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help desk","url":"https://monarchinitiative.org/help","x-role":"responsible developer"},"description":"The [Monarch Application Programming Interface (API)](https://api-v3.monarchinitiative.org/v3/docs#/) is a RESTful API that wraps functionality required by the [Monarch Initiative website](https://monarchinitiative.org/), including the retrieval of disease, gene, and phenotype associations, phenotypic profile comparisons, and other graph operations.","termsOfService":"https://monarchinitiative.org/terms","title":"Monarch API","version":"0.1.0","x-translator":{"biolink-version":"4.1.6","component":"KP","infores":"infores:monarchinitiative","team":["Service Provider","Standards Reference Implementation Team"]}},"paths":{"/v3/api/association":{"get":{"description":"Retrieves all associations for a given entity, or between two entities.","operationId":"_get_associations_v3_api_association_get","parameters":[{"in":"query","name":"category","required":false,"schema":{"items":{"$ref":"#/components/schemas/AssociationCategory"},"title":"Category","type":"array"}},{"in":"query","name":"subject","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Subject"}},{"in":"query","name":"subject_category","required":false,"schema":{"items":{"$ref":"#/components/schemas/EntityCategory"},"title":"Subject Category","type":"array"}},{"in":"query","name":"subject_namespace","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Subject Namespace"}},{"in":"query","name":"subject_taxon","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Subject 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the entity with the specified id\n\nArgs:
\n id (str): ID for the entity to retrieve, ex: MONDO:0019391\n\nRaises:
\n HTTPException: 404 if the entity is not found\n\nReturns:
\n Node: Entity details for the specified id","operationId":"_get_entity_v3_api_entity__id__get","parameters":[{"in":"path","name":"id","required":true,"schema":{"title":"ID of the entity to retrieve","type":"string"}},{"in":"query","name":"format","required":false,"schema":{"allOf":[{"$ref":"#/components/schemas/OutputFormat"}],"default":"json","title":"Output format for the response"}}],"responses":{"200":{"content":{"application/json":{"schema":{"anyOf":[{"$ref":"#/components/schemas/Node"},{"type":"string"}],"title":"Response Get Entity V3 Api Entity Id Get"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Get Entity","tags":["entity"]}},"/v3/api/entity/{id}/{category}":{"get":{"description":"Retrieves association table data for a given entity and association type\n\nArgs:
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\n category (str): Category of association to retrieve association table data for, ex: biolink:DiseaseToPhenotypicFeatureAssociation
\n Path (str, optional): Path string to limit results to a subset. Defaults to None.
\n pagination (PaginationParams, optional): Pagination parameters. Defaults to Depends().
\n\nReturns:
\n AssociationResults: Association table data for the specified entity and association type","operationId":"_association_table_v3_api_entity__id___category__get","parameters":[{"in":"path","name":"id","required":true,"schema":{"title":"ID of the entity to retrieve association table data for","type":"string"}},{"in":"path","name":"category","required":true,"schema":{"allOf":[{"$ref":"#/components/schemas/AssociationCategory"}],"title":"Type of association to retrieve association table data for"}},{"in":"query","name":"query","required":false,"schema":{"title":"query string to limit results to a subset","type":"string"}},{"in":"query","name":"traverse_orthologs","required":false,"schema":{"default":false,"title":"Traverse orthologs to get associations","type":"boolean"}},{"in":"query","name":"sort","required":false,"schema":{"items":{"type":"string"},"title":"Sort results by a list of field + direction statements","type":"array"}},{"in":"query","name":"format","required":false,"schema":{"allOf":[{"$ref":"#/components/schemas/OutputFormat"}],"default":"json","title":"Output format for the response"}},{"in":"query","name":"download","required":false,"schema":{"default":false,"title":"Download the results as a file","type":"boolean"}},{"in":"query","name":"limit","required":false,"schema":{"default":20,"maximum":500,"minimum":0,"title":"Limit","type":"integer"}},{"in":"query","name":"offset","required":false,"schema":{"default":0,"minimum":0,"title":"Offset","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"anyOf":[{"$ref":"#/components/schemas/AssociationTableResults"},{"type":"string"}],"title":"Response Association Table V3 Api Entity Id Category Get"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Association Table","tags":["entity"]}},"/v3/api/histopheno/{id}":{"get":{"description":"Retrieves the entity with the specified id","operationId":"_get_histopheno_v3_api_histopheno__id__get","parameters":[{"in":"path","name":"id","required":true,"schema":{"title":"ID of the entity to get histopheno data for","type":"string"}},{"in":"query","name":"format","required":false,"schema":{"allOf":[{"$ref":"#/components/schemas/OutputFormat"}],"default":"json","title":"Output format for the response"}}],"responses":{"200":{"content":{"application/json":{"schema":{"anyOf":[{"$ref":"#/components/schemas/HistoPheno"},{"type":"string"}],"title":"Response Get Histopheno V3 Api Histopheno Id Get"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Get Histopheno","tags":["histopheno"]}},"/v3/api/search":{"get":{"description":"Search for entities by label, with optional filters\n\nArgs:\n q (str, optional): Query string. 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Defaults to 20.