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Value can be ontology class ID or subset ID","explode":true,"in":"query","name":"slim","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2","in":"query","name":"evidence","schema":{"type":"string"}},{"description":"Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False","in":"query","name":"direct","schema":{"default":false,"type":"boolean"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AssociationResults"}}},"description":"Success"}},"summary":"Returns variants associated with a case","tags":["bioentity"]},"parameters":[{"description":"CURIE identifier for a case","in":"path","name":"id","required":true,"schema":{"type":"string"}}]},"/bioentity/disease/{id}/cases":{"get":{"operationId":"get_disease_case_associations","parameters":[{"description":"number of rows","in":"query","name":"rows","schema":{"default":100,"type":"integer"}},{"description":"beginning row","in":"query","name":"start","schema":{"type":"integer"}},{"description":"Enable faceting","in":"query","name":"facet","schema":{"default":false,"type":"boolean"}},{"description":"Fields to facet on","explode":true,"in":"query","name":"facet_fields","schema":{"items":{"type":"string"},"type":"array"}},{"description":"If true, excludes evidence objects in response","in":"query","name":"unselect_evidence","schema":{"default":false,"type":"boolean"}},{"description":"If true, excludes associations that involve IEAs (ECO:0000501)","in":"query","name":"exclude_automatic_assertions","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload","in":"query","name":"fetch_objects","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns results in compact associations format","in":"query","name":"use_compact_associations","schema":{"default":false,"type":"boolean"}},{"description":"Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID","explode":true,"in":"query","name":"slim","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2","in":"query","name":"evidence","schema":{"type":"string"}},{"description":"Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False","in":"query","name":"direct","schema":{"default":false,"type":"boolean"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AssociationResults"}}},"description":"Success"}},"summary":"Returns cases associated with a disease","tags":["bioentity"]},"parameters":[{"description":"CURIE identifier of disease, e.g. MONDO:0007103, MONDO:0010918. Equivalent IDs can be used with same results","in":"path","name":"id","required":true,"schema":{"type":"string"}}]},"/bioentity/disease/{id}/genes":{"get":{"operationId":"get_disease_gene_associations","parameters":[{"description":"number of rows","in":"query","name":"rows","schema":{"default":100,"type":"integer"}},{"description":"beginning row","in":"query","name":"start","schema":{"type":"integer"}},{"description":"Enable faceting","in":"query","name":"facet","schema":{"default":false,"type":"boolean"}},{"description":"Fields to facet on","explode":true,"in":"query","name":"facet_fields","schema":{"items":{"type":"string"},"type":"array"}},{"description":"If true, excludes evidence objects in response","in":"query","name":"unselect_evidence","schema":{"default":false,"type":"boolean"}},{"description":"If true, excludes associations that involve IEAs (ECO:0000501)","in":"query","name":"exclude_automatic_assertions","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload","in":"query","name":"fetch_objects","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns results in compact associations format","in":"query","name":"use_compact_associations","schema":{"default":false,"type":"boolean"}},{"description":"Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID","explode":true,"in":"query","name":"slim","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2","in":"query","name":"evidence","schema":{"type":"string"}},{"description":"Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False","in":"query","name":"direct","schema":{"default":false,"type":"boolean"}},{"description":"One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default","explode":true,"in":"query","name":"taxon","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Set true to exclude inferred taxa","in":"query","name":"direct_taxon","schema":{"default":false,"type":"boolean"}},{"description":"A relation CURIE to filter associations","in":"query","name":"relation","schema":{"type":"string"}},{"description":"Sorting responses <field> <desc,asc>","in":"query","name":"sort","schema":{"type":"string"}},{"description":"Query string to filter documents","in":"query","name":"q","schema":{"type":"string"}},{"description":"Additional filters: causal, non_causal, both","explode":true,"in":"query","name":"association_type","schema":{"default":"both","enum":["causal","non_causal","both"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AssociationResults"}}},"description":"Success"}},"summary":"Returns genes associated with a