Cell Ontology
The Cell Ontology is a structured controlled vocabulary for cell types in animals.
[{"category": "Individual", "contact_details": [{"contact_type": "email", "value": "do12@sanger.ac.uk"}, {"contact_type": "github", "value": "dosumis"}], "label": "David Osumi-Sutherland", "orcid": "0000-0002-7073-9172"}]
[{"category": "OntologyProduct", "description": "Complete ontology, plus inter-ontology axioms, and imports modules", "format": "owl", "id": "cl.owl", "name": "Main CL OWL edition", "product_file_size": 66753027, "product_url": "http://purl.obolibrary.org/obo/cl.owl"}, {"category": "OntologyProduct", "description": "Complete ontology, plus inter-ontology axioms, and imports modules merged in", "format": "obo", "id": "cl.obo", "name": "CL obo format edition", "product_file_size": 17349355, "product_url": "http://purl.obolibrary.org/obo/cl.obo"}, {"category": "OntologyProduct", "description": "Complete ontology, plus inter-ontology axioms, and imports modules merged in", "format": "json", "id": "cl.json", "name": "CL OBOGraph-JSON format edition", "product_file_size": 38790011, "product_url": "http://purl.obolibrary.org/obo/cl.json"}, {"category": "OntologyProduct", "description": "Basic version, no inter-ontology axioms", "format": "owl", "id": "cl.cl-basic.owl", "name": "Basic CL", "product_file_size": 8979957, "product_url": "http://purl.obolibrary.org/obo/cl/cl-basic.owl"}, {"category": "OntologyProduct", "description": "Basic version, no inter-ontology axioms", "format": "obo", "id": "cl.cl-basic.obo", "name": "Basic CL (OBO version)", "product_file_size": 3112081, "product_url": "http://purl.obolibrary.org/obo/cl/cl-basic.obo"}, {"category": "OntologyProduct", "description": "Basic version, no inter-ontology axioms", "format": "json", "id": "cl.cl-basic.json", "name": "Basic CL (OBOGraph-JSON version)", "product_file_size": 5189872, "product_url": "http://purl.obolibrary.org/obo/cl/cl-basic.json"}, {"category": "OntologyProduct", "description": "complete CL but with no imports or external axioms", "format": "owl", "id": "cl.cl-base.owl", "name": "CL base module", "product_file_size": 12017204, "product_url": "http://purl.obolibrary.org/obo/cl/cl-base.owl"}, {"category": "OntologyProduct", "description": "complete CL but with no imports or external axioms", "format": "obo", "id": "cl.cl-base.obo", "name": "CL base module (OBO version)", "product_file_size": 3514034, "product_url": "http://purl.obolibrary.org/obo/cl/cl-base.obo"}, {"category": "OntologyProduct", "description": "complete CL but with no imports or external axioms", "format": "json", "id": "cl.cl-base.json", "name": "CL base module (OBOGraph-JSON version)", "product_file_size": 6852450, "product_url": "http://purl.obolibrary.org/obo/cl/cl-base.json"}, {"category": "GraphProduct", "description": "Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access.", "dump_format": "neo4j", "id": "ubkg.neo4j", "name": "UBKG Neo4j Docker Distribution", "original_source": ["hgnc", "loinc", "icd10", "snomedct", "uberon", "pato", "cl", "doid", "obi", "obib", "edam", "hsapdv", "sbo", "mi", "chebi", "mp", "ordo", "uniprot", "uo", "mondo", "efo", "pgo", "gencode", "reactome", "hra", "hubmap", "sennet", "stellar", "dct", "clinvar", "connectivitymap", "hp", "mp", "msigdb", "wikipathways", "clingen", "string", "4dn", "erccrbp", "erccreg", "faldo", "glycordf", "glycocoo", "gtex", "kidsfirst", "lincs", "motrpac", "mw", "npo", "sckan", "disgenet", "biomarker", "opentargets"], "product_url": "https://ubkg-downloads.xconsortia.org/", "secondary_source": ["ubkg"]}, {"category": "GraphProduct", "description": "Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access.", "format": "csv", "id": "ubkg.csv", "name": "UBKG