{ "openapi": "3.0.3", "info": { "contact": { "email": "info@monarchinitiative.org", "name": "Monarch help desk", "x-role": "responsible developer", "url": "https://monarchinitiative.org/help" }, "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": { "infores": "infores:monarchinitiative", "component": "KP", "team": [ "Service Provider", "Standards Reference Implementation Team" ], "biolink-version": "4.2.2" } }, "servers": [ { "description": "Production server", "url": "https://api-v3.monarchinitiative.org", "x-maturity": "production" } ], "tags": [ { "name": "translator" } ], "paths": { "/v3/api/association": { "get": { "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" } ], "tags": [ "association" ], "summary": " Get Associations", "description": "Retrieves all associations for a given entity, or between two entities.", "operationId": "_get_associations_v3_api_association_get", "parameters": [ { "name": "category", "in": "query", "required": false, "schema": { "type": "array", "items": { "$ref": "#/components/schemas/AssociationCategory" }, "title": "Category" } }, { "name": "subject", "in": "query", "required": false, "schema": { "anyOf": [ { "type": "array", "items": { "type": "string" } } ], "title": "Subject" } }, { "name": "subject_category", "in": "query", "required": false, "schema": { "type": "array", "items": { "$ref": "#/components/schemas/EntityCategory" }, "title": "Subject Category" } }, { "name": "subject_namespace", "in": "query", "required": false, "schema": { "anyOf": [ { "type": "array", "items": { "type": "string" } } ], "title": "Subject Namespace" } }, { "name": "subject_taxon", "in": "query", "required": false, "schema": { "anyOf": [ { "type": "array", "items": { "type": "string" } } ], "title": "Subject Taxon" } }, { "name": "predicate", "in": "query", "required": false, "schema": { "type": "array", "items": { "$ref": "#/components/schemas/AssociationPredicate" }, "title": "Predicate" } }, { "name": "object", "in": "query", "required": false, "schema": { "anyOf": [ { "type": "array", "items": { "type": "string" } } ], "title": "Object" } }, { "name": "object_category", "in": "query", "required": false, "schema": { "type": "array", "items": { "$ref": "#/components/schemas/EntityCategory" }, "title": "Object Category" } }, { "name": "object_namespace", "in": "query", "required": false, "schema": { "anyOf": [ { "type": "array", "items": { "type": "string" } } ], "title": "Object Namespace" } }, { "name": "object_taxon", "in": "query", "required": false, "schema": { "anyOf": [ { "type": "array", "items": { "type": "string" } } ], "title": "Object Taxon" } }, { "name": "entity", "in": "query", "required": false, "schema": { "anyOf": [ { "type": "array", "items": { "type": "string" } } ], "title": "Entity" } }, { "name": "direct", "in": "query", "required": false, "schema": { "type": "boolean", "default": false, "title": "Direct" } }, { "name": "compact", "in": "query", "required": false, "schema": { "type": "boolean", "default": false, "title": "Compact" } }, { "name": "format", "in": "query", "required": false, "schema": { "allOf": [ { "$ref": "#/components/schemas/OutputFormat" } ], "title": "Output format for the response", "default": "json" } }, { "name": "limit", "in": "query", "required": false, "schema": { "type": "integer", "maximum": 500, "minimum": 0, "default": 20, "title": "Limit" } }, { "name": "offset", "in": "query", "required": false, "schema": { "type": "integer", "minimum": 0, "default": 0, "title": "Offset" } } ], "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": { "anyOf": [ { "$ref": "#/components/schemas/AssociationResults" }, { "$ref": "#/components/schemas/CompactAssociationResults" }, { "type": "string" } ], "title": "Response Get Associations V3 Api Association Get" } } } }, "404": { "description": "Not Found" }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } } }, "/v3/api/entity/{id}": { "get": { "tags": [ "entity" ], "summary": " Get Entity", "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": [ { "name": "id", "in": "path", "required": true, "schema": { "type": "string", "title": "ID of the entity to retrieve" } }, { "name": "format", "in": "query", "required": false, "schema": { "allOf": [ { "$ref": "#/components/schemas/OutputFormat" } ], "title": "Output format for the response", "default": "json" } } ], "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": { "anyOf": [ { "$ref": "#/components/schemas/Node" }, { "type": "string" } ], "title": "Response Get Entity V3 Api Entity Id Get" } } } }, "404": { "description": "Not Found" }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } } }, "/v3/api/entity/{id}/{category}": { "get": { "tags": [ "entity" ], "summary": " Association Table", "description": "Retrieves association table data for a given entity and association type\n\nArgs:
\n id (str): ID of the entity to retrieve association table data, ex: MONDO:0019391
\n category (str): Category of association to retrieve association table data for, ex: biolink:DiseaseToPhenotypicFeatureAssociation
\n Path (str, optional): Path string to limit results to a subset. Defaults to None.
\n pagination (PaginationParams, optional): Pagination parameters. Defaults to Depends().
\n\nReturns:
\n AssociationResults: Association table data for the specified entity and association type", "operationId": "_association_table_v3_api_entity__id___category__get", "parameters": [ { "name": "id", "in": "path", "required": true, "schema": { "type": "string", "title": "ID of the entity to retrieve association table data for" } }, { "name": "category", "in": "path", "required": true, "schema": { "allOf": [ { "$ref": "#/components/schemas/AssociationCategory" } ], "title": "Type of association to retrieve association table data for" } }, { "name": "query", "in": "query", "required": false, "schema": { "type": "string", "title": "query string to limit results to a subset" } }, { "name": "traverse_orthologs", "in": "query", "required": false, "schema": { "type": "boolean", "title": "Traverse orthologs to get associations", "default": false } }, { "name": "sort", "in": "query", "required": false, "schema": { "type": "array", "items": { "type": "string" }, "title": "Sort results by a list of field + direction statements" } }, { "name": "format", "in": "query", "required": false, "schema": { "allOf": [ { "$ref": "#/components/schemas/OutputFormat" } ], "title": "Output format for the response", "default": "json" } }, { "name": "download", "in": "query", "required": false, "schema": { "type": "boolean", "title": "Download the results as a file", "default": false } }, { "name": "limit", "in": "query", "required": false, "schema": { "type": "integer", "maximum": 500, "minimum": 0, "default": 20, "title": "Limit" } }, { "name": "offset", "in": "query", "required": false, "schema": { "type": "integer", "minimum": 0, "default": 0, "title": "Offset" } } ], "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": { "anyOf": [ { "$ref": "#/components/schemas/AssociationTableResults" }, { "type": "string" } ], "title": "Response Association Table V3 Api Entity Id Category Get" } } } }, "404": { "description": "Not Found" }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } } }, "/v3/api/histopheno/{id}": { "get": { "tags": [ "histopheno" ], "summary": " Get Histopheno", "description": "Retrieves the entity with the specified id", "operationId": "_get_histopheno_v3_api_histopheno__id__get", "parameters": [ { "name": "id", "in": "path", "required": true, "schema": { "type": "string", "title": "ID of the entity to get histopheno data for" } }, { "name": "format", "in": "query", "required": false, "schema": { "allOf": [ { "$ref": "#/components/schemas/OutputFormat" } ], "title": "Output format for the response", "default": "json" } } ], "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": { "anyOf": [ { "$ref": "#/components/schemas/HistoPheno" }, { "type": "string" } ], "title": "Response Get Histopheno V3 Api Histopheno Id Get" } } } }, "404": { "description": "Not Found" }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } } }, "/v3/api/search": { "get": { "tags": [ "search" ], "summary": "Search", "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": [ { "name": "q", "in": "query", "required": false, "schema": { "type": "string", "title": "Q" } }, { "name": "category", "in": "query", "required": false, "schema": { "anyOf": [ { "type": "array", "items": { "$ref": "#/components/schemas/EntityCategory" } } ], "title": "Category" } }, { "name": "in_taxon_label", "in": "query", "required": false, "schema": { "anyOf": [ { "type": "array", "items": { "type": "string" } } ], "title": "In Taxon Label" } }, { "name": "limit", "in": "query", "required": false, "schema": { "type": "integer", "maximum": 500, "minimum": 0, "default": 20, "title": "Limit" } }, { "name": "offset", "in": "query", "required": false, "schema": { "type": "integer", "minimum": 0, "default": 0, "title": "Offset" } } ], "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/SearchResults" } } } }, "404": { "description": "Not Found" }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } } }, "/v3/api/autocomplete": { "get": { "tags": [ "search" ], "summary": "Autocomplete", "description": "Autocomplete for entities by label\n\nArgs:\n q (str): Query string to autocomplete against\n\nReturns:\n SearchResults", "operationId": "autocomplete_v3_api_autocomplete_get", "parameters": [ { "name": "q", "in": "query", "required": false, "schema": { "type": "string", "title": "Query string to autocomplete