disease","tags":["bioentity"]},"parameters":[{"description":"CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results","in":"path","name":"id","required":true,"schema":{"type":"string"}}]},"/bioentity/disease/{id}/genotypes":{"get":{"operationId":"get_disease_genotype_associations","parameters":[{"description":"number of rows","in":"query","name":"rows","schema":{"default":100,"type":"integer"}},{"description":"beginning row","in":"query","name":"start","schema":{"type":"integer"}},{"description":"Enable faceting","in":"query","name":"facet","schema":{"default":false,"type":"boolean"}},{"description":"Fields to facet on","explode":true,"in":"query","name":"facet_fields","schema":{"items":{"type":"string"},"type":"array"}},{"description":"If true, excludes evidence objects in response","in":"query","name":"unselect_evidence","schema":{"default":false,"type":"boolean"}},{"description":"If true, excludes associations that involve IEAs (ECO:0000501)","in":"query","name":"exclude_automatic_assertions","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload","in":"query","name":"fetch_objects","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns results in compact associations format","in":"query","name":"use_compact_associations","schema":{"default":false,"type":"boolean"}},{"description":"Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID","explode":true,"in":"query","name":"slim","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2","in":"query","name":"evidence","schema":{"type":"string"}},{"description":"Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False","in":"query","name":"direct","schema":{"default":false,"type":"boolean"}},{"description":"One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default","explode":true,"in":"query","name":"taxon","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Set true to exclude inferred taxa","in":"query","name":"direct_taxon","schema":{"default":false,"type":"boolean"}},{"description":"A relation CURIE to filter associations","in":"query","name":"relation","schema":{"type":"string"}},{"description":"Sorting responses <field> <desc,asc>","in":"query","name":"sort","schema":{"type":"string"}},{"description":"Query string to filter documents","in":"query","name":"q","schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AssociationResults"}}},"description":"Success"}},"summary":"Returns genotypes associated with a disease","tags":["bioentity"]},"parameters":[{"description":"CURIE identifier of disease, e.g. Orphanet:399158, DOID:0080008. Equivalent IDs can be used with same results","in":"path","name":"id","required":true,"schema":{"type":"string"}}]},"/bioentity/disease/{id}/models":{"get":{"description":"In the association object returned, the subject will be the disease, and the object will be the model.\nThe model may be a gene or genetic element.\n\nIf the query disease is a general class, the association subject may be to a specific disease.\n\nIn some cases the association will be *direct*, for example if a paper asserts a genotype is a model of a disease.\n\nIn other cases, the association will be *indirect*, for\nexample, chaining over orthology. In these cases the chain\nwill be reflected in the *evidence graph*\n\n* TODO: provide hook into owlsim for dynamic computation of models by similarity","operationId":"get_disease_model_associations","parameters":[{"description":"number of rows","in":"query","name":"rows","schema":{"default":100,"type":"integer"}},{"description":"beginning row","in":"query","name":"start","schema":{"type":"integer"}},{"description":"Enable faceting","in":"query","name":"facet","schema":{"default":false,"type":"boolean"}},{"description":"Fields to facet on","explode":true,"in":"query","name":"facet_fields","schema":{"items":{"type":"string"},"type":"array"}},{"description":"If true, excludes evidence objects in response","in":"query","name":"unselect_evidence","schema":{"default":false,"type":"boolean"}},{"description":"If true, excludes associations that involve IEAs (ECO:0000501)","in":"query","name":"exclude_automatic_assertions","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload","in":"query","name":"fetch_objects","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns results in compact associations format","in":"query","name":"use_compact_associations","schema":{"default":false,"type":"boolean"}},{"description":"Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID","explode":true,"in":"query","name":"slim","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2","in":"query","name":"evidence","schema":{"type":"string"}},{"description":"Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False","in":"query","name":"direct","schema":{"default":false,"type":"boolean"}},{"description":"One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default","explode":true,"in":"query","name":"taxon","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Set true to exclude inferred taxa","in":"query","name":"direct_taxon","schema":{"default":false,"type":"boolean"}},{"description":"A relation CURIE to filter associations","in":"query","name":"relation","schema":{"type":"string"}},{"description":"Sorting