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This is a newer version where each record is a unique combination of subjectID-predicate- objectID and contains a count of the unique pmids and predications supporting it.","termsOfService":"https://biothings.io/about","title":"BioThings SEMMEDDB API","version":"43_2024R","x-translator":{"biolink-version":"4.2.6","component":"KP","infores":"infores:biothings-semmeddb","team":["Service Provider"]}},"openapi":"3.0.3","paths":{"/association/{id}":{"get":{"description":"By default, this will return the complete association in JSON format. If the input is not valid, 404 (NOT FOUND) will be returned.\n\nOptionally, you can pass a \"fields\" parameter to return only the annotation you want  (by filtering returned object fields). \"fields\" accepts any attributes (a.k.a fields) available  from the association. Multiple attributes should be separated by commas. If an attribute is not  available for a specific association, it will be ignored. 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Unlike the call files/actions/copy, this lets you batch the copy operation and copy a list of files at a time.","operationId":"GET_action-files-copy","parameters":[{"$ref":"#/components/parameters/trait_pageable_limit"},{"$ref":"#/components/parameters/trait_pageable_offset"}],"requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/RequestBatchFileCopy"}}},"required":true},"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/FileCopyStatus"},"type":"array"}}},"description":""}},"security":[{"sevenbridges":[]}],"summary":"Copy files between projects. 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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. Use user1 for testing. ","in":"path","name":"username","required":true,"type":"string"}],"produces":["application/xml","application/json"],"responses":{"200":{"description":"successful operation","schema":{"$ref":"#/definitions/User"}},"400":{"description":"Invalid username supplied"},"404":{"description":"User not found"}},"summary":"Get user by user name","tags":["user"]},"put":{"description":"This can only be done by the logged in user.","operationId":"updateUser","parameters":[{"description":"name that need to be updated","in":"path","name":"username","required":true,"type":"string"},{"description":"Updated user object","in":"body","name":"body","required":true,"schema":{"$ref":"#/definitions/User"}}],"produces":["application/xml","application/json"],"responses":{"400":{"description":"Invalid user supplied"},"404":{"description":"User not found"}},"summary":"Updated user","tags":["user"]}}},"schemes":["https","http"],"securityDefinitions":{"api_key":{"in":"header","name":"api_key","type":"apiKey"},"petstore_auth":{"authorizationUrl":"http://petstore.swagger.io/oauth/dialog","flow":"implicit","scopes":{"read:pets":"read your pets","write:pets":"modify pets in your account"},"type":"oauth2"}},"swagger":"2.0","tags":[{"description":"Everything about your Pets","externalDocs":{"description":"Find out more","url":"http://fancy.io"},"name":"pet"},{"description":"Access to Petstore orders","name":"store"},{"description":"Operations about user","externalDocs":{"description":"Find out more about our fancy store","url":"http://fancy.io"},"name":"user"}],"x-externalServices":[{"description":"Pact Broker","url":"https://github.com/pact-foundation/pact_broker"},{"description":"Dynatrace","url":"https://www.dynatrace.de/"}]},{"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"},"multipleGenesJSON":{"summary":"JSON query for multiple developmental genes","value":"{\n  \"from\": \"Gene\",\n  \"select\": [\"primaryIdentifier\", \"symbol\", \"name\", \"length\", \"chromosome.primaryIdentifier\"],\n  \"where\": [\n    {\"path\": \"organism.name\", \"op\": \"=\", \"value\": \"Drosophila melanogaster\"},\n    {\"path\": \"symbol\", \"op\": \"ONE OF\", \"values\": [\"eve\", \"ftz\", \"zen\", \"hb\", \"Kr\"]}\n  ],\n  \"orderBy\": [{\"path\": \"symbol\", \"direction\": \"ASC\"}]\n}\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 name=\"short genes on the X chromosome\" model=\"genomic\" view=\"Gene.id Gene.exons.id\">\n  <constraint path=\"Gene.chromosome.primaryIdentifier\" op=\"=\" value=\"X\"/>\n  <constraint path=\"Gene.length\" op=\"<\" value=\"1000\"/>\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 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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 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<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 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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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(must contain Gene or Protein objects)","example":"Gap_Genes","in":"query","name":"list","required":true,"schema":{"type":"string"}},{"description":"Extra information to include in FASTA headers","example":["Gene.length","Gene.chromosome.primaryIdentifier"],"in":"query","name":"view","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Authentication token for private lists","in":"query","name":"token","schema":{"type":"string"}}],"responses":{"200":{"content":{"text/plain":{"example":">FBgn0000606 type=gene; loc=2R:9979319..9984780; name=eve; length=5462;\nATGGAGATCAAACAAGCGAAGAGTGGAGAGAAGTGGAGAAGCAGCCAAGCAAG\nCAACAGCACAAGGGCTCGTCGAGCAAGTCCAGCGAGGAGGATCTGCTGAGCGG\nCGAGGAGGATCTGCTGAGCGGCGACAGCGACAGCGACAGCGACAGCGACAGC\n>FBgn0001077 type=gene; loc=3R:2648685..2653456; name=ftz; length=4772;\nATGGCAATGGAAGTGTCCAGCAGTCCCGTGATGGTTCATCACGTCGGTCGCTC\nTCAGTCGTCGGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGT\n","schema":{"type":"string"}}},"description":"FASTA formatted 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The query must return\nobjects of a single type that can be stored in a list.