Ontology CSV Files", "original_source": ["hgnc", "loinc", "icd10", "snomedct", "uberon", "pato", "cl", "doid", "obi", "obib", "edam", "hsapdv", "sbo", "mi", "chebi", "mp", "ordo", "uniprot", "uo", "mondo", "efo", "pgo", "gencode", "reactome", "hra", "hubmap", "sennet", "stellar", "dct", "clinvar", "connectivitymap", "hp", "mp", "msigdb", "wikipathways", "clingen", "string", "4dn", "erccrbp", "erccreg", "faldo", "glycordf", "glycocoo", "gtex", "kidsfirst", "lincs", "motrpac", "mw", "npo", "sckan", "disgenet", "biomarker", "opentargets"], "product_url": "https://ubkg-downloads.xconsortia.org/", "secondary_source": ["ubkg"]}, {"category": "GraphProduct", "description": "The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources.", "id": "spoke.graph", "name": "SPOKE Graph", "original_source": ["ncbigene", "pubmed", "mesh", "pid", "doid", "diseases", "drugcentral", "go", "gwascatalog", "reactome", "lincs-l1000", "uberon", "wikipathways", "bindingdb", "drugbank", "sider", "bgee", "uniprot", "string", "omim", "chembl", "foodb", "civic", "gdsc", "clinicaltrialsgov", "hpa", "cl", "kegg", "metacyc", "bv-brc", "ncbitaxon", "pathophenodb", "pfam", "interpro", "protcid"], "secondary_source": ["spoke"]}, {"category": "GraphProduct", "description": "PheKnowLator graph files, including subsets with and without inverse relations.", "format": "owl", "id": "pheknowlator.graph", "latest_version": "current_build", "name": "PheKnowLator graph", "original_source": ["cl", "clo", "chebi", "go", "hp", "mondo", "pw", "pr", "ro", "so", "uberon", "vo", "bioportal", "clinvar", "ctd", "disgenet", "ensembl", "genemania", "hgnc", "hpa", "ncbigene", "medgen", "reactome", "string", "uniprot"], "product_url": "https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator", "secondary_source": ["pheknowlator"], "versions": ["v1.0.0", "v2.0.0", "v2.1.0", "v3.0.2", "v4.0.0", "current_build"]}, {"description": "The MechRepoNet knowledge graph in its original format", "id": "mechreponet.kg", "name": "MechRepoNet Knowledge Graph", "original_source": ["ctd", "doid", "go", "chebi", "reactome", "interpro", "hp", "cl", "pr", "uberon", "ncbitaxon", "hetionet", "complexportal", "rnacentral", "mirtarbase", "unii", "biolink"], "product_url": "https://github.com/SuLab/MechRepoNet/releases/tag/publication", "secondary_source": ["mechreponet"]}, {"category": "GraphProduct", "description": "RNA-KG as a Neo4j Dump", "format": "neo4j", "id": "rna-kg.kg.neo4j", "name": "RNA-KG Neo4j Dump", "original_source": ["dbsnp", "cosmic", "rnacentral", "ensembl", "circbase", "chebi", "pr", "ncbigene", "cl", "go", "mondo", "hp", "uberon", "vo", "pw", "reactome", "wikipathways"], "product_file_size": 3976840239, "product_url": "https://rna-kg.biodata.di.unimi.it/rnakgv20.dump", "secondary_source": ["rna-kg"]}, {"category": "GraphProduct", "description": "RNA-KG Nodes in CSV format", "format": "csv", "id": "rna-kg.kg.nodes", "name": "RNA-KG