responses <field> <desc,asc>","in":"query","name":"sort","schema":{"type":"string"}},{"description":"Query string to filter documents","in":"query","name":"q","schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AssociationResults"}}},"description":"Success"}},"summary":"Returns associations to models of the disease","tags":["bioentity"]},"parameters":[{"description":"CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results","in":"path","name":"id","required":true,"schema":{"type":"string"}}]},"/bioentity/disease/{id}/models/{taxon}":{"get":{"deprecated":true,"description":"See /disease/<id>/models route for full details","operationId":"get_disease_model_taxon_associations","parameters":[{"description":"number of rows","in":"query","name":"rows","schema":{"default":100,"type":"integer"}},{"description":"beginning row","in":"query","name":"start","schema":{"type":"integer"}},{"description":"Enable faceting","in":"query","name":"facet","schema":{"default":false,"type":"boolean"}},{"description":"Fields to facet on","explode":true,"in":"query","name":"facet_fields","schema":{"items":{"type":"string"},"type":"array"}},{"description":"If true, excludes evidence objects in response","in":"query","name":"unselect_evidence","schema":{"default":false,"type":"boolean"}},{"description":"If true, excludes associations that involve IEAs (ECO:0000501)","in":"query","name":"exclude_automatic_assertions","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload","in":"query","name":"fetch_objects","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns results in compact associations format","in":"query","name":"use_compact_associations","schema":{"default":false,"type":"boolean"}},{"description":"Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID","explode":true,"in":"query","name":"slim","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2","in":"query","name":"evidence","schema":{"type":"string"}},{"description":"Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False","in":"query","name":"direct","schema":{"default":false,"type":"boolean"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AssociationResults"}}},"description":"Success"}},"summary":"Returns associations to models of the disease constrained by taxon","tags":["bioentity"]},"parameters":[{"description":"CURIE of organism taxonomy class to constrain models, e.g NCBITaxon:10090 (M. musculus).\n\n Higher level taxa may be used","in":"path","name":"taxon","required":true,"schema":{"type":"string"}},{"description":"CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results","in":"path","name":"id","required":true,"schema":{"type":"string"}}]},"/bioentity/disease/{id}/pathways":{"get":{"operationId":"get_disease_pathway_associations","parameters":[{"description":"number of rows","in":"query","name":"rows","schema":{"default":100,"type":"integer"}},{"description":"beginning row","in":"query","name":"start","schema":{"type":"integer"}},{"description":"Enable faceting","in":"query","name":"facet","schema":{"default":false,"type":"boolean"}},{"description":"Fields to facet on","explode":true,"in":"query","name":"facet_fields","schema":{"items":{"type":"string"},"type":"array"}},{"description":"If true, excludes evidence objects in response","in":"query","name":"unselect_evidence","schema":{"default":false,"type":"boolean"}},{"description":"If true, excludes associations that involve IEAs (ECO:0000501)","in":"query","name":"exclude_automatic_assertions","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload","in":"query","name":"fetch_objects","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns results in compact associations format","in":"query","name":"use_compact_associations","schema":{"default":false,"type":"boolean"}},{"description":"Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID","explode":true,"in":"query","name":"slim","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2","in":"query","name":"evidence","schema":{"type":"string"}},{"description":"Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False","in":"query","name":"direct","schema":{"default":false,"type":"boolean"}},{"description":"One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default","explode":true,"in":"query","name":"taxon","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Set true to exclude inferred taxa","in":"query","name":"direct_taxon","schema":{"default":false,"type":"boolean"}},{"description":"A relation CURIE to filter associations","in":"query","name":"relation","schema":{"type":"string"}},{"description":"Sorting responses <field> <desc,asc>","in":"query","name":"sort","schema":{"type":"string"}},{"description":"Query string to filter documents","in":"query","name":"q","schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AssociationResults"}}},"description":"Success"}},"summary":"Returns pathways associated with a disease","tags":["bioentity"]},"parameters":[{"description":"CURIE identifier of disease, e.g. DOID:4450. Equivalent IDs can be used with same