\n","operationId":"queryToListGet","parameters":[{"description":"PathQuery in XML or JSON format","example":"<query model=\"genomic\" view=\"Gene.primaryIdentifier\">\n  <constraint path=\"Gene.goAnnotation.ontologyTerm.name\" op=\"CONTAINS\" value=\"transcription\"/>\n  <constraint path=\"Gene.organism.name\" op=\"=\" value=\"Drosophila melanogaster\"/>\n</query>\n","in":"query","name":"query","required":true,"schema":{"type":"string"}},{"description":"Name for the new list (must be unique)","example":"Transcription_Factors_Query","in":"query","name":"name","required":true,"schema":{"type":"string"}},{"description":"Description for the new list","example":"Genes involved in transcription regulation","in":"query","name":"description","schema":{"type":"string"}},{"description":"Tags to categorize the list","example":["gene-function","transcription"],"in":"query","name":"tags","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Whether to replace existing list with same name","in":"query","name":"replaceExisting","schema":{"default":false,"type":"boolean"}},{"description":"Authentication token","in":"query","name":"token","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"executionTime":876,"listName":"Transcription_Factors_Query","size":234,"type":"Gene","wasSuccessful":true},"schema":{"properties":{"executionTime":{"type":"integer"},"listName":{"type":"string"},"size":{"type":"integer"},"type":{"type":"string"},"wasSuccessful":{"type":"boolean"}},"type":"object"}}},"description":"List created from query results"}},"summary":"Save query results as a list","tags":["query","list"]},"post":{"description":"Execute a query and save the results as a new list using POST method.\n","operationId":"queryToListPost","requestBody":{"content":{"application/x-www-form-urlencoded":{"example":{"description":"Genes in hedgehog signaling pathway","name":"Hedgehog_Pathway_Genes","query":"{\n  \"from\": \"Gene\",\n  \"select\": [\"primaryIdentifier\"],\n  \"where\": [\n    {\"path\": \"pathways.name\", \"op\": \"CONTAINS\", \"value\": \"hedgehog\"},\n    {\"path\": \"organism.name\", \"op\": \"=\", \"value\": \"Drosophila melanogaster\"}\n  ]\n}\n","tags":["pathway","signaling"]},"schema":{"properties":{"description":{"description":"Description for the new list","type":"string"},"name":{"description":"Name for the new list","type":"string"},"query":{"description":"PathQuery in XML or JSON format","type":"string"},"replaceExisting":{"default":false,"description":"Whether to replace existing list","type":"boolean"},"tags":{"description":"Tags to categorize the list","items":{"type":"string"},"type":"array"},"token":{"description":"Authentication token","type":"string"}},"required":["query","name"],"type":"object"}}}},"responses":{"200":{"description":"List created from query results"}},"summary":"Save query results as a list","tags":["query","list"]}},"/lists/append":{"post":{"description":"Add items to an existing list by providing identifiers. The list must exist\nand belong to the authenticated user.\n","operationId":"listsAppend","parameters":[{"description":"Authentication token","in":"query","name":"token","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/x-www-form-urlencoded":{"example":{"format":"json","name":"Gap_Genes"},"schema":{"properties":{"format":{"default":"json","description":"Output format","enum":["json","text"],"type":"string"},"name":{"description":"Name of the existing list to append to","type":"string"},"token":{"description":"Authentication token","type":"string"}},"required":["name"],"type":"object"}},"text/plain":{"example":"hb\nKr\nkni\ngt\n","schema":{"description":"Identifiers to add, separated by commas, tabs, or 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intersection of lists","tags":["list"]}},"/lists/subtract":{"post":{"description":"Create a new list containing items from the first list that are not in the second list.\n","operationId":"listsSubtract","parameters":[{"in":"query","name":"token","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/x-www-form-urlencoded":{"example":{"description":"Eye development genes not involved in wing development","from":"Eye_Development_Genes","name":"Unique_Eye_Genes","subtract":"Wing_Development_Genes"},"schema":{"properties":{"description":{"type":"string"},"format":{"default":"json","enum":["json","text"],"type":"string"},"from":{"description":"Name of the source list","type":"string"},"name":{"description":"Name for the new list","type":"string"},"subtract":{"description":"Name of the list to 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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":{"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 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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 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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 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]\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 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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. 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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. 