Nodes", "original_source": ["dbsnp", "cosmic", "rnacentral", "ensembl", "circbase", "chebi", "pr", "ncbigene", "cl", "go", "mondo", "hp", "uberon", "vo", "pw", "reactome", "wikipathways"], "product_file_size": 4424633304, "product_url": "https://rna-kg.biodata.di.unimi.it/nodes.csv", "secondary_source": ["rna-kg"]}, {"category": "GraphProduct", "description": "RNA-KG Edges in CSV format", "format": "csv", "id": "rna-kg.kg.edges", "name": "RNA-KG Edges", "original_source": ["dbsnp", "cosmic", "rnacentral", "ensembl", "circbase", "chebi", "pr", "ncbigene", "cl", "go", "mondo", "hp", "uberon", "vo", "pw", "reactome", "wikipathways"], "product_file_size": 18370248815, "product_url": "https://rna-kg.biodata.di.unimi.it/edges.csv", "secondary_source": ["rna-kg"]}, {"category": "GraphProduct", "description": "The integrative Biomedical Knowledge Hub (iBKH) knowledge graph, harmonizing and integrating information from diverse biomedical resources including DRKG, iDISK, and multiple databases (BRENDA, CTD, DrugBank, KEGG, PharmGKB, Reactome, SIDER, and others).", "id": "ibkh.graph", "name": "iBKH Knowledge Graph", "original_source": ["drkg", "idisk", "brenda", "ctd", "drugbank", "kegg", "pharmgkb", "reactome", "sider", "tissues", "bgee", "doid", "uberon", "cl", "hgnc", "chembl", "chebi"]}, {"category": "GraphProduct", "compatibility": [{"standard": "biolink"}], "compression": "zip", "description": "Curated mechanistic drug\u2013disease paths comprising the DrugMechDB dataset packaged as a downloadable archive.", "dump_format": "other", "format": "mixed", "id": "drugmechdb.graph", "latest_version": "2.0.1", "name": "DrugMechDB Graph Dataset", "original_source": ["go", "cl", "mesh", "chebi", "drugbank", "interpro", "uberon", "pr", "ncbitaxon", "reactome", "hp", "uniprot"], "product_url": "https://doi.org/10.5281/zenodo.8139357", "repository": "https://github.com/SuLab/DrugMechDB", "versions": ["2.0.1", "2.0.0", "1.0.2", "1.0"]}, {"category": "OntologyProduct", "description": "The latest release of EFO in OWL format", "format": "owl", "id": "efo.owl", "name": "EFO OWL", "original_source": ["bfo", "bto", "chebi", "cl", "clo", "cob", "dc", "doid", "ecto", "efo", "fbbt", "fbdv", "fma", "go", "hancestro", "hp", "iao", "ido", "ma", "mondo", "mp", "mpath", "ncbitaxon", "ncit", "oba", "obi", "ogms", "oio", "omit", "omo", "ordo", "pato", "po", "pr", "ro", "semapv", "skos", "so", "to", "uberon", "uo", "wbls", "zfa"], "product_file_size": 240665663, "product_url": "https://www.ebi.ac.uk/efo/efo.owl", "secondary_source": ["efo"]}, {"category": "OntologyProduct", "description": "The latest release of EFO in OBO format", "format": "obo", "id": "efo.obo", "name": "EFO OBO", "original_source": ["bfo", "bto", "chebi", "cl", "clo", "cob", "dc", "doid", "ecto", "efo", "fbbt", "fbdv", "fma", "go", "hancestro", "hp", "iao", "ido", "ma", "mondo", "mp", "mpath", "ncbitaxon", "ncit", "oba", "obi", "ogms", "oio", "omit", "omo", "ordo", "pato", "po", "pr", "ro", "semapv", "skos", "so", "to", "uberon", "uo", "wbls", "zfa"], "product_file_size": 64058275, "product_url": "https://www.ebi.ac.uk/efo/efo.obo", "secondary_source": ["efo"]}]