against", "default": "*:*" } } ], "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/SearchResults" } } } }, "404": { "description": "Not Found" }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } } }, "/v3/api/mappings": { "get": { "tags": [ "search" ], "summary": "Mappings", "operationId": "mappings_v3_api_mappings_get", "parameters": [ { "name": "entity_id", "in": "query", "required": false, "schema": { "anyOf": [ { "type": "array", "items": { "type": "string" } } ], "title": "Entity Id" } }, { "name": "subject_id", "in": "query", "required": false, "schema": { "anyOf": [ { "type": "array", "items": { "type": "string" } } ], "title": "Subject Id" } }, { "name": "predicate_id", "in": "query", "required": false, "schema": { "anyOf": [ { "type": "array", "items": { "$ref": "#/components/schemas/MappingPredicate" } } ], "title": "Predicate Id" } }, { "name": "object_id", "in": "query", "required": false, "schema": { "anyOf": [ { "type": "array", "items": { "type": "string" } } ], "title": "Object Id" } }, { "name": "mapping_justification", "in": "query", "required": false, "schema": { "anyOf": [ { "type": "array", "items": { "type": "string" } } ], "title": "Mapping Justification" } }, { "name": "format", "in": "query", "required": false, "schema": { "allOf": [ { "$ref": "#/components/schemas/OutputFormat" } ], "title": "Output format for the response", "default": "json" } }, { "name": "limit", "in": "query", "required": false, "schema": { "type": "integer", "maximum": 500, "minimum": 0, "default": 20, "title": "Limit" } }, { "name": "offset", "in": "query", "required": false, "schema": { "type": "integer", "minimum": 0, "default": 0, "title": "Offset" } } ], "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": {} } } }, "404": { "description": "Not Found" }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } } }, "/v3/api/semsim/autocomplete": { "get": { "tags": [ "semsim" ], "summary": "Autocomplete", "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": [ { "name": "q", "in": "query", "required": false, "schema": { "type": "string", "title": "Query string to autocomplete against", "default": "*:*" } } ], "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/SearchResults" } } } }, "404": { "description": "Not Found" }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } } }, "/v3/api/semsim/compare/{subjects}/{objects}": { "get": { "tags": [ "semsim" ], "summary": " Compare", "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": [ { "name": "subjects", "in": "path", "required": true, "schema": { "type": "string", "title": "List of subjects for comparison" } }, { "name": "objects", "in": "path", "required": true, "schema": { "type": "string", "title": "List of objects for comparison" } }, { "name": "metric", "in": "query", "required": false, "schema": { "allOf": [ { "$ref": "#/components/schemas/SemsimMetric" } ], "title": "Similarity metric to use", "default": "ancestor_information_content" } } ], "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": {} } } }, "404": { "description": "Not Found" }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } } }, "/v3/api/semsim/compare": { "post": { "tags": [ "semsim" ], "summary": " Post Compare", "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": { "$ref": "#/components/schemas/SemsimCompareRequest" } } }, "required": true }, "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": {} } } }, "404": { "description": "Not Found" }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } } }, "/v3/api/semsim/multicompare": { "post": { "tags": [ "semsim" ], "summary": " Post Multicompare", "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": { "$ref": "#/components/schemas/SemsimMultiCompareRequest" } } }, "required": true }, "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": {} } } }, "404": { "description": "Not Found" }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } } }, "/v3/api/semsim/search/{termset}/{group}": { "get": { "tags": [ "semsim" ], "summary": " Search", "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": [ { "name": "termset", "in": "path", "required": true, "schema": { "type": "string", "title": "Termset to search" } }, { "name": "group", "in": "path", "required": true, "schema": { "allOf": [ { "$ref": "#/components/schemas/SemsimSearchGroup" } ], "title": "Group of entities to search within (e.g. Human Genes)" } }, { "name": "metric", "in": "query", "required": false, "schema": { "allOf": [ { "$ref": "#/components/schemas/SemsimMetric" } ], "title": "Similarity metric to use", "default": "ancestor_information_content" } }, { "name": "limit", "in": "query", "required": false, "schema": { "type": "integer", "maximum": 50, "minimum": 1, "default": 10, "title": "Limit" } } ], "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": {} } } }, "404": { "description": "Not Found" }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } } }, "/v3/api/semsim/search": { "post": { "tags": [ "semsim" ], "summary": " Post Search", "description": "Search for terms in a termset
\n
\n Example:
\n
\n{\n  \"termset\": [\"HP:0002104\", \"HP:0012378\", \"HP:0012378\", \"HP:0012378\"],\n  \"group\": \"Human Diseases\",\n  \"metric\": \"ancestor_information_content\",\n  \"limit\": 5\n}\n
", "operationId": "_post_search_v3_api_semsim_search_post", "requestBody": { "content": { "application/json": { "schema": { "$ref": "#/components/schemas/SemsimSearchRequest" } } }, "required": true }, "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": {} } } }, "404": { "description": "Not Found" }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } } }, "/v3/api/annotate": { "get": { "tags": [ "text_annotation" ], "summary": " Annotate", "operationId": "_annotate_v3_api_annotate_get", "parameters": [ { "name": "text", "in": "query", "required": false, "schema": { "type": "string", "title": "The text content to annotate", "default": "" } } ], "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": { "type": "string", "title": "Response Annotate V3 Api Annotate Get" } } } }, "404": { "description": "Not Found" }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } }, "post": { "tags": [ "text_annotation" ], "summary": " Post Annotate", "operationId": "_post_annotate_v3_api_annotate_post", "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/TextAnnotationRequest" } } } }, "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": { "type": "string", "title": "Response Post Annotate V3 Api Annotate Post" } } } }, "404": { "description": "Not Found" }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } } }, "/v3/api/annotate/entities": { "get": { "tags": [ "text_annotation" ], "summary": " Entities", "operationId": "_entities_v3_api_annotate_entities_get", "parameters": [ { "name": "text", "in": "query", "required": false, "schema": { "type": "string", "default": "", "title": "Text" } } ], "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": { "type": "array", "items": { "$ref": "#/components/schemas/TextAnnotationResult" }, "title": "Response Entities V3 Api Annotate Entities Get" } } } }, "404": { "description": "Not Found" }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } }, "post": { "tags": [ "text_annotation" ], "summary": " Post Entities", "operationId": "_post_entities_v3_api_annotate_entities_post", "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/TextAnnotationRequest" } } } }, "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": { "type": "array", "items": { "$ref": "#/components/schemas/TextAnnotationResult" }, "title": "Response Post Entities V3 Api Annotate Entities Post" } } } }, "404": { "description": "Not Found" }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } } }, "/": { "get": { "summary": " Root", "operationId": "_root__get", "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": {} } } } } } }, "/api": { "get": { "summary": " Api", "operationId": "_api_api_get", "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": {} } } } } } }, "/v3/api/releases": { "get": { "summary": " V3", "operationId": "_v3_v3_api_releases_get", "parameters": [ { "name": "dev", "in": "query", "required": false, "schema": { "type": "boolean", "title": "Get dev releases of the KG (default False)", "default": false } }, { "name": "limit", "in": "query", "required": false, "schema": { "type": "integer", "title": "The number of releases to return (default 0 for no limit)", "default": 0 } }, { "name": "release", "in": "query", "required": false, "schema": { "type": "string", "title": "Get metadata for a specific release" } } ], "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": {} } } }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } } } }, "components": { "schemas": { "Association": { "properties": { "id": { "type": "string", "title": "Id" }, "category": { "anyOf": [ { "type": "string" } ], "title": "Category" }, "subject": { "type": "string", "title": "Subject" }, "original_subject": { "anyOf": [ { "type": "string" } ], "title": "Original Subject" }, "subject_namespace": { "anyOf": [ { "type": "string" } ], "title": "Subject Namespace", "description": "The namespace/prefix of the subject entity" }, "subject_category": { "anyOf": [ { "type": "string" } ], "title": "Subject Category", "description": "The category of the subject entity" }, "subject_closure": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Subject Closure", "description": "Field containing subject id and the ids of all of it's ancestors" }, "subject_label": { "anyOf": [ { "type": "string" } ], "title": "Subject Label", "description": "The name of the subject entity" }, "subject_closure_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Subject