407,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process + @@ -9362,7 +9479,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process macroglia doi:10.1152/physrev.2001.81.2.871 - + @@ -9528,20 +9645,20 @@ MH: sexual subtypes should probably be logically defined based on sexual process mesenchymal progenitor cells MESH:D044982 - + mesenchymal stromal cells - + stem cells, mesenchymal MESH:D044982 - + @@ -9584,7 +9701,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -9609,12 +9725,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process melanocyte - - - - - true - @@ -9628,7 +9738,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - pigment cell visual pigment cell @@ -9641,7 +9750,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9649,7 +9758,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9676,7 +9785,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose primary function is to shorten. contractile cell @@ -9694,7 +9803,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -9787,7 +9895,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9854,7 +9962,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose function is determined by the generation or the reception of an electric signal. electrically active cell @@ -9887,7 +9995,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose primary function is to prevent the transport of stuff across compartments. barrier cell @@ -9906,7 +10014,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9914,7 +10022,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10096,7 +10204,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10104,7 +10212,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10149,7 +10257,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism. structural cell @@ -10176,7 +10284,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell that is specialised to accumulate a particular substance(s). stuff accumulating cell @@ -10196,7 +10304,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10204,7 +10312,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10283,7 +10391,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10318,7 +10426,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -10359,7 +10466,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -10417,7 +10523,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process + + + + + + + Diploid cell produced by the fusion of sperm cell nucleus and egg cell. zygote BTO:0000854 @@ -10524,12 +10637,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process satellite cell smooth muscle myoblast - - - - - true - @@ -10617,7 +10724,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -10843,36 +10949,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - - - - - - - - - - - - - - - - - A native cell that is part of some Metazoa. - metazoan cell - - animal cell - https://www.swissbiopics.org/api/image/Animal_cells.svg - - - - @@ -11652,8 +11728,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process ACs doi:10.1038/s41598-020-66092-9 + - @@ -11932,7 +12008,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -12035,7 +12110,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -12048,12 +12122,6 @@ radial glial cells acting as neural progenitors throughout life. MESH:D053687 somatic stem cell - - - - - true - @@ -12104,8 +12172,8 @@ radial glial cells acting as neural progenitors throughout life. RGCs doi:10.1038/s41598-020-66092-9 + - @@ -12148,8 +12216,8 @@ radial glial cells acting as neural progenitors throughout life. HCs doi:10.1038/s41598-020-66092-9 + - @@ -12221,16 +12289,16 @@ radial glial cells acting as neural progenitors throughout life. BCs doi:10.1038/s41598-020-66092-9 + - BPs GSE137537 + - @@ -12726,7 +12794,7 @@ radial glial cells acting as neural progenitors throughout life. - + A cell of a hematopoietic lineage. BTO:0000574 CALOHA:TS-2017 @@ -12851,7 +12919,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -12889,7 +12956,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -12963,7 +13029,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -12993,7 +13058,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -13001,7 +13066,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -13121,7 +13186,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -13129,7 +13194,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -13159,7 +13224,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -13167,7 +13232,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -13184,12 +13249,6 @@ radial glial cells acting as neural progenitors throughout life. connective tissue cell - - - - - true - @@ -13203,7 +13262,7 @@ radial glial cells acting as neural progenitors throughout life. - + A cell of the embryo. 2010-09-15T03:39:21Z @@ -13263,29 +13322,6 @@ radial glial cells acting as neural progenitors throughout life. - - - - - A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). - - 2010-09-24T09:44:42Z - BTO:0001268 - FMA:72300 - WBbt:0008378 - - somatic cell - - - - - A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). - GOC:tfm - ISBN:0721662544 - - - - @@ -13314,12 +13350,6 @@ radial glial cells acting as neural progenitors throughout life. retinal melanocyte - - - - - true - @@ -13336,7 +13366,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -13344,7 +13374,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -13362,12 +13392,6 @@ radial glial cells acting as neural progenitors throughout life. From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cardiocyte - - - - - true - @@ -13381,7 +13405,6 @@ radial glial cells acting as neural progenitors throughout life. - An endothelial progenitor cell that participates in angiogenesis during development. 2011-02-28T04:20:39Z @@ -13526,12 +13549,6 @@ radial glial cells acting as neural progenitors throughout life. retinal pigment epithelial cell - - - - - true - @@ -13709,7 +13726,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -13822,7 +13838,7 @@ radial glial cells acting as neural progenitors throughout life. - + A zygote in a plant or an animal. MESH:D015053 zygote @@ -13920,7 +13936,7 @@ plexiform layer. - + @@ -13928,7 +13944,7 @@ plexiform layer. - + @@ -14104,7 +14120,6 @@ plexiform layer. - @@ -14295,8 +14310,8 @@ plexiform layer. retinal astroglia - PMID:33796062 + @@ -15229,32 +15244,32 @@ plexiform layer. - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -23903,6 +23918,8 @@ plexiform layer. GC_ID:1 + PMID:30365038 + PMID:32761142 ncbi_taxonomy all NCBITaxon:1 @@ -27283,7 +27300,7 @@ plexiform layer. - + @@ -27324,14 +27341,14 @@ plexiform layer. camera-type eye - + - + definitional @@ -28432,7 +28449,7 @@ plexiform layer. - + The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube) @@ -28457,7 +28474,7 @@ plexiform layer. external ectoderm http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png - + @@ -28470,7 +28487,7 @@ plexiform layer. - + EHDAA2 @@ -28839,7 +28856,7 @@ plexiform layer. - + @@ -28875,14 +28892,14 @@ plexiform layer. gastrula stage - + - + BILS @@ -29148,7 +29165,7 @@ plexiform layer. - + @@ -29221,7 +29238,7 @@ plexiform layer. https://github.com/obophenotype/uberon/issues/661 http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg - + @@ -29234,7 +29251,7 @@ plexiform layer. - + exceptions in some taxa @@ -29359,15 +29376,15 @@ plexiform layer. - + - - + + A fluid that is composed of blood plasma and erythrocytes. This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. @@ -29409,34 +29426,34 @@ plexiform layer. blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -29740,7 +29757,7 @@ plexiform layer. - + @@ -29782,14 +29799,14 @@ plexiform layer. organism substance - + - + this relationship may be too strong and may be weakened in future @@ -31122,7 +31139,7 @@ plexiform layer. - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] @@ -31160,14 +31177,14 @@ plexiform layer. ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -31220,7 +31237,7 @@ plexiform layer. - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] endodermal @@ -31257,14 +31274,14 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -31309,7 +31326,7 @@ plexiform layer. - + The middle germ layer of the embryo, between the endoderm and ectoderm. Primary germ layer that is the middle of the embryonic germ layers.[AAO] @@ -31354,7 +31371,7 @@ plexiform layer. mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + @@ -31367,7 +31384,7 @@ plexiform layer. - + Bgee:AN @@ -31589,7 +31606,7 @@ plexiform layer. - + @@ -31655,14 +31672,14 @@ plexiform layer. cranial nerve II - + - + EHDAA2 @@ -31806,7 +31823,7 @@ plexiform layer. - + @@ -31879,15 +31896,18 @@ plexiform layer. Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706 heart + https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + MA @@ -31965,7 +31985,7 @@ plexiform layer. - + @@ -31990,7 +32010,7 @@ plexiform layer. - + The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. requires review for applicability to invertebrate structures, e.g. synganglion @@ -32050,12 +32070,14 @@ plexiform layer. brain + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb - + - + @@ -32068,13 +32090,13 @@ plexiform layer. - + FMA - + Bgee:AN @@ -32375,9 +32397,9 @@ plexiform layer. - - - + + + @@ -32402,7 +32424,7 @@ plexiform layer. - + @@ -32458,44 +32480,44 @@ plexiform layer. cornea http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - + - + MA - + MA - + FMA-isa - + definitional @@ -32684,10 +32706,10 @@ plexiform layer. - - - - + + + + The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. @@ -32738,44 +32760,44 @@ plexiform layer. retina http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png - + - + - + - + - + FMA - + FMA - + FMA - + EHDAA2 @@ -32849,8 +32871,8 @@ plexiform layer. - - + + @@ -32886,24 +32908,24 @@ plexiform layer. eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -33125,6 +33147,11 @@ plexiform layer. respiratory system http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg + https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb @@ -33503,7 +33530,7 @@ plexiform layer. - + @@ -33556,14 +33583,14 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -33651,7 +33678,7 @@ plexiform layer. - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. Part of the nervous system which includes the brain and spinal cord.[AAO] @@ -33698,7 +33725,7 @@ plexiform layer. central nervous system - + @@ -33712,7 +33739,7 @@ plexiform layer. - + Bgee:AN @@ -34459,7 +34486,7 @@ plexiform layer. - + Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). AEO:0000111 BTO:0002422 @@ -34484,14 +34511,14 @@ plexiform layer. mesothelium http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg - + - + FMA @@ -34864,7 +34891,7 @@ plexiform layer. - + A tube extending from the mouth to the anus. @@ -34904,14 +34931,14 @@ plexiform layer. digestive tract - + - + NCBIBook:NBK10107 @@ -34991,7 +35018,7 @@ plexiform layer. - + The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. BTO:0000654 @@ -35014,7 +35041,7 @@ plexiform layer. ciliary muscle http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png - + @@ -35033,7 +35060,7 @@ plexiform layer. - + FMA @@ -35174,7 +35201,7 @@ plexiform layer. - + @@ -35226,14 +35253,14 @@ plexiform layer. eyelid https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg - + - + multiple @@ -35528,7 +35555,7 @@ plexiform layer. - + @@ -35571,14 +35598,14 @@ plexiform layer. iris - + - + XAO @@ -35650,7 +35677,7 @@ plexiform layer. - + @@ -35702,14 +35729,14 @@ plexiform layer. corneal epithelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png - + - + ISBN:0781772214 @@ -35805,16 +35832,16 @@ plexiform layer. - - + + - - + + @@ -35856,44 +35883,44 @@ plexiform layer. sclera http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - + - + FMA - + ZFA - + ISBN:0781772214 - + cjm ISBN:0781772214 Wikipedia @@ -35953,7 +35980,7 @@ plexiform layer. - + @@ -35992,14 +36019,14 @@ plexiform layer. ciliary body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + ISBN:0781772214 @@ -36047,14 +36074,14 @@ plexiform layer. - + - + @@ -36117,24 +36144,24 @@ plexiform layer. optic choroid http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + MA - + Wikipedia @@ -36234,7 +36261,7 @@ plexiform layer. - + @@ -36283,14 +36310,14 @@ plexiform layer. substantia propria of cornea http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png - + - + cjm ISBN:0781772214 Wikipedia @@ -36367,9 +36394,9 @@ plexiform layer. - - - + + + A double layer covering the ciliary body that produces aqueous humor. BTO:0001770 @@ -36389,15 +36416,15 @@ plexiform layer. ciliary epithelium - + - + - + @@ -36410,19 +36437,19 @@ plexiform layer. - + MA - + MP - + Wikipedia @@ -36545,7 +36572,7 @@ plexiform layer. - + @@ -36606,14 +36633,14 @@ plexiform layer. pigmented layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + Wikipedia @@ -36717,7 +36744,7 @@ plexiform layer. - + @@ -36751,14 +36778,14 @@ plexiform layer. photoreceptor layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + ZFA @@ -36931,7 +36958,7 @@ plexiform layer. - + @@ -36978,14 +37005,14 @@ plexiform layer. outer nuclear layer of retina - + - + soma ZFA @@ -37323,7 +37350,7 @@ plexiform layer. - + @@ -37382,7 +37409,7 @@ plexiform layer. ganglionic layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + @@ -37395,7 +37422,7 @@ plexiform layer. - + FMA @@ -37471,7 +37498,7 @@ plexiform layer. - + @@ -37527,14 +37554,14 @@ plexiform layer. nerve fiber layer of retina - + - + FMA @@ -37912,7 +37939,7 @@ plexiform layer. - + @@ -37948,14 +37975,14 @@ plexiform layer. aqueous humor of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + FMA def states A and P located_in in EHDAA2 VHOG @@ -38137,7 +38164,7 @@ plexiform layer. - + @@ -38161,7 +38188,7 @@ plexiform layer. vitreous body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + @@ -38174,7 +38201,7 @@ plexiform layer. - + neural ectoderm of optic cup ISBN:0781772214 @@ -38309,8 +38336,8 @@ plexiform layer. - - + + @@ -38343,24 +38370,24 @@ plexiform layer. anterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png - + - + - + FMA - + cjm @@ -38411,8 +38438,8 @@ plexiform layer. - - + + @@ -38442,24 +38469,24 @@ plexiform layer. posterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + FMA - + cjm @@ -38495,9 +38522,9 @@ plexiform layer. - - - + + + @@ -38547,15 +38574,15 @@ plexiform layer. conjunctiva http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png - + - + - + @@ -38568,19 +38595,19 @@ plexiform layer. - + cjm - + MA - + ISBN:0781772214 @@ -38644,7 +38671,7 @@ plexiform layer. - + The most anterior region of the brain including both the telencephalon and diencephalon. @@ -38691,14 +38718,14 @@ plexiform layer. forebrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + - + definitional @@ -38774,14 +38801,14 @@ plexiform layer. - + - + The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. developmental relationships need revised @@ -38834,24 +38861,24 @@ plexiform layer. midbrain http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG - + - + - + definitional - + Bgee:AN @@ -38954,14 +38981,14 @@ plexiform layer. - + - + The division of the forebrain that develops from the foremost primary cerebral vesicle. @@ -39024,24 +39051,24 @@ plexiform layer. diencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + - + - + definitional - + definitional @@ -39409,6 +39436,8 @@ plexiform layer. optic tract http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb @@ -39477,7 +39506,7 @@ plexiform layer. - + Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] @@ -39517,14 +39546,14 @@ plexiform layer. midbrain tegmentum http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png - + - + ZFA @@ -39703,8 +39732,8 @@ plexiform layer. - - + + @@ -39717,7 +39746,7 @@ plexiform layer. - + @@ -39732,7 +39761,6 @@ plexiform layer. A vessel through which blood circulates in the body. consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus - Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] Any of the vessels through which blood circulates in the body.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] @@ -39769,41 +39797,40 @@ plexiform layer. vas sanguineum UBERON:0001981 - blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -40162,7 +40189,7 @@ plexiform layer. - + @@ -40175,7 +40202,7 @@ plexiform layer. - + The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. @@ -40226,25 +40253,25 @@ plexiform layer. hindbrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + - + - + modified-source-relation ABA - + Bgee:AN @@ -41063,7 +41090,7 @@ plexiform layer. - + Vasculature that is part of the eye region. not part of the eye in ZFA. Note this changed to a blood vessel in ZFA @@ -41083,15 +41110,17 @@ plexiform layer. vasculature of eye + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb - + - + ISBN:0781772214 @@ -41150,7 +41179,7 @@ plexiform layer. - + @@ -41184,14 +41213,14 @@ plexiform layer. musculoskeletal system - + - + check ctenophore @@ -41329,15 +41358,15 @@ plexiform layer. - + - - + + Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO). TODO - add superclass to unify with VNC? @@ -41393,35 +41422,37 @@ plexiform layer. spinal cord http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb - + - + - + - + ZFA - + definitional - + definitional @@ -41863,7 +41894,7 @@ plexiform layer. - + @@ -41904,14 +41935,14 @@ plexiform layer. coelemic cavity lumen - + - + definitional @@ -42019,9 +42050,9 @@ plexiform layer. - - - + + + @@ -42076,15 +42107,15 @@ plexiform layer. notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -42103,19 +42134,19 @@ plexiform layer. - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -42200,8 +42231,8 @@ plexiform layer. - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk @@ -42247,11 +42278,11 @@ plexiform layer. somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -42264,13 +42295,13 @@ plexiform layer. - + GOTAX:0000352 - + ZFA @@ -42383,12 +42414,12 @@ plexiform layer. - - - - - - + + + + + + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). @@ -42428,66 +42459,66 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells ISBN:0073040584 - + BTO - + PMID:11523831 - + pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest - + PMID:11523831 @@ -42870,14 +42901,14 @@ plexiform layer. - + - + Anatomical system that is involved in the production of hematopoietic cells. Anatomical system that consists of the blood and blood forming tissues.[AAO] @@ -42920,24 +42951,24 @@ plexiform layer. hematopoietic system - + - + - + FMA - + definitional @@ -43002,8 +43033,8 @@ plexiform layer. - - + + @@ -43029,11 +43060,11 @@ plexiform layer. iris epithelium - + - + @@ -43046,13 +43077,13 @@ plexiform layer. - + MA - + MP @@ -43202,7 +43233,7 @@ plexiform layer. - + Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. Do not merge with neurogenic placode Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons @@ -43222,7 +43253,7 @@ plexiform layer. cranial placode - + @@ -43235,7 +43266,7 @@ plexiform layer. - + PMID:11523831 PMID:22512454 @@ -43440,7 +43471,7 @@ plexiform layer. - + @@ -43453,7 +43484,7 @@ plexiform layer. - + The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. consider adding class for organizer. Consider adding separate class for isthmus as a structure Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] @@ -43483,11 +43514,11 @@ plexiform layer. midbrain-hindbrain boundary - + - + @@ -43501,13 +43532,13 @@ plexiform layer. - + ZFA - + ZFA @@ -43672,7 +43703,7 @@ plexiform layer. - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] @@ -43697,14 +43728,14 @@ plexiform layer. presomitic mesoderm - + - + Bgee:AN @@ -43946,7 +43977,7 @@ plexiform layer. - + @@ -43984,7 +44015,7 @@ plexiform layer. eye primordium - + @@ -43997,7 +44028,7 @@ plexiform layer. - + PMID:16496288 XAO @@ -44053,8 +44084,8 @@ plexiform layer. - - + + @@ -44083,24 +44114,24 @@ plexiform layer. optic cup - + - + - + ZFA - + ZFA @@ -44165,7 +44196,7 @@ plexiform layer. - + @@ -44206,7 +44237,7 @@ plexiform layer. lens placode http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png - + @@ -44219,7 +44250,7 @@ plexiform layer. - + ZFA @@ -44283,9 +44314,9 @@ plexiform layer. - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] @@ -44317,34 +44348,34 @@ plexiform layer. neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -44455,7 +44486,7 @@ plexiform layer. - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] @@ -44484,7 +44515,7 @@ plexiform layer. paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -44497,7 +44528,7 @@ plexiform layer. - + Bgee:AN @@ -44609,7 +44640,7 @@ plexiform layer. - + @@ -44653,7 +44684,7 @@ plexiform layer. lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -44666,7 +44697,7 @@ plexiform layer. - + EHDAA2 VHOG @@ -44750,15 +44781,15 @@ plexiform layer. - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] @@ -44778,15 +44809,15 @@ plexiform layer. heart primordium - + - + - + @@ -44799,19 +44830,19 @@ plexiform layer. - + ZFA - + ZFA - + XAO @@ -44866,8 +44897,8 @@ plexiform layer. - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. Skeletogenic portion of somites.