diff --git a/tests/resources/goslim_generic_missing_components.json b/tests/resources/goslim_generic_missing_components.json new file mode 100644 index 00000000..ba4e6a00 --- /dev/null +++ b/tests/resources/goslim_generic_missing_components.json @@ -0,0 +1,5882 @@ +{ + "graphs" : [ { + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/GO_0005615", + "meta" : { + "definition" : { + "val" : "That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid." + }, + "comments" : [ "Note that for multicellular organisms, the extracellular space refers to everything outside a cell, but still within the organism (excluding the extracellular matrix). 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at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell junction. 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It is notably the site of tissue respiration.", + "xrefs" : [ "GOC:giardia", "ISBN:0198506732" ] + }, + "comments" : [ "Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_aspergillus", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon" ], + "xrefs" : [ { + "val" : "NIF_Subcellular:sao1860313010" + }, { + "val" : "MIPS_funcat:70.16" + }, { + "val" : "Wikipedia:Mitochondrion" + } ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "mitochondria", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "cellular_component" + } ] + }, + "type" : "CLASS", + "lbl" : "mitochondrion" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0003723", + "meta" : { + "definition" : { + "val" : "Interacting selectively and non-covalently with an RNA molecule or a portion thereof.", + "xrefs" : [ "GOC:jl", "GOC:mah" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_aspergillus", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon" ], + "xrefs" : [ { + "val" : "MIPS_funcat:16.03.03" + }, { + "val" : "Reactome:R-HSA-203922" + } ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "poly(A) RNA binding", + "xrefs" : [ ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "base pairing with RNA", + "xrefs" : [ ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "poly(A)-RNA binding", + "xrefs" : [ ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "poly-A RNA binding", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "molecular_function" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0044822" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0000498" + } ] + }, + "type" : "CLASS", + "lbl" : "RNA binding" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0005622", + "meta" : { + "definition" : { + "val" : "The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. 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When information is provided on the cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Also, if experimental data suggest that a gene product influences cell death indirectly, rather than being involved in the death process directly, consider annotating to a 'regulation' term." ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_agr" ], + "xrefs" : [ { + "val" : "MIPS_funcat:40.10" + } ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "accidental cell death", + "xrefs" : [ ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "necrosis", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + }, + "type" : "CLASS", + "lbl" : "cell death" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0007009", + "meta" : { + "definition" : { + "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane.", + "xrefs" : [ "GOC:dph", "GOC:jl", "GOC:mah" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_generic" ], + "xrefs" : [ { + "val" : "MIPS_funcat:42.02" + } ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "plasma membrane organisation", + "xrefs" : [ "GOC:curators" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "plasma membrane organization and biogenesis", + "xrefs" : [ "GOC:mah" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + }, + "type" : "CLASS", + "lbl" : "plasma membrane organization" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0005623", + "meta" : { + "definition" : { + "val" : "The basic structural and functional unit of all organisms. 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Instead, select a child term or, if no appropriate child term exists, please request a new term. 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In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon." ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_aspergillus", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], + "xrefs" : [ { + "val" : "MIPS_funcat:70.08" + }, { + "val" : "NIF_Subcellular:sao451912436" + }, { + "val" : "Wikipedia:Golgi_apparatus" + } ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Golgi complex", + "xrefs" : [ ] + }, { + "pred" : "hasBroadSynonym", + "val" : "Golgi", + "xrefs" : [ ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "Golgi ribbon", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "cellular_component" + } ] + }, + "type" : "CLASS", + "lbl" : "Golgi apparatus" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0007059", + "meta" : { + "definition" : { + "val" : "The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.", + "xrefs" : [ "GOC:jl", "GOC:mah", "GOC:mtg_cell_cycle", "GOC:vw" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], + "xrefs" : [ { + "val" : "MIPS_funcat:10.03.04.05" + }, { + "val" : "Wikipedia:Chromosome_segregation" + }, { + "val" : "MIPS_funcat:10.03.04" + } ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "chromosome transmission", + "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "chromosome division", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosome segregation" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0048646", + "meta" : { + "definition" : { + "val" : "The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.", + "xrefs" : [ "GOC:dph", "GOC:jid", "GOC:tb" ] + }, + "comments" : [ "Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense." ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_chembl" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "formation of an anatomical structure involved in morphogenesis", + "xrefs" : [ "GOC:dph", "GOC:tb" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + }, + "type" : "CLASS", + "lbl" : "anatomical structure formation involved in morphogenesis" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0043473", + "meta" : { + "definition" : { + "val" : "The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells.", + "xrefs" : [ "GOC:jl" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_chembl" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + }, + "type" : "CLASS", + "lbl" : "pigmentation" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0040007", + "meta" : { + "definition" : { + "val" : "The increase in size or mass of an entire organism, a part of an organism or a cell.", + "xrefs" : [ "GOC:bf", "GOC:ma" ] + }, + "comments" : [ "See also the biological process term 'cell growth ; GO:0016049'." ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "growth pattern", + "xrefs" : [ ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "non-developmental growth", + "xrefs" : [ "GOC:mah" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0048590" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + }, + "type" : "CLASS", + "lbl" : "growth" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0008150", + "meta" : { + "definition" : { + "val" : "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.", + "xrefs" : [ "GOC:pdt" ] + }, + "comments" : [ "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code \"no data\" (ND), is used to indicate this." ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_aspergillus", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_candida" ], + "xrefs" : [ { + "val" : "Wikipedia:Biological_process" + } ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "biological process", + "xrefs" : [ ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "single organism process", + "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "physiological process", + "xrefs" : [ ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "single-organism process", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0044699" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0000004" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2012-09-19T15:05:24Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "janelomax" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0007582" + } ] + }, + "type" : "CLASS", + "lbl" : "biological_process" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0006091", + "meta" : { + "definition" : { + "val" : "The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.", + "xrefs" : [ "GOC:jl" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_chembl" ], + "xrefs" : [ { + "val" : "MIPS_funcat:02.45.15" + } ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "energy pathways", + "xrefs" : [ ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "metabolic energy generation", + "xrefs" : [ ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "intermediary metabolism", + "xrefs" : [ "GOC:mah" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + }, + "type" : "CLASS", + "lbl" : "generation of precursor metabolites and energy" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "type" : "PROPERTY", + "lbl" : "has_obo_namespace" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion", + "type" : "PROPERTY", + "lbl" : "has_obo_format_version" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0030234", + "meta" : { + "definition" : { + "val" : "Binds to and modulates the activity of an enzyme.", + "xrefs" : [ "GOC:dph", "GOC:mah", "GOC:tb" ] + }, + "comments" : [ "GO:0030234 is reserved for cases when the regulator directly interacts with the enzyme. When regulation of enzyme activity is achieved without enzyme binding, or when the mechanism of regulation is unknown, instead annotate to 'regulation of catalytic activity ; GO:0050790'." ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_aspergillus" ], + "xrefs" : [ { + "val" : "MIPS_funcat:18.02.01" + } ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "metalloenzyme regulator activity", + "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "enzyme modulator", + "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "catalytic regulator activity", + "xrefs" : [ "GOC:dph" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0010576" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "molecular_function" + } ] + }, + "type" : "CLASS", + "lbl" : "enzyme regulator activity" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0071941", + "meta" : { + "definition" : { + "val" : "A nitrogen compound metabolic process that contributes to the nitrogen cycle. The nitrogen cycle is a series of metabolic pathways by which nitrogen is converted between various forms and redox states; it encompasses pathways in which nitrogen is acted upon directly, such as nitrification, denitrification, nitrogen fixation, and mineralization.", + "xrefs" : [ "GOC:mah", "PMID:16675690", "Wikipedia:Nitrogen_cycle" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_chembl" ], + "xrefs" : [ { + "val" : "Wikipedia:Nitrogen_cycle" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "midori" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-09-30T05:21:03Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + }, + "type" : "CLASS", + "lbl" : "nitrogen cycle metabolic process" + 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"http://purl.obolibrary.org/obo/GO_0022857", + "meta" : { + "definition" : { + "val" : "Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other.", + "xrefs" : [ "GOC:jid", "GOC:mtg_transport", "ISBN:0815340729" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], + "xrefs" : [ { + "val" : "Reactome:R-HSA-6784436" + }, { + "val" : "Reactome:R-HSA-6784434" + }, { + "val" : "Reactome:R-HSA-5638209" + }, { + "val" : "Reactome:R-HSA-429036" + }, { + "val" : "Reactome:R-HSA-1236947" + }, { + "val" : "Reactome:R-HSA-5671707" + } ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "uptake transmembrane transporter activity", + "xrefs" : [ ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "substrate-specific transmembrane transporter activity", + "xrefs" : [ ] + }, { + "pred" 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non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.", + "xrefs" : [ "GOC:txnOH-2018" ] + }, + "comments" : [ "Curator guidance: Note that most DNA-binding transcription factors do not have enzymatic activity. The presence of specific domains known to be present in DNA-binding transcription factors (HOX, GATA etc) should be used to help decide whether a protein is a DNA binding transcription factor or a coregulator. If a protein has an enzymatic activity (for example, ubiquitin ligase, histone acetyl transferase) and no known DNA binding domain, consider annotating to GO:0003712 transcription coregulator activity. Special care should be taken with proteins containing Myb/SANT and ARID domains, since only a subset of proteins containing these domains are DNA-binding transcription factors for specific genes. \nChanged definition see https://github.com/geneontology/go-ontology/issues/15704\nMerged term see https://github.com/geneontology/go-ontology/issues/16534" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#goslim_aspergillus", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_generic" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "gene-specific transcription factor activity", + "xrefs" : [ ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "bacterial-type RNA polymerase transcription enhancer sequence-specific DNA binding transcription factor activity", + "xrefs" : [ ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity", + "xrefs" : [ ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity", + "xrefs" : [ ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "transcription factor activity, bacterial-type RNA polymerase transcription enhancer sequence-specific binding", + "xrefs" : [ ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "transcription factor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding", + "xrefs" : [ ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "metal ion regulated sequence-specific DNA binding transcription factor activity", + "xrefs" : [ ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "bacterial-type RNA polymerase transcription factor activity, sequence-specific DNA binding", + "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "sequence-specific DNA binding transcription factor activity", + "xrefs" : [ ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "bacterial-type RNA polymerase transcription factor activity, metal ion regulated sequence-specific DNA binding", + "xrefs" : [ ] + }, { + "pred" : "hasBroadSynonym", + "val" : "transcription factor activity", + "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "DNA binding transcription factor activity", + "xrefs" : [ ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "transcription factor activity, bacterial-type RNA polymerase proximal promoter sequence-specific DNA binding", + "xrefs" : [ ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "transcription factor activity, metal ion regulated sequence-specific DNA binding", + "xrefs" : [ ] + }, { + "pred" : "hasBroadSynonym", + "val" : "nucleic acid binding transcription factor activity", + "xrefs" : [ ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "bacterial-type DNA binding transcription factor activity", + "xrefs" : [ ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0001131" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0001130" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-10-21T04:37:54Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0001151" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0001199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0001071" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "kchris" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0000130" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "molecular_function" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0001204" + } ] + }, + "type" : "CLASS", + "lbl" : "DNA-binding transcription factor activity" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0051301", + "meta" : { + "definition" : { + "val" : "The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.", + "xrefs" : [ "GOC:di", "GOC:go_curators", "GOC:pr" ] + }, + "comments" : [ "Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division." ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_chembl" ], + "xrefs" : [ { + "val" : "Wikipedia:Cell_division" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + }, + "type" : "CLASS", + "lbl" : "cell division" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "type" : "PROPERTY", + "lbl" : "term replaced by" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0006810", + "meta" : { + "definition" : { + "val" : "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.", + "xrefs" : [ "GOC:dos", "GOC:dph", "GOC:jl", "GOC:mah" ] + }, + "comments" : [ "Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport." ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_aspergillus" ], + "xrefs" : [ { + "val" : "MIPS_funcat:20" + } ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "single-organism transport", + "xrefs" : [ ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "small molecule transport", + "xrefs" : [ ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "solute:solute exchange", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "janelomax" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0015457" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0015460" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0044765" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2012-12-13T16:25:32Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + }, + "type" : "CLASS", + "lbl" : "transport" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0006412", + "meta" : { + "definition" : { + "val" : "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.", + "xrefs" : [ "GOC:go_curators" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_aspergillus" ], + "xrefs" : [ { + "val" : "Wikipedia:Translation_(genetics)" + }, { + "val" : "MIPS_funcat:12" + } ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "protein synthesis", + "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "protein anabolism", + "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "protein translation", + "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "protein biosynthetic process", + "xrefs" : [ "GOC:curators" ] + }, { + "pred" : "hasExactSynonym", + "val" : "protein formation", + "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "protein biosynthesis", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0043037" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006416" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006453" + } ] + }, + "type" : "CLASS", + "lbl" : "translation" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0005840", + "meta" : { + "definition" : { + "val" : "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.", + "xrefs" : [ "ISBN:0198506732" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#goslim_aspergillus", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_chembl" ], + "xrefs" : [ { + "val" : "Wikipedia:Ribosome" + }, { + "val" : "NIF_Subcellular:sao1429207766" + } ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "free ribosome", + "xrefs" : [ "NIF_Subcellular:sao1139385046" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "ribosomal RNA", + "xrefs" : [ ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "membrane bound ribosome", + "xrefs" : [ "NIF_Subcellular:sao1291545653" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0033279" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "cellular_component" + } ] + }, + "type" : "CLASS", + "lbl" : "ribosome" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0006259", + "meta" : { + "definition" : { + "val" : "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.", + "xrefs" : [ "ISBN:0198506732" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_aspergillus", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_agr" ], + "xrefs" : [ { + "val" : "MIPS_funcat:10.01" + }, { + "val" : "MIPS_funcat:10" + } ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cellular DNA metabolism", + "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "DNA metabolism", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0055132" + } ] + }, + "type" : "CLASS", + "lbl" : "DNA metabolic process" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0000278", + "meta" : { + "definition" : { + "val" : "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.", + "xrefs" : [ "GOC:mah", "ISBN:0815316194", "Reactome:69278" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], + "xrefs" : [ { + "val" : "MIPS_funcat:10.03.01.01" + }, { + "val" : "Wikipedia:Mitosis" + }, { + "val" : "MIPS_funcat:10.03.01" + } ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "mitosis", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0007067" + } ] + }, + "type" : "CLASS", + "lbl" : "mitotic cell cycle" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0040011", + "meta" : { + "definition" : { + "val" : "Self-propelled movement of a cell or organism from one location to another.", + "xrefs" : [ "GOC:dgh" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_chembl" ], + "xrefs" : [ { + "val" : "MIPS_funcat:02.45.11" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + }, + "type" : "CLASS", + "lbl" : "locomotion" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0042393", + "meta" : { + "definition" : { + "val" : "Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. 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ontobio.obograph_util import convert_json_object, obograph_to_assoc_results +from pprint import pprint + +from ontobio.obograph_util import convert_json_object, obograph_to_assoc_results, convert_json_file from ontobio.golr.golr_query import GolrAssociationQuery from unittest.mock import MagicMock @@ -45,3 +47,14 @@ def test_obograph_to_assoc_results(self): expected_results = json.dumps(json.load(open(expected_fh))) assert results == expected_results + + def test_obograph_to_digraph_null_properties(self): + expected_fh = os.path.join(os.path.dirname(__file__), + 'resources/goslim_generic_missing_components.json') + with open(expected_fh, 'r') as f: + json_dict = json.load(f) + result = convert_json_object(json_dict, reverse_edges=False) + assert result is not None + assert result['graph'] is not None + +