Closure Label", "description": "Field containing subject name and the names of all of it's ancestors" }, "subject_taxon": { "anyOf": [ { "type": "string" } ], "title": "Subject Taxon" }, "subject_taxon_label": { "anyOf": [ { "type": "string" } ], "title": "Subject Taxon Label" }, "predicate": { "type": "string", "title": "Predicate" }, "object": { "type": "string", "title": "Object" }, "original_object": { "anyOf": [ { "type": "string" } ], "title": "Original Object" }, "object_namespace": { "anyOf": [ { "type": "string" } ], "title": "Object Namespace", "description": "The namespace/prefix of the object entity" }, "object_category": { "anyOf": [ { "type": "string" } ], "title": "Object Category", "description": "The category of the object entity" }, "object_closure": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Object Closure", "description": "Field containing object id and the ids of all of it's ancestors" }, "object_label": { "anyOf": [ { "type": "string" } ], "title": "Object Label", "description": "The name of the object entity" }, "object_closure_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Object Closure Label", "description": "Field containing object name and the names of all of it's ancestors" }, "object_taxon": { "anyOf": [ { "type": "string" } ], "title": "Object Taxon" }, "object_taxon_label": { "anyOf": [ { "type": "string" } ], "title": "Object Taxon Label" }, "primary_knowledge_source": { "anyOf": [ { "type": "string" } ], "title": "Primary Knowledge Source" }, "aggregator_knowledge_source": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Aggregator Knowledge Source" }, "negated": { "anyOf": [ { "type": "boolean" } ], "title": "Negated" }, "pathway": { "anyOf": [ { "type": "string" } ], "title": "Pathway" }, "evidence_count": { "anyOf": [ { "type": "integer" } ], "title": "Evidence Count", "description": "count of supporting documents, evidence codes, and sources supplying evidence" }, "knowledge_level": { "type": "string", "title": "Knowledge Level", "description": "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." }, "agent_type": { "type": "string", "title": "Agent Type", "description": "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." }, "has_evidence": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Has Evidence" }, "has_evidence_links": { "anyOf": [ { "items": { "$ref": "#/components/schemas/ExpandedCurie" }, "type": "array" } ], "title": "Has Evidence Links", "description": "List of ExpandedCuries with id and url for evidence" }, "has_count": { "anyOf": [ { "type": "integer" } ], "title": "Has Count", "description": "count of out of has_total representing a frequency" }, "has_total": { "anyOf": [ { "type": "integer" } ], "title": "Has Total", "description": "total, devided by has_count, representing a frequency" }, "has_percentage": { "anyOf": [ { "type": "number" } ], "title": "Has Percentage", "description": "percentage, which may be calculated from has_count and has_total, as 100 * quotient or provided directly, rounded to the integer level" }, "has_quotient": { "anyOf": [ { "type": "number" } ], "title": "Has Quotient", "description": "quotient, which should be 1/100 of has_percentage" }, "grouping_key": { "anyOf": [ { "type": "string" } ], "title": "Grouping Key", "description": "A concatenation of fields used to group associations with the same essential/defining properties" }, "provided_by": { "anyOf": [ { "type": "string" } ], "title": "Provided By" }, "provided_by_link": { "anyOf": [ { "$ref": "#/components/schemas/ExpandedCurie" } ], "description": "A link to the docs for the knowledge source that provided the node/edge." }, "publications": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Publications" }, "publications_links": { "anyOf": [ { "items": { "$ref": "#/components/schemas/ExpandedCurie" }, "type": "array" } ], "title": "Publications Links", "description": "List of ExpandedCuries with id and url for publications" }, "frequency_qualifier": { "anyOf": [ { "type": "string" } ], "title": "Frequency Qualifier" }, "onset_qualifier": { "anyOf": [ { "type": "string" } ], "title": "Onset Qualifier" }, "sex_qualifier": { "anyOf": [ { "type": "string" } ], "title": "Sex Qualifier" }, "stage_qualifier": { "anyOf": [ { "type": "string" } ], "title": "Stage Qualifier" }, "qualifiers": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Qualifiers" }, "qualifiers_label": { "anyOf": [ { "type": "string" } ], "title": "Qualifiers Label", "description": "The name of the frequency_qualifier entity" }, "qualifiers_namespace": { "anyOf": [ { "type": "string" } ], "title": "Qualifiers Namespace", "description": "The namespace/prefix of the frequency_qualifier entity" }, "qualifiers_category": { "anyOf": [ { "type": "string" } ], "title": "Qualifiers Category", "description": "The category of the frequency_qualifier entity" }, "qualifiers_closure": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Qualifiers Closure", "description": "Field containing frequency_qualifier id and the ids of all of it's ancestors" }, "qualifiers_closure_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Qualifiers Closure Label", "description": "Field containing frequency_qualifier name and the names of all of it's ancestors" }, "qualifier": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Qualifier" }, "qualifier_label": { "anyOf": [ { "type": "string" } ], "title": "Qualifier Label", "description": "The name of the frequency_qualifier entity" }, "qualifier_namespace": { "anyOf": [ { "type": "string" } ], "title": "Qualifier Namespace", "description": "The namespace/prefix of the frequency_qualifier entity" }, "qualifier_category": { "anyOf": [ { "type": "string" } ], "title": "Qualifier Category", "description": "The category of the frequency_qualifier entity" }, "qualifier_closure": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Qualifier Closure", "description": "Field containing frequency_qualifier id and the ids of all of it's ancestors" }, "qualifier_closure_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Qualifier Closure Label", "description": "Field containing frequency_qualifier name and the names of all of it's ancestors" }, "frequency_qualifier_label": { "anyOf": [ { "type": "string" } ], "title": "Frequency Qualifier Label", "description": "The name of the frequency_qualifier entity" }, "frequency_qualifier_namespace": { "anyOf": [ { "type": "string" } ], "title": "Frequency Qualifier Namespace", "description": "The namespace/prefix of the frequency_qualifier entity" }, "frequency_qualifier_category": { "anyOf": [ { "type": "string" } ], "title": "Frequency Qualifier Category", "description": "The category of the frequency_qualifier entity" }, "frequency_qualifier_closure": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Frequency Qualifier Closure", "description": "Field containing frequency_qualifier id and the ids of all of it's ancestors" }, "frequency_qualifier_closure_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Frequency Qualifier Closure Label", "description": "Field containing frequency_qualifier name and the names of all of it's ancestors" }, "onset_qualifier_label": { "anyOf": [ { "type": "string" } ], "title": "Onset Qualifier Label", "description": "The name of the onset_qualifier entity" }, "onset_qualifier_namespace": { "anyOf": [ { "type": "string" } ], "title": "Onset Qualifier Namespace", "description": "The namespace/prefix of the onset_qualifier entity" }, "onset_qualifier_category": { "anyOf": [ { "type": "string" } ], "title": "Onset Qualifier Category", "description": "The category of the onset_qualifier entity" }, "onset_qualifier_closure": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Onset Qualifier Closure", "description": "Field containing onset_qualifier id and the ids of all of it's ancestors" }, "onset_qualifier_closure_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Onset Qualifier Closure Label", "description": "Field containing onset_qualifier name and the names of all of it's ancestors" }, "sex_qualifier_label": { "anyOf": [ { "type": "string" } ], "title": "Sex Qualifier Label", "description": "The name of the sex_qualifier entity" }, "sex_qualifier_namespace": { "anyOf": [ { "type": "string" } ], "title": "Sex Qualifier Namespace", "description": "The namespace/prefix of the sex_qualifier entity" }, "sex_qualifier_category": { "anyOf": [ { "type": "string" } ], "title": "Sex Qualifier Category", "description": "The category of the sex_qualifier entity" }, "sex_qualifier_closure": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Sex Qualifier Closure", "description": "Field containing sex_qualifier id and the ids of all of it's ancestors" }, "sex_qualifier_closure_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Sex Qualifier Closure Label", "description": "Field containing sex_qualifier name and the names of all of it's ancestors" }, "stage_qualifier_label": { "anyOf": [ { "type": "string" } ], "title": "Stage Qualifier Label", "description": "The name of the stage_qualifier entity" }, "stage_qualifier_namespace": { "anyOf": [ { "type": "string" } ], "title": "Stage Qualifier Namespace", "description": "The namespace/prefix of the stage_qualifier entity" }, "stage_qualifier_category": { "anyOf": [ { "type": "string" } ], "title": "Stage Qualifier Category", "description": "The category of the stage_qualifier entity" }, "stage_qualifier_closure": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Stage Qualifier Closure", "description": "Field containing stage_qualifier id and the ids of all of it's