[AAO] The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] @@ -44894,11 +44925,11 @@ plexiform layer. sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -44917,13 +44948,13 @@ plexiform layer. - + VHOG:0000680 - + ZFA @@ -45341,7 +45372,7 @@ plexiform layer. - + Mesenchyme that is part of a developing camera-type eye. TODO - change mesenchyme relationships to precursor_of EHDAA2:0000485 @@ -45353,14 +45384,14 @@ plexiform layer. UBERON:0003314 eye mesenchyme - + - + EHDAA2 @@ -46218,7 +46249,7 @@ plexiform layer. - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] @@ -46234,14 +46265,14 @@ plexiform layer. intraembryonic coelom - + - + Wikipedia @@ -46346,7 +46377,7 @@ plexiform layer. - + The part of the retina that contains neurons and photoreceptor cells[GO]. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] @@ -46378,14 +46409,14 @@ plexiform layer. retinal neural layer - + - + Bgee:AN @@ -46643,7 +46674,7 @@ plexiform layer. - + The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium. consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure The layer of undifferentiated, proliferating cells that line the neural tube lumen @@ -46661,7 +46692,7 @@ plexiform layer. neural tube ventricular layer - + @@ -46674,7 +46705,7 @@ plexiform layer. - + NCBIBook:NBK10047 @@ -46734,7 +46765,7 @@ plexiform layer. - + @@ -46758,7 +46789,7 @@ plexiform layer. neural tube mantle layer - + @@ -46771,7 +46802,7 @@ plexiform layer. - + by division NCBIBook:NBK10047 @@ -46808,7 +46839,7 @@ plexiform layer. - + @@ -46825,14 +46856,14 @@ plexiform layer. neural tube marginal layer - + - + forms from axons @@ -47107,9 +47138,9 @@ plexiform layer. - - - + + + @@ -47142,34 +47173,34 @@ plexiform layer. optic vesicle http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png - + - + - + - + ZFA - + GO-def - + ZFA @@ -47285,8 +47316,8 @@ plexiform layer. - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] XAO:0004185 @@ -47299,24 +47330,24 @@ plexiform layer. UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -47375,7 +47406,7 @@ plexiform layer. - + An epithelial tube that will give rise to the mature heart. the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. AAO:0010411 @@ -47395,14 +47426,14 @@ plexiform layer. heart tube - + - + ZFA-modified @@ -47483,7 +47514,7 @@ plexiform layer. - + @@ -47499,14 +47530,14 @@ plexiform layer. eye muscle - + - + MA @@ -47710,7 +47741,7 @@ plexiform layer. - + A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN] @@ -47740,14 +47771,14 @@ plexiform layer. Descemet's membrane https://github.com/obophenotype/uberon/issues/15 - + - + Cline et al @@ -48157,6 +48188,8 @@ plexiform layer. UBERON:0004537 blood vasculature + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb @@ -48528,7 +48561,7 @@ plexiform layer. - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] @@ -48544,14 +48577,14 @@ plexiform layer. skeletal element - + - + VSAO @@ -48596,7 +48629,7 @@ plexiform layer. - + @@ -48635,14 +48668,14 @@ plexiform layer. UBERON:0004770 articular system - + - + FMA @@ -49549,7 +49582,7 @@ plexiform layer. - + Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO] EFO:0003492 @@ -49571,14 +49604,14 @@ plexiform layer. head mesenchyme - + - + EHDAA2 @@ -49645,7 +49678,7 @@ plexiform layer. - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -49661,14 +49694,14 @@ plexiform layer. trunk mesenchyme - + - + EHDAA2 @@ -49691,7 +49724,7 @@ plexiform layer. - + The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]. The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] @@ -49716,14 +49749,14 @@ plexiform layer. myelencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + - + definitional @@ -50250,7 +50283,7 @@ plexiform layer. - + Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. TAO:0002188 ZFA:0001688 @@ -50258,7 +50291,7 @@ plexiform layer. UBERON:0005427 corneal primordium - + @@ -50277,7 +50310,7 @@ plexiform layer. - + ZFA @@ -50300,7 +50333,7 @@ plexiform layer. - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -50318,14 +50351,14 @@ plexiform layer. primitive heart tube - + - + ZFA @@ -50528,7 +50561,7 @@ plexiform layer. - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -50538,7 +50571,7 @@ plexiform layer. UBERON:0005856 developing mesenchymal condensation - + @@ -50557,7 +50590,7 @@ plexiform layer. - + AEO-modified-relation @@ -50616,9 +50649,9 @@ plexiform layer. - - - + + + A serous sac which is the aggregate of the conjunctiva plus the conjunctival space. EMAPA:18233 FMA:20291 @@ -50629,15 +50662,15 @@ plexiform layer. UBERON:0005908 conjunctival sac - + - + - + @@ -50650,19 +50683,19 @@ plexiform layer. - + FMA - + HPO:pr - + MA @@ -50917,7 +50950,7 @@ plexiform layer. - + @@ -50940,14 +50973,14 @@ plexiform layer. future diencephalon - + - + EHDAA2 @@ -51130,7 +51163,7 @@ plexiform layer. - + @@ -51154,14 +51187,14 @@ plexiform layer. future spinal cord - + - + EHDAA2 @@ -51198,7 +51231,7 @@ plexiform layer. - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] @@ -51213,7 +51246,7 @@ plexiform layer. notochordal plate - + @@ -51226,7 +51259,7 @@ plexiform layer. - + EHDAA2 @@ -51263,7 +51296,7 @@ plexiform layer. - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -51280,14 +51313,14 @@ plexiform layer. The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -52192,7 +52225,7 @@ plexiform layer. - + A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis SPD:0000130 @@ -52207,14 +52240,14 @@ plexiform layer. Gene notes: Bmp, Nkx, Gata primary circulatory organ - + - + GO uses blood circulation generically to include the haemolymphatic fluid of arthropods @@ -52369,8 +52402,8 @@ plexiform layer. - - + + @@ -52397,24 +52430,24 @@ plexiform layer. presumptive hindbrain - + - + - + XAO-abduced - + cjm @@ -52471,7 +52504,7 @@ plexiform layer. - + @@ -52490,14 +52523,14 @@ plexiform layer. presumptive midbrain hindbrain boundary - + - + ZFA @@ -52536,7 +52569,7 @@ plexiform layer. - + @@ -52553,14 +52586,14 @@ plexiform layer. presumptive segmental plate - + - + https://github.com/obophenotype/uberon/wiki/The-neural-crest EDHAA2 @@ -52659,7 +52692,7 @@ plexiform layer. - + @@ -52685,7 +52718,7 @@ plexiform layer. presumptive paraxial mesoderm - + @@ -52701,7 +52734,7 @@ plexiform layer. - + https://github.com/obophenotype/uberon/issues/1277 @@ -52783,7 +52816,7 @@ plexiform layer. - + A neural decussation that is part of a diencephalon. FMA:62446 diencephalon decussation @@ -52791,7 +52824,7 @@ plexiform layer. UBERON:0007425 decussation of diencephalon - + @@ -52804,7 +52837,7 @@ plexiform layer. - + Obol @@ -52879,7 +52912,7 @@ plexiform layer. - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -52887,7 +52920,7 @@ plexiform layer. UBERON:0007524 dense mesenchyme tissue - + @@ -52900,7 +52933,7 @@ plexiform layer. - + AEO @@ -53140,7 +53173,7 @@ plexiform layer. - + An axon tract that is part of a brain. the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts FMA:83848 @@ -53150,14 +53183,14 @@ plexiform layer. UBERON:0007702 tract of brain - + - + cjm @@ -53185,7 +53218,7 @@ plexiform layer. - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. @@ -53202,14 +53235,14 @@ plexiform