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If not specified in the request, this will start at the beginning of the results.","in":"query","name":"offset","schema":{"type":"string"}},{"description":"Amount of records to return in a given page.","in":"query","name":"limit","schema":{"default":1000,"format":"int32","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Tool"},"type":"array"}}},"description":"An array of Tools that match the filter."}},"security":[{"BEARER":[]}],"summary":"List all tools","tags":["GA4GHV20"]}},"/ga4gh/trs/v2/tools/{id}":{"get":{"description":"This endpoint returns one specific tool (which has ToolVersions nested inside it).","operationId":"toolsIdGet","parameters":[{"description":"A unique identifier of the tool, scoped to this registry, for example `123456`.","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Tool"}},"text/plain":{"schema":{"$ref":"#/components/schemas/Tool"}}},"description":"A tool."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Error"}},"text/plain":{"schema":{"$ref":"#/components/schemas/Error"}}},"description":"The tool can not be found."}},"security":[{"BEARER":[]}],"summary":"List one specific tool, acts as an anchor for self references","tags":["GA4GHV20"]}},"/ga4gh/trs/v2/tools/{id}/versions":{"get":{"description":"Returns all versions of the specified tool.","operationId":"toolsIdVersionsGet","parameters":[{"description":"A unique identifier of the tool, scoped to this registry, for example `123456`.","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ToolVersion"},"type":"array"}}},"description":"An array of tool versions."}},"security":[{"BEARER":[]}],"summary":"List versions of a tool","tags":["GA4GHV20"]}},"/ga4gh/trs/v2/tools/{id}/versions/{version_id}/containerfile":{"get":{"description":"Returns the container specifications(s) for the specified image. 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We recommend that versions use semantic versioning https://semver.org/spec/v2.0.0.html  (For example, `1.0.0` instead of `develop`)","in":"path","name":"version_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/FileWrapper"},"type":"array"}}},"description":"The tool payload."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Error"}}},"description":"There are no container specifications for this tool."}},"security":[{"BEARER":[]}],"summary":"Get the container specification(s) for the specified image.","tags":["GA4GHV20"]}},"/ga4gh/trs/v2/tools/{id}/versions/{version_id}":{"get":{"description":"This endpoint returns one specific tool version.","operationId":"toolsIdVersionsVersionIdGet","parameters":[{"description":"A unique identifier of the tool, scoped to this registry, for example `123456`.","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"An identifier of the tool version, scoped to this registry, for example `v1`. We recommend that versions use semantic versioning https://semver.org/spec/v2.0.0.html  (For example, `1.0.0` instead of `develop`)","in":"path","name":"version_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ToolVersion"}}},"description":"A tool version."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Error"}}},"description":"The tool can not be found."}},"security":[{"BEARER":[]}],"summary":"List one specific tool version, acts as an anchor for self references","tags":["GA4GHV20"]}},"/ga4gh/trs/v2/tools/{id}/versions/{version_id}/{type}/descriptor":{"get":{"description":"Returns the descriptor for the specified tool (examples include CWL, WDL, Nextflow, Galaxy, or Snakemake documents).","operationId":"toolsIdVersionsVersionIdTypeDescriptorGet","parameters":[{"description":"A unique identifier of the tool, scoped to this registry, for example `123456`.","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"The output type of the descriptor. 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This returns additional descriptors for the specified tool in the same or other directories that can be reached as a relative path. This endpoint can be useful for workflow engine implementations like cwltool to programmatically download all the descriptors for a tool and run it. This can optionally include other files described with FileWrappers such as test parameters and containerfiles.","operationId":"toolsIdVersionsVersionIdTypeDescriptorRelativePathGet","parameters":[{"description":"A unique identifier of the tool, scoped to this registry, for example `123456`.","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"The output type of the descriptor. 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Unencoded paths such 'sampleDirectory/foo.cwl' should also be allowed.","in":"path","name":"relative_path","required":true,"schema":{"pattern":".+","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/FileWrapper"}},"text/plain":{"schema":{"$ref":"#/components/schemas/FileWrapper"}}},"description":"The tool descriptor."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Error"}},"text/plain":{"schema":{"$ref":"#/components/schemas/Error"}}},"description":"The tool can not be output in the specified type."}},"security":[{"BEARER":[]}],"summary":"Get additional tool descriptor files relative to the main file","tags":["GA4GHV20"]}},"/ga4gh/trs/v2/tools/{id}/versions/{version_id}/{type}/files":{"get":{"description":"Get a list of objects that contain the relative path and file type. The descriptors are intended for use with the /tools/{id}/versions/{version_id}/{type}/descriptor/{relative_path : .+} endpoint. Returns a zip file of all files when format=zip is specified.","operationId":"toolsIdVersionsVersionIdTypeFilesGet","parameters":[{"description":"A unique identifier of the tool, scoped to this registry, for example `123456`.","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"The output type of the descriptor.","in":"path","name":"type","required":true,"schema":{"enum":["CWL","WDL","NFL","GALAXY","SMK","SERVICE","JUPYTER"],"type":"string"}},{"description":"An identifier of the tool version, scoped to this registry, for example `v1`. We recommend that versions use semantic versioning https://semver.org/spec/v2.0.0.html  (For example, `1.0.0` instead of `develop`)","in":"path","name":"version_id","required":true,"schema":{"type":"string"}},{"description":"Returns a zip file of all files when format=zip is specified.","in":"query","name":"format","schema":{"enum":["zip"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ToolFile"},"type":"array"}},"application/zip":{"schema":{"items":{"$ref":"#/components/schemas/ToolFile"},"type":"array"}}},"description":"The array of File JSON responses."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Error"}},"application/zip":{"schema":{"$ref":"#/components/schemas/Error"}}},"description":"The tool can not be output in the specified type."}},"security":[{"BEARER":[]}],"summary":"Get a list of objects that contain the relative path and file type","tags":["GA4GHV20"]}},"/ga4gh/trs/v2/tools/{id}/versions/{version_id}/{type}/tests":{"get":{"description":"Get a list of test JSONs (these allow you to execute the tool successfully) suitable for use with this descriptor type.","operationId":"toolsIdVersionsVersionIdTypeTestsGet","parameters":[{"description":"A unique identifier of the tool, scoped to this registry, for example `123456`.","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"The output type of the descriptor. Plain types return the bare descriptor while the \"non-plain\" types return a descriptor wrapped with metadata.","in":"path","name":"type","required":true,"schema":{"enum":["CWL","WDL","NFL","GALAXY","SMK","JUPYTER","PLAIN_CWL","PLAIN_WDL","PLAIN_NFL","PLAIN_GALAXY","PLAIN_GXFORMAT2","PLAIN_SMK","PLAIN_JUPYTER"],"type":"string"}},{"description":"An identifier of the tool version, scoped to this registry, for example `v1`. We recommend that versions use semantic versioning https://semver.org/spec/v2.0.0.html  (For example, `1.0.0` instead of `develop`)","in":"path","name":"version_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/FileWrapper"},"type":"array"}},"text/plain":{"schema":{"items":{"$ref":"#/components/schemas/FileWrapper"},"type":"array"}}},"description":"The tool test JSON response."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Error"}},"text/plain":{"schema":{"$ref":"#/components/schemas/Error"}}},"description":"The tool can not be output in the specified type."}},"security":[{"BEARER":[]}],"summary":"Get a list of test JSONs","tags":["GA4GHV20"]}},"/api/ga4gh/v2/metadata":{"get":{"description":"Return some metadata that is useful for describing this registry","operationId":"metadataGet","responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetadataV20beta"}},"text/plain":{"schema":{"$ref":"#/components/schemas/MetadataV20beta"}}},"description":"A Metadata object describing this service."}},"summary":"Return some metadata that is useful for describing this registry","tags":["GA4GHV20BETA"]}},"/api/ga4gh/v1/metadata":{"get":{"operationId":"metadataGet_1","responses":{"default":{"content":{"application/json":{},"text/plain":{}},"description":"default response"}},"tags":["GA4GHV1"]}},"/api/ga4gh/v2/toolClasses":{"get":{"description":"This endpoint returns all tool-classes available ","operationId":"toolClassesGet_1","responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ToolClassV20beta"},"type":"array"}},"text/plain":{"schema":{"items":{"$ref":"#/components/schemas/ToolClassV20beta"},"type":"array"}}},"description":"A list of potential tool classes."}},"summary":"List all tool types","tags":["GA4GHV20BETA"]}},"/api/ga4gh/v1/tool-classes":{"get":{"operationId":"toolClassesGet_2","responses":{"default":{"content":{"application/json":{},"text/plain":{}},"description":"default response"}},"tags":["GA4GHV1"]}},"/api/ga4gh/v2/tools":{"get":{"description":"This endpoint returns all tools available or a filtered subset using metadata query parameters. ","operationId":"toolsGet_1","parameters":[{"in":"query","name":"id","schema":{"type":"string"}},{"in":"query","name":"alias","schema":{"type":"string"}},{"in":"query","name":"registry","schema":{"type":"string"}},{"in":"query","name":"organization","schema":{"type":"string"}},{"in":"query","name":"name","schema":{"type":"string"}},{"in":"query","name":"toolname","schema":{"type":"string"}},{"in":"query","name":"description","schema":{"type":"string"}},{"in":"query","name":"author","schema":{"type":"string"}},{"in":"query","name":"checker","schema":{"type":"boolean"}},{"in":"query","name":"offset","schema":{"type":"string"}},{"in":"query","name":"limit","schema":{"default":1000,"format":"int32","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ToolV20beta"},"type":"array"}},"text/plain":{"schema":{"items":{"$ref":"#/components/schemas/ToolV20beta"},"type":"array"}}},"description":"An array of Tools that match the filter."}},"summary":"List all tools","tags":["GA4GHV20BETA"]}},"/api/ga4gh/v2/tools/{id}":{"get":{"description":"This endpoint returns one specific tool (which has ToolVersions nested inside it)","operationId":"toolsIdGet_1","parameters":[{"in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ToolV20beta"}},"text/plain":{"schema":{"$ref":"#/components/schemas/ToolV20beta"}}},"description":"A tool."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorV20beta"}},"text/plain":{"schema":{"$ref":"#/components/schemas/ErrorV20beta"}}},"description":"The tool can not be found."}},"summary":"List one specific tool, acts as an anchor for self references","tags":["GA4GHV20BETA"]}},"/api/ga4gh/v2/tools/{id}/versions":{"get":{"description":"Returns all versions of the specified tool","operationId":"toolsIdVersionsGet_1","parameters":[{"in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ToolVersionV20beta"},"type":"array"}},"text/plain":{"schema":{"items":{"$ref":"#/components/schemas/ToolVersionV20beta"},"type":"array"}}},"description":"An array of tool versions"}},"summary":"List versions of a tool","tags":["GA4GHV20BETA"]}},"/api/ga4gh/v2/tools/{id}/versions/{version_id}/containerfile":{"get":{"description":"Returns the container specifications(s) for the specified image. For example, a CWL CommandlineTool can be associated with one specification for a container, a CWL Workflow can be associated with multiple specifications for containers","operationId":"toolsIdVersionsVersionIdContainerfileGet_1","parameters":[{"in":"path","name":"id","required":true,"schema":{"type":"string"}},{"in":"path","name":"version_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/FileWrapperV20beta"},"type":"array"}},"text/plain":{"schema":{"items":{"$ref":"#/components/schemas/FileWrapperV20beta"},"type":"array"}}},"description":"The tool payload."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorV20beta"}},"text/plain":{"schema":{"$ref":"#/components/schemas/ErrorV20beta"}}},"description":"There are no container specifications for this tool"}},"summary":"Get the container specification(s) for the specified image.","tags":["GA4GHV20BETA"]}},"/api/ga4gh/v2/tools/{id}/versions/{version_id}":{"get":{"description":"This endpoint returns one specific tool version","operationId":"toolsIdVersionsVersionIdGet_1","parameters":[{"in":"path","name":"id","required":true,"schema":{"type":"string"}},{"in":"path","name":"version_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ToolVersionV20beta"}},"text/plain":{"schema":{"$ref":"#/components/schemas/ToolVersionV20beta"}}},"description":"A tool version."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorV20beta"}},"text/plain":{"schema":{"$ref":"#/components/schemas/ErrorV20beta"}}},"description":"The tool can not be found."}},"summary":"List one specific tool version, acts as an anchor for self references","tags":["GA4GHV20BETA"]}},"/api/ga4gh/v2/tools/{id}/versions/{version_id}/{type}/descriptor":{"get":{"description":"Returns the descriptor for the specified tool (examples include CWL, WDL, or Nextflow documents).","operationId":"toolsIdVersionsVersionIdTypeDescriptorGet_1","parameters":[{"in":"path","name":"type","required":true,"schema":{"type":"string"}},{"in":"path","name":"id","required":true,"schema":{"type":"string"}},{"in":"path","name":"version_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/FileWrapperV20beta"}},"text/plain":{"schema":{"$ref":"#/components/schemas/FileWrapperV20beta"}}},"description":"The tool descriptor."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorV20beta"}},"text/plain":{"schema":{"$ref":"#/components/schemas/ErrorV20beta"}}},"description":"The tool descriptor can not be found."}},"summary":"Get the tool descriptor for the specified tool","tags":["GA4GHV20BETA"]}},"/api/ga4gh/v2/tools/{id}/versions/{version_id}/{type}/descriptor/{relative_path}":{"get":{"description":"Descriptors can often include imports that refer to additional descriptors. This returns additional descriptors for the specified tool in the same or other directories that can be reached as a relative path. This endpoint can be useful for workflow engine implementations like cwltool to programmatically download all the descriptors for a tool and run it. This can optionally include other files described with FileWrappers such as test parameters and containerfiles. ","operationId":"toolsIdVersionsVersionIdTypeDescriptorRelativePathGet_1","parameters":[{"in":"path","name":"type","required":true,"schema":{"type":"string"}},{"in":"path","name":"id","required":true,"schema":{"type":"string"}},{"in":"path","name":"version_id","required":true,"schema":{"type":"string"}},{"in":"path","name":"relative_path","required":true,"schema":{"pattern":".+","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/FileWrapperV20beta"}},"text/plain":{"schema":{"$ref":"#/components/schemas/FileWrapperV20beta"}}},"description":"The tool descriptor."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorV20beta"}},"text/plain":{"schema":{"$ref":"#/components/schemas/ErrorV20beta"}}},"description":"The tool can not be output in the specified type."}},"summary":"Get additional tool descriptor files relative to the main file","tags":["GA4GHV20BETA"]}},"/api/ga4gh/v2/tools/{id}/versions/{version_id}/{type}/files":{"get":{"description":"Get a list of objects that contain the relative path and file type. The descriptors are intended for use with the /tools/{id}/versions/{version_id}/{type}/descriptor/{relative_path : .+} endpoint.","operationId":"toolsIdVersionsVersionIdTypeFilesGet_1","parameters":[{"in":"path","name":"type","required":true,"schema":{"type":"string"}},{"in":"path","name":"id","required":true,"schema":{"type":"string"}},{"in":"path","name":"version_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ToolFileV20beta"},"type":"array"}},"text/plain":{"schema":{"items":{"$ref":"#/components/schemas/ToolFileV20beta"},"type":"array"}}},"description":"The array of File JSON responses."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorV20beta"}},"text/plain":{"schema":{"$ref":"#/components/schemas/ErrorV20beta"}}},"description":"The tool can not be output in the specified type."}},"summary":"Get a list of objects that contain the relative path and file type","tags":["GA4GHV20BETA"]}},"/api/ga4gh/v2/tools/{id}/versions/{version_id}/{type}/tests":{"get":{"description":"Get a list of test JSONs (these allow you to execute the tool successfully) suitable for use with this descriptor type.","operationId":"toolsIdVersionsVersionIdTypeTestsGet_1","parameters":[{"in":"path","name":"type","required":true,"schema":{"type":"string"}},{"in":"path","name":"id","required":true,"schema":{"type":"string"}},{"in":"path","name":"version_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/FileWrapperV20beta"},"type":"array"}},"text/plain":{"schema":{"items":{"$ref":"#/components/schemas/FileWrapperV20beta"},"type":"array"}}},"description":"The tool test JSON response."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorV20beta"}},"text/plain":{"schema":{"$ref":"#/components/schemas/ErrorV20beta"}}},"description":"The tool 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that match the filter."}},"summary":"List all tools","tags":["GA4GHV1"]}},"/api/ga4gh/v1/tools/{id}":{"get":{"description":"This endpoint returns one specific tool (which has ToolVersions nested inside it)","operationId":"toolsIdGetV1","parameters":[{"in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ToolV1"}}},"description":"A tool."}},"summary":"List one specific tool, acts as an anchor for self references","tags":["GA4GHV1"]}},"/api/ga4gh/v1/tools/{id}/versions":{"get":{"description":"Returns all versions of the specified tool","operationId":"toolsIdVersionGetV1","parameters":[{"in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ToolVersionV1"},"type":"array"}}},"description":"An array of tool versions"}},"summary":"List versions of a tool","tags":["GA4GHV1"]}},"/api/ga4gh/v1/tools/{id}/versions/{version_id}/dockerfile":{"get":{"description":"Returns the dockerfile for the specified image.","operationId":"dockerfileGetV1","parameters":[{"in":"path","name":"id","required":true,"schema":{"type":"string"}},{"in":"path","name":"version_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ToolDockerfile"}}},"description":"The tool payload."}},"summary":"Get the dockerfile for the specified image.","tags":["GA4GHV1"]}},"/api/ga4gh/v1/tools/{id}/versions/{version_id}":{"get":{"description":"This endpoint returns one specific tool version","operationId":"versionIdGetV1","parameters":[{"in":"path","name":"id","required":true,"schema":{"type":"string"}},{"in":"path","name":"version_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ToolVersionV1"}}},"description":"A tool version."}},"summary":"List one specific tool version, acts as an anchor for self references","tags":["GA4GHV1"]}},"/api/ga4gh/v1/tools/{id}/versions/{version_id}/{type}/descriptor":{"get":{"description":"Returns the CWL or WDL descriptor for the specified tool.","operationId":"descriptorGetV1","parameters":[{"in":"path","name":"type","required":true,"schema":{"type":"string"}},{"in":"path","name":"id","required":true,"schema":{"type":"string"}},{"in":"path","name":"version_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ToolDescriptor"}}},"description":"The tool descriptor."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ToolDescriptor"}}},"description":"The tool can not be output in the specified type."}},"summary":"Get the tool descriptor (CWL/WDL) for the specified tool.","tags":["GA4GHV1"]}},"/api/ga4gh/v1/tools/{id}/versions/{version_id}/{type}/descriptor/{relative_path}":{"get":{"description":"Returns additional CWL or WDL descriptors for the specified tool in the same or subdirectories","operationId":"relativeDescriptorGetV1","parameters":[{"in":"path","name":"type","required":true,"schema":{"type":"string"}},{"in":"path","name":"id","required":true,"schema":{"type":"string"}},{"in":"path","name":"version_id","required":true,"schema":{"type":"string"}},{"in":"path","name":"relative_path","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ToolDescriptor"}}},"description":"The tool descriptor."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ToolDescriptor"}}},"description":"The tool can not be output in the specified type."}},"summary":"Get additional tool descriptor files (CWL/WDL) relative to the main file","tags":["GA4GHV1"]}},"/api/ga4gh/v1/tools/{id}/versions/{version_id}/{type}/tests":{"get":{"operationId":"testsGetV1","parameters":[{"in":"path","name":"type","required":true,"schema":{"type":"string"}},{"in":"path","name":"id","required":true,"schema":{"type":"string"}},{"in":"path","name":"version_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ToolTestsV1"},"type":"array"}}},"description":"The tool test JSON response."},"404":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ToolTestsV1"},"type":"array"}}},"description":"The tool can not be output in the specified type."}},"summary":"Get an array of test JSONs suitable for use with this descriptor type.","tags":["GA4GHV1"]}}},"servers":[{"description":"Current server when hosted on AWS","url":"/api"},{"description":"When working locally","url":"/"},{"description":"Production server","url":"https://dockstore.org/api"},{"description":"Staging server","url":"https://staging.dockstore.org/api"},{"description":"Nightly build server","url":"https://dev.dockstore.net/api"}],"tags":[{"description":"Create, update list aliases for accessing entries","name":"aliases"},{"description":"Operations on Dockstore categories","name":"categories"},{"description":"Operations on Dockstore organizations","name":"organizations"},{"description":"Needed for SmartAPI compatibility apparantly, might be cargo cult behaviour","name":"NIHdatacommons"},{"description":"Interact with entries in Dockstore regardless of whether they are containers or workflows","name":"entries"},{"description":"List and register entries in the dockstore (pairs of images + metadata (CWL and Dockerfile))","name":"containers"},{"description":"List and modify tags for containers","name":"containertags"},{"description":"A curated subset of resources proposed as a common standard for tool repositories. Implements TRS [1.0.0](https://github.com/ga4gh/tool-registry-service-schemas/releases/tag/1.0.0) and is considered final (not subject to change)","name":"GA4GHV1"},{"description":"A curated subset of resources proposed as a common standard for tool repositories. Implements TRS [2.0.0-beta.2](https://github.com/ga4gh/tool-registry-service-schemas/releases/tag/2.0.0-beta.2) . Integrators are welcome to use these endpoints but they are subject to change based on community input.","name":"GA4GHV20BETA"},{"description":"A curated subset of resources proposed as a common standard for tool repositories. Implements TRS [2.0.1](https://github.com/ga4gh/tool-registry-service-schemas/releases/tag/2.0.1).","name":"GA4GHV20"},{"description":"Optional experimental extensions of the GA4GH API","name":"extendedGA4GH"},{"description":"List, modify, refresh, and delete tokens for external services","name":"tokens"},{"description":"List and register workflows in the dockstore (CWL, Nextflow, WDL)","name":"workflows"},{"description":"Interactions with the Dockstore-support's ToolTester application","name":"toolTester"},{"description":"List and modify notifications for users of Dockstore","name":"curation"},{"description":"Created and modify hosted entries in the dockstore","name":"hosted"},{"description":"List, modify, and manage end users of the dockstore","name":"users"},{"description":"Information about Dockstore like RSS, sitemap, lists of dependencies, etc.","name":"metadata"},{"description":"Query lambda events triggered by GitHub Apps","name":"lambdaEvents"}]},{"components":{"securitySchemes":{"tokenAuth":{"description":"FlyMine authentication token obtained from /user/token endpoint","in":"query","name":"token","type":"apiKey"}}},"info":{"contact":{"email":"support@flymine.org","name":"FlyMine Support","url":"https://www.flymine.org/"},"description":"FlyMine is an integrated database for Drosophila genomics providing powerful search and\ndata warehousing capabilities for accessing integrated genomic, proteomic, and genetic data\nfor Drosophila and related organisms. This API provides RESTful web services powered by\nInterMine, an open-source biological data warehouse system.\n\n## Authentication\nSome endpoints require authentication via API token. Obtain a token using the /user/token endpoint\nwith username and password, then include it as a query parameter in subsequent requests.\n\n## Formats\nMost endpoints support multiple output formats including JSON, XML, TSV, and CSV.\n","license":{"name":"LGPL-2.1","url":"https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html"},"title":"FlyMine Web Services API","version":"31.0.0"},"openapi":"3.0.3","paths":{"/query/results":{"get":{"description":"Execute a PathQuery to retrieve data from FlyMine. Queries can be submitted\nin XML or JSON format and results can be returned in various formats.