{"activity_status": "active", "category": "Ontology", "collection": ["obo-foundry"], "contacts": [{"category": "Individual", "contact_details": [{"contact_type": "email", "value": "do12@sanger.ac.uk"}, {"contact_type": "github", "value": "dosumis"}], "label": "David Osumi-Sutherland", "orcid": "0000-0002-7073-9172"}], "description": "The Cell Ontology is a structured controlled vocabulary for cell types in animals.", "domains": ["anatomy and development"], "homepage_url": "https://obophenotype.github.io/cell-ontology/", "id": "cl", "layout": "resource_detail", "license": {"id": "http://creativecommons.org/licenses/by/4.0/", "label": "CC BY 4.0", "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png"}, "name": "Cell Ontology", "products": [{"category": "OntologyProduct", "description": "Complete ontology, plus inter-ontology axioms, and imports modules", "format": "owl", "id": "cl.owl", "name": "Main CL OWL edition", "product_file_size": 66753027, "product_url": "http://purl.obolibrary.org/obo/cl.owl"}, {"category": "OntologyProduct", "description": "Complete ontology, plus inter-ontology axioms, and imports modules merged in", "format": "obo", "id": "cl.obo", "name": "CL obo format edition", "product_file_size": 17349355, "product_url": "http://purl.obolibrary.org/obo/cl.obo"}, {"category": "OntologyProduct", "description": "Complete ontology, plus inter-ontology axioms, and imports modules merged in", "format": "json", "id": "cl.json", "name": "CL OBOGraph-JSON format edition", "product_file_size": 38790011, "product_url": "http://purl.obolibrary.org/obo/cl.json"}, {"category": "OntologyProduct", "description": "Basic version, no inter-ontology axioms", "format": "owl", "id": "cl.cl-basic.owl", "name": "Basic CL", "product_file_size": 8979957, "product_url": "http://purl.obolibrary.org/obo/cl/cl-basic.owl"}, {"category": "OntologyProduct", "description": "Basic version, no inter-ontology axioms", "format": "obo", "id": "cl.cl-basic.obo", "name": "Basic CL (OBO version)", "product_file_size": 3112081, "product_url": "http://purl.obolibrary.org/obo/cl/cl-basic.obo"}, {"category": "OntologyProduct", "description": "Basic version, no inter-ontology axioms", "format": "json", "id": "cl.cl-basic.json", "name": "Basic CL (OBOGraph-JSON version)", "product_file_size": 5189872, "product_url": "http://purl.obolibrary.org/obo/cl/cl-basic.json"}, {"category": "OntologyProduct", "description": "complete CL but with no imports or external axioms", "format": "owl", "id": "cl.cl-base.owl", "name": "CL base module", "product_file_size": 12017204, "product_url": "http://purl.obolibrary.org/obo/cl/cl-base.owl"}, {"category": "OntologyProduct", "description": "complete CL but with no imports or external axioms", "format": "obo", "id": "cl.cl-base.obo", "name": "CL base module (OBO version)", "product_file_size": 3514034, "product_url": "http://purl.obolibrary.org/obo/cl/cl-base.obo"}, {"category": "OntologyProduct", "description": "complete CL but with no imports or external axioms", "format": "json", "id": "cl.cl-base.json", "name": "CL base module (OBOGraph-JSON version)", "product_file_size": 6852450, "product_url": "http://purl.obolibrary.org/obo/cl/cl-base.json"}, {"category": "GraphProduct", "description": "Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access.", "dump_format": "neo4j", "id": "ubkg.neo4j", "name": "UBKG Neo4j Docker