ancestors" }, "stage_qualifier_closure_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Stage Qualifier Closure Label", "description": "Field containing stage_qualifier name and the names of all of it's ancestors" } }, "additionalProperties": true, "type": "object", "required": [ "id", "subject", "predicate", "object", "knowledge_level", "agent_type" ], "title": "Association" }, "AssociationCategory": { "type": "string", "enum": [ "biolink:PairwiseGeneToGeneInteraction", "biolink:GeneToExpressionSiteAssociation", "biolink:MacromolecularMachineToBiologicalProcessAssociation", "biolink:GeneToPhenotypicFeatureAssociation", "biolink:MacromolecularMachineToMolecularActivityAssociation", "biolink:MacromolecularMachineToCellularComponentAssociation", "biolink:Association", "biolink:GeneToGeneHomologyAssociation", "biolink:DiseaseToPhenotypicFeatureAssociation", "biolink:GeneToPathwayAssociation", "biolink:ChemicalToPathwayAssociation", "biolink:CorrelatedGeneToDiseaseAssociation", "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "biolink:CausalGeneToDiseaseAssociation" ], "title": "AssociationCategory", "description": "Association categories" }, "AssociationCount": { "properties": { "label": { "type": "string", "title": "Label" }, "count": { "anyOf": [ { "type": "integer" } ], "title": "Count", "description": "count of documents" }, "category": { "anyOf": [ { "type": "string" } ], "title": "Category" } }, "additionalProperties": true, "type": "object", "required": [ "label" ], "title": "AssociationCount" }, "AssociationDirectionEnum": { "type": "string", "enum": [ "incoming", "outgoing" ], "title": "AssociationDirectionEnum", "description": "The directionality of an association as it relates to a specified entity, with edges being categorized as incoming or outgoing" }, "AssociationPredicate": { "type": "string", "enum": [ "biolink:interacts_with", "biolink:expressed_in", "biolink:has_phenotype", "biolink:enables", "biolink:actively_involved_in", "biolink:orthologous_to", "biolink:located_in", "biolink:subclass_of", "biolink:participates_in", "biolink:acts_upstream_of_or_within", "biolink:related_to", "biolink:active_in", "biolink:part_of", "biolink:acts_upstream_of", "biolink:has_mode_of_inheritance", "biolink:gene_associated_with_condition", "biolink:contributes_to", "biolink:causes", "biolink:colocalizes_with", "biolink:acts_upstream_of_or_within_positive_effect", "biolink:acts_upstream_of_positive_effect", "biolink:acts_upstream_of_or_within_negative_effect", "biolink:acts_upstream_of_negative_effect" ], "title": "AssociationPredicate", "description": "Association predicates" }, "AssociationResults": { "properties": { "limit": { "type": "integer", "title": "Limit", "description": "number of items to return in a response" }, "offset": { "type": "integer", "title": "Offset", "description": "offset into the total number of items" }, "total": { "type": "integer", "title": "Total", "description": "total number of items matching a query" }, "items": { "items": { "$ref": "#/components/schemas/Association" }, "type": "array", "title": "Items", "description": "A collection of items, with the type to be overriden by slot_usage" } }, "additionalProperties": true, "type": "object", "required": [ "limit", "offset", "total" ], "title": "AssociationResults" }, "AssociationTableResults": { "properties": { "limit": { "type": "integer", "title": "Limit", "description": "number of items to return in a response" }, "offset": { "type": "integer", "title": "Offset", "description": "offset into the total number of items" }, "total": { "type": "integer", "title": "Total", "description": "total number of items matching a query" }, "items": { "items": { "$ref": "#/components/schemas/DirectionalAssociation" }, "type": "array", "title": "Items", "description": "A collection of items, with the type to be overriden by slot_usage" } }, "additionalProperties": true, "type": "object", "required": [ "limit", "offset", "total" ], "title": "AssociationTableResults" }, "CompactAssociation": { "properties": { "category": { "anyOf": [ { "type": "string" } ], "title": "Category" }, "subject": { "type": "string", "title": "Subject" }, "subject_label": { "anyOf": [ { "type": "string" } ], "title": "Subject Label", "description": "The name of the subject entity" }, "predicate": { "type": "string", "title": "Predicate" }, "object": { "type": "string", "title": "Object" }, "object_label": { "anyOf": [ { "type": "string" } ], "title": "Object Label", "description": "The name of the object entity" }, "negated": { "anyOf": [ { "type": "boolean" } ], "title": "Negated" } }, "additionalProperties": true, "type": "object", "required": [ "subject", "predicate", "object" ], "title": "CompactAssociation" }, "CompactAssociationResults": { "properties": { "limit": { "type": "integer", "title": "Limit", "description": "number of items to return in a response" }, "offset": { "type": "integer", "title": "Offset", "description": "offset into the total number of items" }, "total": { "type": "integer", "title": "Total", "description": "total number of items matching a query" }, "items": { "items": { "$ref": "#/components/schemas/CompactAssociation" }, "type": "array", "title": "Items", "description": "A collection of items, with the type to be overriden by slot_usage" } }, "additionalProperties": true, "type": "object", "required": [ "limit", "offset", "total" ], "title": "CompactAssociationResults" }, "DirectionalAssociation": { "properties": { "id": { "type": "string", "title": "Id" }, "category": { "anyOf": [ { "type": "string" } ], "title": "Category" }, "subject": { "type": "string", "title": "Subject" }, "original_subject": { "anyOf": [ { "type": "string" } ], "title": "Original Subject" }, "subject_namespace": { "anyOf": [ { "type": "string" } ], "title": "Subject Namespace", "description": "The namespace/prefix of the subject entity" }, "subject_category": { "anyOf": [ { "type": "string" } ], "title": "Subject Category", "description": "The category of the subject entity" }, "subject_closure": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Subject Closure", "description": "Field containing subject id and the ids of all of it's ancestors" }, "subject_label": { "anyOf": [ { "type": "string" } ], "title": "Subject Label", "description": "The name of the subject entity" }, "subject_closure_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Subject Closure Label", "description": "Field containing subject name and the names of all of it's ancestors" }, "subject_taxon": { "anyOf": [ { "type": "string" } ], "title": "Subject Taxon" }, "subject_taxon_label": { "anyOf": [ { "type": "string" } ], "title": "Subject Taxon Label" }, "predicate": { "type": "string", "title": "Predicate" }, "object": { "type": "string", "title": "Object" }, "original_object": { "anyOf": [ { "type": "string" } ], "title": "Original Object" }, "object_namespace": { "anyOf": [ { "type": "string" } ], "title": "Object Namespace", "description": "The namespace/prefix of the object entity" }, "object_category": { "anyOf": [ { "type": "string" } ], "title": "Object Category", "description": "The category of the object entity" }, "object_closure": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Object Closure", "description": "Field containing object id and the ids of all of it's ancestors" }, "object_label": { "anyOf": [ { "type": "string" } ], "title": "Object Label", "description": "The name of the object entity" }, "object_closure_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Object Closure Label", "description": "Field containing object name and the names of all of it's ancestors" }, "object_taxon": { "anyOf": [ { "type": "string" } ], "title": "Object Taxon" }, "object_taxon_label": { "anyOf": [ { "type": "string" } ], "title": "Object Taxon Label" }, "primary_knowledge_source": { "anyOf": [ { "type": "string" } ], "title": "Primary Knowledge Source" }, "aggregator_knowledge_source": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Aggregator Knowledge Source" }, "negated": { "anyOf": [ { "type": "boolean" } ], "title": "Negated" }, "pathway": { "anyOf": [ { "type": "string" } ], "title": "Pathway" }, "evidence_count": { "anyOf": [ { "type": "integer" } ], "title": "Evidence Count", "description": "count of supporting documents, evidence codes, and sources supplying evidence" }, "knowledge_level": { "type": "string", "title": "Knowledge Level", "description": "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." }, "agent_type": { "type": "string", "title": "Agent Type", "description": "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." }, "has_evidence": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Has Evidence" }, "has_evidence_links": { "anyOf": [ { "items": { "$ref": "#/components/schemas/ExpandedCurie" }, "type": "array" } ], "title": "Has Evidence Links", "description": "List of ExpandedCuries with id and url for evidence" }, "has_count": { "anyOf": [ { "type": "integer" } ], "title": "Has Count", "description": "count of out of has_total representing a frequency" }, "has_total": { "anyOf": [ { "type": "integer" } ], "title": "Has Total", "description": "total, devided by has_count, representing a frequency" }, "has_percentage": { "anyOf": [ { "type": "number" } ], "title": "Has Percentage", "description": "percentage, which may be calculated from has_count and has_total, as 100 * quotient or provided directly, rounded to the integer level" }, "has_quotient": { "anyOf": [ { "type": "number" } ], "title": "Has Quotient", "description": "quotient, which should be 1/100 of has_percentage" }, "grouping_key": { "anyOf": [ { "type": "string" } ], "title": "Grouping Key", "description": "A concatenation of fields used to group associations with the same essential/defining properties" }, "provided_by": { "anyOf": [ { "type": "string" } ], "title": "Provided By" }, "provided_by_link": { "anyOf": [ { "$ref": "#/components/schemas/ExpandedCurie" } ], "description": "A link to the docs for the knowledge source that provided the node/edge." }, "publications": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Publications" }, "publications_links": { "anyOf": [ { "items": { "$ref": "#/components/schemas/ExpandedCurie" }, "type": "array" } ], "title": "Publications Links", "description": "List of ExpandedCuries with id and url for publications" }, "frequency_qualifier": { "anyOf": [ { "type": "string" } ], "title": "Frequency Qualifier" }, "onset_qualifier": { "anyOf": [ { "type": "string" } ], "title": "Onset Qualifier" }, "sex_qualifier": { "anyOf": [ { "type": "string" } ], "title": "Sex Qualifier" }, "stage_qualifier": { "anyOf": [ { "type": "string" } ], "title": "Stage Qualifier" }, "qualifiers": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Qualifiers" }, "qualifiers_label": { "anyOf": [ { "type": "string" } ], "title": "Qualifiers Label", "description": "The name of the frequency_qualifier entity" }, "qualifiers_namespace": { "anyOf": [ { "type": "string" } ], "title": "Qualifiers Namespace", "description": "The namespace/prefix of the frequency_qualifier entity" }, "qualifiers_category": { "anyOf": [ { "type": "string" } ], "title": "Qualifiers Category", "description": "The category of the frequency_qualifier entity" }, "qualifiers_closure": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Qualifiers Closure", "description": "Field containing frequency_qualifier id and the ids of all of it's ancestors" }, "qualifiers_closure_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Qualifiers Closure Label", "description": "Field containing frequency_qualifier name and the names of all of it's ancestors" }, "qualifier": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Qualifier" }, "qualifier_label": { "anyOf": [ { "type": "string" } ], "title": "Qualifier Label", "description": "The name of the frequency_qualifier entity" }, "qualifier_namespace": { "anyOf": [ { "type": "string" } ], "title": "Qualifier Namespace", "description": "The namespace/prefix of the frequency_qualifier entity" }, "qualifier_category": { "anyOf": [ { "type": "string" } ], "title": "Qualifier Category", "description": "The category of the frequency_qualifier entity" }, "qualifier_closure": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Qualifier Closure", "description": "Field containing frequency_qualifier id and the ids of all of it's ancestors" }, "qualifier_closure_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Qualifier Closure Label", "description": "Field containing frequency_qualifier name and the names of all of it's ancestors" }, "frequency_qualifier_label": { "anyOf": [ { "type": "string" } ], "title": "Frequency Qualifier Label", "description": "The name of the frequency_qualifier entity" }, "frequency_qualifier_namespace": { "anyOf": [ { "type": "string" } ], "title": "Frequency Qualifier Namespace", "description": "The namespace/prefix of the frequency_qualifier entity" }, "frequency_qualifier_category": { "anyOf": [ { "type": "string" } ], "title": "Frequency Qualifier Category", "description": "The category of the frequency_qualifier entity" }, "frequency_qualifier_closure": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Frequency Qualifier Closure", "description": "Field containing frequency_qualifier id and the ids of all of it's ancestors" }, "frequency_qualifier_closure_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Frequency Qualifier Closure Label", "description": "Field containing frequency_qualifier name and the names of all of it's ancestors" }, "onset_qualifier_label": { "anyOf": [ { "type": "string" } ], "title": "Onset Qualifier Label", "description": "The name of the onset_qualifier entity" }, "onset_qualifier_namespace": { "anyOf": [ { "type": "string" } ], "title": "Onset Qualifier Namespace", "description": "The namespace/prefix of the onset_qualifier entity" }, "onset_qualifier_category": { "anyOf": [ { "type": "string" } ], "title": "Onset Qualifier Category", "description": "The category of the onset_qualifier entity" }, "onset_qualifier_closure": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Onset Qualifier Closure", "description": "Field containing onset_qualifier id and the ids of all of it's ancestors" }, "onset_qualifier_closure_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Onset Qualifier Closure Label", "description": "Field containing onset_qualifier name and the names of all of it's ancestors" }, "sex_qualifier_label": { "anyOf": [ { "type": "string" } ], "title": "Sex Qualifier Label", "description": "The name of the sex_qualifier entity" }, "sex_qualifier_namespace": { "anyOf": [ { "type": "string" } ], "title": "Sex Qualifier Namespace", "description": "The namespace/prefix of the sex_qualifier entity" }, "sex_qualifier_category": { "anyOf": [ { "type": "string" } ], "title": "Sex Qualifier Category", "description": "The category of the sex_qualifier entity" }, "sex_qualifier_closure": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Sex Qualifier Closure", "description": "Field containing sex_qualifier id and the ids of all of it's ancestors" }, "sex_qualifier_closure_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Sex Qualifier Closure Label", "description": "Field containing sex_qualifier name and the names of all of it's ancestors" }, "stage_qualifier_label": { "anyOf": [ { "type": "string" } ], "title": "Stage Qualifier Label", "description": "The name of the stage_qualifier entity" }, "stage_qualifier_namespace": { "anyOf": [ { "type": "string" } ], "title": "Stage Qualifier Namespace", "description": "The namespace/prefix of the stage_qualifier entity" }, "stage_qualifier_category": { "anyOf": [ { "type": "string" } ], "title": "Stage Qualifier Category", "description": "The category of the stage_qualifier entity" }, "stage_qualifier_closure": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Stage Qualifier Closure", "description": "Field containing stage_qualifier id and the ids of all of it's ancestors" }, "stage_qualifier_closure_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Stage Qualifier Closure Label", "description": "Field containing stage_qualifier name and the names of all of it's ancestors" }, "direction": { "allOf": [ { "$ref": "#/components/schemas/AssociationDirectionEnum" } ], "description": "The directionality of the association relative to a given entity for an association_count. If the entity is the subject or in the subject closure, the direction is forwards, if it is the object or in the object closure, the direction is backwards." } }, "additionalProperties": true, "type": "object", "required": [ "id", "subject", "predicate", "object", "knowledge_level", "agent_type", "direction" ], "title": "DirectionalAssociation", "description": "An association that gives it's direction relative to a specified entity" }, "Entity": { "properties": { "id": { "type": "string", "title": "Id" }, "category": { "anyOf": [ { "type": "string" } ], "title": "Category" }, "name": { "anyOf": [ { "type": "string" } ], "title": "Name" }, "full_name": { "anyOf": [ { "type": "string" } ], "title": "Full Name", "description": "The long form name of an entity" }, "deprecated": { "anyOf": [ { "type": "boolean" } ], "title": "Deprecated", "description": "A boolean flag indicating that an entity is no longer considered current or valid." }, "description": { "anyOf": [ { "type": "string" } ], "title": "Description" }, "xref": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Xref" }, "provided_by": { "anyOf": [ { "type": "string" } ], "title": "Provided By" }, "in_taxon": { "anyOf": [ { "type": "string" } ], "title": "In Taxon", "description": "The biolink taxon that the entity is in the closure of." }, "in_taxon_label": { "anyOf": [ { "type": "string" } ], "title": "In Taxon Label", "description": "The label of the biolink taxon that the entity is in the closure of." }, "symbol": { "anyOf": [ { "type": "string" } ], "title": "Symbol" }, "synonym": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Synonym" }, "uri": { "anyOf": [ { "type": "string" } ], "title": "Uri", "description": "The URI of the entity" }, "iri": { "anyOf": [ { "type": "string" } ], "title": "Iri" }, "namespace": { "anyOf": [ { "type": "string" } ], "title": "Namespace", "description": "The namespace/prefix portion of this entity's identifier" }, "has_phenotype": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Has Phenotype", "description": "A list of phenotype identifiers that are known to be associated with this entity" }, "has_phenotype_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Has Phenotype Label", "description": "A list of phenotype labels that are known to be associated with this entity" }, "has_phenotype_closure": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Has Phenotype Closure", "description": "A list of phenotype identifiers that are known to be associated with this entity expanded to include all ancestors" }, "has_phenotype_closure_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Has Phenotype Closure Label", "description": "A list of phenotype labels that are known to be associated with this entity expanded to include all ancestors" }, "has_phenotype_count": { "anyOf": [ { "type": "integer" } ], "title": "Has