\n","operationId":"queryResultsGet","parameters":[{"description":"A definition of the query to execute in Path-Query XML or JSON format","examples":{"eveGeneQuery":{"summary":"Query for even-skipped gene","value":"<query name=\"eve gene query\" model=\"genomic\" view=\"Gene.primaryIdentifier Gene.symbol Gene.name Gene.length Gene.chromosome.primaryIdentifier Gene.chromosomeLocation.start Gene.chromosomeLocation.end\">\n  <constraint path=\"Gene.symbol\" op=\"=\" value=\"eve\"/>\n  <constraint path=\"Gene.organism.name\" op=\"=\" value=\"Drosophila melanogaster\"/>\n</query>\n"},"notchPathwayGenes":{"summary":"Genes in Notch signaling pathway","value":"{\n  \"from\": \"Gene\",\n  \"select\": [\"primaryIdentifier\", \"symbol\", \"name\", \"pathways.name\"],\n  \"where\": [\n    {\"path\": \"organism.name\", \"op\": \"=\", \"value\": \"Drosophila melanogaster\"},\n    {\"path\": \"pathways.name\", \"op\": \"CONTAINS\", \"value\": \"Notch\"}\n  ]\n}\n"},"shortGenesXChromosome":{"summary":"Short genes on X chromosome (from original service.json)","value":"<query model=\"genomic\" view=\"Gene.name Gene.symbol Gene.id Gene.length Gene.chromosome.primaryIdentifier\" constraintLogic=\"(nil and B)\" sortOrder=\"\">\n <constraint path=\"Gene.chromosome.primaryIdentifier\" value=\"X\" op=\"=\" code=\"A\"/>\n <constraint path=\"Gene.length\" value=\"100\" op=\"&lt;=\" code=\"B\"/>\n </query>\n"},"transcriptionFactorGenes":{"summary":"Genes with transcription factor activity","value":"<query name=\"transcription factor genes\" model=\"genomic\" view=\"Gene.primaryIdentifier Gene.symbol Gene.name Gene.goAnnotation.ontologyTerm.name\">\n  <constraint path=\"Gene.goAnnotation.ontologyTerm.name\" op=\"CONTAINS\" value=\"transcription factor\"/>\n  <constraint path=\"Gene.organism.name\" op=\"=\" value=\"Drosophila melanogaster\"/>\n</query>\n"},"winglessProteinDomains":{"summary":"Protein domains of wingless gene","value":"<query name=\"wingless protein domains\" model=\"genomic\" view=\"Gene.symbol Gene.proteins.primaryIdentifier Gene.proteins.proteinDomains.name Gene.proteins.proteinDomains.description\">\n  <constraint path=\"Gene.symbol\" op=\"=\" value=\"wingless\"/>\n  <constraint path=\"Gene.organism.name\" op=\"=\" value=\"Drosophila melanogaster\"/>\n</query>\n"}},"in":"query","name":"query","required":true,"schema":{"type":"string"}},{"description":"Output format","in":"query","name":"format","schema":{"default":"tab","enum":["tab","csv","count","json","jsonobjects","jsoncount","xml","html","rdf+xml"],"type":"string"}},{"description":"The index of the first result to return","in":"query","name":"start","schema":{"default":0,"type":"integer"}},{"description":"The maximum size of the result set","example":50,"in":"query","name":"size","schema":{"default":10,"type":"integer"}},{"description":"Include column headers (only for flat-file formats)","in":"query","name":"columnheaders","schema":{"default":"none","enum":["none","path","friendly"],"type":"string"}},{"description":"Authentication token for private data access","example":"","in":"query","name":"token","schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"examples":{"eveGeneResponse":{"summary":"Response for eve gene query","value":{"executionTime":142,"results":[["FBgn0000606","eve","even-skipped","7784","2R","5865334","5873117"]],"statusCode":200,"wasSuccessful":true}},"shortGenesResponse":{"summary":"Response for short genes query","value":{"executionTime":234,"results":[["FBgn0000008","a","893","X"],["FBgn0000606","eve","7784","2R"],["FBgn0001077","ftz","1062","3R"],["FBgn0004053","zen","583","3R"],["FBgn0001180","hb","746","3R"]],"statusCode":200,"wasSuccessful":true}},"transcriptionFactorResponse":{"summary":"Response for transcription factor genes","value":{"executionTime":567,"results":[["FBgn0000606","eve","even-skipped","DNA-binding transcription factor activity"],["FBgn0001077","ftz","fushi tarazu","DNA-binding transcription factor activity"],["FBgn0004053","zen","zerknüllt","DNA-binding transcription factor activity"],["FBgn0001180","hb","hunchback","DNA-binding transcription factor activity"]],"statusCode":200,"wasSuccessful":true}}},"schema":{"properties":{"error":{"type":"string"},"executionTime":{"type":"integer"},"results":{"items":{"items":{"type":"string"},"type":"array"},"type":"array"},"statusCode":{"type":"integer"},"wasSuccessful":{"type":"boolean"}},"type":"object"}}},"description":"Query results"}},"summary":"Execute a query","tags":["query"]},"post":{"description":"Execute a PathQuery to retrieve data from FlyMine using POST method.\n","operationId":"queryResultsPost","requestBody":{"content":{"application/x-www-form-urlencoded":{"examples":{"chromosomeGenesPost":{"summary":"Genes on specific chromosome region","value":{"columnheaders":"friendly","format":"csv","query":"<query model=\"genomic\" view=\"Gene.primaryIdentifier Gene.symbol Gene.chromosomeLocation.start Gene.chromosomeLocation.end\">\n  <constraint path=\"Gene.chromosome.primaryIdentifier\" op=\"=\" value=\"2L\"/>\n  <constraint path=\"Gene.chromosomeLocation.start\" op=\">\" value=\"14615455\"/>\n  <constraint path=\"Gene.chromosomeLocation.end\" op=\"<\" value=\"14619002\"/>\n  <constraint path=\"Gene.organism.name\" op=\"=\" value=\"Drosophila melanogaster\"/>\n</query>\n","size":50}},"eveGenePost":{"summary":"POST query for eve gene with JSON format","value":{"format":"jsonobjects","query":"{\n  \"from\": \"Gene\",\n  \"select\": [\"primaryIdentifier\", \"symbol\", \"name\", \"proteins.primaryIdentifier\", \"proteins.proteinDomains.name\"],\n  \"where\": [\n    {\"path\": \"organism.name\", \"op\": \"=\", \"value\": \"Drosophila melanogaster\"},\n    {\"path\": \"symbol\", \"op\": \"=\", \"value\": \"eve\"}\n  ]\n}\n","size":10}},"transcriptionFactors":{"summary":"Query for transcription factors","value":{"format":"json","query":"<query model=\"genomic\" view=\"Gene.primaryIdentifier Gene.symbol Gene.goAnnotation.ontologyTerm.name\">\n  <constraint path=\"Gene.goAnnotation.ontologyTerm.name\" op=\"CONTAINS\" value=\"transcription factor\"/>\n  <constraint path=\"Gene.organism.name\" op=\"=\" value=\"Drosophila melanogaster\"/>\n</query>\n","size":20}}},"schema":{"properties":{"columnheaders":{"default":"none","enum":["none","path","friendly"],"type":"string"},"format":{"default":"tab","enum":["tab","csv","count","json","jsonobjects","jsoncount","xml","html","rdf+xml"],"type":"string"},"query":{"type":"string"},"size":{"default":10,"type":"integer"},"start":{"default":0,"type":"integer"},"token":{"type":"string"}},"required":["query"],"type":"object"}}}},"responses":{"200":{"description":"Query results"}},"summary":"Execute a query","tags":["query"]}},"/query/results/gff3":{"get":{"description":"Export sequence features from a query in GFF3 format. Suitable for queries\nreturning SequenceFeature objects.\n","operationId":"queryGFF3Get","parameters":[{"description":"PathQuery in XML or JSON format selecting sequence features","example":"<query model=\"genomic\" view=\"Gene.id Gene.exons.id\">\n  <constraint path=\"Gene.chromosome.primaryIdentifier\" op=\"=\" value=\"2L\"/>\n  <constraint path=\"Gene.chromosomeLocation.start\" op=\">\" value=\"10000000\"/>\n  <constraint path=\"Gene.chromosomeLocation.end\" op=\"<\" value=\"11000000\"/>\n</query>\n","in":"query","name":"query","required":true,"schema":{"type":"string"}},{"description":"Extra columns to include in the ninth column","example":["Gene.symbol","Gene.length"],"in":"query","name":"view","schema":{"items":{"type":"string"},"type":"array"}}],"responses":{"200":{"content":{"text/plain":{"example":"##gff-version 3\n2L\tFlyMine\tgene\t10234567\t10245678\t.\t+\t.\tID=FBgn0031208;Name=CG11023;symbol=CG11023;length=11112\n2L\tFlyMine\texon\t10234567\t10234789\t.\t+\t.\tParent=FBgn0031208\n2L\tFlyMine\texon\t10235001\t10235456\t.\t+\t.\tParent=FBgn0031208\n","schema":{"type":"string"}}},"description":"GFF3 formatted results"}},"summary":"Export query results as GFF3","tags":["query","export"]}},"/query/results/fasta":{"get":{"description":"Export biological sequences from a query in FASTA format.\n","operationId":"queryFASTAGet","parameters":[{"description":"PathQuery selecting sequence objects","example":"{\n  \"from\": \"Gene\",\n  \"select\": [\"id\"],\n  \"where\": [\n    {\"path\": \"symbol\", \"op\": \"ONE OF\", \"values\": [\"eve\", \"ftz\", \"zen\"]}\n  ]\n}\n","in":"query","name":"query","required":true,"schema":{"type":"string"}},{"example":["Gene.length","Gene.chromosome.primaryIdentifier"],"in":"query","name":"view","schema":{"items":{"type":"string"},"type":"array"}}],"responses":{"200":{"content":{"text/plain":{"example":">FBgn0000606 type=gene; loc=2R:9979319..9984780; name=eve; length=5462;\nATGGAGATCAAACAAGCGAAGAGTGGAGAGAAGTGGAGAAGCAGCCAAGCAAG\nCAACAGCACAAGGGCTCGTCGAGCAAGTCCAGCGAGGAGGATCTGCTGAGCGG\n>FBgn0001077 type=gene; loc=3R:2648685..2653456; name=ftz; length=4772;\nATGGCAATGGAAGTGTCCAGCAGTCCCGTGATGGTTCATCACGTCGGTCGCTC\n","schema":{"type":"string"}}},"description":"FASTA formatted sequences"}},"summary":"Export sequences as FASTA","tags":["query","export"]}},"/query/results/bed":{"get":{"description":"Export genomic locations from a query in UCSC BED format.\n","operationId":"queryBEDGet","parameters":[{"description":"PathQuery selecting sequence features","example":"<query model=\"genomic\" view=\"Gene.id\">\n  <constraint path=\"Gene.goAnnotation.ontologyTerm.name\" op=\"=\" value=\"wing disc development\"/>\n  <constraint path=\"Gene.organism.name\" op=\"=\" value=\"Drosophila melanogaster\"/>\n</query>\n","in":"query","name":"query","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"text/plain":{"example":"# UCSC BED format\n# Source: FlyMine\ntrack name=FlyMine_Wing_Development description=\"Wing Development Genes\"\nchr2L\t7529\t9484\tCG11023\t1000\t+\nchr2R\t9979319\t9984780\teve\t1000\t-\nchrX\t2648220\t2653456\trunt\t1000\t+\n","schema":{"type":"string"}}},"description":"BED formatted results"}},"summary":"Export genomic locations as BED","tags":["query","export"]}},"/template/results":{"get":{"description":"Execute a pre-configured template query with parameters.\n","operationId":"templateResults","parameters":[{"description":"The name of the template to run","examples":{"flyAtlas":{"summary":"Template for FlyAtlas expression","value":"Gene_AdultFlyAtlas"},"genePathways":{"summary":"Template for gene pathways","value":"Gene_Pathways"},"proteinDomains":{"summary":"Template for gene protein domains","value":"Gene_Protein"}},"in":"query","name":"name","required":true,"schema":{"type":"string"}},{"description":"Constraint path for parameter 1","examples":{"geneConstraint":{"summary":"Gene constraint","value":"Gene"},"geneSymbol":{"summary":"Gene symbol constraint","value":"Gene.symbol"}},"in":"query","name":"constraint1","schema":{"type":"string"}},{"description":"Constraint operator for parameter 1","examples":{"equals":{"summary":"Equals operator","value":"="},"lookup":{"summary":"Lookup operator","value":"LOOKUP"}},"in":"query","name":"op1","schema":{"type":"string"}},{"description":"Constraint value for parameter 1","examples":{"eveGene":{"summary":"even-skipped gene","value":"eve"},"ftzGene":{"summary":"fushi tarazu gene","value":"ftz"},"hbGene":{"summary":"hunchback gene","value":"hb"},"notchGene":{"summary":"Notch receptor gene","value":"Notch"},"winglessGene":{"summary":"wingless signaling gene","value":"wingless"},"zenGene":{"summary":"zerknullt gene","value":"zen"}},"in":"query","name":"value1","schema":{"type":"string"}},{"description":"Extra constraint value for parameter 1","example":"D. melanogaster","in":"query","name":"extra1","schema":{"type":"string"}},{"example":"json","in":"query","name":"format","schema":{"default":"tab","enum":["tab","csv","count","json","jsonobjects","jsoncount","xml","html"],"type":"string"}},{"example":25,"in":"query","name":"size","schema":{"default":10,"type":"integer"}}],"responses":{"200":{"content":{"application/json":{"examples":{"eveProteinDomainsResponse":{"summary":"Response for eve protein domains","value":{"executionTime":87,"results":[["FBgn0000606","eve","even-skipped","Homeobox","DNA binding"],["FBgn0000606","eve","even-skipped","Helix-turn-helix","DNA binding"]],"statusCode":200,"wasSuccessful":true}},"genePathwaysResponse":{"summary":"Response for gene pathways template","value":{"executionTime":145,"results":[["FBgn0000606","eve","Segmentation","P06602"],["FBgn0001077","ftz","Segmentation","P07713"],["FBgn0004053","zen","Dorsal/ventral axis formation","P09102"]],"statusCode":200,"wasSuccessful":true}}},"schema":{"type":"object"}}},"description":"Template query results"}},"summary":"Execute a template query","tags":["template"]}},"/templates":{"get":{"description":"Retrieve a list of all available query templates","operationId":"listTemplates","parameters":[{"description":"Output format","example":"json","in":"query","name":"format","schema":{"default":"xml","enum":["xml","json"],"type":"string"}},{"description":"Whether to include invalid templates","in":"query","name":"includeBroken","schema":{"default":false,"type":"boolean"}}],"responses":{"200":{"content":{"application/json":{"example":{"templates":{"Gene_Pathways":{"comment":"Shows any pathways that the gene is part of","description":"Show all pathways for a particular gene.","select":["Gene.symbol","Gene.pathways.name","Gene.pathways.identifier"],"tags":["im:aspect:Pathways","im:public"],"title":"Gene --> Pathways","where":[{"editable":true,"op":"LOOKUP","path":"Gene","value":"eve"}]},"Organism_Protein":{"description":"Show all proteins for a particular organism","select":["Protein.primaryIdentifier","Protein.name"],"title":"All proteins for organism"}}},"schema":{"properties":{"templates":{"type":"object"}},"type":"object"}}},"description":"List of templates"}},"summary":"List available templates","tags":["template"]}},"/lists":{"delete":{"description":"Delete a list belonging to the authenticated user","operationId":"deleteList","parameters":[{"description":"Name of the list to delete","example":"Old_Gene_List","in":"query","name":"name","required":true,"schema":{"type":"string"}},{"example":"","in":"query","name":"token","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"List deleted successfully"}},"summary":"Delete a list","tags":["list"]},"get":{"description":"Retrieve lists accessible to the user","operationId":"getLists","parameters":[{"description":"Optional filter by name","examples":{"developmentalGenes":{"summary":"Developmental genes list","value":"Developmental_Genes"},"favoriteGenes":{"summary":"User's favorite genes list","value":"My_Favorite_Genes"},"gapGenes":{"summary":"Gap genes list","value":"Gap_Genes"},"hoxGenes":{"summary":"Homeotic genes list","value":"Hox_genes"},"transcriptionFactors":{"summary":"Transcription factors list","value":"TF_List"}},"in":"query","name":"name","schema":{"type":"string"}},{"in":"query","name":"format","schema":{"default":"json","enum":["json","html","text","csv","tab"],"type":"string"}},{"description":"Authentication token","in":"query","name":"token","schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"examples":{"userLists":{"summary":"User's gene lists","value":{"lists":[{"dateCreated":"2023-01-15T10:30:00Z","description":"All FlyBase gene IDs","name":"PL FlyBase_Annotation_IDs","size":35807,"tags":["im:public","im:aspect:Genes"],"type":"Gene"},{"dateCreated":"2023-03-20T14:15:00Z","description":"Drosophila gap genes (eve, ftz, hb, Kr, etc.)","name":"Gap_Genes","size":9,"tags":["im:private","im:aspect:Development"],"type":"Gene"},{"dateCreated":"2023-03-20T14:15:00Z","description":"Drosophila Hox complex genes","name":"Hox_genes","size":8,"tags":["im:private","im:aspect:Development"],"type":"Gene"},{"dateCreated":"2023-05-10T09:45:00Z","description":"Genes involved in Notch signaling pathway","name":"Notch_Pathway","size":156,"tags":["im:private","im:aspect:Signaling"],"type":"Gene"}]}}},"schema":{"properties":{"lists":{"items":{"type":"object"},"type":"array"}},"type":"object"}}},"description":"User's lists"}},"summary":"Get lists","tags":["list"]},"post":{"description":"Create a new list by uploading identifiers","operationId":"createList","requestBody":{"content":{"application/x-www-form-urlencoded":{"examples":{"gapGenesList":{"summary":"Create gap genes list","value":{"description":"Drosophila gap genes involved in segmentation","extraValue":"D. melanogaster","name":"Gap_Genes","token":"","type":"Gene"}},"hoxGenesList":{"summary":"Create Hox genes list","value":{"description":"Homeotic genes controlling body segment identity","extraValue":"D. melanogaster","name":"Hox_Genes","replaceExisting":false,"token":"","type":"Gene"}},"notchPathwayList":{"summary":"Create Notch pathway genes list","value":{"description":"Genes involved in Notch signaling pathway","extraValue":"D. melanogaster","name":"Notch_Signaling_Genes","token":"","type":"Gene"}}},"schema":{"properties":{"description":{"type":"string"},"extraValue":{"type":"string"},"name":{"description":"Name for the new list","type":"string"},"replaceExisting":{"default":false,"type":"boolean"},"token":{"type":"string"},"type":{"description":"Type of objects in the list","type":"string"}},"required":["name","type"],"type":"object"}},"text/plain":{"examples":{"gapGenes":{"summary":"Gap genes as plain text","value":"eve\nftz\nzen\nhb\nKr\nkni\ngt\ntll\nhkb\n"},"hoxGenes":{"summary":"Hox genes with FlyBase IDs","value":"FBgn0000577,Dfd\nFBgn0003963,Scr\nFBgn0001180,pb\nFBgn0004053,zen\nFBgn0000606,eve\n"},"notchPathwayGenes":{"summary":"Notch signaling pathway genes","value":"Notch\nDelta\nSerrate\nfringe\nbig brain\nneuralized\n"}},"schema":{"description":"Identifiers separated by commas, tabs, or newlines","type":"string"}}}},"responses":{"200":{"content":{"application/json":{"example":{"listName":"Gap_Genes","size":9,"type":"Gene","unmatchedIdentifiers":[],"wasSuccessful":true}}},"description":"List created successfully"}},"summary":"Create a new list","tags":["list"]}},"/search":{"get":{"description":"Perform a keyword search across FlyMine data with faceting support\n","operationId":"search","parameters":[{"description":"Search query string","examples":{"developmentalGenes":{"summary":"Search for developmental genes","value":"even skipped fushi tarazu"},"dnaBinding":{"summary":"Search for DNA binding proteins","value":"DNA binding protein"},"eveGene":{"summary":"Search for eve gene","value":"eve"},"notchSignaling":{"summary":"Search for Notch signaling","value":"notch signaling"},"transcriptionFactors":{"summary":"Search for transcription factors","value":"transcription factor"},"winglessPathway":{"summary":"Search for wingless/Wnt pathway","value":"wingless wnt"}},"in":"query","name":"q","schema":{"type":"string"}},{"description":"Maximum number of results","example":20,"in":"query","name":"size","schema":{"default":10,"type":"integer"}},{"description":"Index of first result","in":"query","name":"start","schema":{"default":0,"type":"integer"}},{"description":"Filter by category facet","example":"Gene","in":"query","name":"facet_Category","schema":{"type":"string"}},{"description":"Search within a specific list","example":"PL_FlyBase_IDs","in":"query","name":"list","schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"examples":{"developmentalGenesSearch":{"summary":"Search results for developmental genes","value":{"facets":{"Category":{"GOTerm":45,"Gene":5,"Publication":1234},"organism":{"D. melanogaster":1284}},"results":[{"fields":{"name":"even-skipped","primaryIdentifier":"FBgn0000606","symbol":"eve"},"id":606,"score":0.98,"type":"Gene"},{"fields":{"name":"fushi tarazu","primaryIdentifier":"FBgn0001077","symbol":"ftz"},"id":1077,"score":0.97,"type":"Gene"},{"fields":{"name":"zerknüllt","primaryIdentifier":"FBgn0004053","symbol":"zen"},"id":4053,"score":0.89,"type":"Gene"}]}},"eveGeneSearch":{"summary":"Search results for \"eve\" gene","value":{"facets":{"Category":{"Gene":1,"Protein":1,"Publication":245},"organism":{"D. melanogaster":247}},"results":[{"fields":{"chromosome":"2R","name":"even-skipped","organism":"D. melanogaster","primaryIdentifier":"FBgn0000606","symbol":"eve"},"id":123456,"score":1.0,"type":"Gene"}]}},"notchSignalingSearch":{"summary":"Search results for \"notch signaling\"","value":{"facets":{"Category":{"GOTerm":23,"Gene":156,"Pathway":12,"Publication":843},"organism":{"D. melanogaster":178,"D. simulans":12}},"results":[{"fields":{"name":"Notch","organism":"D. melanogaster","primaryIdentifier":"FBgn0004647","symbol":"Notch"},"id":1234567,"score":0.95,"type":"Gene"},{"fields":{"identifier":"P00045","name":"Notch signaling pathway"},"id":2345678,"score":0.89,"type":"Pathway"}]}}},"schema":{"properties":{"facets":{"type":"object"},"results":{"items":{"type":"object"},"type":"array"}},"type":"object"}}},"description":"Search results"}},"summary":"Keyword search","tags":["search"]}},"/regions/gff3":{"post":{"operationId":"regionsGFF3Post","requestBody":{"content":{"application/json":{"examples":{"eveGeneRegion":{"summary":"Genomic region around eve gene","value":{"extension":2000,"featureTypes":["Gene","MRNA","Exon","CDS"],"organism":"D. melanogaster","regions":["2R:5865000..5875000"]}},"originalServiceExample":{"summary":"Original genomic regions from service.json","value":{"extension":1000,"featureTypes":["Gene","Exon","Intron"],"organism":"D. melanogaster","regions":["2L:14615455..14619002","2R:5866646..5868384","3R:2578486..2580016"]}},"xChromosomeRegions":{"summary":"Multiple regions on X chromosome","value":{"featureTypes":["Gene","TransposableElement"],"isInterbase":false,"organism":"D. melanogaster","regions":["X:1000000..1100000","X:2000000..2100000","X:15000000..15100000"]}}},"schema":{"properties":{"extension":{"type":"number"},"featureTypes":{"description":"Types of features to find","items":{"type":"string"},"type":"array"},"isInterbase":{"type":"boolean"},"organism":{"description":"Organism name","type":"string"},"regions":{"description":"Genomic intervals","items":{"type":"string"},"type":"array"}},"required":["regions","featureTypes","organism"],"type":"object"}}},"required":true},"responses":{"200":{"content":{"text/plain":{"examples":{"eveRegionGFF3":{"summary":"GFF3 output for eve gene region","value":"##gff-version 3\n2R\tFlyMine\tgene\t5865334\t5873117\t.\t+\t.\tID=FBgn0000606;Name=eve;symbol=eve;biotype=protein_coding\n2R\tFlyMine\tmRNA\t5865334\t5873117\t.\t+\t.\tID=FBtr0070607;Parent=FBgn0000606;Name=eve-RA\n2R\tFlyMine\texon\t5865334\t5865475\t.\t+\t.\tID=FBgn0000606:1;Parent=FBtr0070607\n2R\tFlyMine\texon\t5866646\t5868384\t.\t+\t.\tID=FBgn0000606:2;Parent=FBtr0070607\n2R\tFlyMine\texon\t5872855\t5873117\t.\t+\t.\tID=FBgn0000606:3;Parent=FBtr0070607\n"},"originalRegionsGFF3":{"summary":"GFF3 output for original genomic regions","value":"##gff-version 3\n2L\tFlyMine\tgene\t14615552\t14618902\t.\t+\t.\tID=FBgn0000055;Name=Adh;symbol=Adh;biotype=protein_coding\n2L\tFlyMine\tmRNA\t14615552\t14618902\t.\t+\t.\tID=FBtr0070000;Parent=FBgn0000055;Name=Adh-RA\n2L\tFlyMine\texon\t14615552\t14615700\t.\t+\t.\tID=FBgn0000055:1;Parent=FBtr0070000\n2L\tFlyMine\texon\t14616300\t14618902\t.\t+\t.\tID=FBgn0000055:2;Parent=FBtr0070000\n"}}}},"description":"GFF3 formatted features"}},"summary":"Get features overlapping genomic regions as GFF3","tags":["genomic-regions","export"]}},"/regions/sequence":{"post":{"operationId":"regionsFASTAPost","requestBody":{"content":{"application/json":{"examples":{"eveGeneSequence":{"summary":"Sequences from eve gene region","value":{"featureTypes":["Gene","Exon","CDS"],"organism":"D. melanogaster","regions":["2R:5865334..5873117"]}},"multipleChromosomeSequences":{"summary":"Sequences from multiple chromosomes","value":{"featureTypes":["Gene"],"organism":"D. melanogaster","regions":["2L:14615455..14619002","3R:2578486..2580016","X:1000000..1002000"]}},"xChromosomeSequences":{"summary":"Sequences from X chromosome regions","value":{"featureTypes":["Gene","CDS"],"organism":"D. melanogaster","regions":["X:2000000..2010000","X:15000000..15005000"]}}},"schema":{"properties":{"featureTypes":{"items":{"type":"string"},"type":"array"},"organism":{"type":"string"},"regions":{"items":{"type":"string"},"type":"array"}},"required":["regions","featureTypes","organism"],"type":"object"}}},"required":true},"responses":{"200":{"content":{"text/plain":{"examples":{"eveGeneFASTA":{"summary":"FASTA sequence for eve gene","value":">FBgn0000606 2R:5865334-5873117 symbol=eve name=even-skipped length=7784\nATGGCCAACAACAACAACAACAACAACAACAACAACAACAACAACAACAAC\nCAACAACAACGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGC\nCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGC\n"},"xChromosomeFASTA":{"summary":"FASTA sequences from X chromosome","value":">FBgn0003319 X:2001234-2008765 symbol=white length=7532\nATGGATCGTAGCTACGTAGCTAGCTAGCTAGCATCGATCGATCGATCGATC\nGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCT\nAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGT\n>FBgn0264512 X:15001000-15003500 symbol=Notch length=2501\nATGCCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG\n"}}}},"description":"FASTA formatted sequences"}},"summary":"Get sequences from genomic regions as FASTA","tags":["genomic-regions","export"]}},"/regions/bed":{"post":{"operationId":"regionsBEDPost","requestBody":{"content":{"application/json":{"example":{"featureTypes":["Gene","TransposableElement"],"organism":"D. melanogaster","regions":["2L:10000000..11000000","2R:5000000..6000000"]},"schema":{"properties":{"featureTypes":{"items":{"type":"string"},"type":"array"},"organism":{"type":"string"},"regions":{"items":{"type":"string"},"type":"array"}},"required":["regions","featureTypes","organism"],"type":"object"}}},"required":true},"responses":{"200":{"content":{"text/plain":{"example":"track name=FlyMine_Regions description=\"Selected genomic 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subtract","type":"string"},"tags":{"items":{"type":"string"},"type":"array"},"token":{"type":"string"}},"required":["name","from","subtract"],"type":"object"}}}},"responses":{"200":{"description":"Subtraction list created successfully"}},"summary":"Subtract one list from another","tags":["list"]}},"/lists/diff":{"post":{"description":"Create a new list containing items that are in either list but not in both\n(symmetric difference).