\n\nReturns:\n EntityResults","operationId":"search_v3_api_search_get","parameters":[{"in":"query","name":"q","required":false,"schema":{"title":"Q","type":"string"}},{"in":"query","name":"category","required":false,"schema":{"anyOf":[{"items":{"$ref":"#/components/schemas/EntityCategory"},"type":"array"}],"title":"Category"}},{"in":"query","name":"in_taxon_label","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"In Taxon Label"}},{"in":"query","name":"limit","required":false,"schema":{"default":20,"maximum":500,"minimum":0,"title":"Limit","type":"integer"}},{"in":"query","name":"offset","required":false,"schema":{"default":0,"minimum":0,"title":"Offset","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SearchResults"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":"Search","tags":["search"]}},"/v3/api/autocomplete":{"get":{"description":"Autocomplete for entities by label\n\nArgs:\n q (str): Query string to autocomplete against\n\nReturns:\n SearchResults","operationId":"autocomplete_v3_api_autocomplete_get","parameters":[{"in":"query","name":"q","required":false,"schema":{"default":"*:*","title":"Query string to autocomplete against","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SearchResults"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":"Autocomplete","tags":["search"]}},"/v3/api/mappings":{"get":{"operationId":"mappings_v3_api_mappings_get","parameters":[{"in":"query","name":"entity_id","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Entity Id"}},{"in":"query","name":"subject_id","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Subject Id"}},{"in":"query","name":"predicate_id","required":false,"schema":{"anyOf":[{"items":{"$ref":"#/components/schemas/MappingPredicate"},"type":"array"}],"title":"Predicate Id"}},{"in":"query","name":"object_id","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Object Id"}},{"in":"query","name":"mapping_justification","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Mapping Justification"}},{"in":"query","name":"format","required":false,"schema":{"allOf":[{"$ref":"#/components/schemas/OutputFormat"}],"default":"json","title":"Output format for the response"}},{"in":"query","name":"limit","required":false,"schema":{"default":20,"maximum":500,"minimum":0,"title":"Limit","type":"integer"}},{"in":"query","name":"offset","required":false,"schema":{"default":0,"minimum":0,"title":"Offset","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":"Mappings","tags":["search"]}},"/v3/api/semsim/autocomplete":{"get":{"description":"Autocomplete for semantic similarity lookups, prioritizes entities which have direct phenotype associations.\nNote: This API endpoint is experimental and may evolve or disappear over time.\n\nArgs:\n q (str): Query string to autocomplete against\n\nReturns:\n SearchResults","operationId":"autocomplete_v3_api_semsim_autocomplete_get","parameters":[{"in":"query","name":"q","required":false,"schema":{"default":"*:*","title":"Query string to autocomplete against","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SearchResults"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":"Autocomplete","tags":["semsim"]}},"/v3/api/semsim/compare/{subjects}/{objects}":{"get":{"description":"Get pairwise similarity between two sets of terms\n\nArgs:
\n subjects (str, optional): List of subjects for comparison. Defaults to \"\".
\n objects (str, optional): List of objects for comparison. Defaults to \"\".
\n metric (str, optional): Similarity metric to use. Defaults to \"ancestor_information_content\".\n\nReturns:
\n TermSetPairwiseSimilarity: Pairwise similarity between subjects and objects","operationId":"_compare_v3_api_semsim_compare__subjects___objects__get","parameters":[{"in":"path","name":"subjects","required":true,"schema":{"title":"List of subjects for comparison","type":"string"}},{"in":"path","name":"objects","required":true,"schema":{"title":"List of objects for comparison","type":"string"}},{"in":"query","name":"metric","required":false,"schema":{"allOf":[{"$ref":"#/components/schemas/SemsimMetric"}],"default":"ancestor_information_content","title":"Similarity metric to use"}}],"responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Compare","tags":["semsim"]}},"/v3/api/semsim/compare":{"post":{"description":"Pairwise similarity between two sets of terms
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\n Example:
\n
\n{\n  \"subjects\": [\"MP:0010771\",\"MP:0002169\",\"MP:0005391\",\"MP:0005389\",\"MP:0005367\"],\n  \"objects\": [\"HP:0004325\",\"HP:0000093\",\"MP:0006144\"],\n  \"metric\": \"ancestor_information_content\"\n}\n
","operationId":"_post_compare_v3_api_semsim_compare_post","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SemsimCompareRequest"}}},"required":true},"responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Post Compare","tags":["semsim"]}},"/v3/api/semsim/multicompare":{"post":{"description":"Pairwise similarity between two sets of terms
\n
\n Example:
\n 
\n{\n  \"metric\": \"ancestor_information_content\",\n  \"subjects\": [ \"HP:0002616\", \"HP:0001763\", \"HP:0004944\", \"HP:0010749\", \"HP:0001533\", \"HP:0002020\", \"HP:0012450\", \"HP:0003394\", \"HP:0003771\", \"HP:0012378\", \"HP:0001278\", \"HP:0002827\",\n\"HP:0002829\", \"HP:0002999\", \"HP:0003010\"],\n  \"object_sets\": [\n    {\n      \"id\": \"MGI:97486\",\n      \"label\": \"Pax2\",\n      \"phenotypes\": [ \"MP:0003675\", \"MP:0003675\", \"MP:0003675\", \"MP:0011382\", \"MP:0011366\", \"MP:0010097\", \"MP:0012536\", \"MP:0003558\", \"MP:0004729\", \"MP:0009113\", \"MP:0006090\", \"MP:0001325\", \"MP:0001325\", \"MP:0006309\",\n\"MP:0004017\", \"MP:0012533\", \"MP:0004505\", \"MP:0004505\", \"MP:0004505\"]\n    },\n    {\n      \"id\": \"MGI:95819\",\n      \"label\": \"Grin1\",\n      \"phenotypes\": [\"MP:0001435\", \"MP:0001405\", \"MP:0002797\", \"MP:0001386\", \"MP:0001901\", \"MP:0001901\", \"MP:0001901\", \"MP:0001901\", \"MP:0001901\", \"MP:0002906\", \"MP:0004811\", \"MP:0001900\",\n\"MP:0009748\", \"MP:0008428\", \"MP:0008428\", \"MP:0008428\"]\n    }\n  ]\n}\n
","operationId":"_post_multicompare_v3_api_semsim_multicompare_post","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SemsimMultiCompareRequest"}}},"required":true},"responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Post Multicompare","tags":["semsim"]}},"/v3/api/semsim/search/{termset}/{group}":{"get":{"description":"Search for terms in a termset\n\nArgs:
\n termset (str): Comma separated list of term IDs to find matches for.