layer. vascular system - + - + MA @@ -53342,7 +53375,7 @@ plexiform layer. - + @@ -53359,14 +53392,14 @@ plexiform layer. UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -53462,8 +53495,8 @@ plexiform layer. - - + + TODO - developmental relationships for lines TAO:0007044 ZFA:0007044 @@ -53473,24 +53506,24 @@ plexiform layer. UBERON:0009615 midbrain hindbrain boundary neural plate - + - + - + ZFA - + https://github.com/obophenotype/uberon/issues/438 Bgee:AN @@ -53524,14 +53557,14 @@ plexiform layer. - + - + @@ -53556,24 +53589,24 @@ plexiform layer. presumptive midbrain - + - + - + ZFA - + ZFA @@ -53619,7 +53652,7 @@ plexiform layer. - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -53627,14 +53660,14 @@ plexiform layer. UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -53656,7 +53689,7 @@ plexiform layer. - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -53666,14 +53699,14 @@ plexiform layer. anterior lateral plate mesoderm - + - + ZFA @@ -53729,14 +53762,14 @@ plexiform layer. - + EHDAA2:0001315 EHDAA:1122 uberon UBERON:0009920 optic neural crest - + @@ -53749,7 +53782,7 @@ plexiform layer. - + EHDAA2 @@ -53883,7 +53916,7 @@ plexiform layer. - + @@ -53908,14 +53941,14 @@ plexiform layer. eyeball of camera-type eye - + - + FMA @@ -53956,8 +53989,8 @@ plexiform layer. - - + + Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. DHBA:12322 EFO:0003567 @@ -53971,11 +54004,11 @@ plexiform layer. midbrain basal plate - + - + @@ -53988,13 +54021,13 @@ plexiform layer. - + EHDAA2 - + ZFA @@ -54022,7 +54055,7 @@ plexiform layer. - + Portion of neural tube that gives rise to the midbrain. we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed TAO:0007039 @@ -54031,14 +54064,14 @@ plexiform layer. UBERON:0010286 midbrain neural tube - + - + ZFA @@ -54065,7 +54098,7 @@ plexiform layer. - + @@ -54081,14 +54114,14 @@ plexiform layer. UBERON:0010312 immature eye - + - + definitional @@ -54306,6 +54339,14 @@ plexiform layer. UBERON:0010427 ciliary processes http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Eye_L.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Eye_R.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Eye_L.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Eye_R.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb @@ -54358,8 +54399,8 @@ plexiform layer. - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] FMA:23879 @@ -54372,11 +54413,11 @@ plexiform layer. subdivision of skeleton - + - + @@ -54389,13 +54430,13 @@ plexiform layer. - + UBERONREF:0000003 - + VSAO @@ -54472,7 +54513,7 @@ plexiform layer. - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -54482,7 +54523,7 @@ plexiform layer. postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -54495,7 +54536,7 @@ plexiform layer. - + cjm @@ -54607,7 +54648,7 @@ plexiform layer. - + Muscles within the eye (bulbus oculi).[AAO] AAO:0010038 EMAPA:18808 @@ -54618,14 +54659,14 @@ plexiform layer. UBERON:0011222 intra-ocular muscle - + - + EMAPA @@ -54895,7 +54936,7 @@ plexiform layer. - + @@ -54937,7 +54978,7 @@ plexiform layer. anterior uvea - + @@ -54950,7 +54991,7 @@ plexiform layer. - + MP @@ -55726,7 +55767,7 @@ plexiform layer. - + @@ -55749,7 +55790,7 @@ plexiform layer. UBERON:0016887 entire extraembryonic component - + @@ -55762,7 +55803,7 @@ plexiform layer. - + AEO @@ -56514,6 +56555,209 @@ plexiform layer. + + + + + + + + + example to be eventually removed + example to be eventually removed + + + + + + + + failed exploratory term + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + + + + + + metadata complete + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + organizational term + Term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + ready for release + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + metadata incomplete + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + uncurated + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + pending final vetting + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + placeholder removed + placeholder removed + + + + + + + + terms merged + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + + + + + + term imported + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + + + + + + term split + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + + + + + + universal + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + + + + + + defined class + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + + + + + + named class expression + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + + + + + + to be replaced with external ontology term + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + requires discussion + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. + This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/77 + https://orcid.org/0000-0001-5208-3432 + out of scope + + + + + definition + + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition + definition @@ -85,12 +111,18 @@ + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> IAO:0000116 uberon editor_note true editor_note editor note + editor note @@ -115,7 +147,13 @@ - + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + @@ -128,6 +166,12 @@ + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg IAO:0000233 external uberon @@ -135,15 +179,31 @@ true true term_tracker_item + The 'tracker item' can associate a tracker with a specific ontology term. term tracker item + term tracker item + + + + + + + expand expression to + ObjectProperty: RO_0002104 +Label: has plasma membrane part +Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones + Chris Mungall expand expression to + expand expression to @@ -175,6 +235,9 @@ + has ontology root term + Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. + Nicolas Matentzoglu IAO:0000700 external uberon @@ -183,6 +246,7 @@ true has_ontology_root_term has ontology root term + has ontology root term preferred_root @@ -197,7 +261,14 @@ + term replaced by + + Use on obsolete terms, relating the term to another term that can be used as a substitute + Person:Alan Ruttenberg + Person:Alan Ruttenberg + Add as annotation triples in the granting ontology term replaced by + term replaced by @@ -216,7 +287,44 @@ - + + 'part disjoint with' 'defined by construct' """ + PREFIX owl: <http://www.w3.org/2002/07/owl#> + PREFIX : <http://example.org/ + CONSTRUCT { + [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?a ; + owl:disjointWith [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?b + ] + ] + } + WHERE { + ?a :part_disjoint_with ?b . + } + Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. + + + + defined by construct + + + + + + + + CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) + A synonym type for describing pluralization synonyms + + + 2023-03-03 + plural form + @@ -1102,7 +1210,6 @@ WHERE { - plural term @@ -1396,6 +1503,12 @@ WHERE { + + + + + + @@ -1589,7 +1702,12 @@ WHERE { + An alternative label for a class or property which has a more general meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + has broad synonym has_broad_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 @@ -1605,7 +1723,12 @@ WHERE { + An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + has exact synonym has_exact_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 @@ -1613,7 +1736,12 @@ WHERE { + An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + has narrow synonym has_narrow_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 @@ -1629,7 +1757,12 @@ WHERE { + An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + has related synonym has_related_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 @@ -1894,12 +2027,35 @@ WHERE { + + + + + + + + + + + + + + + + + - - - contains - RO:0001019 - uberon - contains - contains - contains - obsolete contains - - true - - - - @@ -8172,26 +8312,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - CARO:0000013 - cell in vivo - - To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). - native cell - - - - - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - CARO:mah - - - - @@ -8237,7 +8357,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -8245,7 +8365,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -8471,14 +8590,13 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + - A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring. @@ -8598,7 +8716,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -8611,7 +8729,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -8885,7 +9002,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -8922,7 +9039,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube. @@ -9502,20 +9618,20 @@ MH: sexual subtypes should probably be logically defined based on sexual process mesenchymal progenitor cells MESH:D044982 - + mesenchymal stromal cells - + stem cells, mesenchymal MESH:D044982 - + @@ -9632,7 +9748,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -9657,12 +9772,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process melanocyte - - - - - true - @@ -9676,7 +9785,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - pigment cell visual pigment cell @@ -9689,7 +9797,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9697,7 +9805,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9736,7 +9844,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -9763,7 +9870,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9782,7 +9889,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -9825,7 +9931,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose primary function is to shorten. contractile cell @@ -9843,7 +9949,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -9877,7 +9982,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9885,7 +9990,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -9976,7 +10081,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10043,7 +10148,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose function is determined by the generation or the reception of an electric signal. electrically active cell @@ -10062,7 +10167,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10070,7 +10175,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10168,7 +10273,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10202,7 +10307,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10240,7 +10345,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10251,7 +10356,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -10404,7 +10508,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10412,7 +10516,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10428,7 +10532,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell that is specialised to accumulate a particular substance(s). stuff accumulating cell @@ -10499,7 +10603,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10507,7 +10611,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -10588,7 +10692,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process + + + + + + + Diploid cell produced by the fusion of sperm cell nucleus and egg cell. zygote BTO:0000854 @@ -10768,7 +10879,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell whose primary function is to protect the organism. defensive cell @@ -10878,12 +10989,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process satellite cell smooth muscle myoblast - - - - - true - @@ -10933,12 +11038,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process skeletal myoblast skeletal muscle myoblast - - - - - true - @@ -11027,7 +11126,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -11126,36 +11224,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - - - - - - - - - - - - - - - - - A native cell that is part of some Metazoa. - metazoan cell - - animal cell - https://www.swissbiopics.org/api/image/Animal_cells.svg - - - - @@ -11646,7 +11714,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -11686,7 +11753,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -11699,12 +11765,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process MESH:D053687 somatic stem cell - - - - - true - @@ -11781,6 +11841,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process + @@ -12216,6 +12277,24 @@ MH: sexual subtypes should probably be logically defined based on sexual process Most markers only described for human pro NK cells. pro-NK cell + + + + null cell + PMID:11532393 + + + + + preNK cell + PMID:11532393 + + + + + + true + @@ -12236,24 +12315,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process PMID:15032583 PMID:15766674 - - - - null cell - PMID:11532393 - - - - - preNK cell - PMID:11532393 - - - - - - true - @@ -12767,7 +12828,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell of a hematopoietic lineage. BTO:0000574 CALOHA:TS-2017 @@ -12856,7 +12917,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -12864,7 +12925,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -12879,12 +12940,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process bone cell - - - - - true - @@ -13320,7 +13375,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -13437,7 +13491,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -13445,7 +13499,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -13473,7 +13527,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -13481,7 +13535,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -13511,7 +13565,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -13519,7 +13573,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -13536,12 +13590,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process connective tissue cell - - - - - true - @@ -13555,7 +13603,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A cell of the embryo. 2010-09-15T03:39:21Z @@ -13574,29 +13622,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). - - 2010-09-24T09:44:42Z - BTO:0001268 - FMA:72300 - WBbt:0008378 - - somatic cell - - - - - A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). - GOC:tfm - ISBN:0721662544 - - - - @@ -13653,7 +13678,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -13661,7 +13686,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -13679,12 +13704,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cardiocyte - - - - - true - @@ -13697,7 +13716,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized). 