\n","operationId":"listsDiff","parameters":[{"in":"query","name":"token","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/x-www-form-urlencoded":{"example":{"description":"Genes unique to brain or muscle but not both","lists":["Brain_Genes","Muscle_Genes"],"name":"Unique_to_Each_Tissue"},"schema":{"properties":{"description":{"type":"string"},"format":{"default":"json","enum":["json","text"],"type":"string"},"lists":{"description":"Names of exactly two lists to compare","items":{"type":"string"},"maxItems":2,"minItems":2,"type":"array"},"name":{"description":"Name for the new difference list","type":"string"},"tags":{"items":{"type":"string"},"type":"array"},"token":{"type":"string"}},"required":["name","lists"],"type":"object"}}}},"responses":{"200":{"description":"Difference list created successfully"}},"summary":"Create symmetric difference of lists","tags":["list"]}},"/login":{"post":{"description":"Log in a user and obtain authentication token for subsequent requests.\nAlternative to the /user/token endpoint.\n","operationId":"login","requestBody":{"content":{"application/x-www-form-urlencoded":{"example":{"password":"securePassword123","user":"researcher@university.edu"},"schema":{"properties":{"password":{"description":"User password","format":"password","type":"string"},"user":{"description":"Username (email address)","format":"email","type":"string"}},"required":["user","password"],"type":"object"}}}},"responses":{"200":{"content":{"application/json":{"example":{"executionTime":123,"token":"a1b2c3d4e5f6g7h8i9j0k1l2m3n4o5p6","wasSuccessful":true},"schema":{"properties":{"executionTime":{"type":"integer"},"token":{"description":"Authentication token","type":"string"},"wasSuccessful":{"type":"boolean"}},"type":"object"}}},"description":"Login successful"},"401":{"content":{"application/json":{"example":{"error":"Invalid username or password","wasSuccessful":false},"schema":{"properties":{"error":{"type":"string"},"wasSuccessful":{"type":"boolean"}},"type":"object"}}},"description":"Invalid credentials"}},"summary":"User login","tags":["user"]}},"/logout":{"get":{"description":"Log out the current user and invalidate the authentication token.\n","operationId":"logout","parameters":[{"description":"Authentication token to invalidate","in":"query","name":"token","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"message":"User logged out successfully","wasSuccessful":true},"schema":{"properties":{"message":{"type":"string"},"wasSuccessful":{"type":"boolean"}},"type":"object"}}},"description":"Logout successful"},"401":{"description":"Invalid or expired token"}},"security":[{"tokenAuth":[]}],"summary":"User logout","tags":["user"]}},"/sequence":{"get":{"description":"Get either the entire sequence of an object or fetch an indexed subsequence.\nExpects a query with a single output column that resolves to a sequenceable object.\n","operationId":"getSequence","parameters":[{"description":"PathQuery in XML or JSON format selecting sequence objects","example":"<query model=\"genomic\" view=\"Gene.sequence.residues\">\n  <constraint path=\"Gene\" op=\"LOOKUP\" value=\"eve\" extraValue=\"D. melanogaster\"/>\n</query>\n","in":"query","name":"query","required":true,"schema":{"type":"string"}},{"description":"Start index for subsequence (0-based)","example":100,"in":"query","name":"start","schema":{"default":0,"minimum":0,"type":"integer"}},{"description":"End index for subsequence (exclusive)","example":500,"in":"query","name":"end","schema":{"type":"integer"}},{"description":"Output format","in":"query","name":"format","schema":{"default":"fasta","enum":["fasta","text"],"type":"string"}}],"responses":{"200":{"content":{"text/plain":{"examples":{"fasta":{"summary":"FASTA format output","value":">FBgn0000606 even-skipped\nATGGAGATCAAACAAGCGAAGAGTGGAGAGAAGTGGAGAAGCAGCCAAGCAAG\nCAACAGCACAAGGGCTCGTCGAGCAAGTCCAGCGAGGAGGATCTGCTGAGCGG\nCGACAGCGACAGCGACAGCGACAGCGACAGCGACAGCGACAGCGACAGCGAC\n"},"text":{"summary":"Plain text output","value":"ATGGAGATCAAACAAGCGAAGAGTGGAGAGAAGTGGAGAAGCAGCCAAGCAAG"}},"schema":{"type":"string"}}},"description":"Sequence data"}},"summary":"Get sequence data","tags":["export"]}},"/summaryfields":{"get":{"description":"Get the fields used to summarize each class in the data model.\nSummary fields are the key attributes displayed in search results and object summaries.\n","operationId":"getSummaryFields","parameters":[{"description":"Whether to exclude reference fields from summary","in":"query","name":"norefs","schema":{"default":false,"type":"boolean"}},{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"classes":{"Gene":["primaryIdentifier","symbol","name","organism.name"],"Protein":["primaryIdentifier","name","organism.name"],"Publication":["firstAuthor","title","year","journal"]}},"schema":{"properties":{"classes":{"additionalProperties":{"items":{"type":"string"},"type":"array"},"type":"object"}},"type":"object"}}},"description":"Summary fields for all classes"}},"summary":"Get summary fields for classes","tags":["model"]}},"/path/values":{"get":{"description":"Get possible values for a given path in the data model. Useful for auto-complete\nand discovering valid constraint values for queries.\n","operationId":"getPathValues","parameters":[{"description":"Path in the data model (e.g., Gene.symbol, Organism.name)","example":"Gene.organism.name","in":"query","name":"path","required":true,"schema":{"type":"string"}},{"description":"JSON object with type constraints","example":"{\"Gene\": \"SequenceFeature\"}","in":"query","name":"typeConstraints","schema":{"type":"string"}},{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"results":[{"count":35807,"value":"Drosophila melanogaster"},{"count":15420,"value":"Drosophila simulans"},{"count":14520,"value":"Drosophila pseudoobscura"}]},"schema":{"properties":{"results":{"items":{"properties":{"count":{"type":"integer"},"value":{"type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"List of possible values"}},"summary":"Get possible values for a path","tags":["model"]}},"/classkeys":{"get":{"description":"Get the keys used to uniquely identify objects of each class in the data model.\nThese keys are used for object lookups and deduplication.\n","operationId":"getClassKeys","parameters":[{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"classes":{"Gene":[["primaryIdentifier"],["symbol","organism.name"],["name","organism.name"]],"Protein":[["primaryIdentifier"],["primaryAccession"],["name","organism.name"]],"Publication":[["pubMedId"],["doi"]]}},"schema":{"properties":{"classes":{"additionalProperties":{"items":{"items":{"type":"string"},"type":"array"},"type":"array"},"type":"object"}},"type":"object"}}},"description":"Class keys for all classes"}},"summary":"Get class keys","tags":["model"]}},"/web-properties":{"get":{"description":"Get configuration properties for the web application interface, including\nsettings for display, behavior, and available features.\n","operationId":"getWebProperties","parameters":[{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"properties":{"externallink.flybase.url":"http://flybase.org/reports/<<attributeValue>>.html","externallink.uniprot.url":"https://www.uniprot.org/uniprot/<<attributeValue>>","project.contact":"support@flymine.org","project.releaseVersion":"52.0","project.subTitle":"An integrated database for Drosophila and Anopheles genomics","project.title":"FlyMine","webapp.listchooser.size":"10","webapp.max.bag.size":"100000"}},"schema":{"properties":{"properties":{"additionalProperties":{"type":"string"},"type":"object"}},"type":"object"}}},"description":"Web application properties"}},"summary":"Get web application properties","tags":["model"]}},"/query/append/tolist":{"post":{"description":"Execute a query and append the results to an existing list. The query must return\nobjects of the same type as the target list.\n","operationId":"queryAppendToList","parameters":[{"in":"query","name":"token","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/x-www-form-urlencoded":{"example":{"listName":"Signaling_Genes","query":"<query model=\"genomic\" view=\"Gene.primaryIdentifier\">\n  <constraint path=\"Gene.pathways.name\" op=\"CONTAINS\" value=\"insulin\"/>\n  <constraint path=\"Gene.organism.name\" op=\"=\" value=\"Drosophila melanogaster\"/>\n</query>\n"},"schema":{"properties":{"listName":{"description":"Name of the existing list to append to","type":"string"},"query":{"description":"PathQuery in XML or JSON format","type":"string"},"token":{"description":"Authentication token","type":"string"}},"required":["query","listName"],"type":"object"}}}},"responses":{"200":{"content":{"application/json":{"example":{"added":23,"duplicates":5,"listName":"Signaling_Genes","newSize":467,"wasSuccessful":true},"schema":{"properties":{"added":{"type":"integer"},"duplicates":{"type":"integer"},"listName":{"type":"string"},"newSize":{"type":"integer"},"wasSuccessful":{"type":"boolean"}},"type":"object"}}},"description":"Query results appended to list"}},"summary":"Append query results to existing list","tags":["query","list"]}},"/list/tags":{"delete":{"description":"Remove one or more tags from an existing list.\n","operationId":"removeListTags","parameters":[{"description":"Name of the list","example":"Gap_Genes","in":"query","name":"name","required":true,"schema":{"type":"string"}},{"description":"Semicolon-separated list of tags to remove","example":"old;deprecated","in":"query","name":"tags","required":true,"schema":{"type":"string"}},{"in":"query","name":"token","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"Tags removed successfully"}},"summary":"Remove tags from a list","tags":["list"]},"get":{"description":"Get all tags used across lists in the system. Tags help organize and categorize lists.\n","operationId":"getListTags","parameters":[{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml","text"],"type":"string"}},{"description":"Authentication token for private tags","in":"query","name":"token","schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"tags":[{"count":142,"tagName":"im:public"},{"count":67,"tagName":"im:aspect:Genes"},{"count":23,"tagName":"development"},{"count":18,"tagName":"signaling"},{"count":12,"tagName":"transcription"}]},"schema":{"properties":{"tags":{"items":{"properties":{"count":{"type":"integer"},"tagName":{"type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"Available list tags"}},"summary":"Get available list tags","tags":["list"]},"post":{"description":"Add one or more tags to an existing list to help with organization and discovery.\n","operationId":"addListTags","parameters":[{"in":"query","name":"token","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/x-www-form-urlencoded":{"example":{"name":"Gap_Genes","tags":"development;segmentation;maternal"},"schema":{"properties":{"name":{"description":"Name of the list to tag","type":"string"},"tags":{"description":"Semicolon-separated list of tags to add","type":"string"},"token":{"description":"Authentication token","type":"string"}},"required":["name","tags"],"type":"object"}}}},"responses":{"200":{"description":"Tags added successfully"}},"summary":"Add tags to a list","tags":["list"]}},"/lists/rename":{"post":{"description":"Rename an existing list. The list must belong to the authenticated user.\n","operationId":"renameList","parameters":[{"in":"query","name":"token","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/x-www-form-urlencoded":{"example":{"newname":"Validated_Gap_Genes","oldname":"My_Test_Genes"},"schema":{"properties":{"newname":{"description":"New name for the list (must be unique)","type":"string"},"oldname":{"description":"Current name of the list","type":"string"},"token":{"description":"Authentication token","type":"string"}},"required":["oldname","newname"],"type":"object"}}}},"responses":{"200":{"content":{"application/json":{"example":{"newname":"Validated_Gap_Genes","oldname":"My_Test_Genes","wasSuccessful":true},"schema":{"properties":{"newname":{"type":"string"},"oldname":{"type":"string"},"wasSuccessful":{"type":"boolean"}},"type":"object"}}},"description":"List renamed successfully"},"400":{"description":"List not found or name already exists"}},"summary":"Rename a list","tags":["list"]}},"/user/preferences":{"get":{"description":"Retrieve user preferences and settings.\n","operationId":"getUserPreferences","parameters":[{"description":"Authentication token","in":"query","name":"token","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"preferences":{"default-query-format":"json","do_not_spam":"true","email-notifications":"false","galaxy-url":"https://usegalaxy.org/"}},"schema":{"properties":{"preferences":{"additionalProperties":{"type":"string"},"type":"object"}},"type":"object"}}},"description":"User preferences"},"401":{"description":"Authentication required"}},"security":[{"tokenAuth":[]}],"summary":"Get user preferences","tags":["user"]},"post":{"description":"Update user preferences and settings.\n","operationId":"setUserPreferences","parameters":[{"in":"query","name":"token","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/x-www-form-urlencoded":{"example":{"key":"do_not_spam","value":"false"},"schema":{"properties":{"key":{"description":"Preference key to update","type":"string"},"value":{"description":"New preference value","type":"string"}},"type":"object"}}}},"responses":{"200":{"content":{"application/json":{"example":{"message":"Preference updated successfully","wasSuccessful":true},"schema":{"properties":{"message":{"type":"string"},"wasSuccessful":{"type":"boolean"}},"type":"object"}}},"description":"Preference updated successfully"}},"security":[{"tokenAuth":[]}],"summary":"Update user preferences","tags":["user"]}},"/facets":{"get":{"description":"Get available facets for search results. Facets provide categorized counts\nof search results for filtering and navigation.\n","operationId":"getFacets","parameters":[{"description":"Search query string","example":"transcription factor","in":"query","name":"q","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"facets":{"Category":{"Gene":234,"Protein":89,"Publication":567},"Organism":{"D. melanogaster":456,"D. simulans":123}}},"schema":{"properties":{"facets":{"additionalProperties":{"type":"object"},"type":"object"}},"type":"object"}}},"description":"Available facets"}},"summary":"Get search facets","tags":["search"]}},"/list/chart":{"get":{"description":"Generate chart data for visualization widgets based on list contents.\nDifferent widget types provide different chart visualizations.\n","operationId":"listChart","parameters":[{"description":"Name of the list to analyze","example":"PL FlyTF_site_specific_TFs","in":"query","name":"list","required":true,"schema":{"type":"string"}},{"description":"Name of the chart widget","example":"flyatlas_for_gene","in":"query","name":"widget","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}},{"in":"query","name":"token","schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"results":{"chartData":{"datasets":[{"data":[45.2,67.8,23.1,34.5],"label":"Expression Level"}],"labels":["Brain","Eye","Wing","Leg"]},"chartType":"BarChart"}},"schema":{"properties":{"results":{"type":"object"}},"type":"object"}}},"description":"Chart data"}},"summary":"Get chart widget data for a list","tags":["widget","list"]}},"/list/table":{"get":{"description":"Generate tabular data for table widgets based on list contents.\nProvides structured data for display in table format.\n","operationId":"listTable","parameters":[{"description":"Name of the list","example":"Gap_Genes","in":"query","name":"list","required":true,"schema":{"type":"string"}},{"description":"Name of the table widget","example":"interactions_for_gene","in":"query","name":"widget","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml","tsv","csv"],"type":"string"}},{"in":"query","name":"token","schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"results":[{"confidence":"high","gene1":"eve","gene2":"ftz","type":"genetic"},{"confidence":"medium","gene1":"eve","gene2":"hb","type":"physical"}]},"schema":{"properties":{"results":{"items":{"type":"object"},"type":"array"}},"type":"object"}}},"description":"Table data"}},"summary":"Get table widget data for a list","tags":["widget","list"]}},"/query/upload":{"post":{"description":"Upload a saved query in XML or JSON format and execute it.\nUseful for running complex saved queries.\n","operationId":"queryUpload","parameters":[{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml","tsv","csv"],"type":"string"}},{"in":"query","name":"token","schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"example":{"from":"Gene","select":["primaryIdentifier","symbol","length"],"where":[{"op":"CONTAINS","path":"goAnnotation.ontologyTerm.name","value":"DNA binding"},{"op":"=","path":"organism.name","value":"Drosophila melanogaster"}]},"schema":{"type":"object"}},"application/xml":{"example":"<query name=\"Complex Gene Query\" model=\"genomic\" view=\"Gene.primaryIdentifier Gene.symbol Gene.length\">\n  <constraint path=\"Gene.goAnnotation.ontologyTerm.name\" op=\"CONTAINS\" value=\"DNA binding\"/>\n  <constraint path=\"Gene.organism.name\" op=\"=\" value=\"Drosophila melanogaster\"/>\n  <constraint path=\"Gene.length\" op=\">\" value=\"1000\"/>\n  <constraint path=\"Gene.length\" op=\"<\" value=\"10000\"/>\n</query>\n","schema":{"format":"xml","type":"string"}}},"required":true},"responses":{"200":{"description":"Query results"}},"summary":"Upload and execute a saved query","tags":["query"]}},"/template/tags":{"get":{"description":"Get all tags used for categorizing and organizing templates.\n","operationId":"getTemplateTags","parameters":[{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"tags":["im:aspect:Genomics","im:aspect:Proteins","im:aspect:Function","im:aspect:Homology","im:aspect:Publications","im:frontpage","im:converter"]},"schema":{"properties":{"tags":{"items":{"type":"string"},"type":"array"}},"type":"object"}}},"description":"Template tags"}},"summary":"Get template tags","tags":["template"]}},"/template/tolist":{"post":{"description":"Execute a template query and save the results as a new list.\n","operationId":"templateToList","parameters":[{"in":"query","name":"token","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/x-www-form-urlencoded":{"example":{"constraint1":"Gene.pathways.name","description":"Genes in hedgehog signaling pathway","extra1":"D. melanogaster","listName":"Hedgehog_Pathway_Genes_List","name":"Gene_Pathways","op1":"CONTAINS","value1":"hedgehog"},"schema":{"properties":{"constraint1":{"type":"string"},"description":{"type":"string"},"extra1":{"type":"string"},"listName":{"description":"Name for the new list","type":"string"},"name":{"description":"Name of the template to execute","type":"string"},"op1":{"type":"string"},"tags":{"items":{"type":"string"},"type":"array"},"token":{"type":"string"},"value1":{"type":"string"}},"required":["name","listName"],"type":"object"}}}},"responses":{"200":{"content":{"application/json":{"example":{"listName":"Hedgehog_Pathway_Genes_List","size":42,"type":"Gene"},"schema":{"properties":{"listName":{"type":"string"},"size":{"type":"integer"},"type":{"type":"string"}},"type":"object"}}},"description":"List created from template results"}},"summary":"Save template results as list","tags":["template","list"]}},"/query/code":{"get":{"description":"Generate client code in various programming languages for executing a query.\nUseful for integrating FlyMine queries into custom applications.\n","operationId":"queryCode","parameters":[{"description":"PathQuery in XML or JSON format","example":"<query model=\"genomic\" view=\"Gene.symbol Gene.primaryIdentifier\">\n  <constraint path=\"Gene.symbol\" op=\"=\" value=\"eve\"/>\n</query>\n","in":"query","name":"query","required":true,"schema":{"type":"string"}},{"description":"Target programming language","example":"python","in":"query","name":"lang","required":true,"schema":{"enum":["python","perl","java","ruby","javascript","curl"],"type":"string"}}],"responses":{"200":{"content":{"text/plain":{"example":"#!/usr/bin/env python\n\nfrom intermine.webservice import Service\n\nservice = Service(\"https://www.flymine.org/flymine/service\")\nquery = service.new_query(\"Gene\")\nquery.add_view(\"symbol\", \"primaryIdentifier\")\nquery.add_constraint(\"symbol\", \"=\", \"eve\")\n\nfor row in query:\n    print(row[\"symbol\"], row[\"primaryIdentifier\"])\n","schema":{"type":"string"}}},"description":"Generated code"}},"summary":"Generate code for a query","tags":["query"]}},"/facet-list":{"get":{"description":"Get faceted search results for items in a specific list.\n","operationId":"getFacetList","parameters":[{"description":"Name of the list","example":"PL FlyBase_Annotation_IDs","in":"query","name":"list","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}},{"in":"query","name":"token","schema":{"type":"string"}}],"responses":{"200":{"description":"Faceted list data"}},"summary":"Get facets for a list","tags":["search"]}},"/user/queries":{"get":{"description":"Get all saved queries for the authenticated user.\n","operationId":"getUserQueries","parameters":[{"in":"query","name":"token","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"queries":[{"created":"2023-10-15T14:30:00Z","description":"Transcription factors with DNA binding","name":"My_TF_Search"},{"created":"2023-10-20T09:15:00Z","description":"Genes involved in wing morphogenesis","name":"Wing_Development_Genes"}]},"schema":{"properties":{"queries":{"items":{"properties":{"created":{"format":"date-time","type":"string"},"description":{"type":"string"},"name":{"type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"User's saved queries"}},"security":[{"tokenAuth":[]}],"summary":"Get saved queries","tags":["user","query"]},"post":{"description":"Save a query for later use by the authenticated user.\n","operationId":"saveUserQuery","parameters":[{"in":"query","name":"token","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/x-www-form-urlencoded":{"example":{"description":"Genes involved in neural development","name":"Neural_Genes","query":"{\n  \"from\": \"Gene\",\n  \"select\": [\"symbol\", \"primaryIdentifier\"],\n  \"where\": [\n    {\"path\": \"goAnnotation.ontologyTerm.name\", \"op\": \"CONTAINS\", \"value\": \"neural\"},\n    {\"path\": \"organism.name\", \"op\": \"=\", \"value\": \"Drosophila melanogaster\"}\n  ]\n}\n"},"schema":{"properties":{"description":{"type":"string"},"name":{"description":"Name for the saved query","type":"string"},"query":{"description":"Query in XML or JSON format","type":"string"},"token":{"type":"string"}},"required":["name","query"],"type":"object"}}}},"responses":{"200":{"description":"Query saved successfully"}},"security":[{"tokenAuth":[]}],"summary":"Save a query","tags":["user","query"]}},"/branding":{"get":{"description":"Get branding and customization information for the FlyMine instance,\nincluding colors, logos, and project information.\n","operationId":"getBranding","responses":{"200":{"content":{"application/json":{"example":{"properties":{"logos":{"favicon":"/images/favicon.ico","header":"/images/logo.png"},"project":{"description":"An integrated database for Drosophila and Anopheles genomics","name":"FlyMine","version":"52.0"},"theme":{"primaryColor":"#00539F","secondaryColor":"#FF6600"}}},"schema":{"properties":{"properties":{"type":"object"}},"type":"object"}}},"description":"Branding information"}},"summary":"Get branding information","tags":["model"]}},"/bluegenes-properties":{"get":{"description":"Get configuration properties for the BlueGenes user interface.\nBlueGenes is the modern web interface for InterMine databases.\n","operationId":"getBlueGenesProperties","responses":{"200":{"content":{"application/json":{"example":{"properties":{"listWidgets":["go_enrichment","pathway_enrichment"],"mineName":"FlyMine","reportWidgets":["ProteinAtlasExpression","FlyAtlas","Publications"],"toolsPath":"/tools"}},"schema":{"properties":{"properties":{"type":"object"}},"type":"object"}}},"description":"BlueGenes configuration"}},"summary":"Get BlueGenes properties","tags":["model"]}},"/lists/jaccard-index":{"get":{"description":"Calculate the Jaccard similarity coefficient between two lists.\nThe Jaccard index measures similarity as the size of the intersection\ndivided by the size of the union of the lists.\n","operationId":"listsJaccardIndex","parameters":[{"description":"Semicolon-separated list names to compare","example":"Gap_Genes;Hox_Genes","in":"query","name":"lists","required":true,"schema":{"type":"string"}},{"in":"query","name":"token","schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"intersection":2,"jaccardIndex":0.125,"list1Size":9,"list2Size":9,"union":16},"schema":{"properties":{"intersection":{"type":"integer"},"jaccardIndex":{"maximum":1,"minimum":0,"type":"number"},"list1Size":{"type":"integer"},"list2Size":{"type":"integer"},"union":{"type":"integer"}},"type":"object"}}},"description":"Jaccard similarity coefficient"}},"summary":"Calculate Jaccard index between lists","tags":["list"]}},"/listswithobject":{"get":{"description":"Find all lists that contain a specific object identified by its database ID.\nUseful for discovering which lists include a particular gene or other entity.