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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 regions\"\nchr2L\t10234567\t10245678\tCG11023\t1000\t+\nchr2L\t10456789\t10467890\tCG2187\t1000\t-\nchr2R\t5234567\t5245678\t1360{}1224\t500\t+\n"}},"description":"BED formatted features"}},"summary":"Get features overlapping genomic regions as BED","tags":["genomic-regions","export"]}},"/model":{"get":{"description":"Retrieve the FlyMine data model\n","operationId":"getModel","parameters":[{"description":"Output 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The query must return\nobjects of a single type that can be stored in a list.\n","operationId":"queryToListGet","parameters":[{"description":"PathQuery in XML or JSON format","example":"<query model=\"genomic\" view=\"Gene.primaryIdentifier\">\n  <constraint path=\"Gene.goAnnotation.ontologyTerm.name\" op=\"CONTAINS\" value=\"transcription\"/>\n  <constraint path=\"Gene.organism.name\" op=\"=\" value=\"Drosophila melanogaster\"/>\n</query>\n","in":"query","name":"query","required":true,"schema":{"type":"string"}},{"description":"Name for the new list (must be unique)","example":"Transcription_Factors_Query","in":"query","name":"name","required":true,"schema":{"type":"string"}},{"description":"Description for the new list","example":"Genes involved in transcription regulation","in":"query","name":"description","schema":{"type":"string"}},{"description":"Tags to categorize the list","example":["gene-function","transcription"],"in":"query","name":"tags","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Whether to replace existing list with same name","in":"query","name":"replaceExisting","schema":{"default":false,"type":"boolean"}},{"description":"Authentication token","in":"query","name":"token","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"executionTime":876,"listName":"Transcription_Factors_Query","size":234,"type":"Gene","wasSuccessful":true},"schema":{"properties":{"executionTime":{"type":"integer"},"listName":{"type":"string"},"size":{"type":"integer"},"type":{"type":"string"},"wasSuccessful":{"type":"boolean"}},"type":"object"}}},"description":"List created from query results"}},"summary":"Save query results as a list","tags":["query","list"]},"post":{"description":"Execute a query and save the results as a new list using POST method.\n","operationId":"queryToListPost","requestBody":{"content":{"application/x-www-form-urlencoded":{"example":{"description":"Genes in hedgehog signaling pathway","name":"Hedgehog_Pathway_Genes","query":"{\n  \"from\": \"Gene\",\n  \"select\": [\"primaryIdentifier\"],\n  \"where\": [\n    {\"path\": \"pathways.name\", \"op\": \"CONTAINS\", \"value\": \"hedgehog\"},\n    {\"path\": \"organism.name\", \"op\": \"=\", \"value\": \"Drosophila melanogaster\"}\n  ]\n}\n","tags":["pathway","signaling"]},"schema":{"properties":{"description":{"description":"Description for the new list","type":"string"},"name":{"description":"Name for the new list","type":"string"},"query":{"description":"PathQuery in XML or JSON format","type":"string"},"replaceExisting":{"default":false,"description":"Whether to replace existing list","type":"boolean"},"tags":{"description":"Tags to categorize the list","items":{"type":"string"},"type":"array"},"token":{"description":"Authentication token","type":"string"}},"required":["query","name"],"type":"object"}}}},"responses":{"200":{"description":"List created from query results"}},"summary":"Save query results as a list","tags":["query","list"]}},"/lists/append":{"post":{"description":"Add items to an existing list by providing identifiers. 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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":{"callbacks":{},"examples":{},"headers":{},"links":{},"parameters":{},"requestBodies":{},"responses":{},"schemas":{"CurieList":{"description":"list of CURIEs","properties":{"curies":{"items":{"type":"string"},"title":"list of CURIEs","type":"array"}},"type":"object"},"OmopList":{"description":"list of OMOP IDs","properties":{"curies":{"items":{"type":"integer"},"title":"list of OMOP IDs","type":"array"}},"type":"object"}},"securitySchemes":{},"x-bte-kgs-response-mappings":{"chi_square":{"biolink:OMOP":"results.concept_id_2","biolink:chi_squared_statistic":"results.chi_square","biolink:has_count":"results.n_c1_c2","biolink:name":"results.concept_2_name","biolink:p_value":"results.adj_p-value"},"obs_exp_ratio":{"biolink:OMOP":"results.concept_id_2","biolink:has_count":"results.observed_count","biolink:name":"results.concept_2_name"},"relative_frequency":{"biolink:OMOP":"results.concept_id_2","biolink:has_count":"results.concept_pair_count","biolink:has_quotient":"results.relative_frequency","biolink:has_total":"results.concept_2_count","biolink:name":"results.concept_2_name"}}},"info":{"contact":{"email":"ct2865@cumc.columbia.edu","name":"Casey Ta","url":"http://chunhualab.org/","x-role":"responsible developer"},"description":"The Columbia Open Health Data (COHD) API provides access to counts and frequencies (i.e., EHR prevalence) of conditions, procedures, drug exposures, and patient demographics, and the co-occurrence frequencies between them. 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 and outpatient data. Counts are the number of patients associated with the concept, e.g., diagnosed with a condition, exposed to a drug, or who had a procedure. Frequencies are the number of unique patients associated with the concept divided by the total number of patients 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\nFour datasets are available: \n1) 5-year non-hierarchical dataset: Includes clinical data from 2013-2017  \n2) lifetime non-hierarchical dataset: Includes clinical data from all dates  \n3) 5-year hierarchical dataset: Counts for each concept include patients from descendant concepts. Includes clinical data from 2013-2017.