Distribution", "original_source": ["hgnc", "loinc", "icd10", "snomedct", "uberon", "pato", "cl", "doid", "obi", "obib", "edam", "hsapdv", "sbo", "mi", "chebi", "mp", "ordo", "uniprot", "uo", "mondo", "efo", "pgo", "gencode", "reactome", "hra", "hubmap", "sennet", "stellar", "dct", "clinvar", "connectivitymap", "hp", "mp", "msigdb", "wikipathways", "clingen", "string", "4dn", "erccrbp", "erccreg", "faldo", "glycordf", "glycocoo", "gtex", "kidsfirst", "lincs", "motrpac", "mw", "npo", "sckan", "disgenet", "biomarker", "opentargets"], "product_url": "https://ubkg-downloads.xconsortia.org/", "secondary_source": ["ubkg"]}, {"category": "GraphProduct", "description": "Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access.", "format": "csv", "id": "ubkg.csv", "name": "UBKG Ontology CSV Files", "original_source": ["hgnc", "loinc", "icd10", "snomedct", "uberon", "pato", "cl", "doid", "obi", "obib", "edam", "hsapdv", "sbo", "mi", "chebi", "mp", "ordo", "uniprot", "uo", "mondo", "efo", "pgo", "gencode", "reactome", "hra", "hubmap", "sennet", "stellar", "dct", "clinvar", "connectivitymap", "hp", "mp", "msigdb", "wikipathways", "clingen", "string", "4dn", "erccrbp", "erccreg", "faldo", "glycordf", "glycocoo", "gtex", "kidsfirst", "lincs", "motrpac", "mw", "npo", "sckan", "disgenet", "biomarker", "opentargets"], "product_url": "https://ubkg-downloads.xconsortia.org/", "secondary_source": ["ubkg"]}, {"category": "GraphProduct", "description": "The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources.", "id": "spoke.graph", "name": "SPOKE Graph", "original_source": ["ncbigene", "pubmed", "mesh", "pid", "doid", "diseases", "drugcentral", "go", "gwascatalog", "reactome", "lincs-l1000", "uberon", "wikipathways", "bindingdb", "drugbank", "sider", "bgee", "uniprot", "string", "omim", "chembl", "foodb", "civic", "gdsc", "clinicaltrialsgov", "hpa", "cl", "kegg", "metacyc", "bv-brc", "ncbitaxon", "pathophenodb", "pfam", "interpro", "protcid"], "secondary_source": ["spoke"]}, {"category": "GraphProduct", "description": "PheKnowLator graph files, including subsets with and without inverse relations.", "format": "owl", "id": "pheknowlator.graph", "latest_version": "current_build", "name": "PheKnowLator graph", "original_source": ["cl", "clo", "chebi", "go", "hp", "mondo", "pw", "pr", "ro", "so", "uberon", "vo", "bioportal", "clinvar", "ctd", "disgenet", "ensembl", "genemania", "hgnc", "hpa", "ncbigene", "medgen", "reactome", "string", "uniprot"], "product_url": "https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator", "secondary_source": ["pheknowlator"], "versions": ["v1.0.0", "v2.0.0", "v2.1.0", "v3.0.2", "v4.0.0", "current_build"]}, {"description": "The MechRepoNet knowledge graph in its original format", "id": "mechreponet.kg", "name": "MechRepoNet Knowledge Graph", "original_source": ["ctd", "doid", "go", "chebi", "reactome", "interpro", "hp", "cl", "pr", "uberon", "ncbitaxon", "hetionet", "complexportal", "rnacentral", "mirtarbase", "unii", "biolink"], "product_url": "https://github.com/SuLab/MechRepoNet/releases/tag/publication", "secondary_source": ["mechreponet"]}, {"category": "GraphProduct", "description": "RNA-KG as a Neo4j Dump", "format": "neo4j", "id": "rna-kg.kg.neo4j", "name": "RNA-KG Neo4j Dump", "original_source": ["dbsnp", "cosmic", "rnacentral", "ensembl", "circbase", "chebi", "pr", "ncbigene", "cl", "go", "mondo", "hp", "uberon", "vo", "pw", "reactome", "wikipathways"], "product_file_size": 3976840239, "product_url": "https://rna-kg.biodata.di.unimi.it/rnakgv20.dump", "secondary_source": ["rna-kg"]}, {"category": "GraphProduct", "description": "RNA-KG