\n","operationId":"listsWithObject","parameters":[{"description":"Database ID of the object","example":1007656,"in":"query","name":"id","required":true,"schema":{"type":"integer"}},{"in":"query","name":"token","schema":{"type":"string"}},{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"lists":[{"description":"Drosophila gap genes","name":"Gap_Genes","size":9,"type":"Gene"},{"description":"All segmentation genes","name":"Segmentation_Genes","size":45,"type":"Gene"}]},"schema":{"properties":{"lists":{"items":{"properties":{"description":{"type":"string"},"name":{"type":"string"},"size":{"type":"integer"},"type":{"type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"Lists containing the object"}},"summary":"Find lists containing an object","tags":["list"]}},"/schema":{"get":{"description":"Get schema definitions for the API, including available schemas for\nqueries, templates, and other API components.\n","operationId":"getSchema","parameters":[{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"schemas":[{"description":"XML Schema for PathQuery format","name":"query.xsd","url":"/schema/query.xsd"},{"description":"XML Schema for template queries","name":"template.xsd","url":"/schema/template.xsd"}]},"schema":{"properties":{"schemas":{"items":{"properties":{"description":{"type":"string"},"name":{"type":"string"},"url":{"type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"Available schemas"}},"summary":"Get API schema information","tags":["model"]}},"/template/upload":{"post":{"description":"Upload a new template query for reuse. Templates are pre-configured\nqueries with parameters that can be easily executed with different values.\n","operationId":"templateUpload","parameters":[{"in":"query","name":"token","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"example":{"description":"Find all genes in a specified pathway","name":"Genes_In_Pathway","query":{"from":"Gene","select":["symbol","primaryIdentifier","pathways.name"],"where":[{"description":"Pathway name","editable":true,"op":"=","path":"pathways.name","value":""},{"op":"=","path":"organism.name","value":"Drosophila melanogaster"}]},"title":"Genes in a specific pathway"},"schema":{"type":"object"}},"application/xml":{"example":"<template name=\"Genes_In_Pathway\" title=\"Genes in a specific pathway\">\n  <query model=\"genomic\" view=\"Gene.symbol Gene.primaryIdentifier Gene.pathways.name\">\n    <constraint path=\"Gene.pathways.name\" op=\"=\" value=\"\" editable=\"true\" description=\"Pathway name\"/>\n    <constraint path=\"Gene.organism.name\" op=\"=\" value=\"Drosophila melanogaster\"/>\n  </query>\n</template>\n","schema":{"format":"xml","type":"string"}}},"required":true},"responses":{"200":{"content":{"application/json":{"example":{"templateName":"Genes_In_Pathway","wasSuccessful":true},"schema":{"properties":{"templateName":{"type":"string"},"wasSuccessful":{"type":"boolean"}},"type":"object"}}},"description":"Template uploaded successfully"}},"security":[{"tokenAuth":[]}],"summary":"Upload a template","tags":["template"]}},"/user":{"get":{"description":"Get detailed information about the authenticated user's account,\nincluding profile, preferences, and usage statistics.\n","operationId":"getUserInfo","parameters":[{"in":"query","name":"token","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"user":{"email":"researcher@university.edu","id":123456,"isGuest":false,"isSuperuser":false,"lists":42,"profile":{"interests":["genomics","development","evolution"],"organization":"University Research Lab"},"queries":156,"templates":8,"username":"researcher@university.edu"}},"schema":{"properties":{"user":{"properties":{"email":{"type":"string"},"id":{"type":"integer"},"isGuest":{"type":"boolean"},"isSuperuser":{"type":"boolean"},"lists":{"type":"integer"},"profile":{"type":"object"},"queries":{"type":"integer"},"templates":{"type":"integer"},"username":{"type":"string"}},"type":"object"}},"type":"object"}}},"description":"User account information"}},"security":[{"tokenAuth":[]}],"summary":"Get user account information","tags":["user"]}}},"security":[{},{"tokenAuth":[]}],"servers":[{"description":"FlyMine production server","url":"https://www.flymine.org/flymine/service"}],"tags":[{"description":"Query operations for retrieving genomic data","name":"query"},{"description":"Pre-configured query templates","name":"template"},{"description":"List management operations","name":"list"},{"description":"Search operations","name":"search"},{"description":"Data export in specialized formats","name":"export"},{"description":"Genomic interval operations","name":"genomic-regions"},{"description":"User account and authentication","name":"user"},{"description":"Data model operations","name":"model"},{"description":"Data visualization widgets","name":"widget"},{"description":"Identifier resolution services","name":"id-resolution"}],"x-externalResources":[{"x-description":"FlyMine homepage","x-type":"website","x-url":"https://www.flymine.org/flymine/"},{"x-description":"InterMine web services documentation","x-type":"documentation","x-url":"http://intermine.org/im-docs/docs/web-services/"},{"x-description":"FlyMine source code repository","x-type":"repository","x-url":"https://github.com/intermine/flymine"}]},{"components":{"schemas":{"Analysis":{"additionalProperties":true,"description":"An analysis is a dictionary that contains information about the result tied to a particular service. 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Data creators can create an AuxiliaryGraph to assemble a specific collections of edges from the Knowledge Graph into a named graph that can be referenced from an Edge as evidence/explanation supporting that Edge, or from a Result Analysis as information used to generate a score.","properties":{"attributes":{"description":"Attributes of the Auxiliary Graph","items":{"$ref":"#/components/schemas/Attribute"},"minItems":0,"nullable":false,"type":"array"},"edges":{"description":"List of edges that form the Auxiliary Graph. Each item is a reference to a single Knowledge Graph edge","items":{"type":"string"},"minItems":1,"nullable":false,"type":"array"}},"required":["edges","attributes"],"type":"object"},"BiolinkEntity":{"description":"Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name.","example":"biolink:PhenotypicFeature","externalDocs":{"description":"Biolink model entities","url":"https://biolink.github.io/biolink-model/docs/NamedThing.html"},"pattern":"^biolink:[A-Z][a-zA-Z]*$","type":"string"},"BiolinkPredicate":{"description":"CURIE for a Biolink 'predicate' slot, taken from the Biolink slot ('is_a') hierarchy rooted in biolink:related_to (snake_case). This predicate defines the Biolink relationship between the subject and object nodes of a biolink:Association defining a knowledge graph edge.","example":"biolink:interacts_with","externalDocs":{"description":"Biolink model predicates","url":"https://biolink.github.io/biolink-model/docs/related_to.html"},"pattern":"^biolink:[a-z][a-z_]*$","type":"string"},"CURIE":{"description":"A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. 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Nodes are identified by the keys in the KnowledgeGraph Node mapping.","properties":{"attributes":{"description":"A list of attributes describing the node","items":{"$ref":"#/components/schemas/Attribute"},"minItems":0,"nullable":false,"type":"array"},"categories":{"description":"These should be Biolink Model categories and are NOT allowed to be of type 'abstract' or 'mixin'. Returning 'deprecated' categories should also be avoided.","items":{"$ref":"#/components/schemas/BiolinkEntity"},"minItems":1,"nullable":false,"type":"array"},"is_set":{"description":"Indicates that the node represents a set of entities. If this property is missing or null, it is assumed to be false.","nullable":true,"type":"boolean"},"name":{"description":"Formal name of the entity","example":"Haptoglobin","nullable":true,"type":"string"}},"required":["categories","attributes"],"type":"object"},"NodeBinding":{"additionalProperties":true,"description":"An instance of NodeBinding is a single KnowledgeGraph Node mapping, identified by the corresponding 'id' object key identifier of the Node within the Knowledge Graph. Instances of NodeBinding may include extra annotation in the form of additional properties. (such annotation is not yet fully standardized). Each Node Binding must bind directly to node in the original Query Graph.","properties":{"attributes":{"description":"A list of attributes providing further information about the node binding. This is not intended for capturing node attributes and should only be used for properties that vary from result to result.","items":{"$ref":"#/components/schemas/Attribute"},"minItems":0,"nullable":false,"type":"array"},"id":{"description":"The CURIE of a Node within the Knowledge Graph.","nullable":false,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]},"query_id":{"description":"An optional property to provide the CURIE in the QueryGraph to which this binding applies. If the bound QNode does not have an an 'id' property or if it is empty, then this query_id MUST be null or absent. If the bound QNode has one or more CURIEs as an 'id' and this NodeBinding's 'id' refers to a QNode 'id' in a manner where the CURIEs are different (typically due to the NodeBinding.id being a descendant of a QNode.id), then this query_id MUST be provided. In other cases, there is no ambiguity, and this query_id SHOULD NOT be provided.","nullable":true,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]}},"required":["id","attributes"],"type":"object"},"QEdge":{"additionalProperties":true,"description":"An edge in the QueryGraph used as a filter pattern specification in a query. If the optional predicate property is not specified, it is assumed to be a wildcard match to the target knowledge space. If specified, the ontological inheritance hierarchy associated with the term provided is assumed, such that edge bindings returned may be an exact match to the given QEdge predicate term, or to a term that is a descendant of the QEdge predicate term.","properties":{"attribute_constraints":{"default":[],"description":"A list of attribute constraints applied to a query edge. If there are multiple items, they must all be true (equivalent to AND)","items":{"$ref":"#/components/schemas/AttributeConstraint"},"type":"array"},"knowledge_type":{"description":"Indicates the type of knowledge that the client wants from the server between the subject and object. If the value is 'lookup', then the client wants direct lookup information from knowledge sources. If the value is 'inferred', then the client wants the server to get creative and connect the subject and object in more speculative and non-direct-lookup ways. If this property is absent or null, it MUST be assumed to mean 'lookup'. This feature is currently experimental and may be further extended in the future.","example":"lookup","nullable":true,"type":"string"},"object":{"description":"Corresponds to the map key identifier of the object concept node anchoring the query filter pattern for the query relationship edge.","example":"https://www.uniprot.org/uniprot/P00738","type":"string"},"predicates":{"description":"These should be Biolink Model predicates and are allowed to be of type 'abstract' or 'mixin' (only in QGraphs!). Use of 'deprecated' predicates should be avoided.","items":{"$ref":"#/components/schemas/BiolinkPredicate"},"minItems":1,"nullable":true,"type":"array"},"qualifier_constraints":{"default":[],"description":"A list of QualifierConstraints that provide nuance to the QEdge. If multiple QualifierConstraints are provided, there is an OR relationship between them. If the QEdge has multiple predicates or if the QNodes that correspond to the subject or object of this QEdge have multiple categories or multiple curies, then qualifier_constraints MUST NOT be specified because these complex use cases are not supported at this time.","items":{"$ref":"#/components/schemas/QualifierConstraint"},"type":"array"},"subject":{"description":"Corresponds to the map key identifier of the subject concept node anchoring the query filter pattern for the query relationship edge.","example":"https://omim.org/entry/603903","type":"string"}},"required":["subject","object"],"type":"object"},"QNode":{"additionalProperties":true,"description":"A node in the QueryGraph used to represent an entity in a query. If a CURIE is not specified, any nodes matching the category of the QNode will be returned in the Results.","properties":{"categories":{"description":"These should be Biolink Model categories and are allowed to be of type 'abstract' or 'mixin' (only in QGraphs!). Use of 'deprecated' categories should be avoided.","items":{"$ref":"#/components/schemas/BiolinkEntity"},"minItems":1,"nullable":true,"type":"array"},"constraints":{"default":[],"description":"A list of constraints applied to a query node. If there are multiple items, they must all be true (equivalent to AND)","items":{"$ref":"#/components/schemas/AttributeConstraint"},"type":"array"},"ids":{"description":"A CURIE identifier (or list of identifiers) for this node. The 'ids' field will hold a list of CURIEs only in the case of a BATCH set_interpretation, where each CURIE is queried separately. If a list of queried CURIEs is to be considered as a set (as under a MANY or ALL set_interpretation), the 'ids' field will hold a single id representing this set, and the individual members of this set will be captured in a separate 'member_ids' field. Note that the set id MUST be created as a UUID by the system that defines the queried set, using a centralized nodenorm service. Note also that downstream systems MUST re-use the original set UUID in the messages they create/send, which will facilitate merging or caching operations.","example":["OMIM:603903"],"items":{"$ref":"#/components/schemas/CURIE"},"minItems":1,"nullable":true,"type":"array"},"member_ids":{"description":"A list of CURIE identifiers for members of a queried set. This field MUST be populated under a set_interpretation of MANY or ALL, when the 'ids' field holds a UUID representing the set itself. This field MUST NOT be used under a set_interpretation of BATCH.","items":{"$ref":"#/components/schemas/CURIE"},"nullable":true,"type":"array"},"set_interpretation":{"description":"Indicates how multiple CURIEs in the ids property MUST be interpreted. BATCH indicates that the query is intended to be a batch query and each CURIE is treated independently. ALL means that all specified CURIES MUST appear in each Result. MANY means that member CURIEs MUST form one or more sets in the Results, and sets with more members are generally considered more desirable that sets with fewer members. If this property is missing or null, the default is BATCH.","enum":["BATCH","ALL","MANY"],"nullable":true,"type":"string"}},"type":"object"},"Qualifier":{"additionalProperties":false,"description":"An additional nuance attached to an assertion","properties":{"qualifier_type_id":{"$ref":"#/components/schemas/CURIE","description":"CURIE for a Biolink 'qualifier' association slot, generally taken from Biolink association slots designated for this purpose (that is, association slots with names ending in 'qualifier') e.g. biolink:subject_aspect_qualifier, biolink:subject_direction_qualifier, biolink:object_aspect_qualifier, etc. Such qualifiers are used to elaborate a second layer of meaning of a knowledge graph edge. Available qualifiers are edge properties in the Biolink Model (see https://biolink.github.io/biolink-model/docs/edge_properties.html) which have slot names with the suffix string 'qualifier'.","example":"biolink:subject_aspect_qualifier","nullable":false,"pattern":"^biolink:[a-z][a-z_]*$"},"qualifier_value":{"description":"The value associated with the type of the qualifier, drawn from a set of controlled values by the type as specified in the Biolink model (e.g. 'expression' or 'abundance' for the qualifier type 'biolink:subject_aspect_qualifier', etc). The enumeration of qualifier values for a given qualifier type is generally going to be constrained by the category of edge (i.e. biolink:Association subtype) of the (Q)Edge.","example":"expression","nullable":false,"type":"string"}},"required":["qualifier_type_id","qualifier_value"],"type":"object"},"QualifierConstraint":{"additionalProperties":false,"description":"Defines a query constraint based on the qualifier_types and qualifier_values of a set of Qualifiers attached to an edge. For example, it can constrain a \"ChemicalX - affects - ?Gene\" query to return only edges where ChemicalX specifically affects the 'expression' of the Gene, by constraining on the qualifier_type \"biolink:object_aspect_qualifier\" with a qualifier_value of \"expression\".","properties":{"qualifier_set":{"description":"A set of Qualifiers that serves to add nuance to a query, by constraining allowed values held by Qualifiers on queried Edges.","items":{"$ref":"#/components/schemas/Qualifier"},"nullable":false,"type":"array"}},"required":["qualifier_set"],"type":"object"},"Query":{"additionalProperties":true,"description":"The Query class is used to package a user request for information. A Query object consists of a required Message object with optional additional properties. Additional properties are intended to convey implementation-specific or query-independent parameters. For example, an additional property specifying a log level could allow a user to override the default log level in order to receive more fine-grained log information when debugging an issue.","properties":{"bypass_cache":{"default":false,"description":"Set to true in order to request that the agent obtain fresh information from its sources in all cases where it has a viable choice between requesting fresh information in real time and using cached information. The agent receiving this flag MUST also include it in TRAPI sent to downstream sources (e.g., ARS -> ARAs -> KPs).","type":"boolean"},"log_level":{"description":"The least critical level of logs to return","nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"message":{"description":"The query Message is a serialization of the user request. Content of the Message object depends on the intended TRAPI operation. For example, the fill operation requires a non-empty query_graph field as part of the Message, whereas other operations, e.g. overlay, require non-empty results and knowledge_graph fields.","nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"submitter":{"description":"Any string for self-identifying the submitter of a query. The purpose of this optional field is to aid in the tracking of the source of queries for development and issue resolution.","nullable":true,"type":"string"},"workflow":{"description":"List of workflow steps to be executed.","nullable":true,"oneOf":[{"$ref":"https://standards.ncats.io/workflow/1.3.5/schema"}]}},"required":["message"],"type":"object","x-body-name":"request_body"},"QueryGraph":{"additionalProperties":true,"description":"A graph representing a biomedical question. It serves as a template for each result (answer), where each bound knowledge graph node/edge is expected to obey the constraints of the associated query graph element.","properties":{"edges":{"additionalProperties":{"$ref":"#/components/schemas/QEdge"},"description":"The edge specifications. The keys of this map are unique edge identifiers and the corresponding values include the constraints on bound edges, in addition to specifying the subject and object QNodes.","type":"object"},"nodes":{"additionalProperties":{"$ref":"#/components/schemas/QNode"},"description":"The node specifications. The keys of this map are unique node identifiers and the corresponding values include the constraints on bound nodes.","type":"object"}},"required":["nodes","edges"],"type":"object"},"ResourceRoleEnum":{"description":"The role played by the InformationResource in serving as a source for an Edge. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources.  This enumeration is found in Biolink Model, but is repeated here for convenience.","enum":["primary_knowledge_source","aggregator_knowledge_source","supporting_data_source"],"type":"string"},"Response":{"additionalProperties":true,"description":"The Response object contains the main payload when a TRAPI query endpoint interprets and responds to the submitted query successfully (i.e., HTTP Status Code 200). The message property contains the knowledge of the response (query graph, knowledge graph, and results). The status, description, and logs properties provide additional details about the response.","properties":{"biolink_version":{"description":"Version label of the Biolink model used in this document","example":"3.1.2","nullable":true,"type":"string"},"description":{"description":"A brief human-readable description of the outcome","example":"Success. 42 results found.","nullable":true,"type":"string"},"logs":{"description":"A list of LogEntry items, containing errors, warnings, debugging information, etc. List items MUST be in chronological order with earliest first.","items":{"$ref":"#/components/schemas/LogEntry"},"minItems":0,"nullable":false,"type":"array"},"message":{"description":"Contains the knowledge of the response (query graph, knowledge graph, and results).","nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"schema_version":{"description":"Version label of the TRAPI schema used in this document","example":"1.4.0","nullable":true,"type":"string"},"status":{"description":"One of a standardized set of short codes, e.g. Success, QueryNotTraversable, KPsNotAvailable","example":"Success","nullable":true,"type":"string"},"workflow":{"description":"List of workflow steps that were executed.","nullable":true,"oneOf":[{"$ref":"https://standards.ncats.io/workflow/1.3.5/schema"}]}},"required":["message"],"type":"object"},"Result":{"additionalProperties":true,"description":"A Result object specifies the nodes and edges in the knowledge graph that satisfy the structure or conditions of a user-submitted query graph. It must contain a NodeBindings object (list of query graph node to knowledge graph node mappings) and a list of Analysis objects.","properties":{"analyses":{"description":"The list of all Analysis components that contribute to the result. See below for Analysis components.","items":{"$ref":"#/components/schemas/Analysis"},"minItems":0,"nullable":false,"type":"array"},"node_bindings":{"additionalProperties":{"items":{"$ref":"#/components/schemas/NodeBinding"},"minItems":1,"type":"array"},"description":"The dictionary of Input Query Graph to Result Knowledge Graph node bindings where the dictionary keys are the key identifiers of the Query Graph nodes and the associated values of those keys are instances of NodeBinding schema type (see below). This value is an array of NodeBindings since a given query node may have multiple knowledge graph Node bindings in the result.","nullable":false,"type":"object"}},"required":["node_bindings","analyses"],"type":"object"},"RetrievalSource":{"additionalProperties":true,"description":"Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved.","properties":{"resource_id":{"$ref":"#/components/schemas/CURIE","description":"The CURIE for an Information Resource that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.","example":"infores:drugbank","nullable":false},"resource_role":{"$ref":"#/components/schemas/ResourceRoleEnum","description":"The role played by the InformationResource in serving as a source for an Edge. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources."},"source_record_urls":{"description":"A URL linking to a specific web page or document provided by the source, that contains a record of the knowledge expressed in the Edge. If the knowledge is contained in more than one web page on an Information Resource's site, urls MAY be provided for each. For example, Therapeutic Targets Database (TTD) has separate web pages for 'Imatinib' and its protein target KIT, both of which hold the claim that 'the KIT protein is a therapeutic target for Imatinib'.","example":"[https://db.idrblab.net/ttd/data/drug/details/d0az3c, https://db.idrblab.net/ttd/data/target/details/t57700]","items":{"type":"string"},"nullable":true,"type":"array"},"upstream_resource_ids":{"description":"An upstream InformationResource from which the resource being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge. This is an array because there are cases where a merged Edge holds knowledge that was retrieved from multiple sources. e.g. an Edge provided by the ARAGORN ARA can expressing knowledge it retrieved from both the automat-mychem-info and molepro KPs, which both provided it with records of this single fact.","example":["infores:automat-mychem-info","infores:molepro"],"items":{"$ref":"#/components/schemas/CURIE"},"nullable":true,"type":"array"}},"required":["resource_id","resource_role"],"type":"object"}}},"externalDocs":{"description":"Documentation for the NCATS Biomedical Translator Reasoners web services","url":"https://github.com/NCATSTranslator/ReasonerAPI"},"info":{"contact":{"email":"qi.wei@isbscience.org","name":"Qi Wei"},"description":"TRAPI 1.5 endpoint for the CATRAX Pharmacogenomics KP, an NCATS Biomedical Translator Knowledge Provider","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"termsOfService":"https://github.com/RTXteam/PloverDB/blob/main/LICENSE","title":"CATRAX Pharmacogenomics KP - TRAPI 1.5.0","version":"2.7.8","x-translator":{"biolink-version":"4.2.1","component":"KP","externalDocs":{"description":"The values for component and team are restricted according to this external JSON schema. See schema and examples at url","url":"https://github.com/NCATSTranslator/translator_extensions/blob/\\ production/x-translator/"},"infores":"infores:catrax-pharmacogenomics","team":["Multiomics Provider"]},"x-trapi":{"asyncquery":false,"externalDocs":{"description":"The values for version are restricted according to the regex in this external JSON schema. See schema and examples at url","url":"https://github.com/NCATSTranslator/translator_extensions/blob/\\ production/x-trapi/"},"multicuriequery":false,"operations":["lookup"],"pathfinderquery":false,"test_data_location":{"default":{"url":"https://multiomics.rtx.ai:9990/PharmacogenomicsKG/sri_test_triples"}},"version":"1.5.0"}},"openapi":"3.0.1","paths":{"/meta_knowledge_graph":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns meta knowledge graph representation of this TRAPI web service."