\n group (str): Group of entities to search within (e.g. Human Genes)
\n metric: (str, optional): Similarity metric to use. Defaults to \"ancestor_information_content\".
\n limit (int, optional): Limit the number of results. Defaults to 10.\n\nReturns:
\n List[str]: List of matching terms","operationId":"_search_v3_api_semsim_search__termset___group__get","parameters":[{"in":"path","name":"termset","required":true,"schema":{"title":"Termset to search","type":"string"}},{"in":"path","name":"group","required":true,"schema":{"allOf":[{"$ref":"#/components/schemas/SemsimSearchGroup"}],"title":"Group of entities to search within (e.g. Human Genes)"}},{"in":"query","name":"metric","required":false,"schema":{"allOf":[{"$ref":"#/components/schemas/SemsimMetric"}],"default":"ancestor_information_content","title":"Similarity metric to use"}},{"in":"query","name":"limit","required":false,"schema":{"default":10,"maximum":50,"minimum":1,"title":"Limit","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Search","tags":["semsim"]}},"/v3/api/semsim/search":{"post":{"description":"Search for terms in a termset
\n
\n Example:
\n
\n{\n  \"termset\": [\"HP:0002104\", \"HP:0012378\", \"HP:0012378\", \"HP:0012378\"],\n  \"group\": \"Human Diseases\",\n  \"metric\": \"ancestor_information_content\",\n  \"limit\": 5\n}\n
","operationId":"_post_search_v3_api_semsim_search_post","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SemsimSearchRequest"}}},"required":true},"responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Post Search","tags":["semsim"]}},"/v3/api/annotate":{"get":{"operationId":"_annotate_v3_api_annotate_get","parameters":[{"in":"query","name":"text","required":false,"schema":{"default":"","title":"The text content to annotate","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"title":"Response Annotate V3 Api Annotate Get","type":"string"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Annotate","tags":["text_annotation"]},"post":{"operationId":"_post_annotate_v3_api_annotate_post","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/TextAnnotationRequest"}}},"required":true},"responses":{"200":{"content":{"application/json":{"schema":{"title":"Response Post Annotate V3 Api Annotate Post","type":"string"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Post Annotate","tags":["text_annotation"]}},"/v3/api/annotate/entities":{"get":{"operationId":"_entities_v3_api_annotate_entities_get","parameters":[{"in":"query","name":"text","required":false,"schema":{"default":"","title":"Text","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/TextAnnotationResult"},"title":"Response Entities V3 Api Annotate Entities Get","type":"array"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" 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","in":"query","name":"log_level","required":false,"schema":{"enum":["ERROR","WARNING","INFO","DEBUG"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryStatusResponse"}}},"description":"Returns the status and current logs of a previously submitted asyncquery."},"404":{"description":"job_id not found"},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Return code 501 indicates that this endpoint has not been implemented at this site. 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","in":"query","name":"log_level","required":false,"schema":{"enum":["ERROR","WARNING","INFO","DEBUG"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"oneOf":[{"$ref":"#/components/schemas/AsyncQueryStatusResponse"},{"$ref":"#/components/schemas/Response"}]}}},"description":"Response format depends on status of the job (pending/in-progress vs finished)"},"404":{"description":"job_id not found"},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Return code 501 indicates that this endpoint has not been implemented at this site. Sites that implement /asyncquery MUST implement /asyncquery_status/{job_id}, but those that do not implement /asyncquery SHOULD NOT implement /asyncquery_status."}},"summary":"If the previously submitted asyncquery is still pending/in-progress, this endpoint will return the same response as the asyncquery_status endpoint (status, logs). 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"}},"/{node_type}/{curie}":{"get":{"description":"Returns `node` matching `curie`.","operationId":"node__node_type___curie__get","parameters":[{"in":"path","name":"node_type","required":true,"schema":{"title":"Node Type","type":"string"}},{"in":"path","name":"curie","required":true,"schema":{"title":"Curie","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{},"title":"Response Node Node Type Curie Get","type":"array"}}},"description":"Successful Response"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":"Find `node` by `curie`"}},"/simple_spec":{"get":{"description":"Returns a list of available predicates when choosing a single source or target curie. 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Note that the attribute names are case-sensitive.\n\nJust like the query service, you can also pass a \"callback\" parameter to make a JSONP call.","parameters":[{"example":"DDInter1414_DDInter1004_Moderate","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["interaction"]}},"/interaction":{"post":{"description":"Although making simple GET requests above to our service is sufficient in most use cases, there are some times you might find it easier to batch query (e.g., retrieving multiple associations). 