name: Gene Ontology
description: An ontology for describing the function of genes and gene products
contacts: [{"category": "Individual", "contact_details": [{"contact_type": "email", "value": "suzia@stanford.edu"}, {"contact_type": "github", "value": "suzialeksander"}], "label": "Suzi Aleksander", "orcid": "0000-0001-6787-2901"}]
products: [{"category": "OntologyProduct", "description": "The main ontology in OWL. This is self contained and does not have connections to other OBO ontologies", "format": "owl", "id": "go.owl", "name": "GO (OWL edition)", "product_file_size": 127608493, "product_url": "http://purl.obolibrary.org/obo/go.owl"}, {"category": "OntologyProduct", "description": "Equivalent to go.owl, in obo format", "format": "obo", "id": "go.obo", "name": "GO (OBO Format edition)", "product_file_size": 35266549, "product_url": "http://purl.obolibrary.org/obo/go.obo"}, {"category": "OntologyProduct", "description": "Equivalent to go.owl, in obograph json format", "format": "json", "id": "go.json", "name": "GO (JSON edition)", "product_file_size": 77592125, "product_url": "http://purl.obolibrary.org/obo/go.json"}, {"category": "OntologyProduct", "description": "The main ontology plus axioms connecting to select external ontologies, with subsets of those ontologies", "format": "owl", "id": "go.extensions.go-plus.owl", "name": "GO-Plus", "product_file_size": 235965574, "product_url": "http://purl.obolibrary.org/obo/go/extensions/go-plus.owl"}, {"category": "OntologyProduct", "description": "The main ontology plus axioms connecting to select external ontologies, excluding the external ontologies themselves", "format": "owl", "id": "go.go-base.owl", "name": "GO Base Module", "product_file_size": 160571191, "product_url": "http://purl.obolibrary.org/obo/go/go-base.owl"}, {"category": "OntologyProduct", "description": "As go-plus.owl, in obographs json format", "format": "json", "id": "go.extensions.go-plus.json", "name": "GO-Plus", "product_file_size": 131618305, "product_url": "http://purl.obolibrary.org/obo/go/extensions/go-plus.json"}, {"category": "OntologyProduct", "description": "Basic version of the GO, filtered such that the graph is guaranteed to be acyclic and annotations can be propagated up the graph. The relations included are is a, part of, regulates, negatively regulates and positively regulates. This version excludes relationships that cross the 3 GO hierarchies.", "format": "obo", "id": "go.go-basic.obo", "name": "GO-Basic, Filtered, for use with legacy tools", "product_file_size": 31417323, "product_url": "http://purl.obolibrary.org/obo/go/go-basic.obo"}, {"category": "OntologyProduct", "description": "As go-basic.obo, in json format", "format": "json", "id": "go.go-basic.json", "name": "GO-Basic, Filtered, for use with legacy tools (JSON)", "product_file_size": 67130778, "product_url": "http://purl.obolibrary.org/obo/go/go-basic.json"}, {"category": "OntologyProduct", "description": "Classes added to ncbitaxon for groupings such as prokaryotes", "format": "owl", "id": "go.extensions.go-taxon-groupings.owl", "name": "GO Taxon Groupings", "product_url": "http://purl.obolibrary.org/obo/go/extensions/go-taxon-groupings.owl", "warnings": ["File was not able to be retrieved when checked on 2025-10-21: HTTP 404 error when accessing file"]}, {"category": "OntologyProduct", "description": "Equivalent to go.owl, but released daily. Note the snapshot release is not archived.", "format": "owl", "id": "go.snapshot.go.owl", "name": "GO (OWL edition), daily snapshot release", "product_file_size": 127608493, "product_url": "http://purl.obolibrary.org/obo/go/snapshot/go.owl"}, {"category": "OntologyProduct", "description": "Equivalent to go.owl, but released daily. Note the snapshot release is not archived.", "format": "obo", "id": "go.snapshot.go.obo", "name": "GO (OBO Format edition), daily snapshot release", "product_file_size": 35266549, "product_url": "http://purl.obolibrary.org/obo/go/snapshot/go.obo"}, {"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", "medline", "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": "Product", "description": "Network embeddings of the Bioteque graph that represent biological entities and their associations", "id": "bioteque.embeddings", "name": "Bioteque Embeddings", "original_source": ["chebi", "cosmic", "achilles", "depmap", "ccle", "gdsc", "cellosaurus", "clue", "ctd", "pharmacodb", "prism", "drugbank", "lincs", "compartments", "offsides", "sider", "drugcentral", "repohub", "chemicalchecker", "repodb", "disgenet", "opentargets", "creeds", "interpro", "reactome", "tissues", "dorothea", "progeny", "gtex", "hpa", "go", "corum", "huri", "intact", "omnipath", "string", "bto"], "product_url": "https://bioteque.irbbarcelona.org/downloads/embeddings", "secondary_source": ["bioteque"]}, {"category": "GraphProduct", "description": "Neo4j