}},"summary":"Meta knowledge graph representation of this TRAPI web service.","tags":["meta_knowledge_graph"]}},"/query":{"post":{"description":"","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Query"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. 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. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a query and wait to receive a Response","tags":["query"]}},"/asyncquery":{"post":{"description":"","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryResponse"}}},"description":"The query is accepted for processing and the Response will be sent to the callback url when complete."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. 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. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a query with a callback to receive the response","tags":["asyncquery"]}},"/asyncquery_status/{job_id}":{"get":{"operationId":"asyncquery_status","parameters":[{"description":"Identifier of the job for status request","in":"path","name":"job_id","required":true,"schema":{"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. 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":"CTKP TRAPI 1.5 endpoint - development","url":"https://multiomics.rtx.ai:9990/PharmacogenomicsKG","x-maturity":"development"},{"description":"CTKP TRAPI 1.5 endpoint - staging","url":"https://multiomics.ci.transltr.io/PharmacogenomicsKG","x-maturity":"staging"},{"description":"CTKP TRAPI 1.5 endpoint - testing","url":"https://multiomics.test.transltr.io/PharmacogenomicsKG","x-maturity":"testing"},{"description":"CTKP TRAPI 1.5 endpoint - production","url":"https://multiomics.transltr.io/PharmacogenomicsKG","x-maturity":"production"}],"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"}]},{"components":{"x-bte-kgs-operations":{"chemical2pathway_1":[{"agent_type":"manual_agent","inputs":[{"id":"HMDB","semantic":"SmallMolecule"}],"knowledge_level":"knowledge_assertion","outputs":[{"id":"REACT","semantic":"Pathway"}],"parameters":{},"predicate":"participates_in","requestBody":{"body":"{ \n  \"analytes\":\n    {{ queryInputs \n       | replPrefix('hmdb') \n       | dump }}\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":"manual_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"]}},"openapi":"3.0.3","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 associations"}},"/api/analyte_intersects":{"get":{"parameters":[{"description":"specifies type of analyte intersects to return, 'metabolites' or 'genes'","in":"query","name":"analytetype","required":true,"schema":{"enum":["metabolites","genes"],"type":"string"}},{"description":"specifies 'global' or 'mapped-to-pathway'","in":"query","name":"query_scope","required":true,"schema":{"enum":["global","mapped-to-pathway"],"type":"string"}}],"responses":{"200":{"description":"OK"},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal Server Error"},"default":{"description":"Default response."}},"summary":"Return analyte source intersects"}},"/api/ontology-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 all types of ontologies present in RaMP-DB"}},"/api/chemical-class-type":{"get":{"parameters":[{"in":"query","name":"classtype","required":false,"schema":{"type":"string"}}],"responses":{"200":{"description":"OK"},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal Server Error"},"default":{"description":"Default response."}},"summary":"Return available high level chemical class types (from ClassyFire)"}},"/api/pathways-from-analytes":{"post":{"requestBody":{"content":{"application/json":{"schema":{"example":{"analytes":["ensembl:ENSG00000135679","hmdb:HMDB0000064","hmdb:HMDB0000148","ensembl:ENSG00000141510"]},"properties":{"analytes":{"items":{"type":"string"},"type":"array"}},"type":"object"}}},"description":"Retrieve pathway(s) for a given analyte(s). IDs should be prepended by ID source (e.g. **hmdb**:C00412).","required":true},"responses":{"200":{"description":"OK"},"500":{"description":"Internal Server Error"}},"summary":"Return pathways from given list of analytes","x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/chemical2pathway_1"},{"$ref":"#/components/x-bte-kgs-operations/gene2pathway_1"}]}},"/api/analytes-from-pathways":{"post":{"requestBody":{"content":{"application/json":{"schema":{"example":{"analyte_type":"both","match":"exact","pathway":["De Novo Triacylglycerol Biosynthesis","sphingolipid metabolism"]},"properties":{"analyte_type":{"enum":["gene","metabolite","both"],"required":false,"type":"string"},"match":{"enum":["exact","fuzzy"],"required":false,"type":"string"},"names_or_ids":{"enum":["names","ids"],"required":false,"type":"string"},"pathway":{"items":{"type":"string"},"type":"array"}},"type":"object"}}},"description":"Enter exact pathway name(s). `analyte_type` should be `\"gene\"`, `\"metabolite\"`, or `\"both\"` *(default)*","required":true},"responses":{"200":{"description":"OK"},"500":{"description":"Internal Server Error"}},"summary":"Retrieve analytes (genes/proteins, metabolites) by pathway."}},"/api/ontologies-from-metabolites":{"post":{"requestBody":{"content":{"application/json":{"schema":{"example":{"NameOrIds":"ids","metabolite":["ensembl:ENSG00000135679","hmdb:HMDB0000064","hmdb:HMDB0000148","ensembl:ENSG00000141510"]},"properties":{"NameOrIds":{"enum":["name","ids"],"type":"string"},"metabolite":{"items":{"type":"string"},"type":"array"}},"type":"object"}}},"description":"Enter a list of metabolites. 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Count and frequency data were derived from the [Columbia University Medical Center's](http://www.cumc.columbia.edu/) [OHDSI](https://www.ohdsi.org/) database including inpatient. Counts are the number of inpatient visits associated with the concept, e.g., diagnosed with a condition, exposed to a drug, or a procedure was performed. Frequencies are the number of unique visits associated with the concept divided by the total number of visits in the dataset, i.e., prevalence in the electronic health records. To protect patient privacy, all concepts and pairs of concepts where the count <= 10 were excluded, and counts were randomized by the Poisson distribution.         \n\nDatasets from three primary cohorts are available: \n1) COVID-19: Hospitalized patients aged 18 or older with a COVID-19 related condition diagnosis and/or a confirmed positive COVID-19 test during their hospitalization period or within the prior 21 days. Date range: March 1, 2020 to September 1, 2020. This cohort is also further stratified by sex (male and female) and age (adult: 18-64, senior: 65+).\n2) General inpatient: All hospitalized patients aged 18 or older. Date range: January 1, 2014 to December 31, 2019.\n3) Influenza: Hospitalized patients aged 18 or older who had at least one occurrence of influenza conditions or pre-coordinated positive measurements or positive influenza testing in the prior 21 days or during their hospitalization period. Date range: January 1, 2014 to December 31, 2019.\n\nBoth hierarchical and non-hierarchical datasets are available for each cohort. In the hierarchical datasets, the counts for each concept include the visits from all descendant concepts. For example, the count for ibuprofen (ID 1177480) includes visits with Ibuprofen 600 MG Oral Tablet (ID 19019073), Ibuprofen 400 MG Oral Tablet (ID 19019072), Ibuprofen 20 MG/ML Oral Suspension (ID 19019050), etc. \n\nClinical concepts (e.g., conditions, procedures, drugs) are coded by their standard concept ID in the [OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki). API methods are provided to map to/from other vocabularies supported in OMOP and other ontologies using the EMBL-EBI Ontology Xref Service (OxO). \n\n\nThe following resources are available through this API: \n\n\n1. Metadata: Metadata on the COHD database, including dataset descriptions, number of concepts, etc. \n\n\n2. OMOP: Access to the common vocabulary for name and concept identifier mapping\n\n\n3. Clinical Frequencies: Access to the counts and frequencies of conditions, procedures, and drug exposures, and the associations between them. Frequency was determined as the number of visits with the code(s) / total number of visits. \n\n\n4. Concept Associations: Inferred associations between concepts using chi-square analysis, ratio between observed to expected frequency, and relative frequency. \n\n\nA [Python notebook](https://github.com/WengLab-InformaticsResearch/cohd_api/blob/master/notebooks/COHD_API_Example.ipynb) demonstrates simple examples of how to use the COHD API.\n\n\nCOHD was developed at the [Columbia University Department of Biomedical Informatics](https://www.dbmi.columbia.edu/) as a collaboration between the [Weng Lab](http://people.dbmi.columbia.edu/~chw7007/), [Tatonetti Lab](http://tatonettilab.org/), and the [NCATS Biomedical Data Translator](https://ncats.nih.gov/translator) program (TReK Team). This work was supported in part by grants: NCATS 1OT2TR003434, NLM R01LM012895, NCATS OT3TR002027, NLM R01LM009886-08A1, and NIGMS R01GM107145.\n\nThe following external resources may be useful:  \n[OHDSI](https://www.ohdsi.org/)  \n[OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki)  \n[Athena](http://athena.ohdsi.org) (OMOP vocabularies, search, concept relationships, concept hierarchy)  \n[Atlas](http://www.ohdsi.org/web/atlas/) (OMOP vocabularies, search, concept relationships, concept hierarchy, concept sets)\n","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"termsOfService":"http://cohd.nsides.io/terms/","title":"Columbia Open Health Data (COHD) for COVID-19 Research API","version":"5.1.0","x-accessRestriction":"none","x-implementationLanguage":"Python"},"openapi":"3.0.1","paths":{"/metadata/datasets":{"get":{"description":"Returns a list of datasets, including dataset ID, name, and description.","operationId":"datasets","responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"dataset_description":{"example":"Hospitalized patients with a COVID-19 condition and/or positive lab test (non-hierarchical)","type":"string"},"dataset_id":{"example":1,"type":"integer"},"dataset_name":{"example":"COVID Cohort (non-hierarchical)","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of dataset descriptions."},"default":{"description":"Unexpected error"}},"summary":"Enumerates the datasets available in COHD","tags":["Metadata"]}},"/metadata/domainCounts":{"get":{"description":"Returns a list of domains and the number of concepts in each domain.","operationId":"domainCounts","parameters":[{"description":"The dataset_id of the dataset to query. 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The hierarchical definitions were derived from the OMOP concept_ancestor table. See the documentation on OMOP's concept_ancestor table on [ohdsi.org](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:concept_ancestor) and [GitHub](https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT_ANCESTOR).","operationId":"conceptDescendants","parameters":[{"description":"An OMOP concept ID, e.g., 313217","example":313217,"in":"query","name":"concept_id","required":true,"schema":{"type":"integer"}},{"description":"The vocabulary_id to restrict ancestors to. For conditions, SNOMED and MedDRA are used. For drugs, RxNorm and ATC are used. For procedures, SNOMED, MedDRA, and ICD10PCS are used. Default: unrestricted","example":null,"in":"query","name":"vocabulary_id","required":false,"schema":{"type":"string"}},{"description":"The concept_class_id to restrict ancestors to. Only certain hierarchical concept_class_ids are used in each vocabuarly: [ATC](https://en.wikipedia.org/wiki/Anatomical_Therapeutic_Chemical_Classification_System) {ATC 1st, ATC 2nd, ATC 3rd, ATC 4th, ATC 5th}; [MedDRA](https://en.wikipedia.org/wiki/MedDRA) {PT, HLT, HLGT, SOC}; [RxNorm](https://www.nlm.nih.gov/research/umls/rxnorm/docs/2015/appendix5.html) {Ingredient, Clinical Drug Form, Clinical Drug Comp, Clinical Drug}. Default: unrestricted","example":null,"in":"query","name":"concept_class_id","required":false,"schema":{"type":"string"}},{"description":"The dataset_id to retrieve counts from. Default: 3 (5-year hierarchical data set)","example":3,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_class_id":{"example":"Clinical Finding","type":"string"},"concept_code":{"example":"49436004","type":"string"},"concept_count":{"example":53272,"type":"integer"},"concept_name":{"example":"Atrial fibrillation","type":"string"},"descendant_concept_id":{"example":313217,"type":"integer"},"domain_id":{"example":"Condition","type":"string"},"max_levels_of_separation":{"example":0,"type":"integer"},"min_levels_of_separation":{"example":0,"type":"integer"},"standard_concept":{"example":"S","type":"string"},"vocabulary_id":{"example":"SNOMED","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of concepts."},"default":{"description":"Unexpected error"}},"summary":"Retrieve the concept's hierarchical descendants","tags":["OMOP"]}},"/omop/mapToStandardConceptID":{"get":{"description":"Uses the OMOP concept_relationship table to map from a non-standard concept code (e.g., ICD9CM 715.3) to a standard OMOP concept ID (e.g., 72990). This method may return multiple results if vocabulary_id is not specified and the concept_code is not unique across vocabularies. If both concept_code and vocabulary_id are specified, then 1 result will be returned at most.","operationId":"mapToStandardConceptID","parameters":[{"description":"The concept code to map from, e.g., 715.3","example":"715.3","in":"query","name":"concept_code","required":true,"schema":{"type":"string"}},{"description":"The vocabulary (e.g., \"ICD9CM\") that the concept code belongs to. If this parameter is not specified, the method will return mappings from any source vocabulary with matching concept code. See /omop/vocabularies for the list of supported vocabularies.","example":"ICD9CM","in":"query","name":"vocabulary_id","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"source_concept_code":{"example":"715.3","type":"string"},"source_concept_id":{"example":44834979,"type":"integer"},"source_concept_name":{"example":"Osteoarthrosis, localized, not specified whether primary or secondary","type":"string"},"source_vocabulary_id":{"example":"ICD9CM","type":"string"},"standard_concept_id":{"example":72990,"type":"integer"},"standard_concept_name":{"example":"Localized osteoarthrosis uncertain if primary OR secondary","type":"string"},"standard_domain_id":{"example":"Condition","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of concepts."},"default":{"description":"Unexpected error"}},"summary":"Map from a non-standard concept code to a standard OMOP concept ID","tags":["OMOP"]}},"/omop/mapFromStandardConceptID":{"get":{"description":"Uses the OMOP concept_relationship table to map from a standard concept ID (e.g., 72990) to concept code(s) (e.g., ICD9CM 715.3, 715.31, 715.32, etc.). An OMOP standard concept ID may map to many concepts in the external vocabulary.","operationId":"mapFromStandardConceptID","parameters":[{"description":"The standard OMOP concept id to map from, e.g., 72990","example":72990,"in":"query","name":"concept_id","required":true,"schema":{"type":"integer"}},{"description":"The vocabulary (e.g., \"ICD9CM\") to map to. If this parameter is not specified, the method will return mappings to any matching vocabularies. See /omop/vocabularies for the list of supported vocabularies.","example":"ICD9CM","in":"query","name":"vocabulary_id","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_class_id":{"example":"4-dig nonbill code","type":"string"},"concept_code":{"example":"715.3","type":"string"},"concept_id":{"example":44834979,"type":"integer"},"concept_name":{"example":"Osteoarthrosis, localized, not specified whether primary or secondary","type":"string"},"domain_id":{"example":"Condition","type":"string"},"standard_concept":{"example":null,"type":"string"},"vocabulary_id":{"example":"ICD9CM","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of concepts."},"default":{"description":"Unexpected error"}},"summary":"Map from a standard concept ID to concept code(s) in an external vocabulary","tags":["OMOP"]}},"/omop/vocabularies":{"get":{"description":"List of vocabulary_ids. Useful if you need to use /omop/mapToStandardConceptID to map a concept code from a source vocabulary to the OMOP standard vocabulary.","operationId":"vocabularies","responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"vocabulary_id":{"example":"SNOMED","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of vocabularies."},"default":{"description":"Unexpected error"}},"summary":"List of vocabularies","tags":["OMOP"]}},"/omop/xrefToOMOP":{"get":{"deprecated":true,"description":"This endpoint has been deprecated. COHD is now using Translator SRI services to map from OMOP to Biolink model.  Also, the OxO API has been producing internal server errors in some circumstances for several months. This  endpoint is currently still available but may not function correctly.  \n  \nAttempts to map a concept from an external ontology to an OMOP standard concept ID using the EMBL-EBI Ontology Xref Service (OxO): https://www.ebi.ac.uk/spot/oxo/index. This method attempts to use OxO to map from the original ontology to an intermediate ontology that is included in OMOP (ICD9CM, ICD10CM, SNOMEDCT, and MeSH), then uses the OMOP mappings to the standard concepts. Multiple mappings may be returned. Results are sorted by total_distance (OxO distance + OMOP distance) in ascending order.","operationId":"xrefToOMOP","parameters":[{"description":"Compact URI (CURIE) of the concept to map, e.g., DOID:8398","example":"DOID:8398","in":"query","name":"curie","required":true,"schema":{"type":"string"}},{"description":"Mapping distance for OxO. Note: this is the distance used in the OxO API to map from the original concept to an ICD9CM, ICD10CM, SNOMEDCT, or MeSH concept. One additional step may be taken by the COHD API to map to the OMOP standard concept. Default: 2.","example":2,"in":"query","name":"distance","required":false,"schema":{"type":"integer"}},{"description":"COHD can either call the OxO API or use the local implementation of OxO. The full call to the OxO API will have the most updated mappings and term definitions, but is slower. The local implementation of OxO is faster but may contain outdated mappings and term definitions. If the parameter is false, COHD will call the full OxO API. If the parameter is true, COHD will use the local implementation.  Default: false.","example":false,"in":"query","name":"local","required":false,"schema":{"type":"boolean"}},{"description":"By default (false), COHD returns all mappings found. If true, COHD will recommend a mapping based on path distances. Default: false.","example":false,"in":"query","name":"recommend","required":false,"schema":{"type":"boolean"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"intermediate_oxo_id":{"example":"ICD9CM:715.3","type":"string"},"intermediate_oxo_label":{"example":"","type":"string"},"omop_concept_name":{"example":"Localized osteoarthrosis uncertain if primary OR secondary","type":"string"},"omop_distance":{"example":1,"type":"integer"},"omop_domain_id":{"example":"Condition","type":"string"},"omop_standard_concept_id":{"example":72990,"type":"integer"},"oxo_distance":{"example":1,"type":"integer"},"source_oxo_id":{"example":"DOID:8398","type":"string"},"source_oxo_label":{"example":"osteoarthritis","type":"string"},"total_distance":{"example":2,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of mappings from external concepts to OMOP concepts."},"default":{"description":"Unexpected error"}},"summary":"Cross-reference from an ontology to OMOP standard concepts using the Ontology Xref Service","tags":["OMOP"]}},"/omop/xrefFromOMOP":{"get":{"deprecated":true,"description":"This endpoint has been deprecated. COHD is now using Translator SRI services to map from OMOP to Biolink model.  Also, the OxO API has been producing internal server errors in some circumstances for several months. This  endpoint is currently still available but may not function correctly.  \n  \nAttempts to map a concept from an external ontology to an OMOP standard concept ID using the EMBL-EBI Ontology Xref Service (OxO): https://www.ebi.ac.uk/spot/oxo/index. This method maps from the OMOP standard concept to an intermediate vocabulary included is OxO (ICD9CM, ICD10CM, SNOMEDCT, and MeSH), then uses the OxO API to map to other ontologies. Multiple mappings may be returned. Results are sorted by total_distance (OxO distance + OMOP distance) in ascending order.","operationId":"xrefFromOMOP","parameters":[{"description":"OMOP standard concept_id to map, e.g., 192855","example":192855,"in":"query","name":"concept_id","required":true,"schema":{"type":"integer"}},{"description":"Target ontologies for OxO. Comma separated target prefixes, e.g., \"DOID,UMLS\"","example":"UMLS","in":"query","name":"mapping_targets","required":false,"schema":{"type":"string"}},{"description":"Mapping distance for OxO. Note: this is the distance used in the OxO API to map from an ICD9CM, ICD10CM, SNOMEDCT, or MeSH concept to the desired ontology. One additional step may be taken by the COHD API to map to the OMOP standard concept to ICD9CM, ICD10CM, SNOMEDCT, or MeSH. Default: 2.","example":2,"in":"query","name":"distance","required":false,"schema":{"type":"integer"}},{"description":"COHD can either call the OxO API or use the local implementation of OxO. The full call to the OxO API will have the most updated mappings and term definitions, but is slower. The local implementation of OxO is faster but may contain outdated mappings and term definitions. If the parameter is false, COHD will call the full OxO API. If the parameter is true, COHD will use the local implementation.  Default: false.","example":false,"in":"query","name":"local","required":false,"schema":{"type":"boolean"}},{"description":"By default (false), COHD returns all mappings found. If true, COHD will recommend a mapping for each target based on path distances. Default: false.","example":false,"in":"query","name":"recommend","required":false,"schema":{"type":"boolean"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"intermediate_omop_concept_code":{"example":"92546004","type":"string"},"intermediate_omop_concept_id":{"example":192855,"type":"integer"},"intermediate_omop_concept_name":{"example":"Cancer in situ of urinary bladder","type":"string"},"intermediate_omop_vocabulary_id":{"example":"SNOMED","type":"string"},"intermediate_oxo_curie":{"example":"SNOMEDCT:92546004","type":"string"},"intermediate_oxo_label":{"example":"Cancer in situ of urinary bladder","type":"string"},"omop_distance":{"example":0,"type":"integer"},"oxo_distance":{"example":1,"type":"integer"},"source_omop_concept_code":{"example":"92546004","type":"string"},"source_omop_concept_id":{"example":192855,"type":"integer"},"source_omop_concept_name":{"example":"Cancer in situ of urinary bladder","type":"string"},"source_omop_vocabulary_id":{"example":"SNOMED","type":"string"},"target_curie":{"example":"UMLS:C0154091","type":"string"},"target_label":{"example":"Cancer in situ of urinary bladder","type":"string"},"total_distance":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of mappings from OMOP concepts to external concepts."},"default":{"description":"Unexpected error"}},"summary":"Cross-reference from an ontology to OMOP standard concepts using the Ontology Xref Service","tags":["OMOP"]}},"/frequencies/singleConceptFreq":{"get":{"description":"Retrieves observed clinical frequencies of individual concepts. Multiple concepts may be requested in a comma separated list.","operationId":"singleConceptFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"A comma separated list of OMOP concept ids, e.g., \"192855\" or \"192855,2008271\"","example":"192855","in":"query","name":"q","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_count":{"example":368,"type":"integer"},"concept_frequency":{"example":0.0002055371025188907,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of single concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequency of individual concepts","tags":["Clinical Frequencies"]}},"/frequencies/pairedConceptFreq":{"get":{"description":"Retrieves observed clinical frequencies of a pair of concepts.","operationId":"pairedConceptFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"A comma pair of OMOP concept ids, e.g., \"192855,2008271\"","example":"192855,2008271","in":"query","name":"q","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_count":{"example":10,"type":"integer"},"concept_frequency":{"example":5.585247351056813e-6,"type":"integer"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2008271,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequency of a pair of concepts","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id. Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"q","required":true,"schema":{"type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":19041324,"type":"integer"},"associated_concept_name":{"example":"Acetaminophen 325 MG Oral Tablet [Tylenol]","type":"string"},"associated_domain_id":{"example":"Drug","type":"string"},"concept_count":{"example":277,"type":"integer"},"concept_frequency":{"example":0.0001547113516242737,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptDomainFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id restricted by domain of the associated concept_id.  Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptDomainFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id","required":true,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc. See /metadata/domainCounts for a list of valid domain IDs.","example":"Procedure","in":"query","name":"domain","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":2211361,"type":"integer"},"associated_concept_name":{"example":"Radiologic examination, chest, 2 views, frontal and lateral","type":"string"},"associated_domain_id":{"example":"Procedure","type":"string"},"concept_count":{"example":257,"type":"integer"},"concept_frequency":{"example":0.00014354085692216007,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/mostFrequentConcepts":{"get":{"description":"Retrieves the most frequent concepts.","operationId":"mostFrequentConcepts","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The number of concepts to retreieve, e.g., 100. 0 or unspecified will return all matching concepts.","example":100,"in":"query","name":"q","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The domain_id to restrict to, e.g., \"Condition\", \"Drug\", \"Procedure\". See /metadata/domainCounts for a list of valid domain IDs.","example":"Condition","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"(Optional) The vocabulary_id(s) to restrict to, e.g., \"SNOMED\", \"MedDRA\", \"RxNorm\", \"ATC\" etc. Comma separated to include multiple vocabularies, e.g., \"SNOMED,MedDRA\". Default: unrestricted","example":null,"in":"query","name":"vocabulary_id","required":false,"schema":{"type":"string"}},{"description":"(Optional) The concept_class_id(s) to restrict to. concept_class_ids are specific to each vocabulary, e.g.,: [ATC](https://en.wikipedia.org/wiki/Anatomical_Therapeutic_Chemical_Classification_System) {ATC 1st, ATC 2nd, ATC 3rd, ATC 4th, ATC 5th}; [MedDRA](https://en.wikipedia.org/wiki/MedDRA) {PT, HLT, HLGT, SOC}; [RxNorm](https://www.nlm.nih.gov/research/umls/rxnorm/docs/2015/appendix5.html) {Ingredient, Clinical Drug Form, Clinical Drug Comp, Clinical Drug}. Comma separated to include multiple concept_class_ids, e.g., \"PT,HLT\". Default: unrestricted","example":null,"in":"query","name":"concept_class_id","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_class_id":{"example":"Clinical Finding","type":"string"},"concept_count":{"example":233790,"type":"integer"},"concept_frequency":{"example":0.1305774978203572,"type":"integer"},"concept_id":{"example":320128,"type":"integer"},"concept_name":{"example":"Essential hypertension","type":"string"},"dataset_id":{"example":1,"type":"integer"},"domain_id":{"example":"Condition","type":"string"},"vocabulary_id":{"example":"SNOMED","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of most frequent concepts."},"default":{"description":"Unexpected error"}},"summary":"Most frequent concepts [by domain]","tags":["Clinical Frequencies"]}},"/association/chiSquare":{"get":{"description":"Returns the chi-square statistic and p-value between pairs of concepts. Results are returned in descending order of the chi-square statistic. Note that due to large sample sizes, the chi-square can become very large.\n\nThe expected frequencies for the chi-square analysis are calculated based on the single concept frequencies and assuming independence between concepts. P-value is calculated with 1 DOF.\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"chiSquare","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If this parameter is specified, then the chi-square between concept_id_1 and concept_id_2 is returned. If this parameter is not specified, then a list of chi-squared results between concept_id_1 and other concepts is returned.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"adj_p-value":{"description":"Bonferonni adjusted p-value, adjusted with the total number of pairs of concepts in the dataset.","example":0.0314,"type":"number"},"chi_square":{"example":370026.1780081638,"type":"integer"},"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Instillation of therapeutic substance into bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":4021588,"type":"integer"},"dataset_id":{"example":3,"type":"integer"},"p-value":{"example":0.0314,"type":"number"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of concept pairs and chi-squared values."},"default":{"description":"Unexpected error"}},"summary":"Chi-square analysis on pairs of concepts","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/obsExpRatio":{"get":{"description":"Returns the natural logarithm of the ratio between the observed count and expected count. Expected count is calculated from the single concept frequencies and assuming independence between the concepts. Results are returned in descending order of ln_ratio.\n\nexpected_count = Count_1_and_2 * num_visits / (Count_1 * Count_2)\n\nln_ratio = ln(expected_count)\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Results for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"obsExpRatio","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}},{"description":"The confidence level used for calculating confidence intervals (default 0.99).","example":0.99,"in":"query","name":"confidence","required":false,"schema":{"type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Closed [transurethral] biopsy of bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2003784,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"expected_count":{"example":0.060838982345591645,"type":"integer"},"ln_ratio":{"example":7.561698473261244,"type":"integer"},"observed_count":{"example":117,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concepts and observed-expected frequency ratio."},"default":{"description":"Unexpected error"}},"summary":"Observed Count / Expected Count","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/relativeFrequency":{"get":{"description":"Calculates the relative frequency (i.e., conditional probability) between pairs of concepts. Results are returned in descending order of relative frequency. Note that due to the randomization of the counts, the calculated relative frequencies can exceed the limit of 1.0.\n\nRelative Frequency = Count_1_and_2 / Count_2\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"relativeFrequency","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict concept_id_2 (the base concept) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}},{"description":"The confidence level used for calculating confidence intervals (default 0.99).","example":0.99,"in":"query","name":"confidence","required":false,"schema":{"type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_2_count":{"example":82,"type":"integer"},"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Radical cystectomy","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2003805,"type":"integer"},"concept_pair_count":{"example":29,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"relative_frequency":{"example":0.35365853658536583,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concepts and relative frequency."},"default":{"description":"Unexpected error"}},"summary":"Relative frequency between pairs of concepts","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/translator/biolink_to_omop":{"post":{"description":"Map Biolink CURIEs to OMOP concepts","operationId":"biolink_to_omop","requestBody":{"content":{"application/json":{"example":"{\n    \"curies\": [\n        \"HP:0002907\",\n        \"MONDO:0001187\"\n    ]\n}","schema":{"$ref":"#/components/schemas/CurieList"}}},"description":"List of CURIEs","required":true},"responses":{"200":{"content":{"application/json":{"example":"{\n  \"MONDO:0001187\": {\n    \"distance\": 2,\n    \"omop_concept_id\": 197508,\n    \"omop_concept_name\": \"Malignant tumor of urinary bladder\"\n  }\n}","schema":{"additionalProperties":{"description":"Mapping from OMOP concept to Biolink","properties":{"distance":{"description":"mapping distance","type":"integer"},"omop_concept_id":{"type":"integer"},"omop_concept_name":{"type":"string"}},"type":"object"}}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from Biolink to OMOP","tags":["translator"]}},"/translator/omop_to_biolink":{"post":{"description":"Map OMOP concepts to normalized Biolink nodes using SRI Node Normalizer.","operationId":"omop_to_biolink","requestBody":{"content":{"application/json":{"example":"{\n    \"omop_ids\": [\n        78472,\n        197508\n    ]\n}","schema":{"$ref":"#/components/schemas/OmopList"}}},"description":"List of OMOP IDs","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"type":"object"},"example":"{\n  \"197508\": {\n    \"equivalent_identifiers\": [\n        {\n            \"identifier\": \"MONDO:0001187\",\n            \"label\": \"urinary bladder cancer\"\n        },\n        {\n            \"identifier\": \"DOID:11054\"\n        },\n        {\n            \"identifier\": \"OMIM:109800\"\n        },\n        {\n            \"identifier\": \"UMLS:C0005684\"\n        },\n        {\n            \"identifier\": \"NCIT:C9334\"\n        },\n        {\n            \"identifier\": \"SNOMEDCT:399326009\"\n        }\n    ],\n    \"id\": {\n        \"identifier\": \"MONDO:0001187\",\n        \"label\": \"urinary bladder cancer\"\n    },\n    \"type\": [\n        \"biolink:Disease\",\n        \"biolink:DiseaseOrPhenotypicFeature\",\n        \"biolink:BiologicalEntity\",\n        \"biolink:NamedThing\"\n    ]\n  }\n}","type":"object"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized. Mapping from OMOP concept to Biolink normalized nodes. See [SRI Node Normalizer](https://nodenormalization-sri.renci.org/docs#/) for response format"},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from OMOP to Biolink","tags":["translator"]}}},"security":[],"servers":[{"description":"COHD-COVID production server","url":"https://covid.cohd.io/api"}],"tags":[{"description":"COHD metadata","name":"Metadata"},{"description":"OMOP Common Data Model concepts","name":"OMOP"},{"description":"Clinical frequency data","name":"Clinical Frequencies"},{"description":"Estimated association between concepts","name":"Concept Associations"}],"x-externalResources":[{"x-description":"Department of Biomedical Informatics, Columbia University","x-type":"website","x-url":"https://www.dbmi.columbia.edu/"},{"x-description":"Observational Health Data Sciences and Informatics","x-type":"website","x-url":"https://www.ohdsi.org/"},{"x-description":"OMOP CDM","x-type":"website","x-url":"https://github.com/OHDSI/CommonDataModel/wiki"}]},{"basePath":"/v2","definitions":{"ApiResponse":{"properties":{"code":{"format":"int32","type":"integer"},"message":{"type":"string"},"type":{"type":"string"}},"type":"object"},"Category":{"properties":{"id":{"format":"int64","type":"integer"},"name":{"type":"string"}},"type":"object","xml":{"name":"Category"}},"Order":{"properties":{"complete":{"default":false,"type":"boolean"},"id":{"format":"int64","type":"integer"},"petId":{"format":"int64","type":"integer"},"quantity":{"format":"int32","type":"integer"},"shipDate":{"format":"date-time","type":"string"},"status":{"description":"Order 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Status","format":"int32","type":"integer"},"username":{"type":"string"}},"type":"object","xml":{"name":"User"}}},"externalDocs":{"description":"Find out more about Swagger","url":"http://swagger.io"},"host":"petstore.fancy.io","info":{"contact":{"email":"apiteam@fancy.io","x-chat":"https://de.wikipedia.org/wiki/Chat","x-issueTracker":"https://www.atlassian.com/de/software/jira"},"description":"This is a sample server Petstore server.","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"termsOfService":"http://fancy.io/terms/","title":"Fancy Petstore","version":"1.0.0"},"paths":{"/pet":{"post":{"consumes":["application/json","application/xml"],"description":"","operationId":"addPet","parameters":[{"description":"Pet object that needs to be added to the store","in":"body","name":"body","required":true,"schema":{"$ref":"#/definitions/Pet"}}],"produces":["application/xml","application/json"],"responses":{"405":{"description":"Invalid input"}},"security":[{"petstore_auth":["write:pets","read:pets"]}],"summary":"Add a new pet to the store","tags":["pet"]},"put":{"consumes":["application/json","application/xml"],"description":"","operationId":"updatePet","parameters":[{"description":"Pet object that needs to be added to the store","in":"body","name":"body","required":true,"schema":{"$ref":"#/definitions/Pet"}}],"produces":["application/xml","application/json"],"responses":{"400":{"description":"Invalid ID supplied"},"404":{"description":"Pet not found"},"405":{"description":"Validation exception"}},"security":[{"petstore_auth":["write:pets","read:pets"]}],"summary":"Update an existing pet","tags":["pet"]}},"/pet/findByStatus":{"get":{"description":"Multiple status values can be provided with comma separated strings","operationId":"findPetsByStatus","parameters":[{"collectionFormat":"multi","description":"Status values that need to be considered for 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Use         tag1, tag2, tag3 for testing.","operationId":"findPetsByTags","parameters":[{"collectionFormat":"multi","description":"Tags to filter by","in":"query","items":{"type":"string"},"name":"tags","required":true,"type":"array"}],"produces":["application/xml","application/json"],"responses":{"200":{"description":"successful operation","schema":{"items":{"$ref":"#/definitions/Pet"},"type":"array"}},"400":{"description":"Invalid tag value"}},"security":[{"petstore_auth":["write:pets","read:pets"]}],"summary":"Finds Pets by tags","tags":["pet"]}},"/pet/{petId}":{"delete":{"description":"","operationId":"deletePet","parameters":[{"in":"header","name":"api_key","required":false,"type":"string"},{"description":"Pet id to delete","format":"int64","in":"path","name":"petId","required":true,"type":"integer"}],"produces":["application/xml","application/json"],"responses":{"400":{"description":"Invalid ID supplied"},"404":{"description":"Pet not found"}},"security":[{"petstore_auth":["write:pets","read:pets"]}],"summary":"Deletes a pet","tags":["pet"]},"get":{"description":"Returns a single pet","operationId":"getPetById","parameters":[{"description":"ID of pet to return","format":"int64","in":"path","name":"petId","required":true,"type":"integer"}],"produces":["application/xml","application/json"],"responses":{"200":{"description":"successful operation","schema":{"$ref":"#/definitions/Pet"}},"400":{"description":"Invalid ID supplied"},"404":{"description":"Pet not found"}},"security":[{"api_key":[]}],"summary":"Find pet by ID","tags":["pet"]},"post":{"consumes":["application/x-www-form-urlencoded"],"description":"","operationId":"updatePetWithForm","parameters":[{"description":"ID of pet that needs to be updated","format":"int64","in":"path","name":"petId","required":true,"type":"integer"},{"description":"Updated name of the pet","in":"formData","name":"name","required":false,"type":"string"},{"description":"Updated status of the pet","in":"formData","name":"status","required":false,"type":"string"}],"produces":["application/xml","application/json"],"responses":{"405":{"description":"Invalid input"}},"security":[{"petstore_auth":["write:pets","read:pets"]}],"summary":"Updates a pet in the store with form data","tags":["pet"]}},"/pet/{petId}/uploadImage":{"post":{"consumes":["multipart/form-data"],"description":"","operationId":"uploadFile","parameters":[{"description":"ID of pet to update","format":"int64","in":"path","name":"petId","required":true,"type":"integer"},{"description":"Additional data to pass to server","in":"formData","name":"additionalMetadata","required":false,"type":"string"},{"description":"file to upload","in":"formData","name":"file","required":false,"type":"file"}],"produces":["application/json"],"responses":{"200":{"description":"successful operation","schema":{"$ref":"#/definitions/ApiResponse"}}},"security":[{"petstore_auth":["write:pets","read:pets"]}],"summary":"uploads an image","tags":["pet"]}},"/store/inventory":{"get":{"description":"Returns a map of status codes to quantities","operationId":"getInventory","parameters":[],"produces":["application/json"],"responses":{"200":{"description":"successful operation","schema":{"additionalProperties":{"format":"int32","type":"integer"},"type":"object"}}},"security":[{"api_key":[]}],"summary":"Returns pet inventories by status","tags":["store"]}},"/store/order":{"post":{"description":"","operationId":"placeOrder","parameters":[{"description":"order placed for purchasing the pet","in":"body","name":"body","required":true,"schema":{"$ref":"#/definitions/Order"}}],"produces":["application/xml","application/json"],"responses":{"200":{"description":"successful operation","schema":{"$ref":"#/definitions/Order"}},"400":{"description":"Invalid Order"}},"summary":"Place an order for a pet","tags":["store"]}},"/store/order/{orderId}":{"delete":{"description":"For valid response try integer IDs with positive integer value.         Negative or non-integer values will generate API errors","operationId":"deleteOrder","parameters":[{"description":"ID of the order that needs to be deleted","format":"int64","in":"path","minimum":1.0,"name":"orderId","required":true,"type":"integer"}],"produces":["application/xml","application/json"],"responses":{"400":{"description":"Invalid ID supplied"},"404":{"description":"Order not found"}},"summary":"Delete purchase order by ID","tags":["store"]},"get":{"description":"For valid response try integer IDs with value >= 1 and <= 10.         Other values will generated exceptions","operationId":"getOrderById","parameters":[{"description":"ID of pet that needs to be fetched","format":"int64","in":"path","maximum":10.0,"minimum":1.0,"name":"orderId","required":true,"type":"integer"}],"produces":["application/xml","application/json"],"responses":{"200":{"description":"successful operation","schema":{"$ref":"#/definitions/Order"}},"400":{"description":"Invalid ID supplied"},"404":{"description":"Order not found"}},"summary":"Find purchase order by ID","tags":["store"]}},"/user":{"post":{"description":"This can only be done by the logged in user.","operationId":"createUser","parameters":[{"description":"Created user object","in":"body","name":"body","required":true,"schema":{"$ref":"#/definitions/User"}}],"produces":["application/xml","application/json"],"responses":{"default":{"description":"successful operation"}},"summary":"Create user","tags":["user"]}},"/user/createWithArray":{"post":{"description":"","operationId":"createUsersWithArrayInput","parameters":[{"description":"List of user object","in":"body","name":"body","required":true,"schema":{"items":{"$ref":"#/definitions/User"},"type":"array"}}],"produces":["application/xml","application/json"],"responses":{"default":{"description":"successful operation"}},"summary":"Creates list of users with given input array","tags":["user"]}},"/user/createWithList":{"post":{"description":"","operationId":"createUsersWithListInput","parameters":[{"description":"List of user object","in":"body","name":"body","required":true,"schema":{"items":{"$ref":"#/definitions/User"},"type":"array"}}],"produces":["application/xml","application/json"],"responses":{"default":{"description":"successful operation"}},"summary":"Creates list of users with given input array","tags":["user"]}},"/user/login":{"get":{"description":"","operationId":"loginUser","parameters":[{"description":"The user name for login","in":"query","name":"username","required":true,"type":"string"},{"description":"The password for login in clear text","in":"query","name":"password","required":true,"type":"string"}],"produces":["application/xml","application/json"],"responses":{"200":{"description":"successful operation","headers":{"X-Expires-After":{"description":"date in UTC when token expires","format":"date-time","type":"string"},"X-Rate-Limit":{"description":"calls per hour allowed by the user","format":"int32","type":"integer"}},"schema":{"type":"string"}},"400":{"description":"Invalid username/password supplied"}},"summary":"Logs user into the system","tags":["user"]}},"/user/logout":{"get":{"description":"","operationId":"logoutUser","parameters":[],"produces":["application/xml","application/json"],"responses":{"default":{"description":"successful operation"}},"summary":"Logs out current logged in user session","tags":["user"]}},"/user/{username}":{"delete":{"description":"This can only be done by the logged in user.","operationId":"deleteUser","parameters":[{"description":"The name that needs to be deleted","in":"path","name":"username","required":true,"type":"string"}],"produces":["application/xml","application/json"],"responses":{"400":{"description":"Invalid username supplied"},"404":{"description":"User not found"}},"summary":"Delete user","tags":["user"]},"get":{"description":"","operationId":"getUserByName","parameters":[{"description":"The name that needs to be fetched. 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Each item in the list is the key of a single Auxiliary Graph.","items":{"type":"string"},"nullable":true,"type":"array"}},"required":["resource_id","edge_bindings"],"type":"object"},"AsyncQuery":{"additionalProperties":true,"description":"The AsyncQuery class is effectively the same as the Query class but it requires a callback property.","properties":{"bypass_cache":{"default":false,"description":"Set to true in order to request that the agent obtain fresh information from its sources in all cases where it has a viable choice between requesting fresh information in real time and using cached information. The agent receiving this flag MUST also include it in TRAPI sent to downstream sources (e.g., ARS -> ARAs -> KPs).","type":"boolean"},"callback":{"description":"Upon completion, this server will send a POST request to the callback URL with `Content-Type: application/json` header and request body containing a JSON-encoded `Response` object. The server MAY POST `Response` objects before work is fully complete to provide interim results with a Response.status value of 'Running'. If a POST operation to the callback URL does not succeed, the server SHOULD retry the POST at least once.","format":"uri","nullable":false,"pattern":"^https?://","type":"string"},"log_level":{"description":"The least critical level of logs to return","nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"message":{"description":"The query Message is a serialization of the user request. Content of the Message object depends on the intended TRAPI operation. For example, the fill operation requires a non-empty query_graph field as part of the Message, whereas other operations, e.g. overlay, require non-empty results and knowledge_graph fields.","nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"submitter":{"description":"Any string for self-identifying the submitter of a query. The purpose of this optional field is to aid in the tracking of the source of queries for development and issue resolution.","nullable":true,"type":"string"},"workflow":{"description":"List of workflow steps to be executed.","nullable":true}},"required":["message"],"type":"object","x-body-name":"request_body"},"AsyncQueryResponse":{"additionalProperties":true,"description":"The AsyncQueryResponse object contains a payload that must be returned from a submitted async_query.","properties":{"description":{"description":"A brief human-readable description of the result of the async_query submission.","example":"Async_query has been queued","nullable":true,"type":"string"},"job_id":{"description":"An identifier for the submitted job that can be used with /async_query_status to receive an update on the status of the job.","example":"rXEOAosN3L","nullable":false,"type":"string"},"status":{"description":"One of a standardized set of short codes: e.g. Accepted, QueryNotTraversable, KPsNotAvailable","example":"Accepted","nullable":true,"type":"string"}},"required":["job_id"],"type":"object"},"AsyncQueryStatusResponse":{"additionalProperties":true,"description":"The AsyncQueryStatusResponse object contains a payload that describes the current status of a previously submitted async_query.","properties":{"description":{"description":"A brief human-readable description of the current state or summary of the problem if the status is Failed.","example":"Callback URL returned 500","nullable":false,"type":"string"},"logs":{"description":"A list of LogEntry items, containing errors, warnings, debugging information, etc. List items MUST be in chronological order with earliest first. The most recent entry should be last. Its timestamp will be compared against the current time to see if there is still activity.","items":{"$ref":"#/components/schemas/LogEntry"},"minItems":1,"nullable":false,"type":"array"},"response_url":{"description":"Optional URL that can be queried to restrieve the full TRAPI Response.","example":"https://arax.ncats.io/api/arax/v1.3/response/116481","nullable":true,"type":"string"},"status":{"description":"One of a standardized set of short codes: Queued, Running, Completed, Failed","example":"Running","nullable":false,"type":"string"}},"required":["status","description","logs"],"type":"object"},"Attribute":{"additionalProperties":false,"description":"Generic attribute for a node or an edge that expands the key-value pair concept by including fields for additional metadata. These fields can be used to describe the source of the statement made in a key-value pair of the attribute object, or describe the attribute's value itself including its semantic type, or a url providing additional information about it. An attribute may be further qualified with sub-attributes (for example to provide confidence intervals on a value).","properties":{"attribute_source":{"description":"The source of the core assertion made by the key-value pair of an attribute object. Use a CURIE or namespace designator for this resource where possible.","example":"UniProtKB","nullable":true,"type":"string"},"attribute_type_id":{"$ref":"#/components/schemas/CURIE","description":"The 'key' of the attribute object, holding a CURIE of an ontology property defining the attribute (preferably the CURIE of a Biolink association slot). This property captures the relationship asserted to hold between the value of the attribute, and the node or edge from  which it hangs. For example, that