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The detailed query syntax for parameter is explained [here for a core BioThings API](https://docs.mychem.info/en/latest/doc/chem_query_service.html#query-syntax).","example":"drug_a.drugbank:DB08880","in":"query","name":"q","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/from"},{"$ref":"#/components/parameters/fetch_all"},{"$ref":"#/components/parameters/scroll_id"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/facets"},{"$ref":"#/components/parameters/facet_size"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/dotfield"},{"$ref":"#/components/parameters/email"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["query"]},"post":{"description":"Although making simple GET requests above to our query service is sufficient for most use cases, there are times you might find it more efficient to make batch queries (e.g., retrieving data for multiple inputs). 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The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. 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The front-end may show these options as allele names but the backend stores and\nqueries by allele function so that is what must be queried on. Those functions can be found in\nthe `guidelineGenes` property of the `DosingGuideline` object.\n\n**IMPORTANT NOTE**: This data is PharmGKB annotation of CPIC guideline information. Our annotations may contain typos or errors or may be out of date. If you're interested in using this data please get it directly from [the CPIC website](https://cpicpgx.org/).","parameters":[{"description":"The accession ID of a Guideline Annotation with annotations","in":"path","name":"id","required":true,"schema":{"default":"PA166104948","type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"properties":{"CYP2C19":{"items":{"description":"Allele function values, must be 2 per gene","type":"string"},"type":"array"}},"type":"object"}}},"description":"The functional phenotype to query for. Should be a map of gene symbol (key) to an array of 2 allele functions (value). This can have more than 1 gene specified, if needed.","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/GuidelineAnnotationGroup"}}},"description":"success"}},"summary":"Query the annotations for a guideline by allele function","tags":["report"],"x-codegen-request-body-name":"body"}},"/report/variantFrequency":{"get":{"parameters":[{"description":"a variant fingerprint to query (e.g. RSID)","in":"query","name":"fp","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/FrequencyResult"}}},"description":"success"}},"summary":"Get all variant frequency data for a given variant fingerprint","tags":["report"]}},"/report/stats":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/StatsResult"}}},"description":"success"}},"summary":"Get all the statistics for object counts in 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Note that the attribute names are case-sensitive.\n\nJust like the query service, you can also pass a \"callback\" parameter to make a JSONP call.","parameters":[{"example":"RHEA:14669","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["reaction"]}},"/reaction":{"post":{"description":"Although making simple GET requests above to our service is sufficient in most use cases, there are some times you might find it easier to batch query (e.g., retrieving multiple reactions). Fortunately, you can also make batch queries via POST requests when you need to.","parameters":[{"description":"Accepts multiple reaction ids separated by commas. 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Associations","tags":["association"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/gene-anatomy"},{"$ref":"#/components/x-bte-kgs-operations/anatomy-gene"},{"$ref":"#/components/x-bte-kgs-operations/disease-pheno"},{"$ref":"#/components/x-bte-kgs-operations/pheno-disease"},{"$ref":"#/components/x-bte-kgs-operations/gene-disease-causal"},{"$ref":"#/components/x-bte-kgs-operations/disease-gene-causal"},{"$ref":"#/components/x-bte-kgs-operations/gene-disease-contributesTo"},{"$ref":"#/components/x-bte-kgs-operations/disease-gene-contributesTo"},{"$ref":"#/components/x-bte-kgs-operations/gene-disease-associatedCondition"},{"$ref":"#/components/x-bte-kgs-operations/disease-gene-associatedCondition"},{"$ref":"#/components/x-bte-kgs-operations/gene-pheno"},{"$ref":"#/components/x-bte-kgs-operations/pheno-gene"},{"$ref":"#/components/x-bte-kgs-operations/gene-gene-interaction-forward"},{"$ref":"#/components/x-bte-kgs-operations/gene-gene-interaction-backward"}]}},"/v3/api/entity/{id}":{"get":{"description":"Retrieves the entity with the specified id\n\nArgs:
\n id (str): ID for the entity to retrieve, ex: MONDO:0019391\n\nRaises:
\n HTTPException: 404 if the entity is not found\n\nReturns:
\n Node: Entity details for the specified id","operationId":"_get_entity_v3_api_entity__id__get","parameters":[{"in":"path","name":"id","required":true,"schema":{"title":"ID of the entity to retrieve","type":"string"}},{"in":"query","name":"format","required":false,"schema":{"allOf":[{"$ref":"#/components/schemas/OutputFormat"}],"default":"json","title":"Output format for the response"}}],"responses":{"200":{"content":{"application/json":{"schema":{"anyOf":[{"$ref":"#/components/schemas/Node"},{"type":"string"}],"title":"Response Get Entity V3 Api Entity Id Get"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Get Entity","tags":["entity"]}},"/v3/api/entity/{id}/{category}":{"get":{"description":"Retrieves association table data for a given entity and association type\n\nArgs:
\n id (str): ID of the entity to retrieve association table data, ex: MONDO:0019391
\n category (str): Category of association to retrieve association table data for, ex: biolink:DiseaseToPhenotypicFeatureAssociation
\n Path (str, optional): Path string to limit results to a subset. Defaults to None.
\n pagination (PaginationParams, optional): Pagination parameters. Defaults to Depends().