database dump of the Clinical Knowledge Graph and additional relationships", "dump_format": "neo4j", "edge_count": 220000000, "format": "mixed", "id": "clinicalkg.graph", "name": "CKG Graph Dump", "node_count": 16000000, "original_source": ["uniprot", "tissues", "string", "stitch", "smpdb", "signor", "sider", "refseq", "reactome", "phosphositeplus", "pfam", "oncokb", "mutationds", "intact", "hpa", "hmdb", "hgnc", "gwascatalog", "foodb", "drugbank", "disgenet", "diseases", "dgidb", "corum", "cancer-genome-interpreter", "doid", "bto", "efo", "go", "hp", "snomedct", "mod", "mi", "ms", "uo"], "product_url": "https://data.mendeley.com/datasets/mrcf7f4tc2/1"}, {"category": "GraphProduct", "description": "KGX Distribution of KG-Monarch", "edge_count": 14783802, "format": "kgx", "id": "kg-monarch.graph", "name": "KGX Distribution of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1366818, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "zfin"], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 230877741, "product_url": "http://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.tar.gz", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "KGX JSON-Lines Distribution of KG-Monarch", "edge_count": 14783802, "format": "kgx-jsonl", "id": "kg-monarch.graph.jsonl", "name": "KGX JSON-L Distribution of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1366818, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "zfin"], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 315667976, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.jsonl.tar.gz", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "RDF Distribution of KG-Monarch", "edge_count": 14783802, "format": "rdfxml", "id": "kg-monarch.graph.rdf", "name": "RDF Distribution of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1366818, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "zfin"], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 879238775, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.nt.gz", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "Neo4j Dump of KG-Monarch", "dump_format": "neo4j", "edge_count": 14783802, "id": "kg-monarch.graph.neo4j", "name": "Neo4j Dump of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1366818, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "zfin"], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 1438250397, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.neo4j.dump", "secondary_source": ["kg-monarch"], "warnings": []}, {"category": "GraphProduct", "description": "DuckDB database of KG-Monarch", "edge_count": 14783802, "id": "kg-monarch.graph.duckdb", "name": "DuckDB database of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1366818, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "zfin"], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 6827814912, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.duckdb", "secondary_source": ["kg-monarch"]}, {"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"]}, {"category": "GraphProduct", "description": "KGX JSON-Lines Distribution of KG-Monarch (Edges)", "edge_count": 14783802, "format": "kgx-jsonl", "id": "kg-monarch.graph.jsonl.edges", "name": "KGX JSON-L Distribution of KG-Monarch Edges", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1366818, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "zfin"], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 15279494795, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_edges.jsonl", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "KGX JSON-Lines Distribution of KG-Monarch (Nodes)", "edge_count": 14783802, "format": "kgx-jsonl", "id": "kg-monarch.graph.jsonl.nodes", "name": "KGX JSON-L Distribution of KG-Monarch Nodes", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1366818, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "zfin"], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 1149505896, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_nodes.jsonl", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "Neo4j Dump of KG-Monarch Edges", "edge_count": 14783802, "format": "neo4j", "id": "kg-monarch.graph.neo4j.edges", "name": "Neo4j Dump of KG-Monarch Edges", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1366818, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "zfin"], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 