a value of '0.000153' represents a p-value supporting an edge, or that a value of 'ChEMBL' represents the original source of the knowledge expressed in the edge.","example":"biolink:synonym"},"attributes":{"description":"A list of attributes providing further information about the parent attribute (for example to provide provenance information about the parent attribute).","nullable":true},"description":{"description":"Human-readable description for the attribute and its value.","example":"Assertion Authored By Dr. Trans L. Ator","nullable":true,"type":"string"},"original_attribute_name":{"description":"The term used by the original source of an attribute to describe the meaning or significance of the value it captures. This may be a column name in a source tsv file, or a key in a source json document for the field in the data that held the attribute's value. Capturing this information  where possible lets us preserve what the original source said. Note that the data type is string' but the contents of the field could also be a CURIE of a third party ontology term.","example":"p-value","nullable":true,"type":"string"},"value":{"description":"Value of the attribute. May be any data type, including a list.","example":0.000153},"value_type_id":{"description":"CURIE describing the semantic type of an  attribute's value. Use a Biolink class if possible, otherwise a term from an external ontology. If a suitable CURIE/identifier does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority.","example":"EDAM:data_1187","nullable":true,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]},"value_url":{"description":"Human-consumable URL linking to a web document that provides additional information about an  attribute's value (not the node or the edge fom which it hangs).","example":"https://pubmed.ncbi.nlm.nih.gov/32529952","nullable":true,"type":"string"}},"required":["attribute_type_id","value"],"type":"object"},"AttributeConstraint":{"additionalProperties":false,"description":"Generic query constraint for a query node or query edge","properties":{"id":{"description":"CURIE of the concept being constrained. For properties defined by the Biolink model this SHOULD be a biolink CURIE. otherwise, if possible, from the EDAM ontology. If a suitable CURIE does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority.","example":"EDAM:data_0844","oneOf":[{"$ref":"#/components/schemas/CURIE"}]},"name":{"description":"Human-readable name or label for the constraint concept. If appropriate, it SHOULD be the term name of the CURIE used as the 'id'. This is redundant but required for human readability.","example":"molecular mass","type":"string"},"not":{"default":false,"type":"boolean"},"operator":{"description":"Relationship between the database value and the constraint value for the specified id. The operators ==, >, and < mean is equal to, is greater than, and is less than, respectively. The 'matches' operator indicates that the value is a regular expression to be evaluated. If value is a list type, then at least one evaluation must be true (equivalent to OR). This means that the == operator with a list acts like a SQL 'IN' clause. If the value of the compared attribute is a list, then comparisons are performed between each of the constraint values and each of the attribute values, and any one true evaluation counts as an overall true (e.g., [1,2,3] == [6,7,2] is true). The == operator is therefore a broad interpretation of inclusion. The '===' operator requires that the constraint value and the attribute value be the same data type, length, content, and order (e.g. only [1,2,3] === [1,2,3]). The 'not' property negates the operator such that not and == means 'not equal to' (or 'not in' for a list), and not > means <=, and not < means >=, not matches means does not match, and not === means the match between the constraint and attribute values are not exact. The '==' operator SHOULD NOT be used in a manner that describes an \"is a\" subclass relationship for the parent QNode.","enum":["==",">","<","matches","==="],"type":"string"},"unit_id":{"description":"CURIE of the units of the value or list of values in the 'value' property. The Units of Measurement Ontology (UO) should be used if possible. The unit_id MUST be provided for (lists of) numerical values that correspond to a quantity that has units.","example":"UO:0000222","nullable":true},"unit_name":{"description":"Term name that is associated with the CURIE of the units of the value or list of values in the 'value' property. The Units of Measurement Ontology (UO) SHOULD be used if possible. This property SHOULD be provided if a unit_id is provided. This is redundant but recommended for human readability.","example":"kilodalton","nullable":true},"value":{"description":"Value of the attribute. May be any data type, including a list. If the value is a list and there are multiple items, at least one comparison must be true (equivalent to OR) unless the '===' operator is used. If 'value' is of data type 'object', the keys of the object MAY be treated as a list. A 'list' data type paired with the '>' or '<' operators will encode extraneous comparisons, but this is permitted as it is in SQL and other languages.","example":57.0}},"required":["name","id","operator","value"],"type":"object"},"AuxiliaryGraph":{"additionalProperties":true,"description":"A single AuxiliaryGraph instance that is used by Knowledge Graph Edges and Result Analyses. Edges comprising an Auxiliary Graph are a subset of the Knowledge Graph in the message. Data creators can create an AuxiliaryGraph to assemble a specific collections of edges from the Knowledge Graph into a named graph that can be referenced from an Edge as evidence/explanation supporting that Edge, or from a Result Analysis as information used to generate a score.","properties":{"attributes":{"description":"Attributes of the Auxiliary Graph","items":{"$ref":"#/components/schemas/Attribute"},"minItems":0,"nullable":false,"type":"array"},"edges":{"description":"List of edges that form the Auxiliary Graph. Each item is a reference to a single Knowledge Graph edge","items":{"type":"string"},"minItems":1,"nullable":false,"type":"array"}},"required":["edges","attributes"],"type":"object"},"BiolinkEntity":{"description":"Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name.","example":"biolink:PhenotypicFeature","externalDocs":{"description":"Biolink model entities","url":"https://biolink.github.io/biolink-model/docs/NamedThing.html"},"pattern":"^biolink:[A-Z][a-zA-Z]*$","type":"string"},"BiolinkPredicate":{"description":"CURIE for a Biolink 'predicate' slot, taken from the Biolink slot ('is_a') hierarchy rooted in biolink:related_to (snake_case). This predicate defines the Biolink relationship between the subject and object nodes of a biolink:Association defining a knowledge graph edge.","example":"biolink:interacts_with","externalDocs":{"description":"Biolink model predicates","url":"https://biolink.github.io/biolink-model/docs/related_to.html"},"pattern":"^biolink:[a-z][a-z_]*$","type":"string"},"CURIE":{"description":"A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI.","externalDocs":{"url":"https://www.w3.org/TR/2010/NOTE-curie-20101216/"},"type":"string"},"Edge":{"additionalProperties":false,"description":"A specification of the semantic relationship linking two concepts that are expressed as nodes in the knowledge \"thought\" graph resulting from a query upon the underlying knowledge source.","properties":{"attributes":{"description":"A list of additional attributes for this edge","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"object":{"description":"Corresponds to the map key CURIE of the object concept node of this relationship edge.","example":"UniProtKB:P00738","nullable":false,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]},"predicate":{"description":"The type of relationship between the subject and object for the statement expressed in an Edge. These should be Biolink Model predicate terms and are NOT allowed to be of type 'abstract' or 'mixin'. Returning 'deprecated' predicate terms should also be avoided.","example":"biolink:gene_associated_with_condition","nullable":false,"oneOf":[{"$ref":"#/components/schemas/BiolinkPredicate"}]},"qualifiers":{"description":"A set of Qualifiers that act together to add nuance or detail to the statement expressed in an Edge.","items":{"$ref":"#/components/schemas/Qualifier"},"nullable":true,"type":"array"},"sources":{"description":"A list of RetrievalSource objects that provide information about how a particular Information Resource served as a source from which the knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved.","items":{"$ref":"#/components/schemas/RetrievalSource"},"minItems":1,"nullable":false,"type":"array"},"subject":{"description":"Corresponds to the map key CURIE of the subject concept node of this relationship edge.","example":"MONDO:0011382","nullable":false,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]}},"required":["object","predicate","subject","sources"],"type":"object"},"EdgeBinding":{"additionalProperties":true,"description":"A instance of EdgeBinding is a single KnowledgeGraph Edge mapping, identified by the corresponding 'id' object key identifier of the Edge within the Knowledge Graph. Instances of EdgeBinding may include extra annotation (such annotation is not yet fully standardized). Edge bindings are captured within a specific reasoner's Analysis object because the Edges in the Knowledge Graph that get bound to the input Query Graph may differ between reasoners.","properties":{"attributes":{"description":"A list of attributes providing further information about the edge binding. This is not intended for capturing edge attributes and should only be used for properties that vary from result to result.","items":{"$ref":"#/components/schemas/Attribute"},"minItems":0,"nullable":false,"type":"array"},"id":{"description":"The key identifier of a specific KnowledgeGraph Edge.","nullable":false,"type":"string"}},"required":["id","attributes"],"type":"object"},"KnowledgeGraph":{"additionalProperties":true,"description":"The knowledge graph associated with a set of results. The instances of Node and Edge defining this graph represent instances of biolink:NamedThing (concept nodes) and biolink:Association (relationship edges) representing (Attribute) annotated knowledge returned from the knowledge sources and inference agents wrapped by the given TRAPI implementation.","properties":{"edges":{"additionalProperties":{"$ref":"#/components/schemas/Edge"},"description":"Dictionary of Edge instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key.","type":"object"},"nodes":{"additionalProperties":{"$ref":"#/components/schemas/Node"},"description":"Dictionary of Node instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key.","type":"object"}},"required":["nodes","edges"],"type":"object"},"LogEntry":{"additionalProperties":true,"description":"The LogEntry object contains information useful for tracing and debugging across Translator components.  Although an individual component (for example, an ARA or KP) may have its own logging and debugging infrastructure, this internal information is not, in general, available to other components. In addition to a timestamp and logging level, LogEntry includes a string intended to be read by a human, along with one of a standardized set of codes describing the condition of the component sending the message.","properties":{"code":{"description":"One of a standardized set of short codes e.g. QueryNotTraversable, KPNotAvailable, KPResponseMalformed","nullable":true,"type":"string"},"level":{"nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"message":{"description":"A human-readable log message","nullable":true,"type":"string"},"timestamp":{"description":"Timestamp in ISO 8601 format, providing the LogEntry time either in univeral coordinated time (UTC) using the 'Z' tag (e.g 2020-09-03T18:13:49Z), or, if local time is provided, the timezone offset must be provided (e.g. 2020-09-03T18:13:49-04:00).","example":"2020-09-03T18:13:49+00:00","format":"date-time","nullable":false,"type":"string"}},"required":["timestamp","message"],"type":"object"},"LogLevel":{"description":"Logging level","enum":["ERROR","WARNING","INFO","DEBUG"],"type":"string"},"Message":{"additionalProperties":false,"description":"The message object holds the main content of a Query or a Response in three properties: query_graph, results, and knowledge_graph. The query_graph property contains the query configuration, the results property contains any answers that are returned by the service, and knowledge_graph property contains lists of edges and nodes in the thought graph corresponding to this message. The content of these properties is context-dependent to the encompassing object and the TRAPI operation requested.","properties":{"auxiliary_graphs":{"additionalProperties":{"$ref":"#/components/schemas/AuxiliaryGraph"},"description":"Dictionary of AuxiliaryGraph instances that are used by Knowledge Graph Edges and Result Analyses. These are referenced elsewhere by the dictionary key.","nullable":true,"type":"object"},"knowledge_graph":{"description":"KnowledgeGraph object that contains lists of nodes and edges in the thought graph corresponding to the message","nullable":true,"oneOf":[{"$ref":"#/components/schemas/KnowledgeGraph"}]},"query_graph":{"description":"QueryGraph object that contains a serialization of a query in the form of a graph","nullable":true,"oneOf":[{"$ref":"#/components/schemas/QueryGraph"}]},"results":{"description":"List of all returned Result objects for the query posed. The list SHOULD NOT be assumed to be ordered. The 'score' property, if present, MAY be used to infer result rankings. If Results are not expected (such as for a query Message), this property SHOULD be null or absent. If Results are expected (such as for a response Message) and no Results are available, this property SHOULD be an array with 0 Results in it.","items":{"$ref":"#/components/schemas/Result"},"minItems":0,"nullable":true,"type":"array"}},"type":"object"},"MetaAttribute":{"properties":{"attribute_source":{"description":"Source of an attribute provided by this TRAPI web service.","example":"infores:chembl","nullable":true,"type":"string"},"attribute_type_id":{"$ref":"#/components/schemas/CURIE","description":"Type of an attribute provided by this TRAPI web service (preferably the CURIE of a Biolink association slot)","example":"biolink:p_value"},"constraint_name":{"description":"Human-readable name or label for the constraint concept. Required whenever constraint_use is true.","example":"p-value","nullable":true,"type":"string"},"constraint_use":{"default":false,"description":"Indicates whether this attribute can be used as a query constraint.","type":"boolean"},"original_attribute_names":{"description":"Names of an the attribute as provided by the source.","items":{"type":"string"},"minItems":1,"nullable":true,"type":"array"}},"required":["attribute_type_id"],"type":"object"},"MetaEdge":{"additionalProperties":false,"description":"Edge in a meta knowledge map describing relationship between a subject Biolink class and an object Biolink class.","properties":{"association":{"$ref":"#/components/schemas/BiolinkEntity","description":"The Biolink association type (entity) that this edge represents. Associations are classes in Biolink that represent a relationship between two entities. For example, the association 'gene interacts with gene' is represented by the Biolink class, 'biolink:GeneToGeneAssociation'.  If association is filled out, then the testing harness can help validate that the qualifiers are being used correctly.","example":"biolink:ChemicalToGeneAssociation"},"attributes":{"description":"Edge attributes provided by this TRAPI web service.","items":{"$ref":"#/components/schemas/MetaAttribute"},"nullable":true,"type":"array"},"knowledge_types":{"description":"A list of knowledge_types that are supported by the service. If the knowledge_types is null, this means that only 'lookup' is supported. Currently allowed values are 'lookup' or 'inferred'.","items":{"type":"string"},"minItems":1,"nullable":true,"type":"array"},"object":{"$ref":"#/components/schemas/BiolinkEntity","description":"Object node category of this relationship edge.","example":"biolink:Protein"},"predicate":{"$ref":"#/components/schemas/BiolinkPredicate","description":"Biolink relationship between the subject and object categories.","example":"biolink:affects"},"qualifiers":{"description":"Qualifiers that are possible to be found on this edge type.","items":{"$ref":"#/components/schemas/MetaQualifier"},"nullable":true,"type":"array"},"subject":{"$ref":"#/components/schemas/BiolinkEntity","description":"Subject node category of this relationship edge.","example":"biolink:ChemicalEntity"}},"required":["subject","predicate","object"],"type":"object"},"MetaKnowledgeGraph":{"description":"Knowledge-map representation of this TRAPI web service. The meta knowledge graph is composed of the union of most specific categories and predicates for each node and edge.","properties":{"edges":{"description":"List of the most specific edges/predicates provided by this TRAPI web service. A predicate is only exposed here if there is an edge for which the predicate is the most specific available.","items":{"$ref":"#/components/schemas/MetaEdge"},"type":"array"},"nodes":{"additionalProperties":{"$ref":"#/components/schemas/MetaNode"},"description":"Collection of the most specific node categories provided by this TRAPI web service, indexed by Biolink class CURIEs. A node category is only exposed here if there is node for which that is the most specific category available.","type":"object"}},"required":["nodes","edges"],"type":"object"},"MetaNode":{"additionalProperties":false,"description":"Description of a node category provided by this TRAPI web service.","properties":{"attributes":{"description":"Node attributes provided by this TRAPI web service.","items":{"$ref":"#/components/schemas/MetaAttribute"},"nullable":true,"type":"array"},"id_prefixes":{"description":"List of CURIE prefixes for the node category that this TRAPI web service understands and accepts on the input.","example":["CHEMBL.COMPOUND","INCHIKEY"],"items":{"type":"string"},"minItems":1,"type":"array"}},"required":["id_prefixes"],"type":"object"},"MetaQualifier":{"properties":{"applicable_values":{"description":"The list of values that are possible for this qualifier.","items":{"example":["expression","activity","abundance","degradation"],"type":"string"},"type":"array"},"qualifier_type_id":{"$ref":"#/components/schemas/CURIE","description":"The CURIE of the qualifier type.","example":"biolink:subject_aspect_qualifier","nullable":false}},"required":["qualifier_type_id"],"type":"object"},"Node":{"additionalProperties":false,"description":"A node in the KnowledgeGraph which represents some biomedical concept. Nodes are identified by the keys in the KnowledgeGraph Node mapping.","properties":{"attributes":{"description":"A list of attributes describing the node","items":{"$ref":"#/components/schemas/Attribute"},"minItems":0,"nullable":false,"type":"array"},"categories":{"description":"These should be Biolink Model categories and are NOT allowed to be of type 'abstract' or 'mixin'. Returning 'deprecated' categories should also be avoided.","items":{"$ref":"#/components/schemas/BiolinkEntity"},"minItems":1,"nullable":false,"type":"array"},"is_set":{"description":"Indicates that the node represents a set of entities. If this property is missing or null, it is assumed to be false.","nullable":true,"type":"boolean"},"name":{"description":"Formal name of the entity","example":"Haptoglobin","nullable":true,"type":"string"}},"required":["categories","attributes"],"type":"object"},"NodeBinding":{"additionalProperties":true,"description":"An instance of NodeBinding is a single KnowledgeGraph Node mapping, identified by the corresponding 'id' object key identifier of the Node within the Knowledge Graph. Instances of NodeBinding may include extra annotation in the form of additional properties. (such annotation is not yet fully standardized). Each Node Binding must bind directly to node in the original Query Graph.","properties":{"attributes":{"description":"A list of attributes providing further information about the node binding. This is not intended for capturing node attributes and should only be used for properties that vary from result to result.","items":{"$ref":"#/components/schemas/Attribute"},"minItems":0,"nullable":false,"type":"array"},"id":{"description":"The CURIE of a Node within the Knowledge Graph.","nullable":false,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]},"query_id":{"description":"An optional property to provide the CURIE in the QueryGraph to which this binding applies. If the bound QNode does not have an an 'id' property or if it is empty, then this query_id MUST be null or absent. If the bound QNode has one or more CURIEs as an 'id' and this NodeBinding's 'id' refers to a QNode 'id' in a manner where the CURIEs are different (typically due to the NodeBinding.id being a descendant of a QNode.id), then this query_id MUST be provided. In other cases, there is no ambiguity, and this query_id SHOULD NOT be provided.","nullable":true,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]}},"required":["id","attributes"],"type":"object"},"QEdge":{"additionalProperties":true,"description":"An edge in the QueryGraph used as a filter pattern specification in a query. If the optional predicate property is not specified, it is assumed to be a wildcard match to the target knowledge space. If specified, the ontological inheritance hierarchy associated with the term provided is assumed, such that edge bindings returned may be an exact match to the given QEdge predicate term, or to a term that is a descendant of the QEdge predicate term.","properties":{"attribute_constraints":{"default":[],"description":"A list of attribute constraints applied to a query edge. If there are multiple items, they must all be true (equivalent to AND)","items":{"$ref":"#/components/schemas/AttributeConstraint"},"type":"array"},"knowledge_type":{"description":"Indicates the type of knowledge that the client wants from the server between the subject and object. If the value is 'lookup', then the client wants direct lookup information from knowledge sources. If the value is 'inferred', then the client wants the server to get creative and connect the subject and object in more speculative and non-direct-lookup ways. If this property is absent or null, it MUST be assumed to mean 'lookup'. This feature is currently experimental and may be further extended in the future.","example":"lookup","nullable":true,"type":"string"},"object":{"description":"Corresponds to the map key identifier of the object concept node anchoring the query filter pattern for the query relationship edge.","example":"https://www.uniprot.org/uniprot/P00738","type":"string"},"predicates":{"description":"These should be Biolink Model predicates and are allowed to be of type 'abstract' or 'mixin' (only in QGraphs!). Use of 'deprecated' predicates should be avoided.","items":{"$ref":"#/components/schemas/BiolinkPredicate"},"minItems":1,"nullable":true,"type":"array"},"qualifier_constraints":{"default":[],"description":"A list of QualifierConstraints that provide nuance to the QEdge. If multiple QualifierConstraints are provided, there is an OR relationship between them. If the QEdge has multiple predicates or if the QNodes that correspond to the subject or object of this QEdge have multiple categories or multiple curies, then qualifier_constraints MUST NOT be specified because these complex use cases are not supported at this time.","items":{"$ref":"#/components/schemas/QualifierConstraint"},"type":"array"},"subject":{"description":"Corresponds to the map key identifier of the subject concept node anchoring the query filter pattern for the query relationship edge.","example":"https://omim.org/entry/603903","type":"string"}},"required":["subject","object"],"type":"object"},"QNode":{"additionalProperties":true,"description":"A node in the QueryGraph used to represent an entity in a query. If a CURIE is not specified, any nodes matching the category of the QNode will be returned in the Results.","properties":{"categories":{"description":"These should be Biolink Model categories and are allowed to be of type 'abstract' or 'mixin' (only in QGraphs!). Use of 'deprecated' categories should be avoided.","items":{"$ref":"#/components/schemas/BiolinkEntity"},"minItems":1,"nullable":true,"type":"array"},"constraints":{"default":[],"description":"A list of constraints applied to a query node. If there are multiple items, they must all be true (equivalent to AND)","items":{"$ref":"#/components/schemas/AttributeConstraint"},"type":"array"},"ids":{"description":"A CURIE identifier (or list of identifiers) for this node.  The 'ids' field will hold a list of CURIEs only in the case of a BATCH set_interpretation, where each CURIE is queried  separately. If a list of queried CURIEs is to be considered as a   set (as under a MANY or ALL set_interpretation), the 'ids' field  will hold a single id representing this set, and the individual members  of this set will be captured in a separate 'member_ids' field.  Note that the set id MUST be created as a UUID by the system that  defines the queried set, using a centralized nodenorm service.  