results","in":"path","name":"id","required":true,"schema":{"type":"string"}}]},"/bioentity/disease/{id}/phenotypes":{"get":{"operationId":"get_disease_phenotype_associations","parameters":[{"description":"number of rows","in":"query","name":"rows","schema":{"default":100,"type":"integer"}},{"description":"beginning row","in":"query","name":"start","schema":{"type":"integer"}},{"description":"Enable faceting","in":"query","name":"facet","schema":{"default":false,"type":"boolean"}},{"description":"Fields to facet on","explode":true,"in":"query","name":"facet_fields","schema":{"items":{"type":"string"},"type":"array"}},{"description":"If true, excludes evidence objects in response","in":"query","name":"unselect_evidence","schema":{"default":false,"type":"boolean"}},{"description":"If true, excludes associations that involve IEAs (ECO:0000501)","in":"query","name":"exclude_automatic_assertions","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload","in":"query","name":"fetch_objects","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns results in compact associations format","in":"query","name":"use_compact_associations","schema":{"default":false,"type":"boolean"}},{"description":"Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID","explode":true,"in":"query","name":"slim","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2","in":"query","name":"evidence","schema":{"type":"string"}},{"description":"Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False","in":"query","name":"direct","schema":{"default":false,"type":"boolean"}},{"description":"One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default","explode":true,"in":"query","name":"taxon","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Set true to exclude inferred taxa","in":"query","name":"direct_taxon","schema":{"default":false,"type":"boolean"}},{"description":"A relation CURIE to filter associations","in":"query","name":"relation","schema":{"type":"string"}},{"description":"Sorting responses <field> <desc,asc>","in":"query","name":"sort","schema":{"type":"string"}},{"description":"Query string to filter documents","in":"query","name":"q","schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/D2PAssociationResults"}}},"description":"Success"}},"summary":"Returns phenotypes associated with disease","tags":["bioentity"]},"parameters":[{"description":"CURIE identifier of disease, e.g. OMIM:605543, Orphanet:1934, DOID:678. Equivalent IDs can be used with same results","in":"path","name":"id","required":true,"schema":{"type":"string"}}]},"/bioentity/disease/{id}/publications":{"get":{"operationId":"get_disease_publication_associations","parameters":[{"description":"number of rows","in":"query","name":"rows","schema":{"default":100,"type":"integer"}},{"description":"beginning row","in":"query","name":"start","schema":{"type":"integer"}},{"description":"Enable faceting","in":"query","name":"facet","schema":{"default":false,"type":"boolean"}},{"description":"Fields to facet on","explode":true,"in":"query","name":"facet_fields","schema":{"items":{"type":"string"},"type":"array"}},{"description":"If true, excludes evidence objects in response","in":"query","name":"unselect_evidence","schema":{"default":false,"type":"boolean"}},{"description":"If true, excludes associations that involve IEAs (ECO:0000501)","in":"query","name":"exclude_automatic_assertions","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload","in":"query","name":"fetch_objects","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns results in compact associations format","in":"query","name":"use_compact_associations","schema":{"default":false,"type":"boolean"}},{"description":"Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID","explode":true,"in":"query","name":"slim","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2","in":"query","name":"evidence","schema":{"type":"string"}},{"description":"Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False","in":"query","name":"direct","schema":{"default":false,"type":"boolean"}},{"description":"One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default","explode":true,"in":"query","name":"taxon","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Set true to exclude inferred taxa","in":"query","name":"direct_taxon","schema":{"default":false,"type":"boolean"}},{"description":"A relation CURIE to filter associations","in":"query","name":"relation","schema":{"type":"string"}},{"description":"Sorting responses <field> <desc,asc>","in":"query","name":"sort","schema":{"type":"string"}},{"description":"Query string to filter documents","in":"query","name":"q","schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AssociationResults"}}},"description":"Success"}},"summary":"Returns publications associated with a disease","tags":["bioentity"]},"parameters":[{"description":"CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results","in":"path","name":"id","required":true,"schema":{"type":"string"}}]},"/bioentity/disease/{id}/treatment":{"get":{"description":"e.g. drugs or small molecules used