4386388748, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_edges.neo4j.csv", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "Neo4j Dump of KG-Monarch Nodes", "edge_count": 14783802, "format": "neo4j", "id": "kg-monarch.graph.neo4j.nodes", "name": "Neo4j Dump of KG-Monarch Nodes", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1366818, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "zfin"], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 349573789, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_nodes.neo4j.csv", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "Neo4j database dump of the Clinical Knowledge Graph and additional relationships", "dump_format": "neo4j", "edge_count": 220000000, "format": "mixed", "id": "cancer-genome-interpreter.clinicalkg.graph", "name": "CKG Graph Dump", "node_count": 16000000, "original_source": ["uniprot", "tissues", "string", "stitch", "smpdb", "signor", "sider", "refseq", "reactome", "phosphositeplus", "pfam", "oncokb", "mutationds", "intact", "hpa", "hmdb", "hgnc", "gwascatalog", "foodb", "drugbank", "disgenet", "diseases", "dgidb", "corum", "cancer-genome-interpreter", "doid", "bto", "efo", "go", "hp", "snomedct", "mod", "mi", "ms", "uo"], "product_url": "https://data.mendeley.com/datasets/mrcf7f4tc2/1"}, {"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": "GraphicalInterface", "description": "A browser interface for a knowledge graph for Alzheimer's Disease.", "format": "http", "id": "alzkb.browser", "name": "AlzKB Graph Database Browser", "original_source": ["aop-db", "bgee", "disgenet", "doid", "drugbank", "dsstox", "go", "gwascatalog", "hrpimp", "lincs-l1000", "mesh", "ncbigene", "pharmacotherapydb", "pid", "pubchem", "reactome", "sider", "tissues", "uberon", "wikipathways"], "product_url": "https://alzkb.ai:7473/login", "secondary_source": ["alzkb", "hetionet"]}, {"category": "GraphProduct", "description": "Memgraph data release for AlzKB.", "id": "alzkb.data", "name": "AlzKB Data Release (Version 2.0.0)", "original_source": ["aop-db", "bgee", "disgenet", "doid", "drugbank", "dsstox", "go", "gwascatalog", "hrpimp", "lincs-l1000", "mesh", "ncbigene", "pharmacotherapydb", "pid", "pubchem", "reactome", "reactome", "sider", "tissues", "uberon", "wikipathways"], "product_url": "https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0", "secondary_source": ["alzkb", "hetionet"]}, {"category": "GraphProduct", "description": "Nodes for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c)", "format": "kgx-jsonl", "id": "rtx-kg2.graph.nodes", "name": "RTX-KG2.10.1c KGX JSONL Nodes", "original_source": ["chembl", "drugbank", "kegg", "reactome", "go", "drugcentral", "uniprot", "mondo", "hp", "chebi", "uberon", "ncbitaxon", "dgidb", "disgenet", "ensembl", "gtopdb", "rtx-kg2", "semmeddb"], "product_file_size": 376501785, "product_url": "https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-nodes.jsonl.gz", "secondary_source": ["rtx-kg2"]}, {"category": "GraphProduct", "description": "Edges for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c)", "format": "kgx-jsonl", "id": "rtx-kg2.graph.edges", "name": "RTX-KG2.10.1c KGX JSONL Edges", "original_source": ["chembl", "drugbank", "kegg", "reactome", "go", "drugcentral", "uniprot", "mondo", "hp", "chebi", "uberon", "ncbitaxon", "dgidb", "disgenet", "ensembl", "gtopdb", "rtx-kg2", "semmeddb"], "product_file_size": 1807360397, "product_url": "https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-edges.jsonl.gz", "secondary_source": ["rtx-kg2"]}, {"category": "ProgrammingInterface", "description": "Neo4j distribution of the RTX-KG2 as a graph database", "dump_format": "neo4j", "id": "rtx-kg2.neo4j", "is_neo4j": true, "is_public": false, "name": "RTX-KG2 Neo4j", "original_source": ["chembl", "drugbank", "kegg", "reactome", "go", "drugcentral", "uniprot", "mondo", "hp", "chebi", "uberon", "ncbitaxon", "dgidb", "disgenet", "ensembl", "gtopdb", "rtx-kg2", "semmeddb"], "product_url": "https://arax.ncats.io/", "secondary_source": ["rtx-kg2"]}, {"category": "OntologyProduct", "description": "OWL release of Monochrom Ontology", "format": "owl", "id": "chr.model.owl", "name": "Monochrom Ontology OWL release", "original_source": ["ro", "go", "ncbitaxon", "iao", "geno", "skos", "gff"], "product_file_size": 102365, "product_url": "https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.owl", "secondary_source": ["chr"]}, {"category": "ProcessProduct", "description": "INDRA CoGEx is a graph database integrating