From aeea89c867eace66ba485b1c8b146af2a4328912 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 22 Apr 2021 10:07:59 -0700 Subject: [PATCH 01/75] feat: :sparkles: set rate limit to max 3 queries per min --- src/config/index.js | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/config/index.js b/src/config/index.js index 1176e762..536cabae 100644 --- a/src/config/index.js +++ b/src/config/index.js @@ -63,9 +63,9 @@ module.exports = class Config { setLimiter() { const limiter = rateLimit({ - windowMs: 15 * 60 * 1000, //15mins - max: 200 //200 requests + windowMs: 1 * 60 * 1000, //1min + max: 3 //3 requests }); - this.app.use("/query", limiter); + this.app.use("/v1/query", limiter); } } \ No newline at end of file From 8686092a8cbeedacbc38f8670a7be6470eeafc9d Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 22 Apr 2021 10:30:16 -0700 Subject: [PATCH 02/75] feat: :sparkles: allow user to set MAX_QUERIES_PER_MIN as env --- src/config/index.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/config/index.js b/src/config/index.js index 536cabae..661e09f4 100644 --- a/src/config/index.js +++ b/src/config/index.js @@ -64,7 +64,7 @@ module.exports = class Config { setLimiter() { const limiter = rateLimit({ windowMs: 1 * 60 * 1000, //1min - max: 3 //3 requests + max: process.env.MAX_QUERIES_PER_MIN || 3 //3 requests }); this.app.use("/v1/query", limiter); } From d26e13ececf46324d82db92121908257bf219753 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 22 Apr 2021 10:30:44 -0700 Subject: [PATCH 03/75] build: :wrench: set env for jest --- .jest/setEnvVars.js | 1 + jest.config.js | 3 ++- 2 files changed, 3 insertions(+), 1 deletion(-) create mode 100644 .jest/setEnvVars.js diff --git a/.jest/setEnvVars.js b/.jest/setEnvVars.js new file mode 100644 index 00000000..82f4b247 --- /dev/null +++ b/.jest/setEnvVars.js @@ -0,0 +1 @@ +process.env.MAX_QUERIES_PER_MIN = 20; \ No newline at end of file diff --git a/jest.config.js b/jest.config.js index d2582e17..f531eba8 100644 --- a/jest.config.js +++ b/jest.config.js @@ -1,5 +1,6 @@ module.exports = { // setupTestFrameworkScriptFile has been deprecated in // favor of setupFilesAfterEnv in jest 24 - setupFilesAfterEnv: ['./jest.setup.js'] + setupFilesAfterEnv: ['./jest.setup.js'], + setupFiles: ["/.jest/setEnvVars.js"] } \ No newline at end of file From 8a9325d9541ade8b6aa81ca4235d0187e15a1594 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 22 Apr 2021 10:42:51 -0700 Subject: [PATCH 04/75] docs: :memo: add documentation on how to modify default rate limit for BTE --- README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/README.md b/README.md index 94e512d1..5d682ed3 100644 --- a/README.md +++ b/README.md @@ -92,6 +92,10 @@ To enable debug mode, which outputs logging statements to the terminal in real t `$ DEBUG=biothings-explorer-trapi:*,smartapi-kg:*,call-apis:*,biomedical-id-resolver:* npm start` (also outputs debug statements from dependencies) +By default, the `/v1/query` endpoint only supports 3 queries per min, you could modify this behavior by setting MAX_QUERIES_PER_MIN environment variable when starting the service + +`$ MAX_QUERIES_PER_MIN=5 npm start` + ## Simple build for production $ npm build From d214a4dbec36a60d6df7d150f89835a6ea32bac8 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 22 Apr 2021 20:04:06 -0700 Subject: [PATCH 05/75] fix: :fire: temporarily disable text mining co-occurrence kp --- src/routes/v1/config.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/routes/v1/config.js b/src/routes/v1/config.js index 0fab45e0..1eb5b077 100644 --- a/src/routes/v1/config.js +++ b/src/routes/v1/config.js @@ -20,11 +20,11 @@ exports.API_LIST = [ 'DISEASES API', 'EBIgene2phenotype API', 'Gene Ontology Biological Process API', - 'Clinical Risk KP API', + // 'Clinical Risk KP API', 'Gene Ontology Molecular Activity API', 'Gene Ontology Cellular Component API', 'BioThings DGIdb API', - 'Text Mining CO-OCCURRENCE API', + // 'Text Mining CO-OCCURRENCE API', 'Text Mining Targeted Association API', 'Multiomics Wellness KP API', 'BioLink API', From 4464dfcffcb470ee7478cd16b2d93d712367ebd7 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 22 Apr 2021 20:10:48 -0700 Subject: [PATCH 06/75] fix: :sparkles: re-enable clinical risk kp --- src/routes/v1/config.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/routes/v1/config.js b/src/routes/v1/config.js index 1eb5b077..4df63bb4 100644 --- a/src/routes/v1/config.js +++ b/src/routes/v1/config.js @@ -20,7 +20,7 @@ exports.API_LIST = [ 'DISEASES API', 'EBIgene2phenotype API', 'Gene Ontology Biological Process API', - // 'Clinical Risk KP API', + 'Clinical Risk KP API', 'Gene Ontology Molecular Activity API', 'Gene Ontology Cellular Component API', 'BioThings DGIdb API', From 551e4b1f938eb08054f303ec6d2460f558e32d08 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 22 Apr 2021 21:02:31 -0700 Subject: [PATCH 07/75] fix: :bug: fix unable to resolve biocarta id issue --- package-lock.json | 36 ++++++++++++++++++------------------ package.json | 2 +- 2 files changed, 19 insertions(+), 19 deletions(-) diff --git a/package-lock.json b/package-lock.json index a8efad8b..017559dd 100644 --- a/package-lock.json +++ b/package-lock.json @@ -495,13 +495,13 @@ } }, "@biothings-explorer/call-apis": { - "version": "1.17.2", - "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.17.2.tgz", - "integrity": "sha512-i/iiJHDL8giIjVIkv+iudmWukLMjsoAoH/UMvpVvxKPURngvyUEUh5B00wQTXQ0PTqVwEyJd+Ex6pJSZBbYZyA==", + "version": "1.18.0", + "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.18.0.tgz", + "integrity": "sha512-8U8XIemDnZhKygcByZtBWRo5dJ8PVjh59AZcMlwOJYpIcMmevUDzpejqM+gdO9cN4SHWJTwTlueLK3bbo50fiw==", "requires": { "@biothings-explorer/api-response-transform": "^1.10.1", "axios": "^0.21.1", - "biomedical_id_resolver": "^3.5.0", + "biomedical_id_resolver": "^3.6.0", "debug": "^4.3.1", "husky": "^4.3.8" }, @@ -565,14 +565,14 @@ } }, "@biothings-explorer/query_graph_handler": { - "version": "1.8.0", - "resolved": "https://registry.npmjs.org/@biothings-explorer/query_graph_handler/-/query_graph_handler-1.8.0.tgz", - "integrity": "sha512-a9kcY4Uulb/74DIEQ7E1hqljTGGi9BQMgTkCOPvCeELXsdvMxZNSCeauV/9vI4A7GnujJPC13TmYuqQOvW0YjQ==", + "version": "1.9.0", + "resolved": "https://registry.npmjs.org/@biothings-explorer/query_graph_handler/-/query_graph_handler-1.9.0.tgz", + "integrity": "sha512-WFbPn2XDRPirvjkxEZZSndKQxCg5ZzT6wgzau2MOVyvql4D71j6dT67ac5tx0uH5kVlFxija5mr5hD3/CG18EQ==", "requires": { - "@biothings-explorer/call-apis": "^1.17.2", + "@biothings-explorer/call-apis": "^1.18.0", "@biothings-explorer/smartapi-kg": "^3.7.0", "biolink-model": "^0.3.0", - "biomedical_id_resolver": "^3.5.0", + "biomedical_id_resolver": "^3.6.0", "debug": "^4.3.1", "lodash": "^4.17.21", "ms": "^2.1.3", @@ -580,9 +580,9 @@ }, "dependencies": { "@babel/runtime": { - "version": "7.13.16", - "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.13.16.tgz", - "integrity": "sha512-7VsWJsI5USRhBLE/3of+VU2DDNWtYHQlq2IHu2iL15+Yx4qVqP8KllR6JMHQlTKWRyDk9Tw6unkqSusaHXt//A==", + "version": "7.13.17", + "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.13.17.tgz", + "integrity": "sha512-NCdgJEelPTSh+FEFylhnP1ylq848l1z9t9N0j1Lfbcw0+KXGjsTvUmkxy+voLLXB5SOKMbLLx4jxYliGrYQseA==", "requires": { "regenerator-runtime": "^0.13.4" } @@ -617,9 +617,9 @@ } }, "core-js": { - "version": "3.10.2", - "resolved": "https://registry.npmjs.org/core-js/-/core-js-3.10.2.tgz", - "integrity": "sha512-W+2oVYeNghuBr3yTzZFQ5rfmjZtYB/Ubg87R5YOmlGrIb+Uw9f7qjUbhsj+/EkXhcV7eOD3jiM4+sgraX3FZUw==" + "version": "3.11.0", + "resolved": "https://registry.npmjs.org/core-js/-/core-js-3.11.0.tgz", + "integrity": "sha512-bd79DPpx+1Ilh9+30aT5O1sgpQd4Ttg8oqkqi51ZzhedMM1omD2e6IOF48Z/DzDCZ2svp49tN/3vneTK6ZBkXw==" }, "follow-redirects": { "version": "1.5.10", @@ -3297,9 +3297,9 @@ } }, "biomedical_id_resolver": { - "version": "3.5.0", - "resolved": "https://registry.npmjs.org/biomedical_id_resolver/-/biomedical_id_resolver-3.5.0.tgz", - "integrity": "sha512-zXh/4xY+KN7xPldu3d27nQRym2tNuwrax05EwscaVP5m+E6ky6LNIsFLXpBLnYbRkfqJT1qV59pI3bQCkaGYqw==", + "version": "3.6.0", + "resolved": "https://registry.npmjs.org/biomedical_id_resolver/-/biomedical_id_resolver-3.6.0.tgz", + "integrity": "sha512-42id3v2Eg1MvJGSdT31LLRPWQICExce8je3itDgGXAH5Y13xCGw0JKcT7uPArDpc/9b5NkMUX4Vtt+6vj3Jc5g==", "requires": { "@commitlint/cli": "^11.0.0", "@commitlint/config-conventional": "^11.0.0", diff --git a/package.json b/package.json index 87b1b16b..4f16fafa 100644 --- a/package.json +++ b/package.json @@ -41,7 +41,7 @@ "supertest": "^6.1.3" }, "dependencies": { - "@biothings-explorer/query_graph_handler": "^1.8.0", + "@biothings-explorer/query_graph_handler": "^1.9.0", "@biothings-explorer/smartapi-kg": "^3.5.0", "axios": "^0.21.1", "biothings-explorer-graphql": "2.1.1", From 612c943aa910396a33fa1a9ef682e6a41917ec68 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 22 Apr 2021 21:07:32 -0700 Subject: [PATCH 08/75] chore(release): 2.4.0 --- CHANGELOG.md | 15 +++++++++++++++ package-lock.json | 2 +- package.json | 2 +- 3 files changed, 17 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f8d0ea95..6f7f4554 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,21 @@ All notable changes to this project will be documented in this file. See [standard-version](https://github.com/conventional-changelog/standard-version) for commit guidelines. +## [2.4.0](https://github.com/biothings/BioThings_Explorer_TRAPI/compare/v2.3.0...v2.4.0) (2021-04-23) + + +### Features + +* :sparkles: allow user to set MAX_QUERIES_PER_MIN as env ([8686092](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/8686092a8cbeedacbc38f8670a7be6470eeafc9d)) +* :sparkles: set rate limit to max 3 queries per min ([aeea89c](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/aeea89c867eace66ba485b1c8b146af2a4328912)) + + +### Bug Fixes + +* :bug: fix unable to resolve biocarta id issue ([551e4b1](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/551e4b1f938eb08054f303ec6d2460f558e32d08)) +* :fire: temporarily disable text mining co-occurrence kp ([d214a4d](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/d214a4dbec36a60d6df7d150f89835a6ea32bac8)) +* :sparkles: re-enable clinical risk kp ([4464dfc](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/4464dfcffcb470ee7478cd16b2d93d712367ebd7)) + ## [2.3.0](https://github.com/biothings/BioThings_Explorer_TRAPI/compare/v2.2.0...v2.3.0) (2021-04-20) diff --git a/package-lock.json b/package-lock.json index 017559dd..df71e3f2 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/single-hop-app", - "version": "2.3.0", + "version": "2.4.0", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index 4f16fafa..6088cd5d 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/single-hop-app", - "version": "2.3.0", + "version": "2.4.0", "description": "App performing single hop query for BioThings Explorer", "main": "src/server.js", "scripts": { From 898483a89d678e7fc4c95dd43ab607e3bbc4ae46 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 22 Apr 2021 21:43:18 -0700 Subject: [PATCH 09/75] fix: :bug: fix issue when output ids contain special characters https://github.com/biothings/BioThings_Explorer_TRAPI/issues/148 --- package-lock.json | 24 ++++++++++++------------ package.json | 2 +- 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/package-lock.json b/package-lock.json index df71e3f2..31b2b74e 100644 --- a/package-lock.json +++ b/package-lock.json @@ -495,13 +495,13 @@ } }, "@biothings-explorer/call-apis": { - "version": "1.18.0", - "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.18.0.tgz", - "integrity": "sha512-8U8XIemDnZhKygcByZtBWRo5dJ8PVjh59AZcMlwOJYpIcMmevUDzpejqM+gdO9cN4SHWJTwTlueLK3bbo50fiw==", + "version": "1.19.0", + "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.19.0.tgz", + "integrity": "sha512-ukJZmOdf8CQ8hA0bxxsvhZLnGXz5QeX66khFdpQpXa2t4YQkB94twdUsgzJ74VgfrEHnpCL4BnmqbWvNm5PCAQ==", "requires": { "@biothings-explorer/api-response-transform": "^1.10.1", "axios": "^0.21.1", - "biomedical_id_resolver": "^3.6.0", + "biomedical_id_resolver": "^3.7.0", "debug": "^4.3.1", "husky": "^4.3.8" }, @@ -565,14 +565,14 @@ } }, "@biothings-explorer/query_graph_handler": { - "version": "1.9.0", - "resolved": "https://registry.npmjs.org/@biothings-explorer/query_graph_handler/-/query_graph_handler-1.9.0.tgz", - "integrity": "sha512-WFbPn2XDRPirvjkxEZZSndKQxCg5ZzT6wgzau2MOVyvql4D71j6dT67ac5tx0uH5kVlFxija5mr5hD3/CG18EQ==", + "version": "1.10.0", + "resolved": "https://registry.npmjs.org/@biothings-explorer/query_graph_handler/-/query_graph_handler-1.10.0.tgz", + "integrity": "sha512-psP7RQBUli5mC6suRpvy4bJaDT6g8taPRUOxCA2wMjEouB3UgCx2KlzNdeE3sXDjtdMxhmYU8xU+TGFAnu+rmQ==", "requires": { - "@biothings-explorer/call-apis": "^1.18.0", + "@biothings-explorer/call-apis": "^1.19.0", "@biothings-explorer/smartapi-kg": "^3.7.0", "biolink-model": "^0.3.0", - "biomedical_id_resolver": "^3.6.0", + "biomedical_id_resolver": "^3.7.0", "debug": "^4.3.1", "lodash": "^4.17.21", "ms": "^2.1.3", @@ -3297,9 +3297,9 @@ } }, "biomedical_id_resolver": { - "version": "3.6.0", - "resolved": "https://registry.npmjs.org/biomedical_id_resolver/-/biomedical_id_resolver-3.6.0.tgz", - "integrity": "sha512-42id3v2Eg1MvJGSdT31LLRPWQICExce8je3itDgGXAH5Y13xCGw0JKcT7uPArDpc/9b5NkMUX4Vtt+6vj3Jc5g==", + "version": "3.7.0", + "resolved": "https://registry.npmjs.org/biomedical_id_resolver/-/biomedical_id_resolver-3.7.0.tgz", + "integrity": "sha512-J8uWY761qUPbqAfOyNDj+6Ywj3MzfuXO1qmMMSVcIuQx/tIVj6dL/XS0DrC/a0uHer43mtOGBhMfMhtHlnaweA==", "requires": { "@commitlint/cli": "^11.0.0", "@commitlint/config-conventional": "^11.0.0", diff --git a/package.json b/package.json index 6088cd5d..4e3e95c5 100644 --- a/package.json +++ b/package.json @@ -41,7 +41,7 @@ "supertest": "^6.1.3" }, "dependencies": { - "@biothings-explorer/query_graph_handler": "^1.9.0", + "@biothings-explorer/query_graph_handler": "^1.10.0", "@biothings-explorer/smartapi-kg": "^3.5.0", "axios": "^0.21.1", "biothings-explorer-graphql": "2.1.1", From 8fa6fefb38ffa09730be9ab6ab591dc0c7f7d91f Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Fri, 23 Apr 2021 09:56:17 -0700 Subject: [PATCH 10/75] chore(release): 2.5.0 --- CHANGELOG.md | 7 +++++++ package-lock.json | 2 +- package.json | 2 +- 3 files changed, 9 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6f7f4554..08876563 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,13 @@ All notable changes to this project will be documented in this file. See [standard-version](https://github.com/conventional-changelog/standard-version) for commit guidelines. +## [2.5.0](https://github.com/biothings/BioThings_Explorer_TRAPI/compare/v2.4.0...v2.5.0) (2021-04-23) + + +### Bug Fixes + +* :bug: fix issue when output ids contain special characters ([898483a](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/898483a89d678e7fc4c95dd43ab607e3bbc4ae46)) + ## [2.4.0](https://github.com/biothings/BioThings_Explorer_TRAPI/compare/v2.3.0...v2.4.0) (2021-04-23) diff --git a/package-lock.json b/package-lock.json index 31b2b74e..e875c7fd 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/single-hop-app", - "version": "2.4.0", + "version": "2.5.0", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index 4e3e95c5..941772e9 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/single-hop-app", - "version": "2.4.0", + "version": "2.5.0", "description": "App performing single hop query for BioThings Explorer", "main": "src/server.js", "scripts": { From 88d6035d9c9e76451be5514409f3a416da062c55 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 27 Apr 2021 07:56:43 -0700 Subject: [PATCH 11/75] fix: :bug: change from NCBIGENE to NCBIGene --- package-lock.json | 71 +++++++++++------------------------------------ package.json | 2 +- 2 files changed, 17 insertions(+), 56 deletions(-) diff --git a/package-lock.json b/package-lock.json index e875c7fd..1e2c3951 100644 --- a/package-lock.json +++ b/package-lock.json @@ -495,13 +495,13 @@ } }, "@biothings-explorer/call-apis": { - "version": "1.19.0", - "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.19.0.tgz", - "integrity": "sha512-ukJZmOdf8CQ8hA0bxxsvhZLnGXz5QeX66khFdpQpXa2t4YQkB94twdUsgzJ74VgfrEHnpCL4BnmqbWvNm5PCAQ==", + "version": "1.20.0", + "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.20.0.tgz", + "integrity": "sha512-WF6+QEdnY3HmQhbHl6PKOAmNjhoIOpXmAhxlqYL39V2BlHlz7joY7PSebYkW+lQxLBjQjeDam5RaVYXXmfnCYQ==", "requires": { "@biothings-explorer/api-response-transform": "^1.10.1", "axios": "^0.21.1", - "biomedical_id_resolver": "^3.7.0", + "biomedical_id_resolver": "^3.9.0", "debug": "^4.3.1", "husky": "^4.3.8" }, @@ -565,14 +565,14 @@ } }, "@biothings-explorer/query_graph_handler": { - "version": "1.10.0", - "resolved": "https://registry.npmjs.org/@biothings-explorer/query_graph_handler/-/query_graph_handler-1.10.0.tgz", - "integrity": "sha512-psP7RQBUli5mC6suRpvy4bJaDT6g8taPRUOxCA2wMjEouB3UgCx2KlzNdeE3sXDjtdMxhmYU8xU+TGFAnu+rmQ==", + "version": "1.12.1", + "resolved": "https://registry.npmjs.org/@biothings-explorer/query_graph_handler/-/query_graph_handler-1.12.1.tgz", + "integrity": "sha512-AYoYe2C5LwKwUyg+pvEqjX5rqfbqoKDYHKJcICMC0MtCX2i9laP76+/XbGRvpuBhQCG97fTNpRzbbq4/2Lt8Fg==", "requires": { - "@biothings-explorer/call-apis": "^1.19.0", + "@biothings-explorer/call-apis": "^1.20.0", "@biothings-explorer/smartapi-kg": "^3.7.0", "biolink-model": "^0.3.0", - "biomedical_id_resolver": "^3.7.0", + "biomedical_id_resolver": "^3.9.0", "debug": "^4.3.1", "lodash": "^4.17.21", "ms": "^2.1.3", @@ -3271,9 +3271,9 @@ "dev": true }, "biolink-model": { - "version": "0.3.0", - "resolved": "https://registry.npmjs.org/biolink-model/-/biolink-model-0.3.0.tgz", - "integrity": "sha512-eUQE9Xy81FEaQdJGPdqx5ouRDy09zcd0g8Rdj331FHVq3ekcnKvQ3FNwzj/QWJEVsSlezCFp5r6l4X+oUOy6Kg==", + "version": "0.3.1", + "resolved": "https://registry.npmjs.org/biolink-model/-/biolink-model-0.3.1.tgz", + "integrity": "sha512-kqGMG68FkNjYxyOI8D7ZWyDtrRhIVkkEXt977VjomxAUbwgmhVjTqg39QkTvXdfn/SDKs/+HU2wv3xak/vFs+g==", "requires": { "axios": "^0.21.1", "debug": "^4.3.1", @@ -3297,24 +3297,19 @@ } }, "biomedical_id_resolver": { - "version": "3.7.0", - "resolved": "https://registry.npmjs.org/biomedical_id_resolver/-/biomedical_id_resolver-3.7.0.tgz", - "integrity": "sha512-J8uWY761qUPbqAfOyNDj+6Ywj3MzfuXO1qmMMSVcIuQx/tIVj6dL/XS0DrC/a0uHer43mtOGBhMfMhtHlnaweA==", + "version": "3.9.0", + "resolved": "https://registry.npmjs.org/biomedical_id_resolver/-/biomedical_id_resolver-3.9.0.tgz", + "integrity": "sha512-bV8sR9tZi7h9QBmzIdwfkEseG/CCsOuDdlgfKVMQ9ApPSjdHl10ZPcRnm9qFe8e+22jrK/lLw7zAK/gkE6gYnQ==", "requires": { "@commitlint/cli": "^11.0.0", "@commitlint/config-conventional": "^11.0.0", "axios": "^0.19.2", - "biolink-model": "^0.1.2", + "biolink-model": "^0.3.1", "debug": "^4.3.1", "husky": "^4.3.8", "lodash": "^4.17.21" }, "dependencies": { - "argparse": { - "version": "2.0.1", - "resolved": "https://registry.npmjs.org/argparse/-/argparse-2.0.1.tgz", - "integrity": "sha512-8+9WqebbFzpX9OR+Wa6O29asIogeRMzcGtAINdpMHHyAg10f05aSFVBbcEqGf/PXw1EjAZ+q2/bEBg3DvurK3Q==" - }, "axios": { "version": "0.19.2", "resolved": "https://registry.npmjs.org/axios/-/axios-0.19.2.tgz", @@ -3323,32 +3318,6 @@ "follow-redirects": "1.5.10" } }, - "biolink-model": { - "version": "0.1.2", - "resolved": "https://registry.npmjs.org/biolink-model/-/biolink-model-0.1.2.tgz", - "integrity": "sha512-SbTcAdocPz3RfucuQc5ZmCN3HMAKRxOd3LxfeqM5yMqMpkn8jlmTWwb6o1y5Zrkh6VDHvOKqR2n1txg0Ne7uQA==", - "requires": { - "axios": "^0.21.1", - "debug": "^4.3.1", - "js-yaml": "^4.0.0", - "pascal-case": "^3.1.2" - }, - "dependencies": { - "axios": { - "version": "0.21.1", - "resolved": "https://registry.npmjs.org/axios/-/axios-0.21.1.tgz", - "integrity": "sha512-dKQiRHxGD9PPRIUNIWvZhPTPpl1rf/OxTYKsqKUDjBwYylTvV7SjSHJb9ratfyzM6wCdLCOYLzs73qpg5c4iGA==", - "requires": { - "follow-redirects": "^1.10.0" - } - }, - "follow-redirects": { - "version": "1.13.3", - "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.13.3.tgz", - "integrity": "sha512-DUgl6+HDzB0iEptNQEXLx/KhTmDb8tZUHSeLqpnjpknR70H0nC2t9N73BK6fN4hOvJ84pKlIQVQ4k5FFlBedKA==" - } - } - }, "follow-redirects": { "version": "1.5.10", "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.5.10.tgz", @@ -3367,14 +3336,6 @@ } } }, - "js-yaml": { - "version": "4.1.0", - "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-4.1.0.tgz", - "integrity": "sha512-wpxZs9NoxZaJESJGIZTyDEaYpl0FKSA+FB9aJiyemKhMwkxQg63h4T1KJgUGHpTqPDNRcmmYLugrRjJlBtWvRA==", - "requires": { - "argparse": "^2.0.1" - } - }, "ms": { "version": "2.0.0", "resolved": "https://registry.npmjs.org/ms/-/ms-2.0.0.tgz", diff --git a/package.json b/package.json index 941772e9..65471808 100644 --- a/package.json +++ b/package.json @@ -41,7 +41,7 @@ "supertest": "^6.1.3" }, "dependencies": { - "@biothings-explorer/query_graph_handler": "^1.10.0", + "@biothings-explorer/query_graph_handler": "^1.12.1", "@biothings-explorer/smartapi-kg": "^3.5.0", "axios": "^0.21.1", "biothings-explorer-graphql": "2.1.1", From f60a0ceeb1fc691bf2c4c0defda86d36178ad4ff Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 27 Apr 2021 07:58:22 -0700 Subject: [PATCH 12/75] refactor: :recycle: change from NCBIGENE to NCBIGene for all tests --- __test__/integration/TRAPIv1.test.js | 2 +- __test__/integration/routes/v1query_by_api.test.js | 2 +- .../v1/query_chemicals_physically_interacts_with_genes.json | 2 +- examples/v1/query_with_node_to_be_expanded.json | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/__test__/integration/TRAPIv1.test.js b/__test__/integration/TRAPIv1.test.js index ee6bbe2e..d4749582 100644 --- a/__test__/integration/TRAPIv1.test.js +++ b/__test__/integration/TRAPIv1.test.js @@ -51,7 +51,7 @@ describe("Testing endpoints", () => { expect(response.body.message).toHaveProperty("knowledge_graph"); expect(response.body.message.knowledge_graph).toHaveProperty("nodes"); expect(response.body.message.knowledge_graph).toHaveProperty("edges"); - expect(response.body.message.knowledge_graph.nodes).toHaveProperty("NCBIGENE:1017") + expect(response.body.message.knowledge_graph.nodes).toHaveProperty("NCBIGene:1017") }) }) diff --git a/__test__/integration/routes/v1query_by_api.test.js b/__test__/integration/routes/v1query_by_api.test.js index b5a0a209..0a9501d2 100644 --- a/__test__/integration/routes/v1query_by_api.test.js +++ b/__test__/integration/routes/v1query_by_api.test.js @@ -98,7 +98,7 @@ describe("Testing /v1/smartapi/{smartapi_id}/query endpoints", () => { .expect(200) .expect('Content-Type', /json/) .then(response => { - expect(response.body.message.knowledge_graph.nodes).toHaveProperty("NCBIGENE:6530") + expect(response.body.message.knowledge_graph.nodes).toHaveProperty("NCBIGene:6530") }) }) diff --git a/examples/v1/query_chemicals_physically_interacts_with_genes.json b/examples/v1/query_chemicals_physically_interacts_with_genes.json index 19543482..06931a71 100644 --- a/examples/v1/query_chemicals_physically_interacts_with_genes.json +++ b/examples/v1/query_chemicals_physically_interacts_with_genes.json @@ -4,7 +4,7 @@ "nodes": { "n0": { "category": "biolink:Gene", - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" }, "n1": { "category": "biolink:ChemicalSubstance" diff --git a/examples/v1/query_with_node_to_be_expanded.json b/examples/v1/query_with_node_to_be_expanded.json index 8cf368fd..5998a509 100644 --- a/examples/v1/query_with_node_to_be_expanded.json +++ b/examples/v1/query_with_node_to_be_expanded.json @@ -3,7 +3,7 @@ "query_graph": { "nodes": { "n0": { - "id": "NCBIGENE:1017", + "id": "NCBIGene:1017", "category": "biolink:Gene" }, "n1": { From e319442e656ba6c645877a64f6565128998e8074 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 27 Apr 2021 18:40:00 +0000 Subject: [PATCH 13/75] build(deps): bump redis from 3.0.2 to 3.1.1 Bumps [redis](https://github.com/NodeRedis/node-redis) from 3.0.2 to 3.1.1. - [Release notes](https://github.com/NodeRedis/node-redis/releases) - [Changelog](https://github.com/NodeRedis/node-redis/blob/master/CHANGELOG.md) - [Commits](https://github.com/NodeRedis/node-redis/compare/v3.0.2...v3.1.1) Signed-off-by: dependabot[bot] --- package-lock.json | 22 +++++++++++----------- package.json | 2 +- 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/package-lock.json b/package-lock.json index 1e2c3951..a39b6baf 100644 --- a/package-lock.json +++ b/package-lock.json @@ -4965,9 +4965,9 @@ "integrity": "sha1-3zrhmayt+31ECqrgsp4icrJOxhk=" }, "denque": { - "version": "1.4.1", - "resolved": "https://registry.npmjs.org/denque/-/denque-1.4.1.tgz", - "integrity": "sha512-OfzPuSZKGcgr96rf1oODnfjqBFmr1DVoc/TrItj3Ohe0Ah1C5WX5Baquw/9U9KovnQ88EqmJbD66rKYUQYN1tQ==" + "version": "1.5.0", + "resolved": "https://registry.npmjs.org/denque/-/denque-1.5.0.tgz", + "integrity": "sha512-CYiCSgIF1p6EUByQPlGkKnP1M9g0ZV3qMIrqMqZqdwazygIA/YP2vrbcyl1h/WppKJTdl1F85cXIle+394iDAQ==" }, "depd": { "version": "1.1.2", @@ -13201,20 +13201,20 @@ } }, "redis": { - "version": "3.0.2", - "resolved": "https://registry.npmjs.org/redis/-/redis-3.0.2.tgz", - "integrity": "sha512-PNhLCrjU6vKVuMOyFu7oSP296mwBkcE6lrAjruBYG5LgdSqtRBoVQIylrMyVZD/lkF24RSNNatzvYag6HRBHjQ==", + "version": "3.1.1", + "resolved": "https://registry.npmjs.org/redis/-/redis-3.1.1.tgz", + "integrity": "sha512-QhkKhOuzhogR1NDJfBD34TQJz2ZJwDhhIC6ZmvpftlmfYShHHQXjjNspAJ+Z2HH5NwSBVYBVganbiZ8bgFMHjg==", "requires": { - "denque": "^1.4.1", - "redis-commands": "^1.5.0", + "denque": "^1.5.0", + "redis-commands": "^1.7.0", "redis-errors": "^1.2.0", "redis-parser": "^3.0.0" } }, "redis-commands": { - "version": "1.6.0", - "resolved": "https://registry.npmjs.org/redis-commands/-/redis-commands-1.6.0.tgz", - "integrity": "sha512-2jnZ0IkjZxvguITjFTrGiLyzQZcTvaw8DAaCXxZq/dsHXz7KfMQ3OUJy7Tz9vnRtZRVz6VRCPDvruvU8Ts44wQ==" + "version": "1.7.0", + "resolved": "https://registry.npmjs.org/redis-commands/-/redis-commands-1.7.0.tgz", + "integrity": "sha512-nJWqw3bTFy21hX/CPKHth6sfhZbdiHP6bTawSgQBlKOVRG7EZkfHbbHwQJnrE4vsQf0CMNE+3gJ4Fmm16vdVlQ==" }, "redis-errors": { "version": "1.2.0", diff --git a/package.json b/package.json index 65471808..5fcea0ef 100644 --- a/package.json +++ b/package.json @@ -61,7 +61,7 @@ "node-cron": "^2.0.3", "npm": "^6.14.12", "openapi-validator-middleware": "^3.2.2", - "redis": "^3.0.2", + "redis": "^3.1.1", "snake-case": "^3.0.4", "winston": "^3.3.3", "winston-daily-rotate-file": "^4.5.1", From 7347b552b9a24cdbdfdaa437aca4c65d52d833b1 Mon Sep 17 00:00:00 2001 From: Andrew Su Date: Fri, 7 May 2021 10:57:22 -0700 Subject: [PATCH 14/75] nodemon to ignore './data/', addresses #170 --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 65471808..b81d34a4 100644 --- a/package.json +++ b/package.json @@ -4,7 +4,7 @@ "description": "App performing single hop query for BioThings Explorer", "main": "src/server.js", "scripts": { - "start": "nodemon