\n4) BETA! Temporal co-occurrence data\n\nIn the 5-year hierarchical data set, the counts for each concept include the patients from all descendant concepts. For example, the count for ibuprofen (ID 1177480) includes patients with Ibuprofen 600 MG Oral Tablet (ID 19019073 patients), Ibuprofen 400 MG Oral Tablet (ID 19019072), Ibuprofen 20 MG/ML Oral Suspension (ID 19019050), etc. \n\nWhile the lifetime dataset captures a larger patient population and range of concepts, the 5-year dataset has better underlying data consistency. \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 patients with the code(s) / total number of patients. \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 (Red Team). This work was supported in part by grants: 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) 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":"5-year non-hierarchical dataset: Includes clinical data from 2013-2017","type":"string"},"dataset_id":{"example":1,"type":"integer"},"dataset_name":{"example":"5-year 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. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"count":{"example":1000,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"domain_id":{"example":"Condition","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of domain counts."},"default":{"description":"Unexpected error"}},"summary":"The number of concepts in each domain","tags":["Metadata"]}},"/metadata/domainPairCounts":{"get":{"description":"Returns a list of pairs of domains and the number of pairs of concepts in each.","operationId":"domainPairCounts","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"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"count":{"example":1000,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"domain_id_1":{"example":"Condition","type":"string"},"domain_id_2":{"example":"Drug","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of domain pair counts."},"default":{"description":"Unexpected error"}},"summary":"The number of pairs of concepts in each pair of domains","tags":["Metadata"]}},"/metadata/patientCount":{"get":{"description":"Returns the number of patients in the dataset.","operationId":"patientCount","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"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"count":{"example":100000,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of patient counts."},"default":{"description":"Unexpected error"}},"summary":"The number of patients in the dataset","tags":["Metadata"]}},"/omop/concepts":{"get":{"description":"Returns the OMOP concept names and domains for the given list of concept IDs.","operationId":"concepts","parameters":[{"description":"A comma separated list of OMOP concept ids, e.g., \"192855\" or \"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_class_id":{"example":"Clinical Finding","type":"string"},"concept_code":{"example":"92546004","type":"string"},"concept_id":{"example":192855,"type":"integer"},"concept_name":{"example":"Cancer in situ of urinary bladder","type":"string"},"domain_id":{"example":"Condition","type":"string"},"vocabulary_id":{"example":"SNOMED","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of concepts."},"default":{"description":"Unexpected error"}},"summary":"Concept definitions from concept ID","tags":["OMOP"]}},"/omop/findConceptIDs":{"get":{"description":"Searches the OMOP concept table for concept names similar to the query. Returns a list of concepts, including their names and IDs, sorted in decreasing order by the concept's prevalence.","operationId":"findConceptIDs","parameters":[{"description":"The name of the concept to search for, e.g., \"cancer\" or \"ibuprofen\"","example":"cancer","in":"query","name":"q","required":true,"schema":{"type":"string"}},{"description":"The dataset to reference when sorting concepts by their frequency. Default: 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"The domain (e.g., \"Condition\", \"Drug\", \"Procedure\") to restrict the search to. If not specified, the search will be unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Condition","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"The minimum concept count (inclusive) to include a concept in the search results. Setting the min_count to 0 will cause findConceptIDs to return all matching standard OMOP concepts (this can be slow). Setting the min_count to 1 will cause findConceptIDs to only return concepts with count data (much faster). Default: 1.","example":1,"in":"query","name":"min_count","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":"92546004","type":"string"},"concept_count":{"example":368,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"concept_name":{"example":"Cancer in situ of urinary bladder","type":"string"},"domain_id":{"example":"Condition","type":"string"},"vocabulary_id":{"example":"SNOMED","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of concepts."