openapi-directory/api/monarchinitiative.org.json

Building & bundling https://github.com/APIs-guru/openapi-directory for easy use from JS

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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":{