\n\nReturns:
\n AssociationResults: Association table data for the specified entity and association type","operationId":"_association_table_v3_api_entity__id___category__get","parameters":[{"in":"path","name":"id","required":true,"schema":{"title":"ID of the entity to retrieve association table data for","type":"string"}},{"in":"path","name":"category","required":true,"schema":{"allOf":[{"$ref":"#/components/schemas/AssociationCategory"}],"title":"Type of association to retrieve association table data for"}},{"in":"query","name":"query","required":false,"schema":{"title":"query string to limit results to a subset","type":"string"}},{"in":"query","name":"traverse_orthologs","required":false,"schema":{"default":false,"title":"Traverse orthologs to get associations","type":"boolean"}},{"in":"query","name":"sort","required":false,"schema":{"items":{"type":"string"},"title":"Sort results by a list of field + direction statements","type":"array"}},{"in":"query","name":"format","required":false,"schema":{"allOf":[{"$ref":"#/components/schemas/OutputFormat"}],"default":"json","title":"Output format for the response"}},{"in":"query","name":"download","required":false,"schema":{"default":false,"title":"Download the results as a file","type":"boolean"}},{"in":"query","name":"limit","required":false,"schema":{"default":20,"maximum":500,"minimum":0,"title":"Limit","type":"integer"}},{"in":"query","name":"offset","required":false,"schema":{"default":0,"minimum":0,"title":"Offset","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"anyOf":[{"$ref":"#/components/schemas/AssociationTableResults"},{"type":"string"}],"title":"Response Association Table V3 Api Entity Id Category Get"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Association Table","tags":["entity"]}},"/v3/api/histopheno/{id}":{"get":{"description":"Retrieves the entity with the specified id","operationId":"_get_histopheno_v3_api_histopheno__id__get","parameters":[{"in":"path","name":"id","required":true,"schema":{"title":"ID of the entity to get histopheno data for","type":"string"}},{"in":"query","name":"format","required":false,"schema":{"allOf":[{"$ref":"#/components/schemas/OutputFormat"}],"default":"json","title":"Output format for the response"}}],"responses":{"200":{"content":{"application/json":{"schema":{"anyOf":[{"$ref":"#/components/schemas/HistoPheno"},{"type":"string"}],"title":"Response Get Histopheno V3 Api Histopheno Id Get"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Get Histopheno","tags":["histopheno"]}},"/v3/api/search":{"get":{"description":"Search for entities by label, with optional filters\n\nArgs:\n q (str, optional): Query string. Defaults to \"*:*\".\n category (str, optional): Filter by biolink model category. Defaults to None.\n in_taxon_label (str, optional): Filter by taxon label. Defaults to None.\n offset (int, optional): Offset for pagination. Defaults to 0.\n limit (int, optional): Limit results. Defaults to 20.\n\nReturns:\n EntityResults","operationId":"search_v3_api_search_get","parameters":[{"in":"query","name":"q","required":false,"schema":{"title":"Q","type":"string"}},{"in":"query","name":"category","required":false,"schema":{"anyOf":[{"items":{"$ref":"#/components/schemas/EntityCategory"},"type":"array"}],"title":"Category"}},{"in":"query","name":"in_taxon_label","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"In Taxon Label"}},{"in":"query","name":"limit","required":false,"schema":{"default":20,"maximum":500,"minimum":0,"title":"Limit","type":"integer"}},{"in":"query","name":"offset","required":false,"schema":{"default":0,"minimum":0,"title":"Offset","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SearchResults"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":"Search","tags":["search"]}},"/v3/api/autocomplete":{"get":{"description":"Autocomplete for entities by label\n\nArgs:\n q (str): Query string to autocomplete against\n\nReturns:\n SearchResults","operationId":"autocomplete_v3_api_autocomplete_get","parameters":[{"in":"query","name":"q","required":false,"schema":{"default":"*:*","title":"Query string to autocomplete against","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SearchResults"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":"Autocomplete","tags":["search"]}},"/v3/api/mappings":{"get":{"operationId":"mappings_v3_api_mappings_get","parameters":[{"in":"query","name":"entity_id","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Entity Id"}},{"in":"query","name":"subject_id","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Subject Id"}},{"in":"query","name":"predicate_id","required":false,"schema":{"anyOf":[{"items":{"$ref":"#/components/schemas/MappingPredicate"},"type":"array"}],"title":"Predicate Id"}},{"in":"query","name":"object_id","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Object Id"}},{"in":"query","name":"mapping_justification","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Mapping Justification"}},{"in":"query","name":"format","required":false,"schema":{"allOf":[{"$ref":"#/components/schemas/OutputFormat"}],"default":"json","title":"Output format for the response"}},{"in":"query","name":"limit","required":false,"schema":{"default":20,"maximum":500,"minimum":0,"title":"Limit","type":"integer"}},{"in":"query","name":"offset","required":false,"schema":{"default":0,"minimum":0,"title":"Offset","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":"Mappings","tags":["search"]}},"/v3/api/semsim/autocomplete":{"get":{"description":"Autocomplete for semantic similarity lookups, prioritizes entities which have direct phenotype associations.\nNote: This API endpoint is experimental and may evolve or disappear over time.\n\nArgs:\n q (str): Query string to autocomplete against\n\nReturns:\n SearchResults","operationId":"autocomplete_v3_api_semsim_autocomplete_get","parameters":[{"in":"query","name":"q","required":false,"schema":{"default":"*:*","title":"Query string to autocomplete against","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SearchResults"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":"Autocomplete","tags":["semsim"]}},"/v3/api/semsim/compare/{subjects}/{objects}":{"get":{"description":"Get pairwise similarity between two sets of terms\n\nArgs:
\n subjects (str, optional): List of subjects for comparison. Defaults to \"\".
\n objects (str, optional): List of objects for comparison. Defaults to \"\".