},"default":{"description":"Unexpected error"}},"summary":"Search for OMOP concepts by name and domain","tags":["OMOP"]}},"/omop/conceptAncestors":{"get":{"description":"Retrieves the given concept's hierarchical ancestors and their counts. The hierarchical definitions were derived from the OMOP concept_ancestor table. For more information, 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":"conceptAncestors","parameters":[{"description":"An OMOP concept ID, e.g., 19019073","example":19019073,"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 (only and ATC are used. For procedures, SNOMED, MedDRA, and ICD10PCS are used. Default: unrestricted","example":"RxNorm","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":"Ingredient","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":{"ancestor_concept_id":{"example":1177480,"type":"integer"},"concept_class_id":{"example":"Ingredient","type":"string"},"concept_code":{"example":"5640","type":"string"},"concept_count":{"example":233514,"type":"integer"},"concept_name":{"example":"Ibuprofen","type":"string"},"domain_id":{"example":"Drug","type":"string"},"max_levels_of_separation":{"example":2,"type":"integer"},"min_levels_of_separation":{"example":2,"type":"integer"},"standard_concept":{"example":"S","type":"string"},"vocabulary_id":{"example":"RxNorm","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of concepts."},"default":{"description":"Unexpected error"}},"summary":"Retrieve the concept's hierarchical ancestors","tags":["OMOP"]}},"/omop/conceptDescendants":{"get":{"description":"Retrieves the given concept's hierarchical descendants and their counts. 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_patients / (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}]}},"/temporal/conceptAgeCounts":{"get":{"description":"Counts of ages when concepts were first observed in a patient. Different concepts will have different bin_widths. All binning schemes start with age 0, and no bin starts with an age > 90. The largest age bin includes all ages greater or equal to the starting age of the bin. For example, with a bin_width of 4, the ages of each bin are [0-3, 4-7, 8-11, ..., 84-87, 88+]. Counts in each bin are independently perturbed with a Poisson distribution. Counts < 10 are suppressed, represented by the value 1. Counts of 0 are reported as 0.\n","operationId":"conceptAgeCounts","parameters":[{"description":"The dataset_id of the data set to query. Default data set is the Temporal Beta data set.","example":4,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"313217\"","example":313217,"in":"query","name":"concept_id","required":true,"schema":{"type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"bin_width":{"example":2,"type":"integer"},"concept_id":{"example":313217,"type":"integer"},"concept_name":{"example":"Atrial fibrillation","type":"string"},"counts":{"description":"Array of counts ordered from 0 to the largest bin.","items":{"example":9000,"type":"integer"},"type":"array"},"dataset_id":{"example":4,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"The concept's age distribution"},"default":{"description":"Unexpected error"}},"summary":"Counts of ages when concepts were first observed in a patient","tags":["Temporal Clinical Data"]}},"/temporal/findSimilarAgeDistributions":{"get":{"description":"Finds concepts with a similar concept-age distribution as with the desired concept_id.\nUses Jaccard similarity to compare concept-age distributions\n","operationId":"findSimilarAgeDistributions","parameters":[{"description":"The dataset_id of the data set to query. Default data set is the Temporal Beta data set.","example":4,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"313217\"","example":313217,"in":"query","name":"concept_id","required":true,"schema":{"type":"integer"}},{"description":"True: excludes concepts that frequently co-occur (0-day delta) with concept_id. False: do not exclude. Default is True.","example":true,"in":"query","name":"exclude_related","required":false,"schema":{"type":"boolean"}},{"description":"(Optional) True: restricts potentially similar concepts to the same type of concept as concept_id, e.g., the same domain_id for Conditions, Drugs, and Procedures. For drugs, if the concept is an ingredient, also restricts concept_class_id to 'Ingredient'.\n","example":true,"in":"query","name":"restrict_type","required":false,"schema":{"type":"boolean"}},{"description":"Minimum threshold for similarity. Range is 0-1, higher is more similar. Default 0.7.","example":0.7,"in":"query","name":"threshold","required":false,"schema":{"type":"number"}},{"description":"Maximum number of concepts to return at each bin width. Default 20.","example":20,"in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"bin_width":{"example":2,"type":"integer"},"concept_id":{"example":313217,"type":"integer"},"concept_name":{"example":"Atrial fibrillation","type":"string"},"counts":{"description":"Array of counts ordered from 0 to the largest bin.","items":{"example":9000,"type":"integer"},"type":"array"},"dataset_id":{"example":4,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"The concept's age distribution"},"default":{"description":"Unexpected error"}},"summary":"Find concepts with a similar concept-age distribution","tags":["Temporal Clinical Data"]}},"/temporal/conceptPairDeltaCounts":{"get":{"description":"Counts of time differences (deltas) between when a pair of concepts were first observed in a patient. given a pair of concepts (source_concept and target_concept), a positive delta indicates that source_concept was observed before target_concept. Likewise, a negaitve delta indicates that source_concept was observed after target_concept. Performing this query with the two concepts swapped will produce a mirrored distribution.