causal relations, ontological relations, properties, and data, assembled at scale automatically from the scientific literature and structured sources. This is the code to build the graph.", "id": "indra.cogex.code", "name": "INDRA CoGEx Build Code", "original_source": ["chembl", "sider", "reactome", "wikipathways", "hp", "nihreporter", "disgenet", "pubmed", "gwascatalog", "cellmarker", "go", "bgee", "ccle", "clinicaltrialsgov", "indra"], "product_url": "https://github.com/gyorilab/indra_cogex", "secondary_source": ["indra"]}, {"category": "MappingProduct", "compression": "gzip", "description": "Gene to Gene Ontology mapping data providing functional annotations for genes", "format": "tsv", "id": "ncbigene.gene2go", "name": "Gene to GO Mapping", "original_source": ["go", "ncbigene"], "product_file_size": 1223833668, "product_url": "https://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz"}, {"category": "ProgrammingInterface", "description": "TRAPI web API for querying MicrobiomeKG", "format": "http", "id": "microbiomekg.api", "name": "MicrobiomeKG Plover API", "original_source": ["biolink", "chebi", "ncbitaxon", "ncbigene", "mesh", "pubchem", "go", "mondo", "ncit", "efo", "uniprot", "rhea", "pr", "uberon", "panther", "hgnc", "drugbank", "eupathdb"], "product_url": "https://multiomics.transltr.io/mbkp", "secondary_source": ["microbiomekg"]}, {"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": "MappingProduct", "description": "bigg.compartment SSSOM", "format": "sssom", "id": "obo-db-ingest.bigg.compartment.sssom.tsv", "license": {"id": "http://bigg.ucsd.edu/license#license", "label": "Custom"}, "name": "bigg.compartment SSSOM", "original_source": ["bigg", "go"], "product_file_size": 242, "product_url": "https://w3id.org/biopragmatics/resources/bigg.compartment/bigg.compartment.sssom.tsv", "secondary_source": ["obo-db-ingest"]}, {"category": "Product", "description": "Gene ontology annotations from the Gene Ontology Consortium", "format": "http", "id": "genecards.gene.ontology", "name": "GeneCards Gene Ontology Annotations", "original_source": ["go"], "product_url": "https://www.genecards.org/", "warnings": ["File was not able to be retrieved when checked on 2025-10-21_ HTTP 403 error when accessing file", "File was not able to be retrieved when checked on 2025-10-15_ HTTP 403 error when accessing file", "File was not able to be retrieved when checked on 2025-10-21: HTTP 403 error when accessing file"]}, {"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"]}, {"category": "MappingProduct", "description": "Mappings between InterPro entries and Gene Ontology (GO) terms", "format": "tsv", "id": "interpro.interpro2go", "name": "InterPro to GO Mappings", "original_source": ["go", "interpro"], "product_file_size": 3088718, "product_url": "https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/interpro2go", "secondary_source": ["interpro"]}, {"category": "DataModelProduct", "description": "The Basic subset of the Plant Trait Ontology in OBO format", "format": "obo", "id": "to-basic.obo", "latest_version": "v2025-05-20", "license": {"id": "https://creativecommons.org/licenses/by/4.0/", "label": "CC BY 4.0"}, "name": "Plant Trait Ontology Basic OBO", "original_source": ["to", "chebi", "ro", "ncbitaxon", "go", "omo", "ecto", "ido", "oio", "pato", "envo", "ohmi", "iao", "omrse", "obi", "peco", "po", "uberon", "ogms", "bfo"], "product_file_size": 111996, "product_url": "http://purl.obolibrary.org/obo/to/subsets/to-basic.obo", "secondary_source": ["to"], "versions": ["v2025-05-20", "v2023-07-17", "v2022-04-13", "v2022-03-09", "v2021-04-06"]}]
raw_data: {"activity_status": "active", "category": "Ontology", "collection": ["obo-foundry"], "contacts": [{"category": "Individual", "contact_details": [{"contact_type": "email", "value": "suzia@stanford.edu"}, {"contact_type": "github", "value": "suzialeksander"}], "label": "Suzi Aleksander", "orcid": "0000-0001-6787-2901"}], "description": "An ontology for describing the function of genes and gene products", "domains": ["biological systems"], "homepage_url": "http://geneontology.org/", "id": "go", "layout": "resource_detail", "license": {"id": "https://creativecommons.org/licenses/by/4.0/", "label": "CC BY 4.0", "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png"}, "name": "Gene Ontology", "products": [{"category": "OntologyProduct", "description": "The main ontology in OWL. This is self contained and does not have connections to other OBO ontologies", "format": "owl", "id": "go.owl", "name": "GO (OWL edition)", "product_file_size": 