Phenotype Count", "description": "A count of the number of phenotypes that are known to be associated with this entity" } }, "additionalProperties": true, "type": "object", "required": [ "id" ], "title": "Entity", "description": "Represents an Entity in the Monarch KG data model" }, "EntityCategory": { "type": "string", "enum": [ "biolink:Gene", "biolink:PhenotypicFeature", "biolink:BiologicalProcessOrActivity", "biolink:GrossAnatomicalStructure", "biolink:Disease", "biolink:Pathway", "biolink:Cell", "biolink:NamedThing", "biolink:AnatomicalEntity", "biolink:CellularComponent", "biolink:MolecularEntity", "biolink:BiologicalProcess", "biolink:MacromolecularComplex", "biolink:MolecularActivity", "biolink:Protein", "biolink:CellularOrganism", "biolink:PhenotypicQuality", "biolink:Vertebrate", "biolink:Virus", "biolink:BehavioralFeature", "biolink:LifeStage", "biolink:PathologicalProcess", "biolink:ChemicalEntity", "biolink:Drug", "biolink:OrganismTaxon", "biolink:SequenceVariant", "biolink:SmallMolecule", "biolink:InformationContentEntity", "biolink:NucleicAcidEntity", "biolink:EvidenceType", "biolink:GeographicExposure", "biolink:RNAProduct", "biolink:Transcript", "biolink:Fungus", "biolink:Plant", "biolink:Dataset", "biolink:Invertebrate", "biolink:PopulationOfIndividualOrganisms", "biolink:ProteinFamily", "biolink:Activity", "biolink:Agent", "biolink:ChemicalExposure", "biolink:ConfidenceLevel", "biolink:EnvironmentalFeature", "biolink:Exon", "biolink:GeneticInheritance", "biolink:Genome", "biolink:Genotype", "biolink:Haplotype", "biolink:Human", "biolink:IndividualOrganism", "biolink:Mammal", "biolink:MaterialSample", "biolink:MicroRNA", "biolink:Patent", "biolink:ProteinDomain", "biolink:Publication", "biolink:RegulatoryRegion", "biolink:Study", "biolink:Treatment", "biolink:WebPage", "biolink:AccessibleDnaRegion", "biolink:Article", "biolink:Attribute", "biolink:Bacterium", "biolink:BiologicalEntity", "biolink:BiologicalSex", "biolink:CellLine", "biolink:ChemicalMixture", "biolink:CodingSequence", "biolink:DatasetDistribution", "biolink:DiagnosticAid", "biolink:DrugExposure", "biolink:EnvironmentalProcess", "biolink:Event", "biolink:GenotypicSex", "biolink:NoncodingRNAProduct", "biolink:OrganismalEntity", "biolink:PhenotypicSex", "biolink:Polypeptide", "biolink:Procedure", "biolink:ProcessedMaterial", "biolink:ReagentTargetedGene", "biolink:SiRNA", "biolink:Snv", "biolink:StudyVariable", "biolink:TranscriptionFactorBindingSite", "biolink:Zygosity" ], "title": "EntityCategory", "description": "Entity categories" }, "ExpandedCurie": { "properties": { "id": { "type": "string", "title": "Id" }, "url": { "anyOf": [ { "type": "string" } ], "title": "Url" } }, "additionalProperties": true, "type": "object", "required": [ "id" ], "title": "ExpandedCurie", "description": "A curie bundled along with its expanded url" }, "FacetField": { "properties": { "label": { "type": "string", "title": "Label" }, "facet_values": { "anyOf": [ { "items": { "$ref": "#/components/schemas/FacetValue" }, "type": "array" } ], "title": "Facet Values", "description": "Collection of FacetValue label/value instances belonging to a FacetField" } }, "additionalProperties": true, "type": "object", "required": [ "label" ], "title": "FacetField" }, "FacetValue": { "properties": { "label": { "type": "string", "title": "Label" }, "count": { "anyOf": [ { "type": "integer" } ], "title": "Count", "description": "count of documents" } }, "additionalProperties": true, "type": "object", "required": [ "label" ], "title": "FacetValue" }, "HTTPValidationError": { "properties": { "detail": { "items": { "$ref": "#/components/schemas/ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "HistoBin": { "properties": { "label": { "type": "string", "title": "Label" }, "count": { "anyOf": [ { "type": "integer" } ], "title": "Count", "description": "count of documents" }, "id": { "type": "string", "title": "Id" } }, "additionalProperties": true, "type": "object", "required": [ "label", "id" ], "title": "HistoBin" }, "HistoPheno": { "properties": { "id": { "type": "string", "title": "Id" }, "items": { "items": { "$ref": "#/components/schemas/HistoBin" }, "type": "array", "title": "Items", "description": "A collection of items, with the type to be overriden by slot_usage" } }, "additionalProperties": true, "type": "object", "required": [ "id" ], "title": "HistoPheno" }, "MappingPredicate": { "type": "string", "enum": [ "skos:exactMatch", "skos:closeMatch", "skos:broadMatch", "skos:narrowMatch" ], "title": "MappingPredicate", "description": "Mapping predicates" }, "Node": { "properties": { "id": { "type": "string", "title": "Id" }, "category": { "anyOf": [ { "type": "string" } ], "title": "Category" }, "name": { "anyOf": [ { "type": "string" } ], "title": "Name" }, "full_name": { "anyOf": [ { "type": "string" } ], "title": "Full Name", "description": "The long form name of an entity" }, "deprecated": { "anyOf": [ { "type": "boolean" } ], "title": "Deprecated", "description": "A boolean flag indicating that an entity is no longer considered current or valid." }, "description": { "anyOf": [ { "type": "string" } ], "title": "Description" }, "xref": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Xref" }, "provided_by": { "anyOf": [ { "type": "string" } ], "title": "Provided By" }, "in_taxon": { "anyOf": [ { "type": "string" } ], "title": "In Taxon", "description": "The biolink taxon that the entity is in the closure of." }, "in_taxon_label": { "anyOf": [ { "type": "string" } ], "title": "In Taxon Label", "description": "The label of the biolink taxon that the entity is in the closure of." }, "symbol": { "anyOf": [ { "type": "string" } ], "title": "Symbol" }, "synonym": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Synonym" }, "uri": { "anyOf": [ { "type": "string" } ], "title": "Uri", "description": "The URI of the entity" }, "iri": { "anyOf": [ { "type": "string" } ], "title": "Iri" }, "namespace": { "anyOf": [ { "type": "string" } ], "title": "Namespace", "description": "The namespace/prefix portion of this entity's identifier" }, "has_phenotype": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Has Phenotype", "description": "A list of phenotype identifiers that are known to be associated with this entity" }, "has_phenotype_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Has Phenotype Label", "description": "A list of phenotype labels that are known to be associated with this entity" }, "has_phenotype_closure": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Has Phenotype Closure", "description": "A list of phenotype identifiers that are known to be associated with this entity expanded to include all ancestors" }, "has_phenotype_closure_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Has Phenotype Closure Label", "description": "A list of phenotype labels that are known to be associated with this entity expanded to include all ancestors" }, "has_phenotype_count": { "anyOf": [ { "type": "integer" } ], "title": "Has Phenotype Count", "description": "A count of the number of phenotypes that are known to be associated with this entity" }, "inheritance": { "anyOf": [ { "$ref": "#/components/schemas/Entity" } ] }, "causal_gene": { "anyOf": [ { "items": { "$ref": "#/components/schemas/Entity" }, "type": "array" } ], "title": "Causal Gene", "description": "A list of genes that are known to be causally associated with a disease" }, "causes_disease": { "anyOf": [ { "items": { "$ref": "#/components/schemas/Entity" }, "type": "array" } ], "title": "Causes Disease", "description": "A list of diseases that are known to be causally associated with a gene" }, "mappings": { "anyOf": [ { "items": { "$ref": "#/components/schemas/ExpandedCurie" }, "type": "array" } ], "title": "Mappings", "description": "List of ExpandedCuries with id and url for mapped entities" }, "external_links": { "anyOf": [ { "items": { "$ref": "#/components/schemas/ExpandedCurie" }, "type": "array" } ], "title": "External Links", "description": "ExpandedCurie with id and url for xrefs" }, "provided_by_link": { "anyOf": [ { "$ref": "#/components/schemas/ExpandedCurie" } ], "description": "A link to the docs for the knowledge source that provided the node/edge." }, "association_counts": { "items": { "$ref": "#/components/schemas/AssociationCount" }, "type": "array", "title": "Association Counts" }, "node_hierarchy": { "anyOf": [ { "$ref": "#/components/schemas/NodeHierarchy" } ] } }, "additionalProperties": true, "type": "object", "required": [ "id" ], "title": "Node", "description": "UI container class extending Entity with additional information" }, "NodeHierarchy": { "properties": { "super_classes": { "items": { "$ref": "#/components/schemas/Entity" }, "type": "array", "title": "Super Classes" }, "sub_classes": { "items": { "$ref": "#/components/schemas/Entity" }, "type": "array", "title": "Sub Classes" } }, "additionalProperties": true, "type": "object", "title": "NodeHierarchy" }, "OutputFormat": { "type": "string", "enum": [ "json", "tsv" ], "title": "OutputFormat" }, "SearchResult": { "properties": { "id": { "type": "string", "title": "Id" }, "category": { "type": "string", "title": "Category" }, "name": { "type": "string", "title": "Name" }, "full_name": { "anyOf": [ { "type": "string" } ], "title": "Full Name", "description": "The long form name of an entity" }, "deprecated": { "anyOf": [ { "type": "boolean" } ], "title": "Deprecated", "description": "A boolean flag indicating that an entity is no longer considered current or valid." }, "description": { "anyOf": [ { "type": "string" } ], "title": "Description" }, "xref": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Xref" }, "provided_by": { "anyOf": [ { "type": "string" } ], "title": "Provided By" }, "in_taxon": { "anyOf": [ { "type": "string" } ], "title": "In Taxon", "description": "The biolink taxon that the entity is in the closure of." }, "in_taxon_label": { "anyOf": [ { "type": "string" } ], "title": "In Taxon Label", "description": "The label of the biolink taxon that the entity is in the closure of." }, "symbol": { "anyOf": [ { "type": "string" } ], "title": "Symbol" }, "synonym": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Synonym" }, "uri": { "anyOf": [ { "type": "string" } ], "title": "Uri", "description": "The URI of the entity" }, "iri": { "anyOf": [ { "type": "string" } ], "title": "Iri" }, "namespace": { "anyOf": [ { "type": "string" } ], "title": "Namespace", "description": "The namespace/prefix portion of this entity's identifier" }, "has_phenotype": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Has Phenotype", "description": "A list of phenotype identifiers that are known to be associated with this entity" }, "has_phenotype_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Has Phenotype Label", "description": "A list of phenotype labels that are known to be associated with this entity" }, "has_phenotype_closure": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Has Phenotype Closure", "description": "A list of phenotype identifiers that are known to be associated with this entity expanded to include all ancestors" }, "has_phenotype_closure_label": { "anyOf": [ { "items": { "type": "string" }, "type": "array" } ], "title": "Has Phenotype Closure Label", "description": "A list of phenotype labels that are known to be associated with this entity expanded to include all ancestors" }, "has_phenotype_count": { "anyOf": [ { "type": "integer" } ], "title": "Has Phenotype Count", "description": "A count of the number of phenotypes that are known to be associated with this entity" }, "highlight": { "anyOf": [ { "type": "string" } ], "title": "Highlight", "description": "matching text snippet containing html tags" }, "score": { "anyOf": [ { "type": "number" } ], "title": "Score" } }, "additionalProperties": true, "type": "object", "required": [ "id", "category", "name" ], "title": "SearchResult" }, "SearchResults": { "properties": { "limit": { "type": "integer", "title": "Limit", "description": "number of items to return in a response" }, "offset": { "type": "integer", "title": "Offset", "description": "offset into the total number of items" }, "total": { "type": "integer", "title": "Total", "description": "total number of items matching a query" }, "items": { "items": { "$ref": "#/components/schemas/SearchResult" }, "type": "array", "title": "Items", "description": "A collection of items, with the type to be overriden by slot_usage" }, "facet_fields": { "anyOf": [ { "items": { "$ref": "#/components/schemas/FacetField" }, "type": "array" } ], "title": "Facet Fields", "description": "Collection of facet field responses with the field values and counts" }, "facet_queries": { "anyOf": [ { "items": { "$ref": "#/components/schemas/FacetValue" }, "type": "array" } ], "title": "Facet Queries", "description": "Collection of facet query responses with the query string values and counts" } }, "additionalProperties": true, "type": "object", "required": [ "limit", "offset", "total" ], "title": "SearchResults" }, "SemsimCompareRequest": { "properties": { "subjects": { "items": { "type": "string" }, "type": "array", "title": "List of subjects for comparison" }, "objects": { "items": { "type": "string" }, "type": "array", "title": "List of objects for comparison" }, "metric": { "allOf": [ { "$ref": "#/components/schemas/SemsimMetric" } ], "title": "Similarity metric to use", "default": "ancestor_information_content" } }, "type": "object", "required": [ "subjects", "objects" ], "title": "SemsimCompareRequest" }, "SemsimMetric": { "type": "string", "enum": [ "ancestor_information_content", "jaccard_similarity", "phenodigm_score" ], "title": "SemsimMetric" }, "SemsimMultiCompareObject": { "properties": { "id": { "anyOf": [ { "type": "string" } ], "title": "ID of the object set" }, "label": { "type": "string", "title": "Label of the object set" }, "phenotypes": { "items": { "type": "string" }, "type": "array", "title": "List of object for comparison" } }, "type": "object", "required": [ "label", "phenotypes" ], "title": "SemsimMultiCompareObject" }, "SemsimMultiCompareRequest": { "properties": { "subjects": { "items": { "type": "string" }, "type": "array", "title": "List of subjects for comparison" }, "object_sets": { "items": { "$ref": "#/components/schemas/SemsimMultiCompareObject" }, "type": "array", "title": "List of object sets for comparison" }, "metric": { "allOf": [ { "$ref": "#/components/schemas/SemsimMetric" } ], "title": "Similarity metric to use", "default": "ancestor_information_content" } }, "type": "object", "required": [ "subjects", "object_sets" ], "title": "SemsimMultiCompareRequest" }, "SemsimSearchGroup": { "type": "string", "enum": [ "Human Genes", "Mouse Genes", "Rat Genes", "Zebrafish Genes", "C. Elegans Genes", "Human Diseases" ], "title": "SemsimSearchGroup" }, "SemsimSearchRequest": { "properties": { "termset": { "items": { "type": "string" }, "type": "array", "title": "Termset to search" }, "group": { "allOf": [ { "$ref": "#/components/schemas/SemsimSearchGroup" } ], "title": "Group of entities to search within (e.g. Human Genes)" }, "metric": { "allOf": [ { "$ref": "#/components/schemas/SemsimMetric" } ], "title": "Similarity metric to use", "default": "ancestor_information_content" }, "limit": { "anyOf": [ { "type": "integer", "maximum": 50, "minimum": 1 } ], "title": "Limit the number of results", "default": 10 } }, "type": "object", "required": [ "termset", "group" ], "title": "SemsimSearchRequest" }, "TextAnnotationRequest": { "properties": { "content": { "type": "string", "title": "The text content to annotate" } }, "type": "object", "required": [ "content" ], "title": "TextAnnotationRequest" }, "TextAnnotationResult": { "properties": { "text": { "anyOf": [ { "type": "string" } ], "title": "Text", "description": "text without tokens" }, "tokens": { "anyOf": [ { "items": { "$ref": "#/components/schemas/Entity" }, "type": "array" } ], "title": "Tokens", "description": "A collection of entities or concepts" }, "start": { "anyOf": [ { "type": "integer" } ], "title": "Start", "description": "start position of the annotation" }, "end": { "anyOf": [ { "type": "integer" } ], "title": "End", "description": "end position of the annotation" } }, "additionalProperties": true, "type": "object", "title": "TextAnnotationResult" }, "ValidationError": { "properties": { "loc": { "items": { "anyOf": [ { "type": "string" }, { "type": "integer" } ] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": [ "loc", "msg", "type" ], "title": "ValidationError" } }, "x-bte-response-mapping": { "object-anatomy-uberon": { "UBERON": "items.object", "output_name": "items.object_label", "input_name": "items.subject_label", "ref_pmid": "items.publications", "trapi_sources": "items.sources" }, "object-disease-mondo": { "MONDO": "items.object", "output_name": "items.object_label", "input_name": "items.subject_label", "ref_pmid": "items.publications", "trapi_sources": "items.sources" }, "object-gene-hgnc": { "HGNC": "items.object", "output_name": "items.object_label", "input_name": "items.subject_label", "ref_pmid": "items.publications", "trapi_sources": "items.sources" }, "object-pheno-hp": { "HP": "items.object", "output_name": "items.object_label", "input_name": "items.subject_label", "ref_pmid": "items.publications", "trapi_sources": "items.sources" }, "subject-disease-mondo": { "MONDO": "items.subject", "output_name": "items.subject_label", "input_name": "items.object_label", "ref_pmid": "items.publications", "trapi_sources": "items.sources" }, "subject-gene-hgnc": { "HGNC": "items.subject", "output_name": "items.subject_label", "input_name": "items.object_label", "ref_pmid": "items.publications", "trapi_sources": "items.sources" } }, "x-bte-kgs-operations": { "gene-anatomy": [ { "supportBatch": false, "useTemplating": true, "inputs": [ { "id": "HGNC", "semantic": "Gene" } ], "parameters": { "subject": "{{ queryInputs | replPrefix('HGNC') }}", "category": "biolink:GeneToExpressionSiteAssociation", "subject_namespace": "HGNC", "subject_taxon": "NCBITaxon:9606", "predicate": "biolink:expressed_in", "object_namespace": "UBERON", "direct": true, "format": "json", "limit": 500 }, "outputs": [ { "id": "UBERON", "semantic": "GrossAnatomicalStructure" } ], "predicate": "expressed_in", "knowledge_level": "knowledge_assertion", "agent_type": "not_provided", "response_mapping": { "$ref": "#/components/x-bte-response-mapping/object-anatomy-uberon" }, "testExamples": [ { "qInput": "HGNC:28264", "oneOutput": "UBERON:0006566" }, { "qInput": "HGNC:9360", "oneOutput": "UBERON:0002450" } ] } ], "anatomy-gene": [ { "supportBatch": false, "useTemplating": true, "inputs": [ { "id": "UBERON", "semantic": "GrossAnatomicalStructure" } ], "parameters": { "object": "{{ queryInputs | replPrefix('UBERON') }}", "category": "biolink:GeneToExpressionSiteAssociation", "subject_namespace": "HGNC", "subject_taxon": "NCBITaxon:9606", "predicate": "biolink:expressed_in", "object_namespace": "UBERON", "direct": true, "format": "json", "limit": 500 }, "outputs": [ { "id": "HGNC", "semantic": "Gene" } ], "predicate": "expresses", "knowledge_level": "knowledge_assertion", "agent_type": "not_provided", "response_mapping": { "$ref": "#/components/x-bte-response-mapping/subject-gene-hgnc" }, "testExamples": [ { "qInput": "UBERON:0001817", "oneOutput": "HGNC:16430" }, { "qInput": "UBERON:0002073", "oneOutput": "HGNC:25851" } ] } ], "disease-pheno": [ { "supportBatch": false, "useTemplating": true, "inputs": [ { "id": "MONDO", "semantic": "Disease" } ], "parameters": { "subject": "{{ queryInputs | replPrefix('MONDO') }}", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject_namespace": "MONDO", "predicate": "biolink:has_phenotype", "object_namespace": "HP", "direct": true, "format": "json", "limit": 500 }, "outputs": [ { "id": "HP", "semantic": "PhenotypicFeature" } ], "predicate": "has_phenotype", "knowledge_level": "knowledge_assertion", "agent_type": "manual_agent", "response_mapping": { "$ref": "#/components/x-bte-response-mapping/object-pheno-hp" }, "testExamples": [ { "qInput": "MONDO:0007298", "oneOutput": "HP:0006855" }, { "qInput": "MONDO:0008974", "oneOutput": "HP:0000926" } ] } ], "pheno-disease": [ { "supportBatch": false, "useTemplating": true, "inputs": [ { "id": "HP", "semantic": "PhenotypicFeature" } ], "parameters": { "object": "{{ queryInputs | replPrefix('HP') }}", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject_namespace": "MONDO", "predicate": "biolink:has_phenotype", "object_namespace": "HP", "direct": true, "format": "json", "limit": 500 }, "outputs": [ { "id": "MONDO", "semantic": "Disease" } ], "predicate": "phenotype_of", "knowledge_level": "knowledge_assertion", "agent_type": "manual_agent", "response_mapping": { "$ref": "#/components/x-bte-response-mapping/subject-disease-mondo" }, "testExamples": [ { "qInput": "HP:0031629", "oneOutput": "MONDO:0030458" }, { "qInput": "HP:0006855", "oneOutput": "MONDO:0010041" } ] } ], "gene-disease-causal": [ { "supportBatch": false, "useTemplating": true, "inputs": [ { "id": "HGNC", "semantic": "Gene" } ], "parameters": { "subject": "{{ queryInputs | replPrefix('HGNC') }}", "category": "biolink:CausalGeneToDiseaseAssociation", "subject_namespace": "HGNC", "predicate": "biolink:causes", "object_namespace": "MONDO", "direct": true, "format": "json", "limit": 500 }, "outputs": [ { "id": "MONDO", "semantic": "Disease" } ], "predicate": "causes", "knowledge_level": "knowledge_assertion", "agent_type": "manual_agent", "response_mapping": { "$ref": "#/components/x-bte-response-mapping/object-disease-mondo" }, "testExamples": [ { "qInput": "HGNC:11138", "oneOutput": "MONDO:0007488" }, { "qInput": "HGNC:3434", "oneOutput": "MONDO:0012553" } ] } ], "disease-gene-causal": [ { "supportBatch": false, "useTemplating": true, "inputs": [ { "id": "MONDO", "semantic": "Disease" } ], "parameters": { "object": "{{ queryInputs | replPrefix('MONDO') }}", "category": "biolink:CausalGeneToDiseaseAssociation", "subject_namespace": "HGNC", "predicate": "biolink:causes", "object_namespace": "MONDO", "direct": true, "format": "json", "limit": 500 }, "outputs": [ { "id": "HGNC", "semantic": "Gene" } ], "predicate": "caused_by", "knowledge_level": "knowledge_assertion", "agent_type": "manual_agent", "response_mapping": { "$ref": "#/components/x-bte-response-mapping/subject-gene-hgnc" }, "testExamples": [ { "qInput": "MONDO:0011562", "oneOutput": "HGNC:11138" }, { "qInput": "MONDO:0009861", "oneOutput": "HGNC:8582" } ] } ], "gene-disease-contributesTo": [ { "supportBatch": false, "useTemplating": true, "inputs": [ { "id": "HGNC", "semantic": "Gene" } ], "parameters": { "subject": "{{ queryInputs | replPrefix('HGNC') }}", "category": "biolink:CorrelatedGeneToDiseaseAssociation", "subject_namespace": "HGNC", "predicate": "biolink:contributes_to", "object_namespace": "MONDO", "direct": true, "format": "json", "limit": 500 }, "outputs": [ { "id": "MONDO", "semantic": "Disease" } ], "predicate": "contributes_to", "knowledge_level": "knowledge_assertion", "agent_type": "manual_agent", "response_mapping": { "$ref": "#/components/x-bte-response-mapping/object-disease-mondo" }, "testExamples": [ { "qInput": "HGNC:6294", "oneOutput": "MONDO:0100316" }, { "qInput": "HGNC:9652", "oneOutput": "MONDO:0007915" } ] } ], "disease-gene-contributesTo": [ { "supportBatch": false, "useTemplating": true, "inputs": [ { "id": "MONDO", "semantic": "Disease" } ], "parameters": { "object": "{{ queryInputs | replPrefix('MONDO') }}", "category": "biolink:CorrelatedGeneToDiseaseAssociation", "subject_namespace": "HGNC", "predicate": "biolink:contributes_to", "object_namespace": "MONDO", "direct": true, "format": "json", "limit": 500 }, "outputs": [ { "id": "HGNC", "semantic": "Gene" } ], "predicate": "contribution_from", "knowledge_level": "knowledge_assertion", "agent_type": "manual_agent", "response_mapping": { "$ref": "#/components/x-bte-response-mapping/subject-gene-hgnc" }, "testExamples": [ { "qInput": "MONDO:0014629", "oneOutput": "HGNC:2230" }, { "qInput": "MONDO:0013416", "oneOutput": "HGNC:32685" } ] } ], "gene-disease-associatedCondition": [ { "supportBatch": false, "useTemplating": true, "inputs": [ { "id": "HGNC", "semantic": "Gene" } ], "parameters": { "subject": "{{ queryInputs | replPrefix('HGNC') }}", "category": "biolink:CorrelatedGeneToDiseaseAssociation", "subject_namespace": "HGNC", "predicate": "biolink:gene_associated_with_condition", "object_namespace": "MONDO", "direct": true, "format": "json", "limit": 500 }, "outputs": [ { "id": "MONDO", "semantic": "Disease" } ], "predicate": "gene_associated_with_condition", "knowledge_level": "knowledge_assertion", "agent_type": "manual_agent", "response_mapping": { "$ref": "#/components/x-bte-response-mapping/object-disease-mondo" }, "testExamples": [ { "qInput": "HGNC:6493", "oneOutput": "MONDO:0009182" }, { "qInput": "HGNC:9462", "oneOutput": "MONDO:0010699" } ] } ], "disease-gene-associatedCondition": [ { "supportBatch": false, "useTemplating": true, "inputs": [ { "id": "MONDO", "semantic": "Disease" } ], "parameters": { "object": "{{ queryInputs | replPrefix('MONDO') }}", "category": "biolink:CorrelatedGeneToDiseaseAssociation", "subject_namespace": "HGNC", "predicate": "biolink:gene_associated_with_condition", "object_namespace": "MONDO", "direct": true, "format": "json", "limit": 500 }, "outputs": [ { "id": "HGNC", "semantic": "Gene" } ], "predicate": "condition_associated_with_gene", "knowledge_level": "knowledge_assertion", "agent_type": "manual_agent", "response_mapping": { "$ref": "#/components/x-bte-response-mapping/subject-gene-hgnc" }, "testExamples": [ { "qInput": "MONDO:0018961", "oneOutput": "HGNC:1787" }, { "qInput": "MONDO:0018875", "oneOutput": "HGNC:6973" } ] } ], "gene-pheno": [ { "supportBatch": false, "useTemplating": true, "inputs": [ { "id": "HGNC", "semantic": "Gene" } ], "parameters": { "subject": "{{ queryInputs | replPrefix('HGNC') }}", "category": "biolink:GeneToPhenotypicFeatureAssociation", "subject_namespace": "HGNC", "predicate": "biolink:has_phenotype", "object_namespace": "HP", "direct": true, "format": "json", "limit": 500 }, "outputs": [ { "id": "HP", "semantic": "PhenotypicFeature" } ], "predicate": "has_phenotype", "knowledge_level": "logical_entailment", "agent_type": "automated_agent", "response_mapping": { "$ref": "#/components/x-bte-response-mapping/object-pheno-hp" }, "testExamples": [ { "qInput": "HGNC:8548", "oneOutput": "HP:0000944" }, { "qInput": "HGNC:7551", "oneOutput": "HP:0011675" } ] } ], "pheno-gene": [ { "supportBatch": false, "useTemplating": true, "inputs": [ { "id": "HP", "semantic": "PhenotypicFeature" } ], "parameters": { "object": "{{ queryInputs | replPrefix('HP') }}", "category": "biolink:GeneToPhenotypicFeatureAssociation", "subject_namespace": "HGNC", "predicate": "biolink:has_phenotype", "object_namespace": "HP", "direct": true, "format": "json", "limit": 500 }, "outputs": [ { "id": "HGNC", "semantic": "Gene" } ], "predicate": "phenotype_of", "knowledge_level": "logical_entailment", "agent_type": "automated_agent", "response_mapping": { "$ref": "#/components/x-bte-response-mapping/subject-gene-hgnc" }, "testExamples": [ { "qInput": "HP:0000183", "oneOutput": "HGNC:4065" }, { "qInput": "HP:0032543", "oneOutput": "HGNC:2950" } ] } ], "gene-gene-interaction-forward": [ { "supportBatch": false, "useTemplating": true, "inputs": [ { "id": "HGNC", "semantic": "Gene" } ], "parameters": { "subject": "{{ queryInputs | replPrefix('HGNC') }}", "category": "biolink:PairwiseGeneToGeneInteraction", "subject_namespace": "HGNC", "predicate": "biolink:interacts_with", "object_namespace": "HGNC", "direct": true, "format": "json", "limit": 500 }, "outputs": [ { "id": "HGNC", "semantic": "Gene" } ], "predicate": "interacts_with", "knowledge_level": "knowledge_assertion", "agent_type": "not_provided", "response_mapping": { "$ref": "#/components/x-bte-response-mapping/object-gene-hgnc" }, "testExamples": [ { "qInput": "HGNC:2950", "oneOutput": "HGNC:13671" }, { "qInput": "HGNC:7551", "oneOutput": "HGNC:16007" } ] } ], "gene-gene-interaction-backward": [ { "supportBatch": false, "useTemplating": true, "inputs": [ { "id": "HGNC", "semantic": "Gene" } ], "parameters": { "object": "{{ queryInputs | replPrefix('HGNC') }}", "category": "biolink:PairwiseGeneToGeneInteraction", "subject_namespace": "HGNC", "predicate": "biolink:interacts_with", "object_namespace": "HGNC", "direct": true, "format": "json", "limit": 500 }, "outputs": [ { "id": "HGNC", "semantic": "Gene" } ], "predicate": "interacts_with", "knowledge_level": "knowledge_assertion", "agent_type": "not_provided", "response_mapping": { "$ref": "#/components/x-bte-response-mapping/subject-gene-hgnc" }, "testExamples": [ { "qInput": "HGNC:2950", "oneOutput": "HGNC:8607" }, { "qInput": "HGNC:7551", "oneOutput": "HGNC:1476" } ] } ] } } }