2012-06-15T02:51:27Z @@ -13870,7 +13889,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - @@ -13928,7 +13946,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A zygote in a plant or an animal. MESH:D015053 zygote @@ -14023,7 +14041,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -14031,7 +14049,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -15723,32 +15741,32 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -21748,28 +21766,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system. - endocrine physiological process - endocrine physiology - biological_process - GO:0050886 - - - endocrine process - - - - - The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system. - ISBN:0721662544 - - - - @@ -24057,6 +24053,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process GC_ID:1 + PMID:30365038 + PMID:32761142 ncbi_taxonomy all NCBITaxon:1 @@ -28429,8 +28427,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + @@ -28481,11 +28479,11 @@ MH: sexual subtypes should probably be logically defined based on sexual process tendon http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg - + - + @@ -28498,13 +28496,13 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + OG - + AEO @@ -29495,7 +29493,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -29531,14 +29529,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process gastrula stage - + - + BILS @@ -29759,7 +29757,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -29832,7 +29830,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process https://github.com/obophenotype/uberon/issues/661 http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg - + @@ -29845,7 +29843,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + exceptions in some taxa @@ -30154,7 +30152,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -30196,14 +30194,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process organism substance - + - + this relationship may be too strong and may be weakened in future @@ -31435,7 +31433,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] @@ -31473,14 +31471,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -31533,7 +31531,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] endodermal @@ -31570,14 +31568,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -31622,7 +31620,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The middle germ layer of the embryo, between the endoderm and ectoderm. Primary germ layer that is the middle of the embryonic germ layers.[AAO] @@ -31667,7 +31665,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + @@ -31680,7 +31678,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Bgee:AN @@ -31872,17 +31870,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - - - - - - @@ -31890,12 +31877,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - @@ -32003,8 +31984,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + @@ -32040,24 +32021,24 @@ MH: sexual subtypes should probably be logically defined based on sexual process eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -32282,6 +32263,11 @@ MH: sexual subtypes should probably be logically defined based on sexual process respiratory system http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg + https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb + https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb @@ -32664,7 +32650,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -32719,14 +32705,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -32814,7 +32800,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. Part of the nervous system which includes the brain and spinal cord.[AAO] @@ -32861,7 +32847,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process central nervous system - + @@ -32875,7 +32861,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Bgee:AN @@ -33742,7 +33728,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Skeletal element that is composed of bone tissue. @@ -33792,14 +33778,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process bone element - + - + VSAO-modified @@ -33910,7 +33896,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A tube extending from the mouth to the anus. @@ -33950,14 +33936,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process digestive tract - + - + NCBIBook:NBK10107 @@ -34548,7 +34534,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -34584,14 +34570,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process musculoskeletal system - + - + check ctenophore @@ -34654,9 +34640,9 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - + + + @@ -34711,15 +34697,15 @@ MH: sexual subtypes should probably be logically defined based on sexual process notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -34738,19 +34724,19 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -34835,8 +34821,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk @@ -34882,11 +34868,11 @@ MH: sexual subtypes should probably be logically defined based on sexual process somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -34899,13 +34885,13 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + GOTAX:0000352 - + ZFA @@ -35082,12 +35068,12 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - + + + + + + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). @@ -35127,66 +35113,66 @@ MH: sexual subtypes should probably be logically defined based on sexual process http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells ISBN:0073040584 - + BTO - + PMID:11523831 - + pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest - + PMID:11523831 @@ -35541,7 +35527,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -35599,14 +35585,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -35877,14 +35863,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + - + Anatomical system that is involved in the production of hematopoietic cells. @@ -35928,24 +35914,24 @@ MH: sexual subtypes should probably be logically defined based on sexual process hematopoietic system - + - + - + FMA - + definitional @@ -36411,7 +36397,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] @@ -36436,14 +36422,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process presomitic mesoderm - + - + Bgee:AN @@ -36673,9 +36659,9 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] @@ -36707,34 +36693,34 @@ MH: sexual subtypes should probably be logically defined based on sexual process neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -36799,7 +36785,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] @@ -36828,7 +36814,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -36841,7 +36827,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Bgee:AN @@ -36913,7 +36899,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -36957,7 +36943,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -36970,7 +36956,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + EHDAA2 VHOG @@ -37054,7 +37040,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -37097,7 +37083,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process myotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + @@ -37110,7 +37096,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + EHDAA2-abduced @@ -37166,8 +37152,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. Skeletogenic portion of somites.