\n metric (str, optional): Similarity metric to use. Defaults to \"ancestor_information_content\".\n\nReturns:
\n TermSetPairwiseSimilarity: Pairwise similarity between subjects and objects","operationId":"_compare_v3_api_semsim_compare__subjects___objects__get","parameters":[{"in":"path","name":"subjects","required":true,"schema":{"title":"List of subjects for comparison","type":"string"}},{"in":"path","name":"objects","required":true,"schema":{"title":"List of objects for comparison","type":"string"}},{"in":"query","name":"metric","required":false,"schema":{"allOf":[{"$ref":"#/components/schemas/SemsimMetric"}],"default":"ancestor_information_content","title":"Similarity metric to use"}}],"responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Compare","tags":["semsim"]}},"/v3/api/semsim/compare":{"post":{"description":"Pairwise similarity between two sets of terms
\n
\n Example:
\n
\n{\n  \"subjects\": [\"MP:0010771\",\"MP:0002169\",\"MP:0005391\",\"MP:0005389\",\"MP:0005367\"],\n  \"objects\": [\"HP:0004325\",\"HP:0000093\",\"MP:0006144\"],\n  \"metric\": \"ancestor_information_content\"\n}\n
","operationId":"_post_compare_v3_api_semsim_compare_post","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SemsimCompareRequest"}}},"required":true},"responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Post Compare","tags":["semsim"]}},"/v3/api/semsim/multicompare":{"post":{"description":"Pairwise similarity between two sets of terms
\n
\n Example:
\n 
\n{\n  \"metric\": \"ancestor_information_content\",\n  \"subjects\": [ \"HP:0002616\", \"HP:0001763\", \"HP:0004944\", \"HP:0010749\", \"HP:0001533\", \"HP:0002020\", \"HP:0012450\", \"HP:0003394\", \"HP:0003771\", \"HP:0012378\", \"HP:0001278\", \"HP:0002827\",\n\"HP:0002829\", \"HP:0002999\", \"HP:0003010\"],\n  \"object_sets\": [\n    {\n      \"id\": \"MGI:97486\",\n      \"label\": \"Pax2\",\n      \"phenotypes\": [ \"MP:0003675\", \"MP:0003675\", \"MP:0003675\", \"MP:0011382\", \"MP:0011366\", \"MP:0010097\", \"MP:0012536\", \"MP:0003558\", \"MP:0004729\", \"MP:0009113\", \"MP:0006090\", \"MP:0001325\", \"MP:0001325\", \"MP:0006309\",\n\"MP:0004017\", \"MP:0012533\", \"MP:0004505\", \"MP:0004505\", \"MP:0004505\"]\n    },\n    {\n      \"id\": \"MGI:95819\",\n      \"label\": \"Grin1\",\n      \"phenotypes\": [\"MP:0001435\", \"MP:0001405\", \"MP:0002797\", \"MP:0001386\", \"MP:0001901\", \"MP:0001901\", \"MP:0001901\", \"MP:0001901\", \"MP:0001901\", \"MP:0002906\", \"MP:0004811\", \"MP:0001900\",\n\"MP:0009748\", \"MP:0008428\", \"MP:0008428\", \"MP:0008428\"]\n    }\n  ]\n}\n
","operationId":"_post_multicompare_v3_api_semsim_multicompare_post","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SemsimMultiCompareRequest"}}},"required":true},"responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Post Multicompare","tags":["semsim"]}},"/v3/api/semsim/search/{termset}/{group}":{"get":{"description":"Search for terms in a termset\n\nArgs:
\n termset (str): Comma separated list of term IDs to find matches for.
\n group (str): Group of entities to search within (e.g. Human Genes)
\n metric: (str, optional): Similarity metric to use. Defaults to \"ancestor_information_content\".
\n limit (int, optional): Limit the number of results. Defaults to 10.\n\nReturns:
\n List[str]: List of matching terms","operationId":"_search_v3_api_semsim_search__termset___group__get","parameters":[{"in":"path","name":"termset","required":true,"schema":{"title":"Termset to search","type":"string"}},{"in":"path","name":"group","required":true,"schema":{"allOf":[{"$ref":"#/components/schemas/SemsimSearchGroup"}],"title":"Group of entities to search within (e.g. Human Genes)"}},{"in":"query","name":"metric","required":false,"schema":{"allOf":[{"$ref":"#/components/schemas/SemsimMetric"}],"default":"ancestor_information_content","title":"Similarity metric to use"}},{"in":"query","name":"limit","required":false,"schema":{"default":10,"maximum":50,"minimum":1,"title":"Limit","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Search","tags":["semsim"]}},"/v3/api/semsim/search":{"post":{"description":"Search for terms in a termset
\n
\n Example:
\n
\n{\n  \"termset\": [\"HP:0002104\", \"HP:0012378\", \"HP:0012378\", \"HP:0012378\"],\n  \"group\": \"Human Diseases\",\n  \"metric\": \"ancestor_information_content\",\n  \"limit\": 5\n}\n
","operationId":"_post_search_v3_api_semsim_search_post","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SemsimSearchRequest"}}},"required":true},"responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Post Search","tags":["semsim"]}},"/v3/api/annotate":{"get":{"operationId":"_annotate_v3_api_annotate_get","parameters":[{"in":"query","name":"text","required":false,"schema":{"default":"","title":"The text content to annotate","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"title":"Response Annotate V3 Api Annotate Get","type":"string"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Annotate","tags":["text_annotation"]},"post":{"operationId":"_post_annotate_v3_api_annotate_post","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/TextAnnotationRequest"}}},"required":true},"responses":{"200":{"content":{"application/json":{"schema":{"title":"Response Post Annotate V3 Api Annotate Post","type":"string"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Post Annotate","tags":["text_annotation"]}},"/v3/api/annotate/entities":{"get":{"operationId":"_entities_v3_api_annotate_entities_get","parameters":[{"in":"query","name":"text","required":false,"schema":{"default":"","title":"Text","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/TextAnnotationResult"},"title":"Response