to treat","operationId":"get_disease_substance_associations","parameters":[{"description":"number of rows","in":"query","name":"rows","schema":{"default":100,"type":"integer"}},{"description":"beginning row","in":"query","name":"start","schema":{"type":"integer"}},{"description":"Enable faceting","in":"query","name":"facet","schema":{"default":false,"type":"boolean"}},{"description":"Fields to facet on","explode":true,"in":"query","name":"facet_fields","schema":{"items":{"type":"string"},"type":"array"}},{"description":"If true, excludes evidence objects in response","in":"query","name":"unselect_evidence","schema":{"default":false,"type":"boolean"}},{"description":"If true, excludes associations that involve IEAs (ECO:0000501)","in":"query","name":"exclude_automatic_assertions","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload","in":"query","name":"fetch_objects","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns results in compact associations format","in":"query","name":"use_compact_associations","schema":{"default":false,"type":"boolean"}},{"description":"Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID","explode":true,"in":"query","name":"slim","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2","in":"query","name":"evidence","schema":{"type":"string"}},{"description":"Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False","in":"query","name":"direct","schema":{"default":false,"type":"boolean"}}],"responses":{"200":{"description":"Success"}},"summary":"Returns substances associated with a disease","tags":["bioentity"]},"parameters":[{"description":"CURIE identifier of disease, e.g. DOID:2841 (asthma). Equivalent IDs not yet supported","in":"path","name":"id","required":true,"schema":{"type":"string"}}]},"/bioentity/disease/{id}/variants":{"get":{"operationId":"get_disease_variant_associations","parameters":[{"description":"number of rows","in":"query","name":"rows","schema":{"default":100,"type":"integer"}},{"description":"beginning row","in":"query","name":"start","schema":{"type":"integer"}},{"description":"Enable faceting","in":"query","name":"facet","schema":{"default":false,"type":"boolean"}},{"description":"Fields to facet on","explode":true,"in":"query","name":"facet_fields","schema":{"items":{"type":"string"},"type":"array"}},{"description":"If true, excludes evidence objects in response","in":"query","name":"unselect_evidence","schema":{"default":false,"type":"boolean"}},{"description":"If true, excludes associations that involve IEAs (ECO:0000501)","in":"query","name":"exclude_automatic_assertions","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload","in":"query","name":"fetch_objects","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns results in compact associations format","in":"query","name":"use_compact_associations","schema":{"default":false,"type":"boolean"}},{"description":"Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID","explode":true,"in":"query","name":"slim","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2","in":"query","name":"evidence","schema":{"type":"string"}},{"description":"Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False","in":"query","name":"direct","schema":{"default":false,"type":"boolean"}},{"description":"One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default","explode":true,"in":"query","name":"taxon","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Set true to exclude inferred taxa","in":"query","name":"direct_taxon","schema":{"default":false,"type":"boolean"}},{"description":"A relation CURIE to filter associations","in":"query","name":"relation","schema":{"type":"string"}},{"description":"Sorting responses <field> <desc,asc>","in":"query","name":"sort","schema":{"type":"string"}},{"description":"Query string to filter documents","in":"query","name":"q","schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AssociationResults"}}},"description":"Success"}},"summary":"Returns variants associated with a disease","tags":["bioentity"]},"parameters":[{"description":"CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results","in":"path","name":"id","required":true,"schema":{"type":"string"}}]},"/bioentity/function/{id}":{"get":{"operationId":"get_function_associations","parameters":[{"description":"beginning row","in":"query","name":"start","schema":{"default":0,"type":"integer"}},{"description":"number of rows","in":"query","name":"rows","schema":{"default":100,"type":"integer"}},{"description":"Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2","explode":true,"in":"query","name":"evidence","schema":{"items":{"type":"string"},"type":"array"}}],"responses":{"200":{"description":"Success"}},"summary":"Returns annotations associated to a function term","tags":["bioentity"]},"parameters":[{"description":"CURIE identifier of a function term (e.g. GO:0044598)","in":"path","name":"id","required":true,"schema":{"type":"string"}}]},"/bioentity/function/{id}/genes":{"get":{"operationId":"get_function_gene_associations","parameters":[{"description":"number of