\nBin widths grow exponentially, and different concept pairs will have different bin_widths. The binning schemes are as follows (delta bins with negative values mirror the positive delta bins):\n  bin_width=1: [0 day, 1 day, 2-3 days, 4-7 days, 8-15 days, ..., 2048-4095 days (5.6-11.2y), and 4096+ days\n  (11.2+ years)].\n  bin_width=2: [0 day, 1-3 days, 4-15 days, 16-63 days, ..., 256-1023 days, 1024+ days (2.8+ years)]\n  bin_width=4: [0 day, 1-15 days, 16-255 days, 256+ days]\n  bin_width=8: [0 day, 1-255 days, 256+ days]\n  bin_width=16: [0 day, 1+ days]\n  The 0-day bin never gets incorporated into larger bins.\n  \nCounts in each bin are independently perturbed with a Poisson distribution. Counts < 10 are suppressed, represented by the value 1. Counts of 0 are reported as 0.\n","operationId":"conceptPairDeltaCounts","parameters":[{"description":"The dataset_id of the data set to query. Default data set is the Temporal Beta data set.","example":4,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"312327\"","example":312327,"in":"query","name":"source_concept_id","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"313217\"","example":313217,"in":"query","name":"target_concept_id","required":true,"schema":{"type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"bin_width":{"example":2,"type":"integer"},"counts":{"description":"Array of counts ordered from the most negative bin to the largest positive bin.","items":{"example":9000,"type":"integer"},"type":"array"},"dataset_id":{"example":4,"type":"integer"},"n":{"example":6,"type":"integer"},"source_concept_id":{"example":312327,"type":"integer"},"source_concept_name":{"example":"Acute myocardial infarction","type":"string"},"target_concept_id":{"example":313217,"type":"integer"},"target_concept_name":{"example":"Atrial fibrillation","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"The concept pair's delta distribution"},"default":{"description":"Unexpected error"}},"summary":"Counts of time deltas between","tags":["Temporal Clinical Data"]}},"/temporal/sourceToTarget":{"get":{"description":"Analysis to determine if there's a temporal relationship between the source_concept and the target_concept.\nCompares the delta distribution between source_concept and target_concept against delta distributions from other concepts to the target_concept. Find comparable concepts by measuring similarity of the age distributions to the age distribution of the source_concept.\n","operationId":"sourceToTarget","parameters":[{"description":"The dataset_id of the data set to query. Default data set is the Temporal Beta data set.","example":4,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"312327\"","example":312327,"in":"query","name":"source_concept_id","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"313217\"","example":313217,"in":"query","name":"target_concept_id","required":true,"schema":{"type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"type":"object"}}},"description":"The concept pair's delta distribution"},"default":{"description":"Unexpected error"}},"summary":"Temporal relationship between source_concept and target_concept.","tags":["Temporal Clinical Data"]}},"/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. 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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. 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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. 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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"},"QueryOptions":{"description":"Additional query options that apply to COHD","properties":{"biolink_only":{"description":"Whether to only include nodes in the knowledge graph and results that are Biolink compliant (as defined by ontology_targets). Default: true","example":true,"type":"boolean"},"confidence_interval":{"description":"Criteria that the results are significant to the specified criteria level. This only applies when the method is 'obsExpRatio'. Default: not required.","example":0.99,"type":"number"},"dataset_id":{"description":"The COHD dataset to query","example":3,"type":"integer"},"local_oxo":{"description":"Whether to use the local implementation of OxO or the real implementation of OxO. Note, the local OxO implementation may contain outdated definitions and xrefs but runs faster. The real OxO has the most updated definitions and xrefs, but is slower (~1-2 seconds/concept). Default: true","example":false,"type":"boolean"},"max_results":{"description":"The maximum number of results to be returned.","example":10,"type":"integer"},"min_cooccurrence":{"description":"Criteria that the results have a minimum co-occurrence count. Default: not required.","example":50,"type":"integer"},"threshold":{"description":"Criteria threshold to apply to the association metric. chiSquare: p-value < threshold. obsExpRatio: abs(ln_ratio) >= threshold. relativeFrequency: relative_frequency >= threshold.","example":0.5,"type":"number"}},"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":"ct2865@cumc.columbia.edu","name":"Casey Ta","url":"http://chunhualab.org/","x-role":"responsible developer"},"description":"The Columbia Open Health Data (COHD) TRAPI API provides access to associations derived from clinical data between\ndiseases, phenotypic features, drugs, procedures, and demographic features.\n\nCOHD was developed at the [Columbia University Department of Biomedical Informatics](https://www.dbmi.columbia.edu/)\nas a collaboration between the [Weng Lab](http://people.dbmi.columbia.edu/~chw7007/),\n[Tatonetti Lab](http://tatonettilab.org/), and the\n[NCATS Biomedical Data Translator](https://ncats.nih.gov/translator) program.