Nodes in CSV format", "format": "csv", "id": "rna-kg.kg.nodes", "name": "RNA-KG Nodes", "original_source": ["dbsnp", "cosmic", "rnacentral", "ensembl", "circbase", "chebi", "pr", "ncbigene", "cl", "go", "mondo", "hp", "uberon", "vo", "pw", "reactome", "wikipathways"], "product_file_size": 4424633304, "product_url": "https://rna-kg.biodata.di.unimi.it/nodes.csv", "secondary_source": ["rna-kg"]}, {"category": "GraphProduct", "description": "RNA-KG Edges in CSV format", "format": "csv", "id": "rna-kg.kg.edges", "name": "RNA-KG Edges", "original_source": ["dbsnp", "cosmic", "rnacentral", "ensembl", "circbase", "chebi", "pr", "ncbigene", "cl", "go", "mondo", "hp", "uberon", "vo", "pw", "reactome", "wikipathways"], "product_file_size": 18370248815, "product_url": "https://rna-kg.biodata.di.unimi.it/edges.csv", "secondary_source": ["rna-kg"]}, {"category": "GraphProduct", "description": "The integrative Biomedical Knowledge Hub (iBKH) knowledge graph, harmonizing and integrating information from diverse biomedical resources including DRKG, iDISK, and multiple databases (BRENDA, CTD, DrugBank, KEGG, PharmGKB, Reactome, SIDER, and others).", "id": "ibkh.graph", "name": "iBKH Knowledge Graph", "original_source": ["drkg", "idisk", "brenda", "ctd", "drugbank", "kegg", "pharmgkb", "reactome", "sider", "tissues", "bgee", "doid", "uberon", "cl", "hgnc", "chembl", "chebi"]}, {"category": "GraphProduct", "compatibility": [{"standard": "biolink"}], "compression": "zip", "description": "Curated mechanistic drug\u2013disease paths comprising the DrugMechDB dataset packaged as a downloadable archive.", "dump_format": "other", "format": "mixed", "id": "drugmechdb.graph", "latest_version": "2.0.1", "name": "DrugMechDB Graph Dataset", "original_source": ["go", "cl", "mesh", "chebi", "drugbank", "interpro", "uberon", "pr", "ncbitaxon", "reactome", "hp", "uniprot"], "product_url": "https://doi.org/10.5281/zenodo.8139357", "repository": "https://github.com/SuLab/DrugMechDB", "versions": ["2.0.1", "2.0.0", "1.0.2", "1.0"]}, {"category": "OntologyProduct", "description": "The latest release of EFO in OWL format", "format": "owl", "id": "efo.owl", "name": "EFO OWL", "original_source": ["bfo", "bto", "chebi", "cl", "clo", "cob", "dc", "doid", "ecto", "efo", "fbbt", "fbdv", "fma", "go", "hancestro", "hp", "iao", "ido", "ma", "mondo", "mp", "mpath", "ncbitaxon", "ncit", "oba", "obi", "ogms", "oio", "omit", "omo", "ordo", "pato", "po", "pr", "ro", "semapv", "skos", "so", "to", "uberon", "uo", "wbls", "zfa"], "product_file_size": 240665663, "product_url": "https://www.ebi.ac.uk/efo/efo.owl", "secondary_source": ["efo"]}, {"category": "OntologyProduct", "description": "The latest release of EFO in OBO format", "format": "obo", "id": "efo.obo", "name": "EFO OBO", "original_source": ["bfo", "bto", "chebi", "cl", "clo", "cob", "dc", "doid", "ecto", "efo", "fbbt", "fbdv", "fma", "go", "hancestro", "hp", "iao", "ido", "ma", "mondo", "mp", "mpath", "ncbitaxon", "ncit", "oba", "obi", "ogms", "oio", "omit", "omo", "ordo", "pato", "po", "pr", "ro", "semapv", "skos", "so", "to", "uberon", "uo", "wbls", "zfa"], "product_file_size": 64058275, "product_url": "https://www.ebi.ac.uk/efo/efo.obo", "secondary_source": ["efo"]}], "repository": "https://github.com/obophenotype/cell-ontology", "taxon": ["NCBITaxon:33208"]}