rows","in":"query","name":"rows","schema":{"default":100,"type":"integer"}},{"description":"beginning row","in":"query","name":"start","schema":{"type":"integer"}},{"description":"Enable faceting","in":"query","name":"facet","schema":{"default":false,"type":"boolean"}},{"description":"Fields to facet on","explode":true,"in":"query","name":"facet_fields","schema":{"items":{"type":"string"},"type":"array"}},{"description":"If true, excludes evidence objects in response","in":"query","name":"unselect_evidence","schema":{"default":false,"type":"boolean"}},{"description":"If true, excludes associations that involve IEAs (ECO:0000501)","in":"query","name":"exclude_automatic_assertions","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload","in":"query","name":"fetch_objects","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns results in compact associations format","in":"query","name":"use_compact_associations","schema":{"default":false,"type":"boolean"}},{"description":"Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID","explode":true,"in":"query","name":"slim","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2","in":"query","name":"evidence","schema":{"type":"string"}},{"description":"Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False","in":"query","name":"direct","schema":{"default":false,"type":"boolean"}},{"description":"One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default","explode":true,"in":"query","name":"taxon","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Set true to exclude inferred taxa","in":"query","name":"direct_taxon","schema":{"default":false,"type":"boolean"}},{"description":"A relation CURIE to filter associations","in":"query","name":"relation","schema":{"type":"string"}},{"description":"Sorting responses <field> <desc,asc>","in":"query","name":"sort","schema":{"type":"string"}},{"description":"Query string to filter documents","in":"query","name":"q","schema":{"type":"string"}},{"description":"relationship type ('involved_in', 'involved_in_regulation_of' or 'acts_upstream_of_or_within')","explode":true,"in":"query","name":"relationship_type","schema":{"default":"involved_in","enum":["involved_in","involved_in_regulation_of","acts_upstream_of_or_within"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AssociationResults"}}},"description":"Success"}},"summary":"Returns genes associated to a GO term","tags":["bioentity"]},"parameters":[{"description":"CURIE identifier of a GO term, e.g. GO:0044598","in":"path","name":"id","required":true,"schema":{"type":"string"}}]},"/bioentity/function/{id}/publications":{"get":{"operationId":"get_function_publication_associations","parameters":[{"description":"beginning row","in":"query","name":"start","schema":{"default":0,"type":"integer"}},{"description":"number of rows","in":"query","name":"rows","schema":{"default":100,"type":"integer"}},{"description":"Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2","explode":true,"in":"query","name":"evidence","schema":{"items":{"type":"string"},"type":"array"}}],"responses":{"200":{"description":"Success"}},"summary":"Returns publications associated to a GO term","tags":["bioentity"]},"parameters":[{"description":"CURIE identifier of a GO term, e.g. GO:0044598","in":"path","name":"id","required":true,"schema":{"type":"string"}}]},"/bioentity/function/{id}/taxons":{"get":{"operationId":"get_function_taxon_associations","parameters":[{"description":"beginning row","in":"query","name":"start","schema":{"default":0,"type":"integer"}},{"description":"number of rows","in":"query","name":"rows","schema":{"default":100,"type":"integer"}},{"description":"Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2","explode":true,"in":"query","name":"evidence","schema":{"items":{"type":"string"},"type":"array"}}],"responses":{"200":{"description":"Success"}},"summary":"Returns taxons associated to a GO term","tags":["bioentity"]},"parameters":[{"description":"CURIE identifier of a GO term, e.g. GO:0044598","in":"path","name":"id","required":true,"schema":{"type":"string"}}]},"/bioentity/gene/{id}/anatomy":{"get":{"operationId":"get_gene_anatomy_associations","parameters":[{"description":"number of rows","in":"query","name":"rows","schema":{"default":100,"type":"integer"}},{"description":"beginning row","in":"query","name":"start","schema":{"type":"integer"}},{"description":"Enable faceting","in":"query","name":"facet","schema":{"default":false,"type":"boolean"}},{"description":"Fields to facet on","explode":true,"in":"query","name":"facet_fields","schema":{"items":{"type":"string"},"type":"array"}},{"description":"If true, excludes evidence objects in response","in":"query","name":"unselect_evidence","schema":{"default":false,"type":"boolean"}},{"description":"If true, excludes associations that involve IEAs (ECO:0000501)","in":"query","name":"exclude_automatic_assertions","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns a distinct set of association.objects (typically ontology terms). 