\nThis work was supported in part by grants: NCATS OT2TR003434, NCATS OT3TR002027, NLM R01LM009886-08A1, and\nNIGMS 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,\nconcept sets)\n","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"termsOfService":"http://cohd.nsides.io/terms/","title":"COHD TRAPI","version":"6.5.0","x-translator":{"biolink-version":"4.1.6","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:cohd","team":["Clinical Data Provider"]},"x-trapi":{"asyncquery":false,"batch_size_limit":100,"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":true,"operations":["lookup_and_score"],"pathfinderquery":false,"rate_limit":10,"test_data_location":{"default":{"url":"https://raw.githubusercontent.com/WengLab-InformaticsResearch/cohd_api/master/cohd/translator/sri_testing_triples.json"}},"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":"Query the COHD API following the [NCATS Translator Reasoner Standard API](https://github.com/NCATSTranslator/ReasonerAPI). Only single hop queries are supported. See the example query_graph.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n  \"message\": {\n    \"query_graph\": {\n      \"nodes\": {\n        \"n00\": {\n          \"ids\": [\"DOID:9053\"],\n          \"categories\": [\"biolink:Disease\"]\n        },\n        \"n01\": {\n          \"categories\": [\"biolink:Procedure\"]\n        }\n      },\n      \"edges\": {\n        \"e00\": {\n          \"predicates\": [\"biolink:correlated_with\"],\n          \"subject\": \"n00\",\n          \"object\": \"n01\"\n        }\n      }\n    }\n  },\n  \"query_options\": {\n    \"dataset_id\": 3,\n    \"confidence_interval\": 0.99,\n    \"min_cooccurrence\": 50,\n    \"threshold\": 0.5,\n    \"local_oxo\": true,\n    \"max_results\": 50,\n    \"biolink_only\": true\n  }\n}","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 COHD following NCATS Translator Reasoner Standard API. Initiate a query and wait to receive a Response","tags":["query"]}}},"servers":[{"description":"COHD ITRB Production Server","url":"https://cohd-api.transltr.io/api","x-maturity":"production"},{"description":"COHD ITRB Test Server","url":"https://cohd-api.test.transltr.io/api","x-maturity":"testing"},{"description":"COHD ITRB CI Server","url":"https://cohd-api.ci.transltr.io/api","x-maturity":"staging"},{"description":"COHD Development Server","url":"https://cohd.io/api","x-maturity":"development"}],"tags":[{"description":"Retrieve the meta knowledge graph representation of this TRAPI web service. KPs MUST provide all subject category - predicate - object category triplets that are supported by the service, NOT including all implied ancestor relationships. ARAs SHOULD provide the union of all meta knowledge graphs of all the KPs that they can consult.","name":"meta_knowledge_graph"},{"description":"Initiate a query and wait to receive the response","name":"query"},{"description":"Required for SmartAPI validation of x-translator","name":"translator"},{"description":"Required for SmartAPI validation of x-trapi","name":"trapi"}]},{"components":{"parameters":{"callback":{"description":"Optional, you can pass a \"callback\" parameter to make a JSONP call.","in":"query","name":"callback","required":false,"schema":{"type":"string"}},"dotfield":{"description":"Optional, can be used to control the format of the returned object. If \"dotfield\" is true, the returned data object is returned flattened (no nested objects) using dotfield notation for key names. Default: false.","in":"query","name":"dotfield","required":false,"schema":{"default":false,"type":"boolean"}},"email":{"description":"Optional, if you are regular users of our services, we encourage you to provide us an email, so that we can better track the usage or follow up with you.","in":"query","name":"email","required":false,"schema":{"type":"string"}},"facet_size":{"description":"Optional, an integer (1 <= facet_size <= 1000) that specifies how many buckets to return in a [faceted query](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#faceted-queries).","in":"query","name":"facet_size","required":false,"schema":{"default":10,"type":"integer"}},"facets":{"description":"Optional, a single field or comma-separated fields to return facets, can only be used on non-free text fields. E.g. \"facets=chembl.molecule_properties.full_mwt\". See [examples of faceted queries for a core BioThings API](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#faceted-queries).","in":"query","name":"facets","required":false,"schema":{"items":{"type":"string"},"type":"array"}},"fetch_all":{"description":"Optional, a boolean, which when TRUE, allows fast retrieval of all unsorted query hits. The return object contains a _scroll_id field, which when passed as a parameter to the query endpoint (see the scroll_id parameter), returns the next 1000 query results. Setting fetch_all = TRUE causes the results to be inherently unsorted, therefore the sort parameter is ignored. For more information, see [examples using fetch_all for a core BioThings API](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#scrolling-queries). Default: FALSE.","in":"query","name":"fetch_all","required":false,"schema":{"default":false,"type":"boolean"}},"fields":{"description":"Optional, can be a comma-separated list to limit the fields returned from the object. If \"fields=all\", all available fields will be returned.