127608493, "product_url": "http://purl.obolibrary.org/obo/go.owl"}, {"category": "OntologyProduct", "description": "Equivalent to go.owl, in obo format", "format": "obo", "id": "go.obo", "name": "GO (OBO Format edition)", "product_file_size": 35266549, "product_url": "http://purl.obolibrary.org/obo/go.obo"}, {"category": "OntologyProduct", "description": "Equivalent to go.owl, in obograph json format", "format": "json", "id": "go.json", "name": "GO (JSON edition)", "product_file_size": 77592125, "product_url": "http://purl.obolibrary.org/obo/go.json"}, {"category": "OntologyProduct", "description": "The main ontology plus axioms connecting to select external ontologies, with subsets of those ontologies", "format": "owl", "id": "go.extensions.go-plus.owl", "name": "GO-Plus", "product_file_size": 235965574, "product_url": "http://purl.obolibrary.org/obo/go/extensions/go-plus.owl"}, {"category": "OntologyProduct", "description": "The main ontology plus axioms connecting to select external ontologies, excluding the external ontologies themselves", "format": "owl", "id": "go.go-base.owl", "name": "GO Base Module", "product_file_size": 160571191, "product_url": "http://purl.obolibrary.org/obo/go/go-base.owl"}, {"category": "OntologyProduct", "description": "As go-plus.owl, in obographs json format", "format": "json", "id": "go.extensions.go-plus.json", "name": "GO-Plus", "product_file_size": 131618305, "product_url": "http://purl.obolibrary.org/obo/go/extensions/go-plus.json"}, {"category": "OntologyProduct", "description": "Basic version of the GO, filtered such that the graph is guaranteed to be acyclic and annotations can be propagated up the graph. The relations included are is a, part of, regulates, negatively regulates and positively regulates. This version excludes relationships that cross the 3 GO hierarchies.", "format": "obo", "id": "go.go-basic.obo", "name": "GO-Basic, Filtered, for use with legacy tools", "product_file_size": 31417323, "product_url": "http://purl.obolibrary.org/obo/go/go-basic.obo"}, {"category": "OntologyProduct", "description": "As go-basic.obo, in json format", "format": "json", "id": "go.go-basic.json", "name": "GO-Basic, Filtered, for use with legacy tools (JSON)", "product_file_size": 67130778, "product_url": "http://purl.obolibrary.org/obo/go/go-basic.json"}, {"category": "OntologyProduct", "description": "Classes added to ncbitaxon for groupings such as prokaryotes", "format": "owl", "id": "go.extensions.go-taxon-groupings.owl", "name": "GO Taxon Groupings", "product_url": "http://purl.obolibrary.org/obo/go/extensions/go-taxon-groupings.owl", "warnings": ["File was not able to be retrieved when checked on 2025-10-21: HTTP 404 error when accessing file"]}, {"category": "OntologyProduct", "description": "Equivalent to go.owl, but released daily. Note the snapshot release is not archived.", "format": "owl", "id": "go.snapshot.go.owl", "name": "GO (OWL edition), daily snapshot release", "product_file_size": 127608493, "product_url": "http://purl.obolibrary.org/obo/go/snapshot/go.owl"}, {"category": "OntologyProduct", "description": "Equivalent to go.owl, but released daily. Note the snapshot release is not archived.", "format": "obo", "id": "go.snapshot.go.obo", "name": "GO (OBO Format edition), daily snapshot release", "product_file_size": 35266549, "product_url": "http://purl.obolibrary.org/obo/go/snapshot/go.obo"}, {"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", "medline", "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": "Product", "description": "Network embeddings of the Bioteque graph that represent biological entities and their associations", "id": "bioteque.embeddings", "name": "Bioteque Embeddings", "original_source": ["chebi", "cosmic", "achilles", "depmap", "ccle", "gdsc", "cellosaurus", "clue", "ctd", "pharmacodb", "prism", "drugbank", "lincs", "compartments", "offsides", "sider", "drugcentral", "repohub", "chemicalchecker", "repodb", "disgenet", "opentargets", "creeds", "interpro", "reactome", "tissues", "dorothea", "progeny", "gtex", "hpa", "go", "corum", "huri", "intact", "omnipath", "string", "bto"], "product_url": "https://bioteque.irbbarcelona.org/downloads/embeddings", "secondary_source": ["bioteque"]}, {"category": "GraphProduct", "description": "Neo4j database dump of the Clinical Knowledge Graph and additional relationships", "dump_format": "neo4j", "edge_count": 220000000, "format": "mixed", "id": "clinicalkg.graph", "name": "CKG Graph Dump", "node_count": 