[AAO] The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] @@ -37194,11 +37180,11 @@ MH: sexual subtypes should probably be logically defined based on sexual process sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -37217,13 +37203,13 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + VHOG:0000680 - + ZFA @@ -37432,7 +37418,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] @@ -37448,14 +37434,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process intraembryonic coelom - + - + Wikipedia @@ -37783,7 +37769,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The bilaminar epithelium formed from the myotome and dermatome. Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]. Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO] @@ -37806,7 +37792,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0004290 dermomyotome - + @@ -37825,7 +37811,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + EHDAA2 ZFA @@ -38151,7 +38137,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]. A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] EMAPA:37744 @@ -38165,7 +38151,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from skeletal tissue - + @@ -38178,7 +38164,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + 2012-08-14 VSAO:0000015 VSAO @@ -38217,7 +38203,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] @@ -38233,14 +38219,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process skeletal element - + - + VSAO @@ -38285,7 +38271,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -38324,14 +38310,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0004770 articular system - + - + FMA @@ -38798,7 +38784,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -38814,14 +38800,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process trunk mesenchyme - + - + EHDAA2 @@ -39118,7 +39104,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -39128,7 +39114,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0005856 developing mesenchymal condensation - + @@ -39147,7 +39133,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + AEO-modified-relation @@ -39252,7 +39238,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] @@ -39267,7 +39253,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process notochordal plate - + @@ -39280,7 +39266,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + EHDAA2 @@ -39317,7 +39303,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -39334,14 +39320,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -39799,7 +39785,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis SPD:0000130 @@ -39814,14 +39800,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process Gene notes: Bmp, Nkx, Gata primary circulatory organ - + - + GO uses blood circulation generically to include the haemolymphatic fluid of arthropods @@ -39911,7 +39897,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -39928,14 +39914,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process presumptive segmental plate - + - + https://github.com/obophenotype/uberon/wiki/The-neural-crest EDHAA2 @@ -40034,7 +40020,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -40060,7 +40046,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process presumptive paraxial mesoderm - + @@ -40076,7 +40062,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + https://github.com/obophenotype/uberon/issues/1277 @@ -40125,7 +40111,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -40133,7 +40119,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0007524 dense mesenchyme tissue - + @@ -40146,7 +40132,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + AEO @@ -40456,7 +40442,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -40473,14 +40459,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -40502,7 +40488,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -40510,14 +40496,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -40677,8 +40663,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] FMA:23879 @@ -40691,11 +40677,11 @@ MH: sexual subtypes should probably be logically defined based on sexual process subdivision of skeleton - + - + @@ -40708,13 +40694,13 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + UBERONREF:0000003 - + VSAO @@ -41085,7 +41071,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -41110,7 +41096,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0011899 epimysium - + @@ -41123,7 +41109,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + FMA @@ -41229,7 +41215,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -41251,7 +41237,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0012429 hematopoietic tissue - + @@ -41264,7 +41250,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + defitional @@ -41832,7 +41818,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -41855,7 +41841,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process UBERON:0016887 entire extraembryonic component - + @@ -41868,7 +41854,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + AEO @@ -41954,7 +41940,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process - + @@ -41970,14 +41956,14 @@ MH: sexual subtypes should probably be logically defined based on sexual process skeletal musculature - + - + MA @@ -42265,6 +42251,209 @@ MH: sexual subtypes should probably be logically defined based on sexual process + + + + + + + + + example to be eventually removed + example to be eventually removed + + + + + + + + failed exploratory term + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + + + + + + metadata complete + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + organizational term + Term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + ready for release + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + metadata incomplete + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + uncurated + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + pending final vetting + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + placeholder removed + placeholder removed + + + + + + + + terms merged + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + + + + + + term imported + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + + + + + + term split + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + + + + + + universal + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + + + + + + defined class + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + + + + + + named class expression + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + + + + + + to be replaced with external ontology term + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + requires discussion + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. + This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/77 + https://orcid.org/0000-0001-5208-3432 + out of scope + + + +