\nNote that it supports dot notation as well, e.g., you can pass \"chebi.name\". Default: \"fields=all\". The parameter \"filter\" is an alias for this parameter.","in":"query","name":"fields","required":false,"schema":{"default":"all","type":"string"}},"from":{"description":"Optional, the number of matching hits to skip, starting from 0. Default: 0.","in":"query","name":"from","required":false,"schema":{"default":0,"type":"integer"}},"scroll_id":{"description":"Optional, a string containing the _scroll_id returned from a query request with fetch_all = TRUE. Supplying a valid scroll_id will return the next 1000 unordered results. If the next results are not obtained within 1 minute of the previous set of results, the scroll_id becomes stale, and a new one must be obtained with another query request with fetch_all = TRUE. All other parameters are ignored when the scroll_id parameter is supplied. For more information see [examples using scroll_id for a core BioThings API](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#scrolling-queries).","in":"query","name":"scroll_id","required":false,"schema":{"type":"string"}},"size":{"description":"Optional, the maximum number of matching hits to return (with a cap of 1000 at the moment). Default: 10. The combination of \"size\" and \"from\" parameters can be used to get paging for a large query.","in":"query","name":"size","required":false,"schema":{"default":10,"type":"integer"}},"sort":{"description":"Optional, the comma-separated fields to sort on. Prefix with \"-\" for descending order, otherwise in ascending order. Default: sort by matching scores in descending order.","in":"query","name":"sort","required":false,"schema":{"items":{"type":"string"},"type":"array"}}}},"info":{"contact":{"email":"help@biothings.io","name":"BioThings Team","x-id":"https://github.com/biothings","x-role":"responsible organization"},"description":"The BioThings Disbiome API provides access to the [Disbiome database](https://disbiome.ugent.be/), which catalogs associations between human diseases and changes in microbiome composition. This database systematically curates literature-derived evidence linking microbial taxa to various human health conditions. The API enables researchers to query disease-microbiome associations, microbial abundance changes, and study metadata. Disbiome supports microbiome research, precision medicine, and therapeutic development by providing standardized access to curated disease-microbiome relationships. This resource facilitates hypothesis generation, biomarker discovery, and understanding of host-microbiome interactions in health and disease.","termsOfService":"https://biothings.io/about","title":"BioThings Disbiome API","version":"2018-09-20","x-translator":{"component":"KP","team":["Service Provider"]}},"openapi":"3.0.3","paths":{"/association/{id}":{"get":{"description":"By default, the full record for each ID is returned in JSON. Invalid input returns a 404 (Not Found). Use the \"fields\" parameter to return specific attributes (comma-separated, case-sensitive). Unavailable attributes are ignored. You can also use the \"callback\" parameter for JSONP requests.","parameters":[{"example":"bccf236adbdd453cbf2717267212c43f","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["association"]}},"/association":{"post":{"description":"To fetch multiple items in one request, use a batch query with POST.","parameters":[{"description":"Accepts up to 1,000 IDs (comma-separated); extra IDs are ignored. IDs can also be sent in the request body.","in":"query","name":"ids","required":false,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"requestBody":{"content":{"application/json":{"example":{"ids":["bc49e24685224a2f9775f6a3b38b003e","bc94efd8341240dca51e4f15b1701343","bc9de0d73f3f4f968335e54eb97c3abb"]},"schema":{"properties":{"ids":{"description":"Accepts multiple association ids. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted.","items":{"type":"string"},"type":"array"}},"type":"object"}}}},"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["association"]}},"/metadata":{"get":{"description":"Get metadata about the data available from the API","responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["metadata"]}},"/metadata/fields":{"get":{"description":"Get metadata about the data fields available from the API","responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["metadata"]}},"/query":{"get":{"description":"Query service. In the output, \"total\" in the output gives the total number of matching hits, while the actual hits are returned under \"hits\" field.","parameters":[{"description":"Required, passing user query. The detailed query syntax for parameter is explained [here for a core BioThings API](https://docs.mychem.info/en/latest/doc/chem_query_service.html#query-syntax).","example":"object.meddra_level:preferred_term","in":"query","name":"q","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/from"},{"$ref":"#/components/parameters/fetch_all"},{"$ref":"#/components/parameters/scroll_id"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/facets"},{"$ref":"#/components/parameters/facet_size"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/dotfield"},{"$ref":"#/components/parameters/email"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["query"]},"post":{"description":"Although making simple GET requests above to our query service is sufficient for most use cases, there are times you might find it more efficient to make batch queries (e.g., retrieving data for multiple inputs). 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