Note also that downstream systems MUST re-use the original set UUID  in the messages they create/send, which will facilitate merging or  caching operations.","example":["OMIM:603903"],"items":{"$ref":"#/components/schemas/CURIE"},"minItems":1,"nullable":true,"type":"array"},"member_ids":{"description":"A list of CURIE identifiers for members of a queried set. This  field MUST be populated under a set_interpretation of MANY or ALL, when the 'ids' field holds a UUID representing the set  itself. This field MUST NOT be used under a set_interpretation  of BATCH.","items":{"$ref":"#/components/schemas/CURIE"},"nullable":true,"type":"array"},"set_interpretation":{"description":"Indicates how multiple CURIEs in the ids property MUST be interpreted. BATCH indicates that the query is intended to be a batch query and each CURIE is treated independently. ALL means that all specified CURIES MUST appear in each Result. MANY means that member CURIEs MUST form one or more sets in the Results, and sets with more members are generally considered more desirable that sets with fewer members. If this property is missing or null, the default is BATCH.","enum":["BATCH","ALL","MANY"],"nullable":true,"type":"string"}},"type":"object"},"Qualifier":{"additionalProperties":false,"description":"An additional nuance attached to an assertion","properties":{"qualifier_type_id":{"$ref":"#/components/schemas/CURIE","description":"CURIE for a Biolink 'qualifier' association slot, generally taken from Biolink association slots designated for this purpose (that is, association slots with names ending in 'qualifier') e.g. biolink:subject_aspect_qualifier,  biolink:subject_direction_qualifier, biolink:object_aspect_qualifier, etc. Such qualifiers are used to elaborate a second layer of meaning of a knowledge graph edge. Available qualifiers are edge properties in the Biolink Model (see https://biolink.github.io/biolink-model/docs/edge_properties.html) which have slot names with the suffix string 'qualifier'.","example":"biolink:subject_aspect_qualifier","nullable":false,"pattern":"^biolink:[a-z][a-z_]*$"},"qualifier_value":{"description":"The value associated with the type of the qualifier, drawn from a set of controlled values by the type as specified in the Biolink model (e.g. 'expression' or 'abundance' for the qualifier type 'biolink:subject_aspect_qualifier', etc). The enumeration of qualifier values for a given qualifier type is generally going to be constrained by the category of edge (i.e. biolink:Association subtype) of the (Q)Edge.","example":"expression","nullable":false,"type":"string"}},"required":["qualifier_type_id","qualifier_value"],"type":"object"},"QualifierConstraint":{"additionalProperties":false,"description":"Defines a query constraint based on the qualifier_types and qualifier_values of a set of Qualifiers attached to an edge. For example, it can constrain a \"ChemicalX - affects - ?Gene\" query to return only edges where ChemicalX specifically affects the 'expression' of the Gene, by constraining on the qualifier_type \"biolink:object_aspect_qualifier\" with a qualifier_value of \"expression\".","properties":{"qualifier_set":{"description":"A set of Qualifiers that serves to add nuance to a query, by constraining allowed values held by Qualifiers on queried Edges.","items":{"$ref":"#/components/schemas/Qualifier"},"nullable":false,"type":"array"}},"required":["qualifier_set"],"type":"object"},"Query":{"additionalProperties":true,"description":"The Query class is used to package a user request for information. A Query object consists of a required Message object with optional additional properties. Additional properties are intended to convey implementation-specific or query-independent parameters. For example, an additional property specifying a log level could allow a user to override the default log level in order to receive more fine-grained log information when debugging an issue.","properties":{"bypass_cache":{"default":false,"description":"Set to true in order to request that the agent obtain fresh information from its sources in all cases where it has a viable choice between requesting fresh information in real time and using cached information. The agent receiving this flag MUST also include it in TRAPI sent to downstream sources (e.g., ARS -> ARAs -> KPs).","type":"boolean"},"log_level":{"description":"The least critical level of logs to return","nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"message":{"description":"The query Message is a serialization of the user request. Content of the Message object depends on the intended TRAPI operation. For example, the fill operation requires a non-empty query_graph field as part of the Message, whereas other operations, e.g. overlay, require non-empty results and knowledge_graph fields.","nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"submitter":{"description":"Any string for self-identifying the submitter of a query. The purpose of this optional field is to aid in the tracking of the source of queries for development and issue resolution.","nullable":true,"type":"string"},"workflow":{"description":"List of workflow steps to be executed.","nullable":true}},"required":["message"],"type":"object","x-body-name":"request_body"},"QueryGraph":{"additionalProperties":true,"description":"A graph representing a biomedical question. It serves as a template for each result (answer), where each bound knowledge graph node/edge is expected to obey the constraints of the associated query graph element.","properties":{"edges":{"additionalProperties":{"$ref":"#/components/schemas/QEdge"},"description":"The edge specifications. The keys of this map are unique edge identifiers and the corresponding values include the constraints on bound edges, in addition to specifying the subject and object QNodes.","type":"object"},"nodes":{"additionalProperties":{"$ref":"#/components/schemas/QNode"},"description":"The node specifications. The keys of this map are unique node identifiers and the corresponding values include the constraints on bound nodes.","type":"object"}},"required":["nodes","edges"],"type":"object"},"ResourceRoleEnum":{"description":"The role played by the InformationResource in serving as a source for an Edge. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources.  This enumeration is found in Biolink Model, but is repeated here for convenience.","enum":["primary_knowledge_source","aggregator_knowledge_source","supporting_data_source"],"type":"string"},"Response":{"additionalProperties":true,"description":"The Response object contains the main payload when a TRAPI query endpoint interprets and responds to the submitted query successfully (i.e., HTTP Status Code 200). The message property contains the knowledge of the response (query graph, knowledge graph, and results). The status, description, and logs properties provide additional details about the response.","properties":{"biolink_version":{"description":"Version label of the Biolink model used in this document","example":"3.1.2","nullable":true,"type":"string"},"description":{"description":"A brief human-readable description of the outcome","example":"Success. 42 results found.","nullable":true,"type":"string"},"logs":{"description":"A list of LogEntry items, containing errors, warnings, debugging information, etc. List items MUST be in chronological order with earliest first.","items":{"$ref":"#/components/schemas/LogEntry"},"minItems":0,"nullable":false,"type":"array"},"message":{"description":"Contains the knowledge of the response (query graph, knowledge graph, and results).","nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"schema_version":{"description":"Version label of the TRAPI schema used in this document","example":"1.4.0","nullable":true,"type":"string"},"status":{"description":"One of a standardized set of short codes, e.g. Success, QueryNotTraversable, KPsNotAvailable","example":"Success","nullable":true,"type":"string"},"workflow":{"description":"List of workflow steps that were executed.","nullable":true}},"required":["message"],"type":"object"},"Result":{"additionalProperties":true,"description":"A Result object specifies the nodes and edges in the knowledge graph that satisfy the structure or conditions of a user-submitted query graph. It must contain a NodeBindings object (list of query graph node to knowledge graph node mappings) and a list of Analysis objects.","properties":{"analyses":{"description":"The list of all Analysis components that contribute to the result. See below for Analysis components.","items":{"$ref":"#/components/schemas/Analysis"},"minItems":0,"nullable":false,"type":"array"},"node_bindings":{"additionalProperties":{"items":{"$ref":"#/components/schemas/NodeBinding"},"minItems":1,"type":"array"},"description":"The dictionary of Input Query Graph to Result Knowledge Graph node bindings where the dictionary keys are the key identifiers of the Query Graph nodes and the associated values of those keys are instances of NodeBinding schema type (see below). This value is an array of NodeBindings since a given query node may have multiple knowledge graph Node bindings in the result.","nullable":false,"type":"object"}},"required":["node_bindings","analyses"],"type":"object"},"RetrievalSource":{"additionalProperties":true,"description":"Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved.","properties":{"resource_id":{"$ref":"#/components/schemas/CURIE","description":"The CURIE for an Information Resource that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.","example":"infores:drugbank","nullable":false},"resource_role":{"$ref":"#/components/schemas/ResourceRoleEnum","description":"The role played by the InformationResource in serving as a source for an Edge. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources."},"source_record_urls":{"description":"A URL linking to a specific web page or document provided by the  source, that contains a record of the knowledge expressed in the  Edge. If the knowledge is contained in more than one web page on  an Information Resource's site, urls MAY be provided for each.  For example, Therapeutic Targets Database (TTD) has separate web  pages for 'Imatinib' and its protein target KIT, both of which hold  the claim that 'the KIT protein is a therapeutic target for Imatinib'.         ","example":"[https://db.idrblab.net/ttd/data/drug/details/d0az3c,  https://db.idrblab.net/ttd/data/target/details/t57700]","items":{"type":"string"},"nullable":true,"type":"array"},"upstream_resource_ids":{"description":"An upstream InformationResource from which the resource being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge. This is an array because there are cases where a merged Edge holds knowledge that was retrieved from multiple sources. e.g. an Edge provided by the ARAGORN ARA can expressing knowledge it retrieved from both the automat-mychem-info and molepro KPs, which both provided it with records of this single fact.","example":["infores:automat-mychem-info","infores:molepro"],"items":{"$ref":"#/components/schemas/CURIE"},"nullable":true,"type":"array"}},"required":["resource_id","resource_role"],"type":"object"}}},"info":{"contact":{"email":"asu@scripps.edu","name":"Andrew Su","url":"https://github.com/andrewsu"},"description":"A TRAPI/Reasoner Standard API for BioThings Explorer (BTE)","termsOfService":"https://biothings.io/about","title":"BioThings Explorer (BTE) TRAPI","version":"3.0.0","x-translator":{"biolink-version":"4.2.2","component":"ARA","infores":"infores:biothings-explorer","team":["Exploring Agent"]},"x-trapi":{"asyncquery":true,"batch_size_limit":150,"multicuriequery":false,"operations":["lookup_and_score"],"pathfinderquery":true,"rate_limit":15,"test_data_location":{"default":{"url":"https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biothings_explorer/sri-test-bte-ara.json"}},"version":"1.5.0"}},"openapi":"3.0.3","paths":{"/meta_knowledge_graph":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns meta knowledge graph representation of this TRAPI web service."}},"summary":"Meta knowledge graph representation of this TRAPI web service.","tags":["meta_knowledge_graph"]}},"/smartapi/{smartapi_id}/meta_knowledge_graph":{"get":{"parameters":[{"description":"SmartAPI ID of an API with x-bte annotation. The easiest way to find these is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js","example":"09c8782d9f4027712e65b95424adba79","in":"path","name":"smartapi_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns a TRAPI-compliant meta-knowledge-graph representation for an individual SmartAPI KP API (that has x-bte annotation)"}},"summary":"TRAPI-compliant meta-knowledge-graph representation for an individual SmartAPI KP API (that has x-bte annotation)","tags":["meta_knowledge_graph"]}},"/team/{team_name}/meta_knowledge_graph":{"get":{"parameters":[{"description":"Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. Note that Service Provider endpoints are also registered separately as a KP in the SmartAPI Registry","example":"Service Provider","in":"path","name":"team_name","required":true,"schema":{"enum":["Multiomics Provider","Text Mining Provider","Service Provider"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns a TRAPI-compliant meta-knowledge-graph representation for one KP team's SmartAPI KP APIs (that have x-bte annotation)"}},"summary":"TRAPI-compliant meta-knowledge-graph representation for one KP team's SmartAPI KP APIs (that have x-bte annotation)","tags":["meta_knowledge_graph"]}},"/query":{"post":{"parameters":[{"description":"Legacy option to explicitly enable/disable caching.","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"Dryrun a query (logs the queries BTE would make without running them)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}},{"description":"Dryrun a pathfinder query (logs the tempalted-queries BTE would make without running them)","in":"query","name":"dryrun_pathfinder","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/Query"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. 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. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a TRAPI-format query to BTE (operating as an ARA) and wait to receive a Response","tags":["query"]}},"/smartapi/{smartapi_id}/query":{"post":{"parameters":[{"description":"SmartAPI ID of an API with x-bte annotation. The easiest way to find these is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js","example":"09c8782d9f4027712e65b95424adba79","in":"path","name":"smartapi_id","required":true,"schema":{"type":"string"}},{"description":"Legacy option to explicitly enable/disable caching.","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"Dryrun a query (logs the queries BTE would make without running them)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/Query"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. 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. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Query individual SmartAPI KP API (that has x-bte annotation) as a TRAPI KP API","tags":["query"]}},"/team/{team_name}/query":{"post":{"parameters":[{"description":"Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. Note that Service Provider endpoints are also registered separately as a KP in the SmartAPI Registry","example":"Service Provider","in":"path","name":"team_name","required":true,"schema":{"enum":["Multiomics Provider","Text Mining Provider","Service Provider"],"type":"string"}},{"description":"Legacy option to explicitly enable/disable caching.","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"Dryrun a query (logs the queries BTE would make without running them)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/Query"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Query an individual Translator team's SMARTAPI KP APIs (that have x-bte annotation) as an individual TRAPI service by specifying the team name","tags":["query"]}},"/asyncquery":{"post":{"parameters":[{"description":"Legacy option to explicitly enable/disable caching.","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"Dryrun a query (logs the queries BTE would make without running them)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}},{"description":"Dryrun a pathfinder query (logs the tempalted-queries BTE would make without running them)","in":"query","name":"dryrun_pathfinder","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryResponse"}}},"description":"The query is accepted for processing. The behavior will depend on whether the callback property is included. If the callback property is included, the Response will be sent to the callback url when complete. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. 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. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response.","tags":["asyncquery"]}},"/smartapi/{smartapi_id}/asyncquery":{"post":{"parameters":[{"description":"SmartAPI ID of an API with x-bte annotation. The easiest way to find these is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js","example":"09c8782d9f4027712e65b95424adba79","in":"path","name":"smartapi_id","required":true,"schema":{"type":"string"}},{"description":"Legacy option to explicitly enable/disable caching.","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"Dryrun a query (logs the queries BTE would make without running them)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryResponse"}}},"description":"The query is accepted for processing. The behavior will depend on whether the callback property is included. If the callback property is included, the Response will be sent to the callback url when complete. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. 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. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"This endpoint is for asynchronously querying an individual SmartAPI KP API (that has x-bte annotation)  as a TRAPI KP API.\nInitiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response.","tags":["asyncquery"]}},"/team/{team_name}/asyncquery":{"post":{"parameters":[{"description":"Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. Note that Service Provider endpoints are also registered separately as a KP in the SmartAPI Registry","example":"Service Provider","in":"path","name":"team_name","required":true,"schema":{"enum":["Multiomics Provider","Text Mining Provider","Service Provider"],"type":"string"}},{"description":"Legacy option to explicitly enable/disable caching.","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"Dryrun a query (logs the queries BTE would make without running them)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryResponse"}}},"description":"The query is accepted for processing. The behavior will depend on whether the callback property is included. If the callback property is included, the Response will be sent to the callback url when complete. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. 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. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"This endpoint is for asynchronously querying an individual Translator team's SMARTAPI KP APIs (that have x-bte annotation)  as an individual TRAPI service by specifying the team name.\nInitiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response.","tags":["asyncquery"]}},"/asyncquery_status/{job_id}":{"get":{"operationId":"asyncquery_status","parameters":[{"description":"Identifier of the job for status request","in":"path","name":"job_id","required":true,"schema":{"type":"string"}},{"description":"When specified, the TRAPI logs returned will be of this level of importance or higher. This setting will override the log_level setting in the job's TRAPI query.\nIf it's not specified, BTE will use the log_level setting in the job's TRAPI query or return all logs (the default). ","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. 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"]}},"/asyncquery_response/{job_id}":{"get":{"operationId":"asyncquery_response","parameters":[{"description":"Identifier of the job for status request","in":"path","name":"job_id","required":true,"schema":{"type":"string"}},{"description":"When specified, the TRAPI logs returned will be of this level of importance or higher. This setting will override the log_level setting in the job's TRAPI query.\nIf it's not specified, BTE will use the log_level setting in the job's TRAPI query or return all logs (the default). ","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). But if the asyncquery job is finished,  the complete TRAPI response to the query will be returned","tags":["asyncquery_response"]}}},"servers":[{"description":"ITRB Production server","url":"https://bte.transltr.io/v1","x-maturity":"production"},{"description":"ITRB Test server","url":"https://bte.test.transltr.io/v1","x-maturity":"testing"},{"description":"ITRB CI server","url":"https://bte.ci.transltr.io/v1","x-maturity":"staging"}],"tags":[{"name":"1.5.0"},{"name":"meta_knowledge_graph"},{"name":"query"},{"name":"asyncquery"},{"name":"asyncquery_status"},{"name":"translator"},{"name":"trapi"},{"name":"biothings"}]},{"info":{"contact":{"email":"gtex-help@broadinstitute.org","name":"GTEx Help"},"termsOfService":"https://sites.google.com/broadinstitute.org/gtex-faqs/home","title":"GTEx API","version":"v1"},"openapi":"3.0.0","paths":{"/admin/ping":{"get":{"description":"This web service sends a request to the ping endpoint to see if the server is available. If it fails to respond then either there is an issue with the server being addressed, or there are connection issues on the network reaching out to the server.","operationId":"ping","parameters":[],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Success"},"default":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Unexpected error."}},"summary":"Heartbeat to check server connectivity.","tags":["admin"]}},"/association/dyneqtl":{"get":{"description":"This service calculates the gene-variant association for any given pair of gene and variant, which may or may not be significant. This requires as input a GENCODE ID, GTEx variant ID, and tissue site detail ID. 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A false discovery rate (FDR) threshold of <= 0.05 was applied to identify genes with a significant eQTL.","operationId":"egene","parameters":[{"description":"Page (slice) of entire results set to return. 0-based.","in":"query","name":"page","required":false,"schema":{"items":{"format":"int32","type":"integer"},"type":"array"}},{"description":"Number of records per page of results.  Max is 2000.","in":"query","name":"pageSize","required":false,"schema":{"default":250,"items":{"format":"int32","type":"integer"},"maximum":2000,"minimum":1,"type":"array"}},{"description":"Filter down results matching the specified term. 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Default empty string will simply return all expression values (no boxplot calculations performed).","in":"query","name":"boxplotDetail","required":false,"schema":{"enum":["full","median","quartiles"],"type":"string"}},{"description":"Format of result.","in":"query","name":"format","required":false,"schema":{"default":"json","enum":["json","tsv","csv"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Success"},"default":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Unexpected error."}},"summary":"Find transcript expression data at the sample level.","tags":["expression"]}},"/metadata/dataset":{"get":{"description":"This service returns information and analysis summary of the datasets that GTEx web services provide. Results may be filtered by dataset ID or organization.","operationId":"dataset","parameters":[{"description":"Unique identifier of a dataset. 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Results may be filtered by tissue site (tissueSite), subsite name (tissueSiteDetail), subsite ID (tissueSiteId), or subsite abbreviation (tissueSiteDetailAbbr).","operationId":"tissueSiteDetail","parameters":[{"description":"Format of result.","in":"query","name":"format","required":false,"schema":{"default":"json","enum":["json","tsv","csv"],"type":"string"}},{"description":"Tissue Site is an anatomical grouping of Tissue Site Details.","in":"query","name":"tissueSite","required":false,"schema":{"enum":["Adipose Tissue","Adrenal Gland","Blood","Blood Vessel","Bladder","Brain","Breast","Cervix Uteri","Colon","Esophagus","Fallopian Tube","Heart","Kidney","Liver","Lung","Muscle","Nerve","Ovary","Pancreas","Pituitary","Prostate","Salivary Gland","Skin","Small Intestine","Spleen","Stomach","Testis","Thyroid","Uterus","Vagina"],"type":"string"}},{"description":"The formatted version of a tissueSiteDetail, e.g., Adipose - Subcutaneous","in":"query","name":"tissueSiteDetail","required":false,"schema":{"type":"string"}},{"description":"Standard abbreviation for the Tissue Site Detail, e.g., ADPSBQ.","in":"query","name":"tissueSiteDetailAbbr","required":false,"schema":{"type":"string"}},{"description":"The URL formatted version of a tissueSiteDetail, e.g., Adipose_Subcutaneous","in":"query","name":"tissueSiteDetailId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Success"},"default":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Unexpected error."}},"summary":"Find metadata of each tissue site detail.","tags":["metadata"]}},"/reference/exon":{"get":{"deprecated":false,"description":"This service returns exons from all known transcripts of the given gene. A versioned GENCODE ID is required to ensure that all exons are from a single gene. A dataset ID or both GENCODE version and genome build must be provided. Although annotated exons are not dataset dependent, specifying a dataset here is equivalent to specifying the GENCODE version and genome build used by that dataset.","operationId":"exon","parameters":[{"description":"Versioned GENCODE ID of a gene, e.g. ENSG00000065613.9.","in":"query","name":"gencodeId","required":true,"schema":{"type":"string"}},{"description":"GENCODE annotation release.","in":"query","name":"gencodeVersion","required":false,"schema":{"enum":["v19"],"type":"string"}},{"description":"Reference genome assembly.","in":"query","name":"genomeBuild","required":false,"schema":{"enum":["GRCh37/hg19"],"type":"string"}},{"description":"Unique identifier of a dataset. 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