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Equivalent IDs can be used with same results","in":"path","name":"id","required":true,"schema":{"type":"string"}}]},"/bioentity/gene/{id}/expression/anatomy":{"get":{"operationId":"get_gene_expression_associations","parameters":[{"description":"number of rows","in":"query","name":"rows","schema":{"default":100,"type":"integer"}},{"description":"beginning row","in":"query","name":"start","schema":{"type":"integer"}},{"description":"Enable faceting","in":"query","name":"facet","schema":{"default":false,"type":"boolean"}},{"description":"Fields to facet on","explode":true,"in":"query","name":"facet_fields","schema":{"items":{"type":"string"},"type":"array"}},{"description":"If true, excludes evidence objects in response","in":"query","name":"unselect_evidence","schema":{"default":false,"type":"boolean"}},{"description":"If true, excludes associations that involve IEAs (ECO:0000501)","in":"query","name":"exclude_automatic_assertions","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns a distinct set of association.objects (typically ontology terms). 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Equivalent IDs can be used with same results","in":"path","name":"id","required":true,"schema":{"type":"string"}}]},"/bioentity/gene/{id}/function":{"get":{"description":"IMPLEMENTATION DETAILS\n----------------------\n\nNote: currently this is implemented as a query to the GO/AmiGO solr instance.\nThis directly supports IDs such as:\n\n - ZFIN e.g. ZFIN:ZDB-GENE-050417-357\n\nNote that the AmiGO GOlr natively stores MGI annotations to MGI:MGI:nn. However,\nthe standard for biolink is MGI:nnnn, so you should use this (will be transparently\nmapped to legacy ID)\n\nAdditionally, for some species such as Human, GO has the annotation attached to the UniProt ID.\nAgain, this should be transparently handled; e.g. you can use NCBIGene:6469, and this will be\nmapped behind the scenes for querying.","operationId":"get_gene_function_associations","parameters":[{"description":"number of rows","in":"query","name":"rows","schema":{"default":100,"type":"integer"}},{"description":"beginning row","in":"query","name":"start","schema":{"type":"integer"}},{"description":"Enable faceting","in":"query","name":"facet","schema":{"default":false,"type":"boolean"}},{"description":"Fields to facet on","explode":true,"in":"query","name":"facet_fields","schema":{"items":{"type":"string"},"type":"array"}},{"description":"If true, excludes evidence objects in response","in":"query","name":"unselect_evidence","schema":{"default":false,"type":"boolean"}},{"description":"If true, excludes associations that involve IEAs (ECO:0000501)","in":"query","name":"exclude_automatic_assertions","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns a distinct set of association.objects (typically ontology terms). 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Equivalent IDs can be used with same results","in":"path","name":"id","required":true,"schema":{"type":"string"}}]},"/bioentity/gene/{id}/genotypes":{"get":{"operationId":"get_gene_genotype_associations","parameters":[{"description":"number of rows","in":"query","name":"rows","schema":{"default":100,"type":"integer"}},{"description":"beginning row","in":"query","name":"start","schema":{"type":"integer"}},{"description":"Enable faceting","in":"query","name":"facet","schema":{"default":false,"type":"boolean"}},{"description":"Fields to facet on","explode":true,"in":"query","name":"facet_fields","schema":{"items":{"type":"string"},"type":"array"}},{"description":"If true, excludes evidence objects in response","in":"query","name":"unselect_evidence","schema":{"default":false,"type":"boolean"}},{"description":"If true, excludes associations that involve IEAs (ECO:0000501)","in":"query","name":"exclude_automatic_assertions","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns a distinct set of association.objects (typically ontology terms). 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Equivalent IDs can be used with same results","in":"path","name":"id","required":true,"schema":{"type":"string"}}]},"/bioentity/gene/{id}/interactions":{"get":{"operationId":"get_gene_interactions","parameters":[{"description":"number of rows","in":"query","name":"rows","schema":{"default":100,"type":"integer"}},{"description":"beginning row","in":"query","name":"start","schema":{"type":"integer"}},{"description":"Enable faceting","in":"query","name":"facet","schema":{"default":false,"type":"boolean"}},{"description":"Fields to facet on","explode":true,"in":"query","name":"facet_fields","schema":{"items":{"type":"string"},"type":"array"}},{"description":"If true, excludes evidence objects in response","in":"query","name":"unselect_evidence","schema":{"default":false,"type":"boolean"}},{"description":"If true, excludes associations that involve IEAs (ECO:0000501)","in":"query","name":"exclude_automatic_assertions","schema":{"default":false,"type":"boolean"}},{"description":"If true, returns a distinct set of association.objects (typically ontology terms). 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