Entities V3 Api Annotate Entities Get","type":"array"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Entities","tags":["text_annotation"]},"post":{"operationId":"_post_entities_v3_api_annotate_entities_post","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/TextAnnotationRequest"}}},"required":true},"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/TextAnnotationResult"},"title":"Response Post Entities V3 Api Annotate Entities Post","type":"array"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Post Entities","tags":["text_annotation"]}},"/":{"get":{"operationId":"_root__get","responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"}},"summary":" Root"}},"/api":{"get":{"operationId":"_api_api_get","responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"}},"summary":" Api"}},"/v3/api/releases":{"get":{"operationId":"_v3_v3_api_releases_get","parameters":[{"in":"query","name":"dev","required":false,"schema":{"default":false,"title":"Get dev releases of the KG (default False)","type":"boolean"}},{"in":"query","name":"limit","required":false,"schema":{"default":0,"title":"The number of releases to return (default 0 for no limit)","type":"integer"}},{"in":"query","name":"release","required":false,"schema":{"title":"Get metadata for a specific release","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" V3"}}},"servers":[{"description":"Production 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queryInputs }}"},"predicate":"part_of","response_mapping":{"$ref":"#/components/x-bte-response-mapping/complex-output"},"supportBatch":false,"testExamples":[{"oneOutput":"ComplexPortal:CPX-2158","qInput":"UniProtKB:P69905"}],"useTemplating":true}]},"x-bte-response-mapping":{"complex-output":{"ComplexPortal":"elements.complexAC","output_name":"elements.complexName"},"complex2chemical":{"CHEBI":"participants.identifier"},"complex2disease":{"orphanet":"disease_ids"},"complex2protein":{"UniProtKB":"participants.identifier"}}},"info":{"contact":{"name":"EMBL-EBI form for support and feedback","url":"https://www.ebi.ac.uk/about/contact/support/complexportal"},"description":"The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms. The majority of complexes are made up of proteins but may also include nucleic acids or small molecules.","termsOfService":"https://www.ebi.ac.uk/complexportal/about#license_privacy","title":"Complex Portal Web Service","version":"1.0","x-translator":{"biolink-version":"4.1.6","component":"KP","infores":"infores:complex-portal","team":["Service Provider"]}},"paths":{"/search/{search_term}":{"get":{"description":"search for complexes matching your search term","parameters":[{"description":"can be a ID (ex: for a protein, chemical, or disease) or a complex name","example":"P69905","in":"path","name":"search_term","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"type":"object"}}},"description":"response 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}}\n}"},"requestBodyType":"object","response_mapping":{"$ref":"#/components/x-bte-response-mapping/reactome"},"supportBatch":false,"testExamples":[{"oneOutput":"REACT:R-HSA-15869","qInput":"HMDB:HMDB0000148"}],"useTemplating":true}],"gene2pathway_1":[{"agent_type":"automated_agent","inputs":[{"id":"NCBIGene","semantic":"Gene"}],"knowledge_level":"knowledge_assertion","outputs":[{"id":"REACT","semantic":"Pathway"}],"parameters":{},"predicate":"participates_in","requestBody":{"body":"{ \n \"analytes\":\n {{ queryInputs \n | replPrefix('entrez') \n | dump }}\n}"},"requestBodyType":"object","response_mapping":{"$ref":"#/components/x-bte-response-mapping/reactome"},"supportBatch":false,"testExamples":[{"oneOutput":"REACT:R-HSA-8939211","qInput":"NCBIGene:5241"}],"useTemplating":true}]},"x-bte-response-mapping":{"reactome":{"REACT":"data.pathwayId","output_name":"data.pathwayName"}}},"info":{"contact":{"email":"NCATSRaMP@nih.gov","name":"RaMP","x-id":"https://github.com/ncats","x-role":"responsible developer"},"description":"Relational Database of Metabolic Pathways (RaMP) API","termsOfService":"https://rampdb.nih.gov","title":"RaMP API v1.0.1","version":"1.0.1","x-translator":{"biolink-version":"3.1.1","component":"KP","infores":"infores:rampdb","team":["Service Provider"]}},"paths":{"/api/source_versions":{"get":{"parameters":[],"responses":{"200":{"content":{"application/json":{"schema":{"type":"object"}}},"description":"OK"},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal Server Error"},"default":{"content":{"application/json":{"schema":{"type":"object"}}},"description":"Default response."}},"summary":"Return source version information"}},"/api/id-types":{"get":{"parameters":[],"responses":{"200":{"content":{"application/json":{"schema":{"type":"object"}}},"description":"OK"},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal Server Error"},"default":{"content":{"application/json":{"schema":{"type":"object"}}},"description":"Default response."}},"summary":"Return analyte ID types"}},"/api/entity_counts":{"get":{"parameters":[],"responses":{"200":{"content":{"application/json":{"schema":{"type":"object"}}},"description":"OK"},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal Server Error"},"default":{"content":{"application/json":{"schema":{"type":"object"}}},"description":"Default response."