src/server.js", + "start": "nodemon --ignore './data/' src/server.js", "test": "jest --forceExit", "test-cov": "jest --coverage", "coveralls": "jest --coverage --forceExit && cat ./coverage/lcov.info | ./node_modules/coveralls/bin/coveralls.js && rm -rf ./coverage", From ebff947aeacee8d81f11da4020df869200c0c83b Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Mon, 10 May 2021 16:31:32 -0700 Subject: [PATCH 15/75] build: :arrow_up: upgrade smartapi-kg package --- package-lock.json | 19779 +++++++++++++++++++++++++++++++++++++++++++- package.json | 2 +- 2 files changed, 19618 insertions(+), 163 deletions(-) diff --git a/package-lock.json b/package-lock.json index 1e2c3951..5bedf859 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,8 +1,19578 @@ { "name": "@biothings-explorer/single-hop-app", "version": "2.5.0", - "lockfileVersion": 1, + 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"lru-cache": "^5.1.1", "make-fetch-happen": "^5.0.0", "npm-package-arg": "^6.1.0", @@ -11968,6 +31423,19 @@ "version": "2.0.0", "bundled": true }, + "string_decoder": { + "version": "1.3.0", + "bundled": true, + "requires": { + "safe-buffer": "~5.2.0" + }, + "dependencies": { + "safe-buffer": { + "version": "5.2.0", + "bundled": true + } + } + }, "string-width": { "version": "2.1.1", "bundled": true, @@ -11993,19 +31461,6 @@ } } }, - "string_decoder": { - "version": "1.3.0", - "bundled": true, - "requires": { - "safe-buffer": "~5.2.0" - }, - "dependencies": { - "safe-buffer": { - "version": "5.2.0", - "bundled": true - } - } - }, "stringify-package": { "version": "1.0.1", "bundled": true @@ -14449,6 +33904,14 @@ "resolved": "https://registry.npmjs.org/streamsearch/-/streamsearch-0.1.2.tgz", "integrity": "sha1-gIudDlb8Jz2Am6VzOOkpkZoanxo=" }, + "string_decoder": { + "version": "1.3.0", + "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.3.0.tgz", + "integrity": "sha512-hkRX8U1WjJFd8LsDJ2yQ/wWWxaopEsABU1XfkM8A+j0+85JAGppt16cr1Whg6KIbb4okU6Mql6BOj+uup/wKeA==", + "requires": { + "safe-buffer": "~5.2.0" + } + }, "string-length": { "version": "4.0.1", "resolved": "https://registry.npmjs.org/string-length/-/string-length-4.0.1.tgz", @@ -14487,14 +33950,6 @@ "es-abstract": "^1.17.5" } }, - "string_decoder": { - "version": "1.3.0", - "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.3.0.tgz", - "integrity": "sha512-hkRX8U1WjJFd8LsDJ2yQ/wWWxaopEsABU1XfkM8A+j0+85JAGppt16cr1Whg6KIbb4okU6Mql6BOj+uup/wKeA==", - "requires": { - "safe-buffer": "~5.2.0" - } - }, "stringify-package": { "version": "1.0.1", "resolved": "https://registry.npmjs.org/stringify-package/-/stringify-package-1.0.1.tgz", diff --git a/package.json b/package.json index 65471808..541d4446 100644 --- a/package.json +++ b/package.json @@ -42,7 +42,7 @@ }, "dependencies": { "@biothings-explorer/query_graph_handler": "^1.12.1", - "@biothings-explorer/smartapi-kg": "^3.5.0", + "@biothings-explorer/smartapi-kg": "^3.8.0", "axios": "^0.21.1", "biothings-explorer-graphql": "2.1.1", "body-parser": "^1.19.0", From d8cc553365a89c9ab1e9bec850e69b01f1020bd2 Mon Sep 17 00:00:00 2001 From: Andrew Su Date: Mon, 10 May 2021 21:04:19 -0700 Subject: [PATCH 16/75] use nodemon delay option --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index b81d34a4..cd5b92e2 100644 --- a/package.json +++ b/package.json @@ -4,7 +4,7 @@ "description": "App performing single hop query for BioThings Explorer", "main": "src/server.js", "scripts": { - "start": "nodemon --ignore './data/' src/server.js", + "start": "nodemon --delay 5 src/server.js", "test": "jest --forceExit", "test-cov": "jest --coverage", "coveralls": "jest --coverage --forceExit && cat ./coverage/lcov.info | ./node_modules/coveralls/bin/coveralls.js && rm -rf ./coverage", From e952cca53b7dfaa6645b74bc9b9d00648214794d Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Tue, 11 May 2021 10:15:19 -0700 Subject: [PATCH 17/75] test: :green_heart: update test to match upstream API --- __test__/integration/TRAPIv1.test.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/__test__/integration/TRAPIv1.test.js b/__test__/integration/TRAPIv1.test.js index d4749582..ed41e0e8 100644 --- a/__test__/integration/TRAPIv1.test.js +++ b/__test__/integration/TRAPIv1.test.js @@ -67,7 +67,7 @@ describe("Testing endpoints", () => { expect(response.body.message).toHaveProperty("knowledge_graph"); expect(response.body.message.knowledge_graph).toHaveProperty("nodes"); expect(response.body.message.knowledge_graph).toHaveProperty("edges"); - expect(response.body.message.knowledge_graph.nodes).toHaveProperty("MONDO:0008315") + expect(response.body.message.knowledge_graph.nodes).toHaveProperty("MONDO:0001583") }) }) From 3cec3f2868864cd4a6501ba441ac4927b8034250 Mon Sep 17 00:00:00 2001 From: Marco Cano Date: Tue, 11 May 2021 11:27:17 -0700 Subject: [PATCH 18/75] feat: :sparkles: upgrade handler to support trapi 1.1.0 --- package-lock.json | 19561 +++++++++++++++++++++++++++++++++++++++++++- package.json | 2 +- 2 files changed, 19404 insertions(+), 159 deletions(-) diff --git a/package-lock.json b/package-lock.json index 1e2c3951..9b090e13 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,8 +1,19353 @@ { "name": "@biothings-explorer/single-hop-app", "version": "2.5.0", - "lockfileVersion": 1, + "lockfileVersion": 2, "requires": true, + "packages": { + "": { + "name": "@biothings-explorer/single-hop-app", + "version": "2.5.0", + "license": "ISC", + "dependencies": { + "@biothings-explorer/query_graph_handler": "^1.15.0", + "@biothings-explorer/smartapi-kg": "^3.5.0", + "axios": "^0.21.1", + "biothings-explorer-graphql": "2.1.1", + "body-parser": "^1.19.0", + "camelcase": "^6.2.0", + "compression": "^1.7.4", + "cors": "^2.8.5", + "debug": "^4.3.1", + "dotenv": "^8.2.0", + "express": "^4.17.1", + 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"make-fetch-happen": "^5.0.0", "npm-package-arg": "^6.1.0", @@ -11968,6 +31222,19 @@ "version": "2.0.0", "bundled": true }, + "string_decoder": { + "version": "1.3.0", + "bundled": true, + "requires": { + "safe-buffer": "~5.2.0" + }, + "dependencies": { + "safe-buffer": { + "version": "5.2.0", + "bundled": true + } + } + }, "string-width": { "version": "2.1.1", "bundled": true, @@ -11993,19 +31260,6 @@ } } }, - "string_decoder": { - "version": "1.3.0", - "bundled": true, - "requires": { - "safe-buffer": "~5.2.0" - }, - "dependencies": { - "safe-buffer": { - "version": "5.2.0", - "bundled": true - } - } - }, "stringify-package": { "version": "1.0.1", "bundled": true @@ -14449,6 +33703,14 @@ "resolved": "https://registry.npmjs.org/streamsearch/-/streamsearch-0.1.2.tgz", "integrity": "sha1-gIudDlb8Jz2Am6VzOOkpkZoanxo=" }, + "string_decoder": { + "version": "1.3.0", + "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.3.0.tgz", + "integrity": 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"sha512-doEwdvm4PCeK4K3RQN2ZC2BYUBaxwLARCqZmMjtF8a51J2Rb0xpVloFRnCODwqjpwnAoao4pelN8l3RJdv3gRQ==", - "dev": true, - "requires": { - "ms": "2.1.2" - } - }, "form-data": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/form-data/-/form-data-3.0.0.tgz", diff --git a/package.json b/package.json index 65471808..c2ebb263 100644 --- a/package.json +++ b/package.json @@ -41,7 +41,7 @@ "supertest": "^6.1.3" }, "dependencies": { - "@biothings-explorer/query_graph_handler": "^1.12.1", + "@biothings-explorer/query_graph_handler": "^1.15.0", "@biothings-explorer/smartapi-kg": "^3.5.0", "axios": "^0.21.1", "biothings-explorer-graphql": "2.1.1", From 1a8dd3a411b8960bd5ac3784cf9625c084a6b375 Mon Sep 17 00:00:00 2001 From: Marco Cano Date: Tue, 11 May 2021 11:40:04 -0700 Subject: [PATCH 19/75] chore(release): 2.6.0 --- CHANGELOG.md | 13 +++++++++++++ package-lock.json | 2 +- package.json | 2 +- 3 files changed, 15 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 08876563..20ccecac 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,19 @@ All notable changes to this project will be documented in this file. See [standard-version](https://github.com/conventional-changelog/standard-version) for commit guidelines. +## [2.6.0](https://github.com/biothings/BioThings_Explorer_TRAPI/compare/v2.5.0...v2.6.0) (2021-05-11) + + +### Features + +* :sparkles: upgrade handler to support trapi 1.1.0 ([3cec3f2](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/3cec3f2868864cd4a6501ba441ac4927b8034250)) +* trapi v1.1.0 support, update handler ([3109a8a](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/3109a8a14071198ae038c5001f0d1bd76c566ad2)) + + +### Bug Fixes + +* :bug: change from NCBIGENE to NCBIGene ([88d6035](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/88d6035d9c9e76451be5514409f3a416da062c55)) + ## [2.5.0](https://github.com/biothings/BioThings_Explorer_TRAPI/compare/v2.4.0...v2.5.0) (2021-04-23) diff --git a/package-lock.json b/package-lock.json index 49b7cbc7..22c14782 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/single-hop-app", - "version": "2.5.0", + "version": "2.6.0", "lockfileVersion": 2, "requires": true, "packages": { diff --git a/package.json b/package.json index 361b5451..84d2436a 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/single-hop-app", - "version": "2.5.0", + "version": "2.6.0", "description": "App performing single hop query for BioThings Explorer", "main": "src/server.js", "scripts": { From 7bca88119675d7fb0a23896f777849917aedbba8 Mon Sep 17 00:00:00 2001 From: Marco Cano Date: Wed, 12 May 2021 14:08:27 -0700 Subject: [PATCH 20/75] build: :arrow_up: upgrade dep, update callapis for trapi 1.1.0 --- package-lock.json | 154 +++++----------------------------------------- package.json | 2 +- 2 files changed, 18 insertions(+), 138 deletions(-) diff --git a/package-lock.json b/package-lock.json index 49b7cbc7..3106e6af 100644 --- a/package-lock.json +++ b/package-lock.json @@ -9,7 +9,7 @@ "version": "2.5.0", "license": "ISC", "dependencies": { - "@biothings-explorer/query_graph_handler": "^1.15.0", + "@biothings-explorer/query_graph_handler": "^1.16.1", "@biothings-explorer/smartapi-kg": "^3.8.0", "axios": "^0.21.1", "biothings-explorer-graphql": "2.1.1", @@ -165,18 +165,6 @@ "node": ">=6.9.0" } }, - "node_modules/@babel/core/node_modules/debug": { - "version": "4.3.1", - "resolved": "https://registry.npmjs.org/debug/-/debug-4.3.1.tgz", - "integrity": "sha512-doEwdvm4PCeK4K3RQN2ZC2BYUBaxwLARCqZmMjtF8a51J2Rb0xpVloFRnCODwqjpwnAoao4pelN8l3RJdv3gRQ==", - "dev": true, - "dependencies": { - "ms": "2.1.2" - }, - "engines": { - "node": ">=6.0" - } - }, "node_modules/@babel/core/node_modules/source-map": { "version": "0.5.7", "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.5.7.tgz", @@ -488,18 +476,6 @@ "lodash": "^4.17.19" } }, - "node_modules/@babel/traverse/node_modules/debug": { - "version": "4.3.1", - "resolved": "https://registry.npmjs.org/debug/-/debug-4.3.1.tgz", - 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"version": "1.16.1", + "resolved": "https://registry.npmjs.org/@biothings-explorer/query_graph_handler/-/query_graph_handler-1.16.1.tgz", + "integrity": "sha512-aokTFVYV1/swNAwFKrhG1QDcny9xgRMYoKS9NdT12uTU70+Q43NyI6GlUwnCqAcx4OwolQUcDi0MbuOvz/gl/Q==", "requires": { - "@biothings-explorer/call-apis": "^1.21.0", - "@biothings-explorer/smartapi-kg": "^3.7.0", + "@biothings-explorer/call-apis": "^1.23.0", + "@biothings-explorer/smartapi-kg": "^3.8.0", "biolink-model": "^0.3.0", "biomedical_id_resolver": "^3.9.0", "debug": "^4.3.1", @@ -22734,14 +22650,6 @@ "lodash": "^4.17.19" } }, - "debug": { - "version": "4.1.1", - "resolved": "https://registry.npmjs.org/debug/-/debug-4.1.1.tgz", - "integrity": "sha512-pYAIzeRo8J6KPEaJ0VWOh5Pzkbw/RetuzehGM7QRRX5he4fPHx2rdKMB256ehJCkX+XRQm16eZLqLNS8RSZXZw==", - "requires": { - "ms": "^2.1.1" - } - }, "follow-redirects": { "version": "1.5.10", "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.5.10.tgz", @@ -22845,14 +22753,6 @@ } } }, - "debug": { - "version": "4.1.1", - "resolved": "https://registry.npmjs.org/debug/-/debug-4.1.1.tgz", - "integrity": "sha512-pYAIzeRo8J6KPEaJ0VWOh5Pzkbw/RetuzehGM7QRRX5he4fPHx2rdKMB256ehJCkX+XRQm16eZLqLNS8RSZXZw==", - "requires": { - "ms": "^2.1.1" - } - }, "follow-redirects": { "version": "1.5.10", "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.5.10.tgz", @@ -26574,17 +26474,6 @@ "debug": "^4.1.1", "istanbul-lib-coverage": "^3.0.0", "source-map": "^0.6.1" - }, - "dependencies": { - "debug": { - "version": "4.3.1", - "resolved": "https://registry.npmjs.org/debug/-/debug-4.3.1.tgz", - "integrity": "sha512-doEwdvm4PCeK4K3RQN2ZC2BYUBaxwLARCqZmMjtF8a51J2Rb0xpVloFRnCODwqjpwnAoao4pelN8l3RJdv3gRQ==", - "dev": true, - "requires": { - "ms": "2.1.2" - } - } } }, "istanbul-reports": { @@ -33953,15 +33842,6 @@ "semver": "^7.3.2" }, "dependencies": { - "debug": { - "version": "4.3.1", - "resolved": "https://registry.npmjs.org/debug/-/debug-4.3.1.tgz", - "integrity": "sha512-doEwdvm4PCeK4K3RQN2ZC2BYUBaxwLARCqZmMjtF8a51J2Rb0xpVloFRnCODwqjpwnAoao4pelN8l3RJdv3gRQ==", - "dev": true, - "requires": { - "ms": "2.1.2" - } - }, "form-data": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/form-data/-/form-data-3.0.0.tgz", diff --git a/package.json b/package.json index 361b5451..670ca5e5 100644 --- a/package.json +++ b/package.json @@ -41,7 +41,7 @@ "supertest": "^6.1.3" }, "dependencies": { - "@biothings-explorer/query_graph_handler": "^1.15.0", + "@biothings-explorer/query_graph_handler": "^1.16.1", "@biothings-explorer/smartapi-kg": "^3.8.0", "axios": "^0.21.1", "biothings-explorer-graphql": "2.1.1", From 