16000000, "original_source": ["uniprot", "tissues", "string", "stitch", "smpdb", "signor", "sider", "refseq", "reactome", "phosphositeplus", "pfam", "oncokb", "mutationds", "intact", "hpa", "hmdb", "hgnc", "gwascatalog", "foodb", "drugbank", "disgenet", "diseases", "dgidb", "corum", "cancer-genome-interpreter", "doid", "bto", "efo", "go", "hp", "snomedct", "mod", "mi", "ms", "uo"], "product_url": "https://data.mendeley.com/datasets/mrcf7f4tc2/1"}, {"category": "GraphProduct", "description": "KGX Distribution of KG-Monarch", "edge_count": 14783802, "format": "kgx", "id": "kg-monarch.graph", "name": "KGX Distribution of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1366818, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "zfin"], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 230877741, "product_url": "http://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.tar.gz", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "KGX JSON-Lines Distribution of KG-Monarch", "edge_count": 14783802, "format": "kgx-jsonl", "id": "kg-monarch.graph.jsonl", "name": "KGX JSON-L Distribution of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1366818, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "zfin"], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 315667976, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.jsonl.tar.gz", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "RDF Distribution of KG-Monarch", "edge_count": 14783802, "format": "rdfxml", "id": "kg-monarch.graph.rdf", "name": "RDF Distribution of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1366818, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "zfin"], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 879238775, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.nt.gz", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "Neo4j Dump of KG-Monarch", "dump_format": "neo4j", "edge_count": 14783802, "id": "kg-monarch.graph.neo4j", "name": "Neo4j Dump of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1366818, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "zfin"], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 1438250397, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.neo4j.dump", "secondary_source": ["kg-monarch"], "warnings": []}, {"category": "GraphProduct", "description": "DuckDB database of KG-Monarch", "edge_count": 14783802, "id": "kg-monarch.graph.duckdb", "name": "DuckDB database of KG-Monarch", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1366818, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "zfin"], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 6827814912, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.duckdb", "secondary_source": ["kg-monarch"]}, {"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"]}, {"category": "GraphProduct", "description": "KGX JSON-Lines Distribution of KG-Monarch (Edges)", "edge_count": 14783802, "format": "kgx-jsonl", "id": "kg-monarch.graph.jsonl.edges", "name": "KGX JSON-L Distribution of KG-Monarch Edges", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1366818, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "zfin"], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 15279494795, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_edges.jsonl", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "KGX JSON-Lines Distribution of KG-Monarch (Nodes)", "edge_count": 14783802, "format": "kgx-jsonl", "id": "kg-monarch.graph.jsonl.nodes", "name": "KGX JSON-L Distribution of KG-Monarch Nodes", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1366818, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "zfin"], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 1149505896, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_nodes.jsonl", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "Neo4j Dump of KG-Monarch Edges", "edge_count": 14783802, "format": "neo4j", "id": "kg-monarch.graph.neo4j.edges", "name": "Neo4j Dump of KG-Monarch Edges", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1366818, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "zfin"], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 4386388748, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_edges.neo4j.csv", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "Neo4j Dump of KG-Monarch Nodes", "edge_count": 14783802, "format": "neo4j", "id": "kg-monarch.graph.neo4j.nodes", "name": "Neo4j Dump of KG-Monarch Nodes", "node_categories": ["biolink:AnatomicalEntity", "biolink:BiologicalProcess", "biolink:Cell", "biolink:CellularComponent", "biolink:ChemicalEntity", "biolink:Disease", "biolink:Gene", "biolink:Genotype", "biolink:LifeStage", "biolink:MolecularActivity", "biolink:MolecularEntity", "biolink:NamedThing", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:SequenceVariant"], "node_count": 