}},"summary":"Return counts on entities and their 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IDs should be prepended by ID source (e.g. **kegg**:C00412).","required":true},"responses":{"200":{"description":"OK"},"500":{"description":"Internal Server Error"}},"summary":"Return ontologies from list of metabolites"}},"/api/metabolites-from-ontologies":{"post":{"requestBody":{"content":{"application/json":{"schema":{"example":{"format":"json","ontology":["Colon","Liver","Lung"]},"properties":{"format":{"enum":["json","tsv"],"type":"string"},"ontology":{"items":{"type":"string"},"type":"array"}},"type":"object"}}},"description":"Enter ontology(ies) and retrieve corresponding analytes (metabolites).","required":true},"responses":{"200":{"description":"OK"},"500":{"description":"Internal Server Error"}},"summary":"Return metabolites from ontology"}},"/api/chemical-classes":{"post":{"requestBody":{"content":{"application/json":{"schema":{"example":{"metabolites":["hmdb:HMDB0000056","hmdb:HMDB0000439","hmdb:HMDB0000479","hmdb:HMDB0000532","hmdb:HMDB0001015","hmdb:HMDB0001138","hmdb:HMDB0029159","hmdb:HMDB0029412","hmdb:HMDB0034365","hmdb:HMDB0035227","hmdb:HMDB0007973","hmdb:HMDB0008057","hmdb:HMDB0011211"]},"properties":{"biospecimen":{"enum":["Blood","Adipose","Heart","Urine","Brain","Liver","Kidney","Saliva","Feces"],"type":"string"},"metabolites":{"items":{"type":"string"},"type":"array"}},"type":"object"}}},"description":"Retrieve chemical class information (from ClassyFire and LIPID MAPS) for input metabolite IDs. 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Sites that implement /asyncquery MUST implement /asyncquery_status/{job_id}, but those that do not implement /asyncquery SHOULD NOT implement /asyncquery_status."}},"summary":"Retrieve the current status of a previously submitted asyncquery given its job_id","tags":["asyncquery_status"]}}},"servers":[{"description":"TRAPI test service for GeLiNEA","url":"https://molepro-gelinea-trapi.test.transltr.io/gelinea-trapi/v1.5","x-maturity":"testing"},{"description":"TRAPI staging service for GeLiNEA","url":"https://molepro-gelinea-trapi.ci.transltr.io/gelinea-trapi/v1.5","x-maturity":"staging"},{"description":"TRAPI development service for GeLiNEA","url":"https://translator.broadinstitute.org/gelinea-trapi/v1.5","x-maturity":"development"}],"tags":[{"description":"Retrieve the meta knowledge graph representation of this TRAPI web service. KPs MUST provide all subject category - predicate - object category triplets that are supported by the service, NOT including all implied ancestor relationships. ARAs SHOULD provide the union of all meta knowledge graphs of all the KPs that they can consult.","name":"meta_knowledge_graph"},{"description":"Initiate a query and wait to receive the response","name":"query"},{"description":"Initiate a query with a callback to receive the response","name":"asyncquery"},{"description":"Retrieve the current status of a previously submitted asyncquery given its job_id","name":"asyncquery_status"},{"description":"Required for SmartAPI validation of x-translator","name":"translator"},{"description":"Required for SmartAPI validation of x-trapi","name":"trapi"}]}]} \ No newline at end of file diff --git a/src/routes/index.ts b/src/routes/index.ts index ffa0673..96049a4 100644 --- a/src/routes/index.ts +++ b/src/routes/index.ts @@ -50,11 +50,10 @@ export const tasks: TaskByRoute = { asyncquery_v1: (taskInfo: TaskInfo) => V1AsyncQuery.task(taskInfo), asyncquery_v1_by_api: (taskInfo: TaskInfo) => V1AsyncQueryByAPI.task(taskInfo), asyncquery_v1_by_team: (taskInfo: TaskInfo) => V1AsyncQueryByTeam.task(taskInfo), - // load MetaKG from global - meta_knowledge_graph_v1: (taskInfo: TaskInfo) => V1MetaKG.task(taskInfo), // Not threaded due to being lightweight/speed being higher priority // performance: (taskInfo: TaskInfo) => Performance.task(taskInfo), // metakg: (taskInfo: TaskInfo) => MetaKG.task(taskInfo), + // meta_knowledge_graph_v1: (taskInfo: TaskInfo) => V1MetaKG.task(taskInfo), // meta_knowledge_graph_v1_by_api: (taskInfo: TaskInfo) => V1MetaKGByAPI.task(taskInfo), // meta_knowledge_graph_v1_by_team: (taskInfo: TaskInfo) => V1MetaKGByTeam.task(taskInfo), }; diff --git a/src/routes/v1/meta_knowledge_graph_v1.ts b/src/routes/v1/meta_knowledge_graph_v1.ts index 947e98c..7bd6610 100644 --- a/src/routes/v1/meta_knowledge_graph_v1.ts +++ b/src/routes/v1/meta_knowledge_graph_v1.ts @@ -1,8 +1,5 @@ -import path from "path"; -import { TaskInfo } from "@biothings-explorer/types"; import handler from "../../controllers/meta_knowledge_graph"; import * as utils from "../../utils/common"; -import { runTask, taskResponse, taskError } from "../../controllers/threading/threadHandler"; import { Express, NextFunction, Request, Response, RequestHandler } from "express"; class MetaKG { @@ -11,33 +8,16 @@ class MetaKG { .route("/v1/meta_knowledge_graph") .get((async (_req: Request, res: Response, next: NextFunction) => { try { - const response = await runTask(_req, res, path.parse(__filename).name); + const metaKGHandler = new handler(undefined); + const kg = await metaKGHandler.getKG(); res.setHeader("Content-Type", "application/json"); - res.end(JSON.stringify(response)); + res.end(JSON.stringify(kg)); } catch (error) { next(error); } }) as RequestHandler) .all(utils.methodNotAllowed); } - - async task(taskInfo: TaskInfo) { - try { - let kg = undefined; - - // read metakg from files if not globally defined - if(!taskInfo.data.options.metakg) { - const metaKGHandler = new handler(undefined); - kg = await metaKGHandler.getKG(); - } else { - kg = taskInfo.data.options.metakg; - } - // response.logs = utils.filterForLogLevel(response.logs, options.logLevel); - return taskResponse(kg); - } catch (error) { - taskError(error as Error); - } - } } export default new MetaKG();