2a41515dc88c04c2b3136ad4d683a5911d602a33 Mon Sep 17 00:00:00 2001 From: Marco Cano Date: Wed, 12 May 2021 17:27:57 -0700 Subject: [PATCH 21/75] build: :arrow_up: trapi 1.1.0 ready, rename predicate endpoints, double throttle size --- __test__/integration/TRAPIv1.test.js | 8 ++++---- __test__/integration/routes/metakg.test.js | 2 +- __test__/integration/routes/v1predicates.test.js | 4 ++-- __test__/integration/routes/v1predicates_by_api.test.js | 6 +++--- __test__/integration/routes/v1predicates_by_team.test.js | 6 +++--- __test__/unittest/routes/predicates.test.js | 4 ++-- __test__/unittest/routes/predicates_team.test.js | 4 ++-- docs/smartapi.yaml | 8 ++++---- examples/v1/branched_query.json | 8 ++++---- .../v1/invalid/query_graph_with_edges_not_specified.json | 6 +++--- .../query_graph_with_nodes_and_edges_not_match.json | 8 ++++---- .../v1/invalid/query_graph_with_nodes_not_specified.json | 2 +- .../clinical_risk_kp/query_attribute_to_disease.json | 6 +++--- .../clinical_risk_kp/query_disease_to_disease.json | 6 +++--- .../clinical_risk_kp/query_drug_to_disease.json | 6 +++--- .../clinical_risk_kp/query_observation_to_disease.json | 6 +++--- .../query_chemicals_physically_interacts_with_genes.json | 8 ++++---- examples/v1/query_disease_has_phenotype.json | 8 ++++---- examples/v1/query_genes_relate_to_disease.json | 6 +++--- examples/v1/query_multihop_disease_gene_chemical.json | 8 ++++---- examples/v1/query_with_category_as_list.json | 6 +++--- examples/v1/query_with_node_to_be_expanded.json | 8 ++++---- examples/v1/query_without_input_category.json | 4 ++-- examples/v1/serviceprovider/mychem.json | 8 ++++---- examples/v1/serviceprovider/mygene.json | 8 ++++---- .../v1/textmining/query_chemicals_related_to_disease.json | 6 +++--- .../query_chemicals_related_to_gene_or_gene_product.json | 6 +++--- src/config/index.js | 2 +- src/routes/v1/predicates_v1.js | 2 +- src/routes/v1/predicates_v1_by_api.js | 2 +- src/routes/v1/predicates_v1_by_team.js | 2 +- 31 files changed, 87 insertions(+), 87 deletions(-) diff --git a/__test__/integration/TRAPIv1.test.js b/__test__/integration/TRAPIv1.test.js index ed41e0e8..496809cd 100644 --- a/__test__/integration/TRAPIv1.test.js +++ b/__test__/integration/TRAPIv1.test.js @@ -16,9 +16,9 @@ describe("Testing endpoints", () => { const query_without_category = JSON.parse(fs.readFileSync(path.join(example_foler, 'query_without_input_category.json'))) const expand_node = JSON.parse(fs.readFileSync(path.join(example_foler, 'query_with_node_to_be_expanded.json'))) - test("GET /v1/predicates", async () => { + test("GET /v1/meta_knowledge_graph", async () => { await request(app) - .get("/v1/predicates") + .get("/v1/meta_knowledge_graph") .expect(200) .expect('Content-Type', /json/) .then((response) => { @@ -28,9 +28,9 @@ describe("Testing endpoints", () => { }) }) - test("GET /v1/smartapi/{smartapi_id}/predicates", async () => { + test("GET /v1/smartapi/{smartapi_id}/meta_knowledge_graph", async () => { await request(app) - .get("/v1/smartapi/978fe380a147a8641caf72320862697b/predicates") + .get("/v1/smartapi/978fe380a147a8641caf72320862697b/meta_knowledge_graph") .expect(200) .expect('Content-Type', /json/) .then((response) => { diff --git a/__test__/integration/routes/metakg.test.js b/__test__/integration/routes/metakg.test.js index b8c42ea0..832de86a 100644 --- a/__test__/integration/routes/metakg.test.js +++ b/__test__/integration/routes/metakg.test.js @@ -86,7 +86,7 @@ describe("Test /metakg endpoint", () => { }) }) - test("Should return info from TRAPI /predicates endpoint", async () => { + test("Should return info from TRAPI /meta_knowledge_graph endpoint", async () => { await request(app) .get("/metakg") .expect(200) diff --git a/__test__/integration/routes/v1predicates.test.js b/__test__/integration/routes/v1predicates.test.js index 83401a7f..54ef33c5 100644 --- a/__test__/integration/routes/v1predicates.test.js +++ b/__test__/integration/routes/v1predicates.test.js @@ -1,10 +1,10 @@ const app = require("../../../src/app"); const request = require('supertest'); -describe("Test /v1/predicates endpoint", () => { +describe("Test /v1/meta_knowledge_graph endpoint", () => { test("Should return 200 with valid response", async () => { await request(app) - .get("/v1/predicates") + .get("/v1/meta_knowledge_graph") .expect(200) .expect('Content-Type', /json/) .then((response) => { diff --git a/__test__/integration/routes/v1predicates_by_api.test.js b/__test__/integration/routes/v1predicates_by_api.test.js index d3a35473..2212836f 100644 --- a/__test__/integration/routes/v1predicates_by_api.test.js +++ b/__test__/integration/routes/v1predicates_by_api.test.js @@ -1,10 +1,10 @@ const app = require("../../../src/app"); const request = require('supertest'); -describe("Test /v1/smartapi/{smartapi_id}/predicates endpoint", () => { +describe("Test /v1/smartapi/{smartapi_id}/meta_knowledge_graph endpoint", () => { test("Query to Text Mining Targeted Association API Should return 200 with valid response", async () => { await request(app) - .get("/v1/smartapi/978fe380a147a8641caf72320862697b/predicates") + .get("/v1/smartapi/978fe380a147a8641caf72320862697b/meta_knowledge_graph") .expect(200) .expect('Content-Type', /json/) .then((response) => { @@ -15,7 +15,7 @@ describe("Test /v1/smartapi/{smartapi_id}/predicates endpoint", () => { test("Query to Invalid API Should return 404 with error message included", async () => { await request(app) - .get("/v1/smartapi/78fe380a147a8641caf72320862697b/predicates") + .get("/v1/smartapi/78fe380a147a8641caf72320862697b/meta_knowledge_graph") .expect(404) .expect('Content-Type', /json/) .then((response) => { diff --git a/__test__/integration/routes/v1predicates_by_team.test.js b/__test__/integration/routes/v1predicates_by_team.test.js index 3c1cb598..c25176c0 100644 --- a/__test__/integration/routes/v1predicates_by_team.test.js +++ b/__test__/integration/routes/v1predicates_by_team.test.js @@ -1,10 +1,10 @@ const app = require("../../../src/app"); const request = require('supertest'); -describe("Test /v1/team/{team_name}/predicates endpoint", () => { +describe("Test /v1/team/{team_name}/meta_knowledge_graph endpoint", () => { test("Query to Text Mining team Should return 200 with valid response", async () => { await request(app) - .get("/v1/team/Text Mining Provider/predicates") + .get("/v1/team/Text Mining Provider/meta_knowledge_graph") .expect(200) .expect('Content-Type', /json/) .then((response) => { @@ -15,7 +15,7 @@ describe("Test /v1/team/{team_name}/predicates endpoint", () => { test("Query to Invalid team Should return 200 with empty response", async () => { await request(app) - .get("/v1/team/wrong team/predicates") + .get("/v1/team/wrong team/meta_knowledge_graph") .expect(404) .expect('Content-Type', /json/) .then((response) => { diff --git a/__test__/unittest/routes/predicates.test.js b/__test__/unittest/routes/predicates.test.js index add0cbf9..77ea2422 100644 --- a/__test__/unittest/routes/predicates.test.js +++ b/__test__/unittest/routes/predicates.test.js @@ -7,7 +7,7 @@ jest.mock('../../../src/controllers/predicates'); -describe("Test /v1/predicates endpoint", () => { +describe("Test /v1/meta_knowledge_graph endpoint", () => { test("Should return 404 with valid response", async () => { @@ -15,7 +15,7 @@ describe("Test /v1/predicates endpoint", () => { throw new PredicatesLoadingError(); }) await request(app) - .get("/v1/predicates") + .get("/v1/meta_knowledge_graph") .expect(404) .expect('Content-Type', /json/) .then(res => { diff --git a/__test__/unittest/routes/predicates_team.test.js b/__test__/unittest/routes/predicates_team.test.js index 53a734fb..07c94b96 100644 --- a/__test__/unittest/routes/predicates_team.test.js +++ b/__test__/unittest/routes/predicates_team.test.js @@ -7,7 +7,7 @@ jest.mock('../../../src/controllers/predicates'); -describe("Test /v1/predicates endpoint", () => { +describe("Test /v1/meta_knowledge_graph endpoint", () => { test("Should return 404 with valid response", async () => { @@ -15,7 +15,7 @@ describe("Test /v1/predicates endpoint", () => { throw new PredicatesLoadingError(); }) await request(app) - .get("/v1/team/Text Mining Provider/predicates") + .get("/v1/team/Text Mining Provider/meta_knowledge_graph") .expect(404) .expect('Content-Type', /json/) .then(res => { diff --git a/docs/smartapi.yaml b/docs/smartapi.yaml index 92b5685a..43724436 100644 --- a/docs/smartapi.yaml +++ b/docs/smartapi.yaml @@ -113,7 +113,7 @@ paths: return all associations tags: - metadata - /predicates: + /meta_knowledge_graph: get: responses: '200': @@ -139,7 +139,7 @@ paths: tags: - metadata - 0.9.2 - /v1/predicates: + /v1/meta_knowledge_graph: get: tags: - predicates @@ -166,7 +166,7 @@ paths: 'biolink:Gene': - biolink:directly_interacts_with - biolink:decreases_activity_of - /v1/smartapi/{smartapi_id}/predicates: + /v1/smartapi/{smartapi_id}/meta_knowledge_graph: get: tags: - predicates @@ -201,7 +201,7 @@ paths: 'biolink:Gene': - biolink:directly_interacts_with - biolink:decreases_activity_of - /v1/team/{team_name}/predicates: + /v1/team/{team_name}/meta_knowledge_graph: get: tags: - predicates diff --git a/examples/v1/branched_query.json b/examples/v1/branched_query.json index e4b58f72..01136c80 100644 --- a/examples/v1/branched_query.json +++ b/examples/v1/branched_query.json @@ -3,14 +3,14 @@ "query_graph": { "nodes": { "n0": { - "category": "biolink:Disease", - "id": "MONDO:0005737" + "categories": "biolink:Disease", + "ids": "MONDO:0005737" }, "n1": { - "category": "biolink:Gene" + "categories": "biolink:Gene" }, "n2": { - "category": "biolink:ChemicalSubstance" + "categories": "biolink:ChemicalSubstance" } }, "edges": { diff --git a/examples/v1/invalid/query_graph_with_edges_not_specified.json b/examples/v1/invalid/query_graph_with_edges_not_specified.json index e405d797..1081ee68 100644 --- a/examples/v1/invalid/query_graph_with_edges_not_specified.json +++ b/examples/v1/invalid/query_graph_with_edges_not_specified.json @@ -3,11 +3,11 @@ "query_graph": { "nodes": { "n0": { - "category": "biolink:Gene", - "id": "NCBIGene:1017" + "categories": "biolink:Gene", + "ids": "NCBIGene:1017" }, "n1": { - "category": "biolink:ChemicalSubstance" + "categories": "biolink:ChemicalSubstance" } }, "edges": {} diff --git a/examples/v1/invalid/query_graph_with_nodes_and_edges_not_match.json b/examples/v1/invalid/query_graph_with_nodes_and_edges_not_match.json index 3f7f1a23..51b0b7c8 100644 --- a/examples/v1/invalid/query_graph_with_nodes_and_edges_not_match.json +++ b/examples/v1/invalid/query_graph_with_nodes_and_edges_not_match.json @@ -3,18 +3,18 @@ "query_graph": { "nodes": { "n0": { - "category": "biolink:Gene", - "id": "NCBIGene:1017" + "categories": "biolink:Gene", + "ids": "NCBIGene:1017" }, "n2": { - "category": "biolink:ChemicalSubstance" + "categories": "biolink:ChemicalSubstance" } }, "edges": { "e01": { "subject": "n0", "object": "n1", - "predicate": "biolink:physically_interacts_with" + "predicates": "biolink:physically_interacts_with" } } } diff --git a/examples/v1/invalid/query_graph_with_nodes_not_specified.json b/examples/v1/invalid/query_graph_with_nodes_not_specified.json index 63ba1478..1c980688 100644 --- a/examples/v1/invalid/query_graph_with_nodes_not_specified.json +++ b/examples/v1/invalid/query_graph_with_nodes_not_specified.json @@ -6,7 +6,7 @@ "e01": { "subject": "n0", "object": "n1", - "predicate": "biolink:physically_interacts_with" + "predicates": "biolink:physically_interacts_with" } } } diff --git a/examples/v1/multiomics/clinical_risk_kp/query_attribute_to_disease.json b/examples/v1/multiomics/clinical_risk_kp/query_attribute_to_disease.json index 45ab7a5d..bfec60b8 100644 --- a/examples/v1/multiomics/clinical_risk_kp/query_attribute_to_disease.json +++ b/examples/v1/multiomics/clinical_risk_kp/query_attribute_to_disease.json @@ -3,11 +3,11 @@ "query_graph": { "nodes": { "n0": { - "category": "biolink:Attribute", - "id": "NCIT:C28421" + "categories": "biolink:Attribute", + "ids": "NCIT:C28421" }, "n3": { - "category": "biolink:DiseaseOrPhenotypicFeature" + "categories": "biolink:DiseaseOrPhenotypicFeature" } }, "edges": { diff --git a/examples/v1/multiomics/clinical_risk_kp/query_disease_to_disease.json b/examples/v1/multiomics/clinical_risk_kp/query_disease_to_disease.json index 048ff5fd..81cf8319 100644 --- a/examples/v1/multiomics/clinical_risk_kp/query_disease_to_disease.json +++ b/examples/v1/multiomics/clinical_risk_kp/query_disease_to_disease.json @@ -3,11 +3,11 @@ "query_graph": { "nodes": { "n0": { - "category": "biolink:DiseaseOrPhenotypicFeature", - "id": "MONDO:0005015" + "categories": "biolink:DiseaseOrPhenotypicFeature", + "ids": "MONDO:0005015" }, "n3": { - "category": "biolink:DiseaseOrPhenotypicFeature" + "categories": "biolink:DiseaseOrPhenotypicFeature" } }, "edges": { diff --git a/examples/v1/multiomics/clinical_risk_kp/query_drug_to_disease.json b/examples/v1/multiomics/clinical_risk_kp/query_drug_to_disease.json index d9a737e6..fd3fc869 100644 --- a/examples/v1/multiomics/clinical_risk_kp/query_drug_to_disease.json +++ b/examples/v1/multiomics/clinical_risk_kp/query_drug_to_disease.json @@ -3,11 +3,11 @@ "query_graph": { "nodes": { "n0": { - "category": "biolink:Drug", - "id": "CHEBI:86990" + "categories": "biolink:Drug", + "ids": "CHEBI:86990" }, "n3": { - "category": "biolink:Disease" + "categories": "biolink:Disease" } }, "edges": { diff --git