1366818, "original_source": ["phenio", "alliance", "bgee", "biogrid", "clingen", "clinvar", "ctd", "dictybase", "go", "hp", "maxo", "panther", "pombase", "reactome", "string", "xenbase", "zfin"], "predicates": ["biolink:actively_involved_in", "biolink:acts_upstream_of", "biolink:acts_upstream_of_negative_effect", "biolink:acts_upstream_of_or_within", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:ameliorates_condition", "biolink:associated_with_increased_likelihood_of", "biolink:caused_by", "biolink:causes", "biolink:colocalizes_with", "biolink:contraindicated_in", "biolink:contributes_to", "biolink:disease_has_location", "biolink:disrupts", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:genetically_associated_with", "biolink:has_mode_of_inheritance", "biolink:has_participant", "biolink:has_phenotype", "biolink:has_sequence_variant", "biolink:interacts_with", "biolink:is_active_in", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:model_of", "biolink:orthologous_to", "biolink:part_of", "biolink:participates_in", "biolink:preventative_for_condition", "biolink:related_to", "biolink:subclass_of", "biolink:treats_or_applied_or_studied_to_treat"], "product_file_size": 349573789, "product_url": "https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_nodes.neo4j.csv", "secondary_source": ["kg-monarch"]}, {"category": "GraphProduct", "description": "Neo4j database dump of the Clinical Knowledge Graph and additional relationships", "dump_format": "neo4j", "edge_count": 220000000, "format": "mixed", "id": "cancer-genome-interpreter.clinicalkg.graph", "name": "CKG Graph Dump", "node_count": 16000000, "original_source": ["uniprot", "tissues", "string", "stitch", "smpdb", "signor", "sider", "refseq", "reactome", "phosphositeplus", "pfam", "oncokb", "mutationds", "intact", "hpa", "hmdb", "hgnc", "gwascatalog", "foodb", "drugbank", "disgenet", "diseases", "dgidb", "corum", "cancer-genome-interpreter", "doid", "bto", "efo", "go", "hp", "snomedct", "mod", "mi", "ms", "uo"], "product_url": "https://data.mendeley.com/datasets/mrcf7f4tc2/1"}, {"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": "GraphicalInterface", "description": "A browser interface for a knowledge graph for Alzheimer's Disease.", "format": "http", "id": "alzkb.browser", "name": "AlzKB Graph Database Browser", "original_source": ["aop-db", "bgee", "disgenet", "doid", "drugbank", "dsstox", "go", "gwascatalog", "hrpimp", "lincs-l1000", "mesh", "ncbigene", "pharmacotherapydb", "pid", "pubchem", "reactome", "sider", "tissues", "uberon", "wikipathways"], "product_url": "https://alzkb.ai:7473/login", "secondary_source": ["alzkb", "hetionet"]}, {"category": "GraphProduct", "description": "Memgraph data release for AlzKB.", "id": "alzkb.data", "name": "AlzKB Data Release (Version 2.0.0)", "original_source": ["aop-db", "bgee", "disgenet", "doid", "drugbank", "dsstox", "go", "gwascatalog", "hrpimp", "lincs-l1000", "mesh", "ncbigene", "pharmacotherapydb", "pid", "pubchem", "reactome", "reactome", "sider", "tissues", "uberon", "wikipathways"], "product_url": "https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0", "secondary_source": ["alzkb", "hetionet"]}, {"category": "GraphProduct", "description": "Nodes for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c)", "format": "kgx-jsonl", "id": "rtx-kg2.graph.nodes", "name": "RTX-KG2.10.1c KGX JSONL Nodes", "original_source": ["chembl", "drugbank", "kegg", "reactome", "go", "drugcentral", "uniprot", "mondo", "hp", "chebi", "uberon", "ncbitaxon", "dgidb", "disgenet", "ensembl", "gtopdb", "rtx-kg2", "semmeddb"], "product_file_size": 376501785, "product_url": "https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-nodes.jsonl.gz", "secondary_source": ["rtx-kg2"]}, {"category": "GraphProduct", "description": "Edges for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c)", "format": "kgx-jsonl", "id": "rtx-kg2.graph.edges", "name": "RTX-KG2.10.1c KGX JSONL Edges", "original_source": ["chembl", "drugbank", "kegg", "reactome", "go", "drugcentral", "uniprot", "mondo", "hp", "chebi", "uberon", "ncbitaxon", "dgidb", "disgenet", "ensembl", "gtopdb", "rtx-kg2", "semmeddb"], "product_file_size": 1807360397, "product_url": "https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-edges.jsonl.gz", "secondary_source": ["rtx-kg2"]}, {"category": "ProgrammingInterface", "description": "Neo4j distribution of the RTX-KG2 as a graph database", "dump_format": "neo4j", "id": "rtx-kg2.neo4j", "is_neo4j": true, "is_public": false, "name": "RTX-KG2 Neo4j", "original_source": ["chembl", "drugbank", "kegg", "reactome", "go", "drugcentral", "uniprot", "mondo", "hp", "chebi", "uberon", "ncbitaxon", "dgidb", "disgenet", "ensembl", "gtopdb", "rtx-kg2", "semmeddb"], "product_url": "https://arax.ncats.io/", "secondary_source": ["rtx-kg2"]}, {"category": "OntologyProduct", "description": "OWL release of Monochrom Ontology", "format": "owl", "id": "chr.model.owl", "name": "Monochrom Ontology OWL release", "original_source": ["ro", "go", "ncbitaxon", "iao", "geno", "skos", "gff"], "product_file_size": 102365, "product_url": "https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.owl", "secondary_source": ["chr"]}, {"category": "ProcessProduct", "description": "INDRA CoGEx is a graph database integrating causal relations, ontological relations, properties, and data, assembled at scale automatically from the scientific literature and structured sources. This is the code to build the graph.", "id": "indra.cogex.code", "name": "INDRA CoGEx Build Code", "original_source": ["chembl", "sider", "reactome", "wikipathways", "hp", "nihreporter", "disgenet", "pubmed", "gwascatalog", "cellmarker", "go", "bgee", "ccle", "clinicaltrialsgov", "indra"], "product_url": "https://github.com/gyorilab/indra_cogex", "secondary_source": ["indra"]}, {"category": "MappingProduct", "compression": "gzip", "description": "Gene to Gene Ontology mapping data providing functional annotations for genes", "format": "tsv", "id": "ncbigene.gene2go", "name": "Gene to GO Mapping", "original_source": ["go", "ncbigene"], "product_file_size": 1223833668, "product_url": "https://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz"}, {"category": "ProgrammingInterface", "description": "TRAPI web API for querying MicrobiomeKG", "format": "http", "id": "microbiomekg.api", "name": "MicrobiomeKG Plover API", "original_source": ["biolink", "chebi", "ncbitaxon", "ncbigene", "mesh", "pubchem", "go", "mondo", "ncit", "efo", "uniprot", "rhea", "pr", "uberon", "panther", "hgnc", "drugbank", "eupathdb"], "product_url": "https://multiomics.transltr.io/mbkp", "secondary_source": ["microbiomekg"]}, {"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": "MappingProduct", "description": "bigg.compartment SSSOM", "format": "sssom", "id": "obo-db-ingest.bigg.compartment.sssom.tsv", "license": {"id": "http://bigg.ucsd.edu/license#license", "label": "Custom"}, "name": "bigg.compartment SSSOM", "original_source": ["bigg", "go"], "product_file_size": 242, "product_url": "https://w3id.org/biopragmatics/resources/bigg.compartment/bigg.compartment.sssom.tsv", "secondary_source": ["obo-db-ingest"]}, {"category": "Product", "description": "Gene ontology annotations from the Gene Ontology Consortium", "format": "http", "id": "genecards.gene.ontology", "name": "GeneCards Gene Ontology Annotations", "original_source": ["go"], "product_url": "https://www.genecards.org/", "warnings": ["File was not able to be retrieved when checked on 2025-10-21_ HTTP 403 error when accessing file", "File was not able to be retrieved when checked on 2025-10-15_ HTTP 403 error when accessing file", "File was not able to be retrieved when checked on 2025-10-21: HTTP 403 error when accessing file"]}, {"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"]}, {"category": "MappingProduct", "description": "Mappings between InterPro entries and Gene Ontology (GO) terms", "format": "tsv", "id": "interpro.interpro2go", "name": "InterPro to GO Mappings", "original_source": ["go", "interpro"], "product_file_size": 3088718, "product_url": "https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/interpro2go", "secondary_source": ["interpro"]}, {"category": "DataModelProduct", "description": "The Basic subset of the Plant Trait Ontology in OBO format", "format": "obo", "id": "to-basic.obo", "latest_version": "v2025-05-20", "license": {"id": "https://creativecommons.org/licenses/by/4.0/", "label": "CC BY 4.0"}, "name": "Plant Trait Ontology Basic OBO", "original_source": ["to", "chebi", "ro", "ncbitaxon", "go", "omo", "ecto", "ido", "oio", "pato", "envo", "ohmi", "iao", "omrse", "obi", "peco", "po", "uberon", "ogms", "bfo"], "product_file_size": 111996, "product_url": "http://purl.obolibrary.org/obo/to/subsets/to-basic.obo", "secondary_source": ["to"], "versions": ["v2025-05-20", "v2023-07-17", "v2022-04-13", "v2022-03-09", "v2021-04-06"]}], "repository": "https://github.com/geneontology/go-ontology", "taxon": ["NCBITaxon:1"]}