a/examples/v1/multiomics/clinical_risk_kp/query_observation_to_disease.json b/examples/v1/multiomics/clinical_risk_kp/query_observation_to_disease.json index 907f35c2..2ebc70b1 100644 --- a/examples/v1/multiomics/clinical_risk_kp/query_observation_to_disease.json +++ b/examples/v1/multiomics/clinical_risk_kp/query_observation_to_disease.json @@ -3,11 +3,11 @@ "query_graph": { "nodes": { "n0": { - "category": "biolink:Observation", - "id": "NCIT:C110935" + "categories": "biolink:Observation", + "ids": "NCIT:C110935" }, "n3": { - "category": "biolink:DiseaseOrPhenotypicFeature" + "categories": "biolink:DiseaseOrPhenotypicFeature" } }, "edges": { diff --git a/examples/v1/query_chemicals_physically_interacts_with_genes.json b/examples/v1/query_chemicals_physically_interacts_with_genes.json index 06931a71..8a8c5186 100644 --- a/examples/v1/query_chemicals_physically_interacts_with_genes.json +++ b/examples/v1/query_chemicals_physically_interacts_with_genes.json @@ -3,18 +3,18 @@ "query_graph": { "nodes": { "n0": { - "category": "biolink:Gene", - "id": "NCBIGene:1017" + "categories": "biolink:Gene", + "ids": "NCBIGene:1017" }, "n1": { - "category": "biolink:ChemicalSubstance" + "categories": "biolink:ChemicalSubstance" } }, "edges": { "e01": { "subject": "n0", "object": "n1", - "predicate": "biolink:physically_interacts_with" + "predicates": "biolink:physically_interacts_with" } } } diff --git a/examples/v1/query_disease_has_phenotype.json b/examples/v1/query_disease_has_phenotype.json index f6c63eda..dfb2f4b9 100644 --- a/examples/v1/query_disease_has_phenotype.json +++ b/examples/v1/query_disease_has_phenotype.json @@ -3,18 +3,18 @@ "query_graph": { "nodes": { "n0": { - "category": "biolink:Disease", - "id": "MONDO:0016575" + "categories": "biolink:Disease", + "ids": "MONDO:0016575" }, "n1": { - "category": "biolink:PhenotypicFeature" + "categories": "biolink:PhenotypicFeature" } }, "edges": { "e01": { "subject": "n0", "object": "n1", - "predicate": "biolink:has_phenotype" + "predicates": "biolink:has_phenotype" } } } diff --git a/examples/v1/query_genes_relate_to_disease.json b/examples/v1/query_genes_relate_to_disease.json index 952d8bea..90d2e88f 100644 --- a/examples/v1/query_genes_relate_to_disease.json +++ b/examples/v1/query_genes_relate_to_disease.json @@ -3,11 +3,11 @@ "query_graph": { "nodes": { "n0": { - "category": "biolink:Disease", - "id": "MONDO:0005737" + "categories": "biolink:Disease", + "ids": "MONDO:0005737" }, "n1": { - "category": "biolink:Gene" + "categories": "biolink:Gene" } }, "edges": { diff --git a/examples/v1/query_multihop_disease_gene_chemical.json b/examples/v1/query_multihop_disease_gene_chemical.json index f1cdd81f..4f7120f5 100644 --- a/examples/v1/query_multihop_disease_gene_chemical.json +++ b/examples/v1/query_multihop_disease_gene_chemical.json @@ -3,14 +3,14 @@ "query_graph": { "nodes": { "n0": { - "category": "biolink:Disease", - "id": "MONDO:0005737" + "categories": "biolink:Disease", + "ids": "MONDO:0005737" }, "n1": { - "category": "biolink:Gene" + "categories": "biolink:Gene" }, "n2": { - "category": "biolink:ChemicalSubstance" + "categories": "biolink:ChemicalSubstance" } }, "edges": { diff --git a/examples/v1/query_with_category_as_list.json b/examples/v1/query_with_category_as_list.json index 6c35534e..00f9f4f6 100644 --- a/examples/v1/query_with_category_as_list.json +++ b/examples/v1/query_with_category_as_list.json @@ -3,11 +3,11 @@ "query_graph": { "nodes": { "n0": { - "id": "UMLS:C0008780", - "category": "biolink:PhenotypicFeature" + "ids": "UMLS:C0008780", + "categories": "biolink:PhenotypicFeature" }, "n1": { - "category": [ + "categories": [ "biolink:Disease", "biolink:BiologicalProcess", "biolink:Pathway" diff --git a/examples/v1/query_with_node_to_be_expanded.json b/examples/v1/query_with_node_to_be_expanded.json index 5998a509..23844d1d 100644 --- a/examples/v1/query_with_node_to_be_expanded.json +++ b/examples/v1/query_with_node_to_be_expanded.json @@ -3,18 +3,18 @@ "query_graph": { "nodes": { "n0": { - "id": "NCBIGene:1017", - "category": "biolink:Gene" + "ids": "NCBIGene:1017", + "categories": "biolink:Gene" }, "n1": { - "category": "biolink:NamedThing" + "categories": "biolink:NamedThing" } }, "edges": { "e01": { "subject": "n0", "object": "n1", - "predicate": "biolink:participates_in" + "predicates": "biolink:participates_in" } } } diff --git a/examples/v1/query_without_input_category.json b/examples/v1/query_without_input_category.json index 487db0dc..722dc067 100644 --- a/examples/v1/query_without_input_category.json +++ b/examples/v1/query_without_input_category.json @@ -3,10 +3,10 @@ "query_graph": { "nodes": { "n0": { - "id": "UMLS:C0008780" + "ids": "UMLS:C0008780" }, "n1": { - "category": "biolink:Gene" + "categories": "biolink:Gene" } }, "edges": { diff --git a/examples/v1/serviceprovider/mychem.json b/examples/v1/serviceprovider/mychem.json index 2272b14b..1ebc4110 100644 --- a/examples/v1/serviceprovider/mychem.json +++ b/examples/v1/serviceprovider/mychem.json @@ -5,16 +5,16 @@ "e00": { "object": "n01", "subject": "n00", - "predicate": "biolink:physically_interacts_with" + "predicates": "biolink:physically_interacts_with" } }, "nodes": { "n00": { - "category": "biolink:ChemicalSubstance", - "id": "CHEMBL.COMPOUND:CHEMBL744" + "categories": "biolink:ChemicalSubstance", + "ids": "CHEMBL.COMPOUND:CHEMBL744" }, "n01": { - "category": "biolink:Gene" + "categories": "biolink:Gene" } } } diff --git a/examples/v1/serviceprovider/mygene.json b/examples/v1/serviceprovider/mygene.json index febd4b6e..e10b9884 100644 --- a/examples/v1/serviceprovider/mygene.json +++ b/examples/v1/serviceprovider/mygene.json @@ -5,16 +5,16 @@ "e00": { "object": "n01", "subject": "n00", - "predicate": "biolink:functional_association" + "predicates": "biolink:functional_association" } }, "nodes": { "n00": { - "category": "biolink:Gene", - "id": "ENSEMBL:ENSG00000123374" + "categories": "biolink:Gene", + "ids": "ENSEMBL:ENSG00000123374" }, "n01": { - "category": "biolink:BiologicalProcess" + "categories": "biolink:BiologicalProcess" } } } diff --git a/examples/v1/textmining/query_chemicals_related_to_disease.json b/examples/v1/textmining/query_chemicals_related_to_disease.json index 3ca24e97..a984e18f 100644 --- a/examples/v1/textmining/query_chemicals_related_to_disease.json +++ b/examples/v1/textmining/query_chemicals_related_to_disease.json @@ -3,11 +3,11 @@ "query_graph": { "nodes": { "n0": { - "category": "biolink:Disease", - "id": "MONDO:0005252" + "categories": "biolink:Disease", + "ids": "MONDO:0005252" }, "n3": { - "category": "biolink:ChemicalSubstance" + "categories": "biolink:ChemicalSubstance" } }, "edges": { diff --git a/examples/v1/textmining/query_chemicals_related_to_gene_or_gene_product.json b/examples/v1/textmining/query_chemicals_related_to_gene_or_gene_product.json index 8c65f0b4..279ae9f7 100644 --- a/examples/v1/textmining/query_chemicals_related_to_gene_or_gene_product.json +++ b/examples/v1/textmining/query_chemicals_related_to_gene_or_gene_product.json @@ -3,11 +3,11 @@ "query_graph": { "nodes": { "n0": { - "category": "biolink:GeneOrGeneProduct", - "id": "PR:000008790" + "categories": "biolink:GeneOrGeneProduct", + "ids": "PR:000008790" }, "n1": { - "category": "biolink:ChemicalSubstance" + "categories": "biolink:ChemicalSubstance" } }, "edges": { diff --git a/src/config/index.js b/src/config/index.js index 661e09f4..640ff1ab 100644 --- a/src/config/index.js +++ b/src/config/index.js @@ -64,7 +64,7 @@ module.exports = class Config { setLimiter() { const limiter = rateLimit({ windowMs: 1 * 60 * 1000, //1min - max: process.env.MAX_QUERIES_PER_MIN || 3 //3 requests + max: process.env.MAX_QUERIES_PER_MIN || 6 //6 requests }); this.app.use("/v1/query", limiter); } diff --git a/src/routes/v1/predicates_v1.js b/src/routes/v1/predicates_v1.js index b672bba9..c59981d0 100644 --- a/src/routes/v1/predicates_v1.js +++ b/src/routes/v1/predicates_v1.js @@ -2,7 +2,7 @@ const handler = require("../../controllers/predicates"); class RoutePredicates { setRoutes(app) { - app.get('/v1/predicates', async (req, res, next) => { + app.get('/v1/meta_knowledge_graph', async (req, res, next) => { try { const predicateHandler = new handler(undefined); const predicates = await predicateHandler.getPredicates(); diff --git a/src/routes/v1/predicates_v1_by_api.js b/src/routes/v1/predicates_v1_by_api.js index 7d659451..a13a4088 100644 --- a/src/routes/v1/predicates_v1_by_api.js +++ b/src/routes/v1/predicates_v1_by_api.js @@ -2,7 +2,7 @@ const PredicatesHandler = require("../../controllers/predicates"); class RoutePredicatesByAPI { setRoutes(app) { - app.get('/v1/smartapi/:smartapiID/predicates', async (req, res, next) => { + app.get('/v1/smartapi/:smartapiID/meta_knowledge_graph', async (req, res, next) => { try { const handler = new PredicatesHandler(req.params.smartapiID); const predicates = await handler.getPredicates(); diff --git a/src/routes/v1/predicates_v1_by_team.js b/src/routes/v1/predicates_v1_by_team.js index 6d218989..2ad86fcf 100644 --- a/src/routes/v1/predicates_v1_by_team.js +++ b/src/routes/v1/predicates_v1_by_team.js @@ -2,7 +2,7 @@ const PredicatesHandler = require("../../controllers/predicates"); class RoutePredicatesByTeam { setRoutes(app) { - app.get('/v1/team/:teamName/predicates', async (req, res, next) => { + app.get('/v1/team/:teamName/meta_knowledge_graph', async (req, res, next) => { try { const handler = new PredicatesHandler(undefined, req.params.teamName); const predicates = await handler.getPredicates(); From c1c50116dcec2c131c36c8c3ec52502f49e65d2d Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Sat, 15 May 2021 17:15:42 -0700 Subject: [PATCH 22/75] feat: :sparkles: add handler logics for creating v1 metakg --- src/controllers/ids.js | 285 ++++++++++++++++++++++++ src/controllers/meta_knowledge_graph.js | 94 ++++++++ 2 files changed, 379 insertions(+) create mode 100644 src/controllers/ids.js create mode 100644 src/controllers/meta_knowledge_graph.js diff --git a/src/controllers/ids.js b/src/controllers/ids.js new file mode 100644 index 00000000..0c52a7e9 --- /dev/null +++ b/src/controllers/ids.js @@ -0,0 +1,285 @@ +module.exports = { + Gene: { + id_ranks: ['NCBIGene', 'ENSEMBL', 'HGNC', 'SYMBOL', 'OMIM', 'UniProtKB', 'UMLS', 'MGI', 'name'], + semantic: 'Gene', + api_name: 'mygene.info', + url: 'https://mygene.info/v3/query', + mapping: { + NCBIGene: ['entrezgene'], + name: ['name'], + SYMBOL: ['symbol'], + UMLS: ['umls.cui', 'umls.protein_cui'], + HGNC: ['HGNC'], + UniProtKB: ['uniprot.Swiss-Prot'], + ENSEMBL: ['ensembl.gene'], + OMIM: ['MIM'], + MGI: ['MGI'], + }, + additional_attributes_mapping: { + interpro: ['interpro.desc'], + type_of_gene: ['type_of_gene'], + }, + }, + Protein: { + id_ranks: ['UniProtKB', 'ENSEMBL', 'SYMBOL', 'UMLS', 'name'], + semantic: 'Protein', + api_name: 'mygene.info', + url: 'https://mygene.info/v3/query', + mapping: { + name: ['name'], + SYMBOL: ['symbol'], + UMLS: ['umls.cui', 'umls.protein_cui'], + UniProtKB: ['uniprot.Swiss-Prot'], + ENSEMBL: ['ensembl.protein'], + }, + additional_attributes_mapping: { + interpro: ['interpro.desc'], + }, + }, + SequenceVariant: { + id_ranks: ['HGVS', 'DBSNP', 'MYVARIANT_HG19', 'CLINVAR'], + api_name: 'myvariant.info', + semantic: 'SequenceVariant', + url: 'https://myvariant.info/v1/query', + mapping: { + MYVARIANT_HG19: ['_id'], + DBSNP: ['dbsnp.rsid', 'clinvar.rsid', 'dbnsfp.rsid'], + HGVS: ['clinvar.hgvs.genomic', 'clinvar.hgvs.protein', 'clinvar.hgvs.coding'], + ClINVAR: ['clinvar.rcv.accession'], + }, + additional_attributes_mapping: { + cadd_consequence: ['cadd.consequence'], + cadd_variant_type: ['cadd.type'], + dbsnp_variant_type: ['dbsnp.vartype'], + clinvar_clinical_significance: ['clinvar.rcv.clinical_significance'], + sift_category: ['cadd.sift.cat'], + }, + }, + ChemicalSubstance: { + id_ranks: [ + 'CHEBI', + 'CHEMBL.COMPOUND', + 'DRUGBANK', + 'PUBCHEM.COMPOUND', + 'MESH', + 'INCHI', + 'INCHIKEY', + 'UNII', + 'KEGG', + 'UMLS', + 'RHEA', + 'name', + ], + semantic: 'ChemicalSubstance', + api_name: 'mychem.info', + url: 'https://mychem.info/v1/query', + mapping: { + 'CHEMBL.COMPOUND': ['chembl.molecule_chembl_id', 'drugbank.xrefs.chembl', 'drugcentral.xrefs.chembl_id'], + DRUGBANK: ['drugcentral.xrefs.drugbank_id', 'pharmgkb.xrefs.drugbank', 'chebi.xrefs.drugbank', 'drugbank.id'], + 'PUBCHEM.COMPOUND': [ + 'pubchem.cid', + 'drugbank.xrefs.pubchem.cid', + 'drugcentral.xrefs.pubchem_cid', + 'pharmgkb.xrefs.pubchem.cid', + ], + CHEBI: ['chebi.id', 'chembl.chebi_par_id', 'drugbank.xrefs.chebi', 'drugcentral.xrefs.chebi'], + UMLS: ['drugcentral.xrefs.umlscui', 'pharmgkb.xrefs.umls', 'umls.cui'], + MESH: ['umls.mesh', 'drugcentral.xrefs.mesh_descriptor_ui', 'ginas.xrefs.MESH', 'pharmgkb.xrefs.mesh'], + UNII: ['drugcentral.xrefs.unii', 'unii.unii', 'aeolus.unii', 'ginas.unii'], + INCHIKEY: ['drugbank.inchi_key', 'ginas.inchikey', 'unii.inchikey', 'chebi.inchikey'], + INCHI: ['drugbank.inchi', 'chebi.inchi', 'chembl.inchi'], + KEGG: ['drugbank.xrefs.kegg.cid'], + LINCS: ['unichem.lincs'], + RHEA: ['chebi.xrefs.rhea'], + name: ['chembl.pref_name', 'drugbank.name', 'umls.name', 'ginas.preferred_name', 'pharmgkb.name', 'chebi.name'], + }, + additional_attributes_mapping: { + chembl_max_phase: ['chembl.max_phase'], + chembl_molecule_type: ['chembl.molecule_type'], + drugbank_drug_category: ['drugbank.categories.category'], + drugbank_taxonomy_class: ['drugbank.taxonomy.class'], + drugbank_groups: ['drugbank.groups'], + drugbank_kingdom: ['drugbank.taxonomy.kingdom'], + drugbank_superclass: ['drugbank.taxonomy.superclass'], + contraindications: ['drugcentral.drug_use.contraindication.concept_name'], + indications: ['drugcentral.drug_use.indication.concept_name'], + mesh_pharmacology_class: ['drugcentral.pharmacology_class.mesh_pa.description'], + fda_epc_pharmacology_class: ['drugcentral.pharmacology_class.fda_epc.description'], + }, + }, + Drug: { + id_ranks: [ + 'CHEBI', + 'CHEMBL.COMPOUND', + 'DRUGBANK', + 'PUBCHEM.COMPOUND', + 'MESH', + 'INCHI', + 'INCHIKEY', + 'UNII', + 'KEGG', + 'UMLS', + 'LINCS', + 'RHEA', + 'name', + ], + semantic: 'ChemicalSubstance', + api_name: 'mychem.info', + url: 'https://mychem.info/v1/query', + mapping: { + 'CHEMBL.COMPOUND': ['chembl.molecule_chembl_id', 'drugbank.xrefs.chembl', 'drugcentral.xrefs.chembl_id'], + DRUGBANK: ['drugcentral.xrefs.drugbank_id', 'pharmgkb.xrefs.drugbank', 'chebi.xrefs.drugbank', 'drugbank.id'], + 'PUBCHEM.COMPOUND': [ + 'pubchem.cid', + 'drugbank.xrefs.pubchem.cid', + 'drugcentral.xrefs.pubchem_cid', + 'pharmgkb.xrefs.pubchem.cid', + ], + CHEBI: ['chebi.id', 'chembl.chebi_par_id', 'drugbank.xrefs.chebi', 'drugcentral.xrefs.chebi'], + UMLS: ['drugcentral.xrefs.umlscui', 'pharmgkb.xrefs.umls', 'umls.cui'], + MESH: ['umls.mesh', 'drugcentral.xrefs.mesh_descriptor_ui', 'ginas.xrefs.MESH', 'pharmgkb.xrefs.mesh'], + UNII: ['drugcentral.xrefs.unii', 'unii.unii', 'aeolus.unii', 'ginas.unii'], + INCHIKEY: ['drugbank.inchi_key', 'ginas.inchikey', 'unii.inchikey', 'chebi.inchikey'], + INCHI: ['drugbank.inchi', 'chebi.inchi', 'chembl.inchi'], + KEGG: ['drugbank.xrefs.kegg.cid'], + RHEA: ['chebi.xrefs.rhea'], + name: ['chembl.pref_name', 'drugbank.name', 'umls.name', 'ginas.preferred_name', 'pharmgkb.name', 'chebi.name'], + }, + additional_attributes_mapping: { + chembl_max_phase: ['chembl.max_phase'], + chembl_molecule_type: ['chembl.molecule_type'], + drugbank_drug_category: ['drugbank.categories.category'], + drugbank_taxonomy_class: ['drugbank.taxonomy.class'], + drugbank_groups: ['drugbank.groups'], + drugbank_kingdom: ['drugbank.taxonomy.kingdom'], + drugbank_superclass: ['drugbank.taxonomy.superclass'], + contraindications: ['drugcentral.drug_use.contraindication.concept_name'], + indications: ['drugcentral.drug_use.indication.concept_name'], + mesh_pharmacology_class: ['drugcentral.pharmacology_class.mesh_pa.description'], + fda_epc_pharmacology_class: ['drugcentral.pharmacology_class.fda_epc.description'], + }, + }, + PhenotypicFeature: { + id_ranks: ['UMLS', 'SNOMEDCT', 'HP', 'MEDDRA', 'EFO', 'NCIT', 'MESH', 'MP', 'name'], + semantic: 'PhenotypicFeature', + api_name: 'HPO API', + url: 'https://biothings.ncats.io/hpo/query', + mapping: { + UMLS: ['xrefs.umls'], + SNOMEDCT: ['xrefs.snomed_ct'], + HP: ['_id'], + MEDDRA: ['xrefs.meddra'], + EFO: ['xrefs.efo'], + NCIT: ['xrefs.ncit'], + MESH: ['xrefs.mesh'], + MP: ['xrefs.mp'], + name: ['name'], + }, + }, + Disease: { + id_ranks: ['MONDO', 'DOID', 'OMIM', 'ORPHANET', 'EFO', 'UMLS', 'MESH', 'HP', 'GARD', 'name'], + semantic: 'Disease', + api_name: 'mydisease.info', + url: 'https://mydisease.info/v1/query', + mapping: { + MONDO: ['mondo.mondo'], + DOID: ['mondo.xrefs.doid'], + UMLS: [ + 'mondo.xrefs.umls', + 'mondo.xrefs.umls_cui', + 'disgenet.xrefs.umls', + 'umls.umls', + 'disease_ontology.xrefs.umls_cui', + ], + name: ['mondo.label', 'disgenet.xrefs.disease_name'], + MESH: ['mondo.xrefs.mesh', 'disease_ontology.xrefs.mesh', 'ctd.mesh'], + OMIM: ['mondo.xrefs.omim', 'hpo.omim', 'disgenet.xrefs.omim'], + EFO: ['mondo.xrefs.efo'], + ORPHANET: ['hpo.orphanet', 'mondo.xrefs.orphanet'], + GARD: ['mondo.xrefs.gard', 'disease_ontology.xrefs.gard'], + HP: ['mondo.xrefs.hp'], + }, + }, + MolecularActivity: { + id_ranks: ['GO', 'MetaCyc', 'RHEA', 'KEGG', 'REACT', 'name'], + semantic: 'MolecularActivity', + api_name: 'Gene Ontology Molecular Function API', + url: 'https://biothings.ncats.io/go_mf/query', + mapping: { + GO: ['_id'], + MetaCyc: ['xrefs.metacyc'], + RHEA: ['xrefs.rhea'], + KEGG: ['xrefs.kegg_reaction'], + REACT: ['xrefs.reactome'], + name: ['name'], + }, + }, + BiologicalProcess: { + id_ranks: ['GO', 'MetaCyc', 'REACT', 'KEGG', 'name'], + semantic: 'BiologicalProcess', + api_name: 'Gene Ontology Biological Process API', + url: 'https://biothings.ncats.io/go_bp/query', + mapping: { + GO: ['_id'], + MetaCyc: ['xrefs.metacyc'], + KEGG: ['xrefs.kegg_pathway'], + REACT: ['xrefs.reactome'], + name: ['name'], + }, + }, + CellularComponent: { + id_ranks: ['GO', 'MetaCyc', 'RHEA', 'name'], + semantic: 'CellularComponent', + api_name: 'Gene Ontology Cellular Component API', + url: 'https://biothings.ncats.io/go_cc/query', + mapping: { + GO: ['_id'], + MetaCyc: ['xrefs.metacyc'], + RHEA: ['xrefs.rhea'], + name: ['name'], + }, + }, + Pathway: { + id_ranks: ['REACT', 'KEGG', 'PHARMGKB', 'WIKIPATHWAYS', 'name'], + semantic: 'Pathway', + api_name: 'geneset API', + url: 'https://biothings.ncats.io/geneset/query', + mapping: { + REACT: ['reactome'], + WIKIPATHWAYS: ['wikipathways'], + KEGG: ['kegg'], + BIOCARTA: ['biocarta'], + PHARMGKB: ['pharmgkb'], + name: ['name'], + }, + additional_attributes_mapping: { + num_of_participants: ['num_of_participants'], + }, + }, + AnatomicalEntity: { + id_ranks: ['UBERON', 'UMLS', 'MESH', 'NCIT', 'name'], + semantic: 'AnatomicalEntity', + api_name: 'UBERON API', + url: 'https://biothings.ncats.io/uberon/query', + mapping: { + UBERON: ['_id'], + UMLS: ['xrefs.umls'], + MESH: ['xrefs.mesh'], + NCIT: ['xrefs.ncit'], + name: ['name'], + }, + }, + Cell: { + id_ranks: ['CL', 'NCIT', 'MESH', 'EFO', 'name'], + semantic: 'Cell', + api_name: 'Cell Onotlogy API', + url: 'https://biothings.ncats.io/cell_ontology/query', + mapping: { + CL: ['_id'], + NCIT: ['xrefs.ncit'], + MESH: ['xrefs.mesh'], + EFO: ['xrefs.efo'], + name: ['name'], + }, + }, +}; \ No newline at end of file diff --git a/src/controllers/meta_knowledge_graph.js b/src/controllers/meta_knowledge_graph.js new file mode 100644 index 00000000..53e926bf --- /dev/null +++ b/src/controllers/meta_knowledge_graph.js @@ -0,0 +1,94 @@ +const meta_kg = require("@biothings-explorer/smartapi-kg"); +const snakeCase = require("snake-case"); +const fs = require("fs"); +var path = require('path'); +const util = require('util'); +const PredicatesLoadingError = require("../utils/errors/predicates_error"); +const ids = require("./ids"); +const readFile = util.promisify(fs.readFile); + +module.exports = class MetaKnowledgeGraphHandler { + constructor(smartapiID = undefined, team = undefined) { + this.smartapiID = smartapiID; + this.team = team; + } + + async _loadMetaKG(smartapiID = undefined, team = undefined) { + const smartapi_specs = path.resolve(__dirname, '../../data/smartapi_specs.json'); + const predicates = path.resolve(__dirname, '../../data/predicates.json'); + const kg = new meta_kg.default(smartapi_specs, predicates); + try { + if (smartapiID !== undefined) { + kg.constructMetaKGSync(false, { smartAPIID: smartapiID }) + } else if (team !== undefined) { + kg.constructMetaKGSync(false, { teamName: team }) + } else { + kg.constructMetaKGSync(true, {}) + } + if (kg.ops.length === 0) { + throw new PredicatesLoadingError("Failed to Load MetaKG"); + } + return kg; + } catch (error) { + throw new PredicatesLoadingError("Failed to Load MetaKG"); + } + + } + + _modifyCategory(category) { + if (category.startsWith("biolink:")) { + return 'biolink:' + category.charAt(8).toUpperCase() + category.slice(9); + } else { + return "biolink:" + category.charAt(0).toUpperCase() + category.slice(1); + } + } + + _modifyPredicate(predicate) { + if (predicate.startsWith("biolink:")) { + return 'biolink:' + snakeCase.snakeCase(predicate.slice(8)); + } else { + return "biolink:" + snakeCase.snakeCase(predicate); + } + } + + async getKG(smartapiID = this.smartapiID, team = this.team) { + const kg = await this._loadMetaKG(smartapiID, team); + let knowledge_graph = { + nodes: {}, + edges: [] + }; + let predicates = {}; + Object.keys(ids).map(semanticType => { + knowledge_graph.nodes[this._modifyCategory(semanticType)] = { + id_prefixes: ids[semanticType].id_ranks + } + }) + kg.ops.map(op => { + let input = this._modifyCategory(op.association.input_type); + let output = this._modifyCategory(op.association.output_type); + let pred = this._modifyPredicate(op.association.predicate); + if (!(input in predicates)) { + predicates[input] = {}; + } + if (!(output in predicates[input])) { + predicates[input][output] = []; + } + if (!(predicates[input][output].includes(pred))) { + predicates[input][output].push(pred); + } + }) + Object.keys(predicates).map(input => { + Object.keys(predicates[input]).map(output => { + predicates[input][output].map(pred => { + knowledge_graph.edges.push({ + subject: input, + predicate: pred, + object: output, + relation: null + }) + }) + }) + }) + return knowledge_graph; + } +} \ No newline at end of file From cd379bc8f16c491090c2982f5c0fb5fbbc4dda3d Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Sat, 15 May 2021 17:15:53 -0700 Subject: [PATCH 23/75] feat: :sparkles: create route for metakg --- src/routes/v1/meta_knowledge_graph_v1.js | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 src/routes/v1/meta_knowledge_graph_v1.js diff --git a/src/routes/v1/meta_knowledge_graph_v1.js b/src/routes/v1/meta_knowledge_graph_v1.js new file mode 100644 index 00000000..d71b74b7 --- /dev/null +++ b/src/routes/v1/meta_knowledge_graph_v1.js @@ -0,0 +1,18 @@ +const handler = require("../../controllers/meta_knowledge_graph"); + +class RouteMetaKG { + setRoutes(app) { + app.get('/v1/meta_knowledge_graph', async (req, res, next) => { + try { + const metaKGHandler = new handler(undefined); + const kg = await metaKGHandler.getKG(); + res.setHeader('Content-Type', 'application/json'); + res.end(JSON.stringify(kg)); + } catch (error) { + next(error) + } + }) + } +} + +module.exports = new RouteMetaKG(); \ No newline at end of file From 7c7b8e1fed0f195c8ab5854b8a49d0cf9b71ae96 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Sat, 15 May 2021 17:16:05 -0700 Subject: [PATCH 24/75] feat: :sparkles: add metakg routes to index --- src/routes/index.js | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/routes/index.js b/src/routes/index.js index c88f48d0..d2711639 100644 --- a/src/routes/index.js +++ b/src/routes/index.js @@ -8,6 +8,7 @@ const routesV1QueryByAPI = require("./v1/query_v1_by_api"); const routesV1QueryByTeam = require("./v1/query_v1_by_team"); const routesQueryTest = require("./v1/query_test"); const routesV1Query = require("./v1/query_v1"); +const routesV1MetaKG = require("./v1/meta_knowledge_graph_v1") const ErrorHandler = require("../middlewares/error"); const LoggingHandler = require("../middlewares/logging"); @@ -15,6 +16,7 @@ class Routes { setRoutes(app) { routesMetaKG.setRoutes(app); routesV1Predicates.setRoutes(app); + routesV1MetaKG.setRoutes(app); routesV1PredicatesByAPI.setRoutes(app); routesV1PredicatesByTeam.setRoutes(app); routesFrontPage.setRoutes(app); From 028eb49dcb2cacecb899d1c01af758e8843266c9 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Sat, 15 May 2021 17:20:17 -0700 Subject: [PATCH 25/75] chore(release): 2.7.0 --- CHANGELOG.md | 9 +++++++++ package-lock.json | 2 +- package.json | 2 +- 3 files changed, 11 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 20ccecac..a05c2940 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,15 @@ All notable changes to this project will be documented in this file. See [standard-version](https://github.com/conventional-changelog/standard-version) for commit guidelines. +## [2.7.0](https://github.com/biothings/BioThings_Explorer_TRAPI/compare/v2.6.0...v2.7.0) (2021-05-16) + + +### Features + +* :sparkles: add handler logics for creating v1 metakg ([c1c5011](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/c1c50116dcec2c131c36c8c3ec52502f49e65d2d)) +* :sparkles: add metakg routes to index ([7c7b8e1](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/7c7b8e1fed0f195c8ab5854b8a49d0cf9b71ae96)) +* :sparkles: create route for metakg ([cd379bc](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/cd379bc8f16c491090c2982f5c0fb5fbbc4dda3d)) + ## [2.6.0](https://github.com/biothings/BioThings_Explorer_TRAPI/compare/v2.5.0...v2.6.0) (2021-05-11) diff --git a/package-lock.json b/package-lock.json index 22c14782..4cab7e7f 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/single-hop-app", - "version": "2.6.0", + "version": "2.7.0", "lockfileVersion": 2, "requires": true, "packages": { diff --git a/package.json b/package.json index 84d2436a..5f4b11ff 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/single-hop-app", - "version": "2.6.0", + "version": "2.7.0", "description": "App performing single hop query for BioThings Explorer", "main": "src/server.js", "scripts": { From 5654b421c436b217d589f802d6b3ec5db3e99ab5 Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Wed, 19 May 2021 16:35:01 -0700 Subject: [PATCH 26/75] test: revert v1 examples --- examples/v1/branched_query.json | 8 ++++---- .../v1/invalid/query_graph_with_edges_not_specified.json | 6 +++--- .../query_graph_with_nodes_and_edges_not_match.json | 8 ++++---- .../v1/invalid/query_graph_with_nodes_not_specified.json | 2 +- .../clinical_risk_kp/query_attribute_to_disease.json | 6 +++--- .../clinical_risk_kp/query_disease_to_disease.json | 6 +++--- .../clinical_risk_kp/query_drug_to_disease.json | 6 +++--- .../clinical_risk_kp/query_observation_to_disease.json | 6 +++--- .../query_chemicals_physically_interacts_with_genes.json | 8 ++++---- examples/v1/query_disease_has_phenotype.json | 8 ++++---- examples/v1/query_genes_relate_to_disease.json | 6 +++--- examples/v1/query_multihop_disease_gene_chemical.json | 8 ++++---- examples/v1/query_with_category_as_list.json | 6 +++--- examples/v1/query_with_node_to_be_expanded.json | 8 ++++---- examples/v1/query_without_input_category.json | 4 ++-- examples/v1/serviceprovider/mychem.json | 8 ++++---- examples/v1/serviceprovider/mygene.json | 8 ++++---- .../v1/textmining/query_chemicals_related_to_disease.json | 6 +++--- .../query_chemicals_related_to_gene_or_gene_product.json | 6 +++--- 19 files changed, 62 insertions(+), 62 deletions(-) diff --git a/examples/v1/branched_query.json b/examples/v1/branched_query.json index 01136c80..e4b58f72 100644 --- a/examples/v1/branched_query.json +++ b/examples/v1/branched_query.json @@ -3,14 +3,14 @@ "query_graph": { "nodes": { "n0": { - "categories": "biolink:Disease", - "ids": "MONDO:0005737" + "category": "biolink:Disease", + "id": "MONDO:0005737" }, "n1": { - "categories": "biolink:Gene" + "category": "biolink:Gene" }, "n2": { - "categories": "biolink:ChemicalSubstance" + "category": "biolink:ChemicalSubstance" } }, "edges": { diff --git a/examples/v1/invalid/query_graph_with_edges_not_specified.json b/examples/v1/invalid/query_graph_with_edges_not_specified.json index 1081ee68..e405d797 100644 --- a/examples/v1/invalid/query_graph_with_edges_not_specified.json +++ b/examples/v1/invalid/query_graph_with_edges_not_specified.json @@ -3,11 +3,11 @@ "query_graph": { "nodes": { "n0": { - "categories": "biolink:Gene", - "ids": "NCBIGene:1017" + "category": "biolink:Gene", + "id": "NCBIGene:1017" }, "n1": { - "categories": "biolink:ChemicalSubstance" + "category": "biolink:ChemicalSubstance" } }, "edges": {} diff --git a/examples/v1/invalid/query_graph_with_nodes_and_edges_not_match.json b/examples/v1/invalid/query_graph_with_nodes_and_edges_not_match.json index 51b0b7c8..3f7f1a23 100644 --- a/examples/v1/invalid/query_graph_with_nodes_and_edges_not_match.json +++ b/examples/v1/invalid/query_graph_with_nodes_and_edges_not_match.json @@ -3,18 +3,18 @@ "query_graph": { "nodes": { "n0": { - "categories": "biolink:Gene", - "ids": "NCBIGene:1017" + "category": "biolink:Gene", + "id": "NCBIGene:1017" }, "n2": { - "categories": "biolink:ChemicalSubstance" + "category": "biolink:ChemicalSubstance" } }, "edges": { "e01": { "subject": "n0", "object": "n1", - "predicates": "biolink:physically_interacts_with" + "predicate": "biolink:physically_interacts_with" } } } diff --git a/examples/v1/invalid/query_graph_with_nodes_not_specified.json b/examples/v1/invalid/query_graph_with_nodes_not_specified.json index 1c980688..63ba1478 100644 --- a/examples/v1/invalid/query_graph_with_nodes_not_specified.json +++ b/examples/v1/invalid/query_graph_with_nodes_not_specified.json @@ -6,7 +6,7 @@ "e01": { "subject": "n0", "object": "n1", - "predicates": "biolink:physically_interacts_with" + "predicate": "biolink:physically_interacts_with" } } } diff --git a/examples/v1/multiomics/clinical_risk_kp/query_attribute_to_disease.json b/examples/v1/multiomics/clinical_risk_kp/query_attribute_to_disease.json index bfec60b8..45ab7a5d 100644 --- a/examples/v1/multiomics/clinical_risk_kp/query_attribute_to_disease.json +++ b/examples/v1/multiomics/clinical_risk_kp/query_attribute_to_disease.json @@ -3,11 +3,11 @@ "query_graph": { "nodes": { "n0": { - "categories": "biolink:Attribute", - "ids": "NCIT:C28421" + "category": "biolink:Attribute", + "id": "NCIT:C28421" }, "n3": { - "categories": "biolink:DiseaseOrPhenotypicFeature" + "category": "biolink:DiseaseOrPhenotypicFeature" } }, "edges": { diff --git a/examples/v1/multiomics/clinical_risk_kp/query_disease_to_disease.json b/examples/v1/multiomics/clinical_risk_kp/query_disease_to_disease.json index 81cf8319..048ff5fd 100644 --- a/examples/v1/multiomics/clinical_risk_kp/query_disease_to_disease.json +++ b/examples/v1/multiomics/clinical_risk_kp/query_disease_to_disease.json @@ -3,11 +3,11 @@ "query_graph": { "nodes": { "n0": { - "categories": "biolink:DiseaseOrPhenotypicFeature", - "ids": "MONDO:0005015" + "category": "biolink:DiseaseOrPhenotypicFeature", + "id": "MONDO:0005015" }, "n3": { - "categories": "biolink:DiseaseOrPhenotypicFeature" + "category": "biolink:DiseaseOrPhenotypicFeature" } }, "edges": { diff --git a/examples/v1/multiomics/clinical_risk_kp/query_drug_to_disease.json b/examples/v1/multiomics/clinical_risk_kp/query_drug_to_disease.json index fd3fc869..d9a737e6 100644 --- a/examples/v1/multiomics/clinical_risk_kp/query_drug_to_disease.json +++ b/examples/v1/multiomics/clinical_risk_kp/query_drug_to_disease.json @@ -3,11 +3,11 @@ "query_graph": { "nodes": { "n0": { - "categories": "biolink:Drug", - "ids": "CHEBI:86990" + "category": "biolink:Drug", + "id": "CHEBI:86990" }, "n3": { - "categories": "biolink:Disease" + "category": "biolink:Disease" } }, "edges": { diff --git a/examples/v1/multiomics/clinical_risk_kp/query_observation_to_disease.json b/examples/v1/multiomics/clinical_risk_kp/query_observation_to_disease.json index 2ebc70b1..907f35c2 100644 --- a/examples/v1/multiomics/clinical_risk_kp/query_observation_to_disease.json +++ b/examples/v1/multiomics/clinical_risk_kp/query_observation_to_disease.json @@ -3,11 +3,11 @@ "query_graph": { "nodes": { "n0": { - "categories": "biolink:Observation", - "ids": "NCIT:C110935" + "category": "biolink:Observation", + "id": "NCIT:C110935" }, "n3": { - "categories": "biolink:DiseaseOrPhenotypicFeature" + "category": "biolink:DiseaseOrPhenotypicFeature" } }, "edges": { diff --git a/examples/v1/query_chemicals_physically_interacts_with_genes.json b/examples/v1/query_chemicals_physically_interacts_with_genes.json index 8a8c5186..06931a71 100644 --- a/examples/v1/query_chemicals_physically_interacts_with_genes.json +++ b/examples/v1/query_chemicals_physically_interacts_with_genes.json @@ -3,18 +3,18 @@ "query_graph": { "nodes": { "n0": { - "categories": "biolink:Gene", - "ids": "NCBIGene:1017" + "category": "biolink:Gene", + "id": "NCBIGene:1017" }, "n1": { - "categories": "biolink:ChemicalSubstance" + "category": "biolink:ChemicalSubstance" } }, "edges": { "e01": { "subject": "n0", "object": "n1", - "predicates": "biolink:physically_interacts_with" + "predicate": "biolink:physically_interacts_with" } } } diff --git a/examples/v1/query_disease_has_phenotype.json b/examples/v1/query_disease_has_phenotype.json index dfb2f4b9..f6c63eda 100644 --- a/examples/v1/query_disease_has_phenotype.json +++ b/examples/v1/query_disease_has_phenotype.json @@ -3,18 +3,18 @@ "query_graph": { "nodes": { "n0": { - "categories": "biolink:Disease", - "ids": "MONDO:0016575" + "category": "biolink:Disease", + "id": "MONDO:0016575" }, "n1": { - "categories": "biolink:PhenotypicFeature" + "category": "biolink:PhenotypicFeature" } }, "edges": { "e01": { "subject": "n0", "object": "n1", - "predicates": "biolink:has_phenotype" + "predicate": "biolink:has_phenotype" } } } diff --git a/examples/v1/query_genes_relate_to_disease.json b/examples/v1/query_genes_relate_to_disease.json index 90d2e88f..952d8bea 100644 --- a/examples/v1/query_genes_relate_to_disease.json +++ b/examples/v1/query_genes_relate_to_disease.json @@ -3,11 +3,11 @@ "query_graph": { "nodes": { "n0": { - "categories": "biolink:Disease", - "ids": "MONDO:0005737" + "category": "biolink:Disease", + "id": "MONDO:0005737" }, "n1": { - "categories": "biolink:Gene" + "category": "biolink:Gene" } }, "edges": { diff --git a/examples/v1/query_multihop_disease_gene_chemical.json b/examples/v1/query_multihop_disease_gene_chemical.json index 4f7120f5..f1cdd81f 100644 --- a/examples/v1/query_multihop_disease_gene_chemical.json +++ b/examples/v1/query_multihop_disease_gene_chemical.json @@ -3,14 +3,14 @@ "query_graph": { "nodes": { "n0": { - "categories": "biolink:Disease", - "ids": "MONDO:0005737" + "category": "biolink:Disease", + "id": "MONDO:0005737" }, "n1": { - "categories": "biolink:Gene" + "category": "biolink:Gene" }, "n2": { - "categories": "biolink:ChemicalSubstance" + "category": "biolink:ChemicalSubstance" } }, "edges": { diff --git a/examples/v1/query_with_category_as_list.json b/examples/v1/query_with_category_as_list.json index 00f9f4f6..6c35534e 100644 --- a/examples/v1/query_with_category_as_list.json +++ b/examples/v1/query_with_category_as_list.json @@ -3,11 +3,11 @@ "query_graph": { "nodes": { "n0": { - "ids": "UMLS:C0008780", - "categories": "biolink:PhenotypicFeature" + "id": "UMLS:C0008780", + "category": "biolink:PhenotypicFeature" }, "n1": { - "categories": [ + "category": [ "biolink:Disease", "biolink:BiologicalProcess", "biolink:Pathway" diff --git a/examples/v1/query_with_node_to_be_expanded.json b/examples/v1/query_with_node_to_be_expanded.json index 23844d1d..5998a509 100644 --- a/examples/v1/query_with_node_to_be_expanded.json +++ b/examples/v1/query_with_node_to_be_expanded.json @@ -3,18 +3,18 @@ "query_graph": { "nodes": { "n0": { - "ids": "NCBIGene:1017", - "categories": "biolink:Gene" + "id": "NCBIGene:1017", + "category": "biolink:Gene" }, "n1": { - "categories": "biolink:NamedThing" + "category": "biolink:NamedThing" } }, "edges": { "e01": { "subject": "n0", "object": "n1", - "predicates": "biolink:participates_in" + "predicate": "biolink:participates_in" } } } diff --git a/examples/v1/query_without_input_category.json b/examples/v1/query_without_input_category.json index 722dc067..487db0dc 100644 --- a/examples/v1/query_without_input_category.json +++ b/examples/v1/query_without_input_category.json @@ -3,10 +3,10 @@ "query_graph": { "nodes": { "n0": { - "ids": "UMLS:C0008780" + "id": "UMLS:C0008780" }, "n1": { - "categories": "biolink:Gene" + "category": "biolink:Gene" } }, "edges": { diff --git a/examples/v1/serviceprovider/mychem.json b/examples/v1/serviceprovider/mychem.json index 1ebc4110..2272b14b 100644 --- a/examples/v1/serviceprovider/mychem.json +++ b/examples/v1/serviceprovider/mychem.json @@ -5,16 +5,16 @@ "e00": { "object": "n01", "subject": "n00", - "predicates": "biolink:physically_interacts_with" + "predicate": "biolink:physically_interacts_with" } }, "nodes": { "n00": { - "categories": "biolink:ChemicalSubstance", - "ids": "CHEMBL.COMPOUND:CHEMBL744" + "category": "biolink:ChemicalSubstance", + "id": "CHEMBL.COMPOUND:CHEMBL744" }, "n01": { - "categories": "biolink:Gene" + "category": "biolink:Gene" } } } diff --git a/examples/v1/serviceprovider/mygene.json b/examples/v1/serviceprovider/mygene.json index e10b9884..febd4b6e 100644 --- a/examples/v1/serviceprovider/mygene.json +++ b/examples/v1/serviceprovider/mygene.json @@ -5,16 +5,16 @@ "e00": { "object": "n01", "subject": "n00", - "predicates": "biolink:functional_association" + "predicate": "biolink:functional_association" } }, "nodes": { "n00": { - "categories": "biolink:Gene", - "ids": "ENSEMBL:ENSG00000123374" + "category": "biolink:Gene", + "id": "ENSEMBL:ENSG00000123374" }, "n01": { - "categories": "biolink:BiologicalProcess" + "category": "biolink:BiologicalProcess" } } } diff --git a/examples/v1/textmining/query_chemicals_related_to_disease.json b/examples/v1/textmining/query_chemicals_related_to_disease.json index a984e18f..3ca24e97 100644 --- a/examples/v1/textmining/query_chemicals_related_to_disease.json +++ b/examples/v1/textmining/query_chemicals_related_to_disease.json @@ -3,11 +3,11 @@ "query_graph": { "nodes": { "n0": { - "categories": "biolink:Disease", - "ids": "MONDO:0005252" + "category": "biolink:Disease", + "id": "MONDO:0005252" }, "n3": { - "categories": "biolink:ChemicalSubstance" + "category": "biolink:ChemicalSubstance" } }, "edges": { diff --git a/examples/v1/textmining/query_chemicals_related_to_gene_or_gene_product.json b/examples/v1/textmining/query_chemicals_related_to_gene_or_gene_product.json index 279ae9f7..8c65f0b4 100644 --- a/examples/v1/textmining/query_chemicals_related_to_gene_or_gene_product.json +++ b/examples/v1/textmining/query_chemicals_related_to_gene_or_gene_product.json @@ -3,11 +3,11 @@ "query_graph": { "nodes": { "n0": { - "categories": "biolink:GeneOrGeneProduct", - "ids": "PR:000008790" + "category": "biolink:GeneOrGeneProduct", + "id": "PR:000008790" }, "n1": { - "categories": "biolink:ChemicalSubstance" + "category": "biolink:ChemicalSubstance" } }, "edges": { From bbc9f375e845e87765235ceaf48864e87806074c Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Wed, 19 May 2021 16:35:45 -0700 Subject: [PATCH 27/75] test: revert v1 TRAPI test --- __test__/integration/TRAPIv1.test.js | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/__test__/integration/TRAPIv1.test.js b/__test__/integration/TRAPIv1.test.js index 496809cd..ed41e0e8 100644 --- a/__test__/integration/TRAPIv1.test.js +++ b/__test__/integration/TRAPIv1.test.js @@ -16,9 +16,9 @@ describe("Testing endpoints", () => { const query_without_category = JSON.parse(fs.readFileSync(path.join(example_foler, 'query_without_input_category.json'))) const expand_node = JSON.parse(fs.readFileSync(path.join(example_foler, 'query_with_node_to_be_expanded.json'))) - test("GET /v1/meta_knowledge_graph", async () => { + test("GET /v1/predicates", async () => { await request(app) - .get("/v1/meta_knowledge_graph") + .get("/v1/predicates") .expect(200) .expect('Content-Type', /json/) .then((response) => { @@ -28,9 +28,9 @@ describe("Testing endpoints", () => { }) }) - test("GET /v1/smartapi/{smartapi_id}/meta_knowledge_graph", async () => { + test("GET /v1/smartapi/{smartapi_id}/predicates", async () => { await request(app) - .get("/v1/smartapi/978fe380a147a8641caf72320862697b/meta_knowledge_graph") + .get("/v1/smartapi/978fe380a147a8641caf72320862697b/predicates") .expect(200) .expect('Content-Type', /json/) .then((response) => { From fbd9b81ac32dbfd780e203792200db233aabaed6 Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Wed, 19 May 2021 16:36:45 -0700 Subject: [PATCH 28/75] test: add v1.1 TRAPI test file --- __test__/integration/TRAPIv1.1.test.js | 142 +++++++++++++++++++++++++ 1 file changed, 142 insertions(+) create mode 100644 __test__/integration/TRAPIv1.1.test.js diff --git a/__test__/integration/TRAPIv1.1.test.js b/__test__/integration/TRAPIv1.1.test.js new file mode 100644 index 00000000..496809cd --- /dev/null +++ b/__test__/integration/TRAPIv1.1.test.js @@ -0,0 +1,142 @@ +const app = require("../../src/app"); +const request = require('supertest'); +const fs = require("fs"); +var path = require('path'); + + +describe("Testing endpoints", () => { + const example_foler = path.resolve(__dirname, '../../examples/v1'); + const clinical_risk_kp_folder = path.resolve(__dirname, '../../examples/v1/multiomics/clinical_risk_kp'); + const old_spec_folder = path.resolve(__dirname, "../../examples/v0.9.2"); + const invalid_example_folder = path.resolve(__dirname, "../../examples/v1/invalid"); + const drug2disease_query = JSON.parse(fs.readFileSync(path.join(clinical_risk_kp_folder, 'query_drug_to_disease.json'))); + const gene2chemical_query = JSON.parse(fs.readFileSync(path.join(example_foler, 'query_chemicals_physically_interacts_with_genes.json'))); + const disease2gene_query = JSON.parse(fs.readFileSync(path.join(example_foler, 'query_genes_relate_to_disease.json'))); + const query_using_earlier_trapi_spec = JSON.parse(fs.readFileSync(path.join(old_spec_folder, 'query_genes_relate_to_disease.json'))); + const query_without_category = JSON.parse(fs.readFileSync(path.join(example_foler, 'query_without_input_category.json'))) + const expand_node = JSON.parse(fs.readFileSync(path.join(example_foler, 'query_with_node_to_be_expanded.json'))) + + test("GET /v1/meta_knowledge_graph", async () => { + await request(app) + .get("/v1/meta_knowledge_graph") + .expect(200) + .expect('Content-Type', /json/) + .then((response) => { + expect(response.body).toHaveProperty("biolink:Gene"); + expect(response.body["biolink:Gene"]).toHaveProperty("biolink:ChemicalSubstance"); + expect(response.body["biolink:Gene"]["biolink:ChemicalSubstance"]).toContain("biolink:related_to"); + }) + }) + + test("GET /v1/smartapi/{smartapi_id}/meta_knowledge_graph", async () => { + await request(app) + .get("/v1/smartapi/978fe380a147a8641caf72320862697b/meta_knowledge_graph") + .expect(200) + .expect('Content-Type', /json/) + .then((response) => { + expect(response.body).toHaveProperty("biolink:Gene"); + expect(response.body["biolink:Gene"]).toHaveProperty("biolink:ChemicalSubstance"); + }) + }) + + test("POST /v1/query with gene2chemical query", async () => { + await request(app) + .post("/v1/query") + .send(gene2chemical_query) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .then(response => { + expect(response.body.message).toHaveProperty("query_graph"); + expect(response.body.message).toHaveProperty("knowledge_graph"); + expect(response.body.message.knowledge_graph).toHaveProperty("nodes"); + expect(response.body.message.knowledge_graph).toHaveProperty("edges"); + expect(response.body.message.knowledge_graph.nodes).toHaveProperty("NCBIGene:1017") + }) + }) + + test("POST /v1/query with clinical risk kp query", async () => { + await request(app) + .post("/v1/query") + .send(drug2disease_query) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .then(response => { + expect(response.body.message).toHaveProperty("query_graph"); + expect(response.body.message).toHaveProperty("knowledge_graph"); + expect(response.body.message.knowledge_graph).toHaveProperty("nodes"); + expect(response.body.message.knowledge_graph).toHaveProperty("edges"); + expect(response.body.message.knowledge_graph.nodes).toHaveProperty("MONDO:0001583") + }) + }) + + test("POST /v1/query with query graph defined in old trapi standard", async () => { + await request(app) + .post("/v1/query") + .send(query_using_earlier_trapi_spec) + .set('Accept', 'application/json') + .expect(400) + .expect('Content-Type', /json/) + .then(response => { + expect(response.body).toHaveProperty("error", "Your input query graph is invalid"); + }) + }) + + test("POST /v1/query with disease2gene query", async () => { + await request(app) + .post("/v1/query") + .send(disease2gene_query) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .then(response => { + expect(response.body).toHaveProperty("message"); + expect(response.body.message).toHaveProperty("query_graph"); + expect(response.body.message).toHaveProperty("knowledge_graph"); + expect(response.body.message.knowledge_graph).toHaveProperty("nodes"); + expect(response.body.message.knowledge_graph).toHaveProperty("edges"); + expect(response.body.message.knowledge_graph.nodes).toHaveProperty("MONDO:0005737"); + }) + }) + + test("POST /v1/query with query that doesn't provide input category", async () => { + await request(app) + .post("/v1/query") + .send(query_without_category) + .set('Accept', 'application/json') + .expect(200) + .expect('Content-Type', /json/) + .then(response => { + expect(response.body).toHaveProperty("message"); + expect(response.body.message).toHaveProperty("query_graph"); + expect(response.body.message).toHaveProperty("knowledge_graph"); + expect(response.body.message.knowledge_graph).toHaveProperty("nodes"); + expect(response.body.message.knowledge_graph).toHaveProperty("edges"); + expect(response.body.message.knowledge_graph.nodes).toHaveProperty("MONDO:0016575"); + expect(response.body.message.knowledge_graph.nodes).toHaveProperty("UMLS:C0008780"); + expect(response.body.message.knowledge_graph.nodes["UMLS:C0008780"]).toHaveProperty("category", "biolink:PhenotypicFeature"); + }) + }) + + // test("POST /v1/query with query that needs to expand node", async () => { + // console.log("expanded node", expand_node); + // await request(app) + // .post("/v1/query") + // .send(expand_node) + // .set('Accept', 'application/json') + // .expect(200) + // .expect('Content-Type', /json/) + // .then(response => { + // console.log(response.body.message.knowledge_graph); + // expect(response.body).toHaveProperty("message"); + // expect(response.body.message).toHaveProperty("query_graph"); + // expect(response.body.message).toHaveProperty("knowledge_graph"); + // expect(response.body.message.knowledge_graph).toHaveProperty("nodes"); + // expect(response.body.message.knowledge_graph).toHaveProperty("edges"); + // expect(response.body.message.knowledge_graph.nodes).toHaveProperty("REACT:R-HSA-109582"); + // expect(response.body.message.knowledge_graph.nodes).toHaveProperty("GO:0000082"); + // }) + // }) + +}) \ No newline at end of file From ec535457864457dae7340b1297c688d44274636d Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Wed, 19 May 2021 16:37:22 -0700 Subject: [PATCH 29/75] test: add v1.1 examples --- examples/v1.1/branched_query.json | 28 +++++++++++++++++++ .../query_graph_with_edges_not_specified.json | 16 +++++++++++ ..._graph_with_nodes_and_edges_not_match.json | 22 +++++++++++++++ .../query_graph_with_nodes_not_specified.json | 14 ++++++++++ .../query_attribute_to_disease.json | 21 ++++++++++++++ .../query_disease_to_disease.json | 21 ++++++++++++++ .../query_drug_to_disease.json | 21 ++++++++++++++ .../query_observation_to_disease.json | 21 ++++++++++++++ ...icals_physically_interacts_with_genes.json | 22 +++++++++++++++ .../v1.1/query_disease_has_phenotype.json | 22 +++++++++++++++ .../v1.1/query_genes_relate_to_disease.json | 21 ++++++++++++++ .../query_multihop_disease_gene_chemical.json | 28 +++++++++++++++++++ .../v1.1/query_with_category_as_list.json | 25 +++++++++++++++++ .../v1.1/query_with_node_to_be_expanded.json | 22 +++++++++++++++ .../v1.1/query_without_input_category.json | 20 +++++++++++++ examples/v1.1/serviceprovider/mychem.json | 22 +++++++++++++++ examples/v1.1/serviceprovider/mygene.json | 22 +++++++++++++++ .../query_chemicals_related_to_disease.json | 21 ++++++++++++++ ...icals_related_to_gene_or_gene_product.json | 21 ++++++++++++++ 19 files changed, 410 insertions(+) create mode 100644 examples/v1.1/branched_query.json create mode 100644 examples/v1.1/invalid/query_graph_with_edges_not_specified.json create mode 100644 examples/v1.1/invalid/query_graph_with_nodes_and_edges_not_match.json create mode 100644 examples/v1.1/invalid/query_graph_with_nodes_not_specified.json create mode 100644 examples/v1.1/multiomics/clinical_risk_kp/query_attribute_to_disease.json create mode 100644 examples/v1.1/multiomics/clinical_risk_kp/query_disease_to_disease.json create mode 100644 examples/v1.1/multiomics/clinical_risk_kp/query_drug_to_disease.json create mode 100644 examples/v1.1/multiomics/clinical_risk_kp/query_observation_to_disease.json create mode 100644 examples/v1.1/query_chemicals_physically_interacts_with_genes.json create mode 100644 examples/v1.1/query_disease_has_phenotype.json create mode 100644 examples/v1.1/query_genes_relate_to_disease.json create mode 100644 examples/v1.1/query_multihop_disease_gene_chemical.json create mode 100644 examples/v1.1/query_with_category_as_list.json create mode 100644 examples/v1.1/query_with_node_to_be_expanded.json create mode 100644 examples/v1.1/query_without_input_category.json create mode 100644 examples/v1.1/serviceprovider/mychem.json create mode 100644 examples/v1.1/serviceprovider/mygene.json create mode 100644 examples/v1.1/textmining/query_chemicals_related_to_disease.json create mode 100644 examples/v1.1/textmining/query_chemicals_related_to_gene_or_gene_product.json diff --git a/examples/v1.1/branched_query.json b/examples/v1.1/branched_query.json new file mode 100644 index 00000000..01136c80 --- /dev/null +++ b/examples/v1.1/branched_query.json @@ -0,0 +1,28 @@ +{ + "message": { + "query_graph": { + "nodes": { + "n0": { + "categories": "biolink:Disease", + "ids": "MONDO:0005737" + }, + "n1": { + "categories": "biolink:Gene" + }, + "n2": { + "categories": "biolink:ChemicalSubstance" + } + }, + "edges": { + "e01": { + "subject": "n0", + "object": "n1" + }, + "e02": { + "subject": "n0", + "object": "n2" + } + } + } + } +} \ No newline at end of file diff --git a/examples/v1.1/invalid/query_graph_with_edges_not_specified.json b/examples/v1.1/invalid/query_graph_with_edges_not_specified.json new file mode 100644 index 00000000..1081ee68 --- /dev/null +++ b/examples/v1.1/invalid/query_graph_with_edges_not_specified.json @@ -0,0 +1,16 @@ +{ + "message": { + "query_graph": { + "nodes": { + "n0": { + "categories": "biolink:Gene", + "ids": "NCBIGene:1017" + }, + "n1": { + "categories": "biolink:ChemicalSubstance" + } + }, + "edges": {} + } + } +} \ No newline at end of file diff --git a/examples/v1.1/invalid/query_graph_with_nodes_and_edges_not_match.json b/examples/v1.1/invalid/query_graph_with_nodes_and_edges_not_match.json new file mode 100644 index 00000000..51b0b7c8 --- /dev/null +++ b/examples/v1.1/invalid/query_graph_with_nodes_and_edges_not_match.json @@ -0,0 +1,22 @@ +{ + "message": { + "query_graph": { + "nodes": { + "n0": { + "categories": "biolink:Gene", + "ids": "NCBIGene:1017" + }, + "n2": { + "categories": "biolink:ChemicalSubstance" + } + }, + "edges": { + "e01": { + "subject": "n0", + "object": "n1", + "predicates": "biolink:physically_interacts_with" + } + } + } + } +} \ No newline at end of file diff --git a/examples/v1.1/invalid/query_graph_with_nodes_not_specified.json b/examples/v1.1/invalid/query_graph_with_nodes_not_specified.json new file mode 100644 index 00000000..1c980688 --- /dev/null +++ b/examples/v1.1/invalid/query_graph_with_nodes_not_specified.json @@ -0,0 +1,14 @@ +{ + "message": { + "query_graph": { + "nodes": {}, + "edges": { + "e01": { + "subject": "n0", + "object": "n1", + "predicates": "biolink:physically_interacts_with" + } + } + } + } +} \ No newline at end of file diff --git a/examples/v1.1/multiomics/clinical_risk_kp/query_attribute_to_disease.json b/examples/v1.1/multiomics/clinical_risk_kp/query_attribute_to_disease.json new file mode 100644 index 00000000..bfec60b8 --- /dev/null +++ b/examples/v1.1/multiomics/clinical_risk_kp/query_attribute_to_disease.json @@ -0,0 +1,21 @@ +{ + "message": { + "query_graph": { + "nodes": { + "n0": { + "categories": "biolink:Attribute", + "ids": "NCIT:C28421" + }, + "n3": { + "categories": "biolink:DiseaseOrPhenotypicFeature" + } + }, + "edges": { + "e03": { + "subject": "n0", + "object": "n3" + } + } + } + } +} \ No newline at end of file diff --git a/examples/v1.1/multiomics/clinical_risk_kp/query_disease_to_disease.json b/examples/v1.1/multiomics/clinical_risk_kp/query_disease_to_disease.json new file mode 100644 index 00000000..81cf8319 --- /dev/null +++ b/examples/v1.1/multiomics/clinical_risk_kp/query_disease_to_disease.json @@ -0,0 +1,21 @@ +{ + "message": { + "query_graph": { + "nodes": { + "n0": { + "categories": "biolink:DiseaseOrPhenotypicFeature", + "ids": "MONDO:0005015" + }, + "n3": { + "categories": "biolink:DiseaseOrPhenotypicFeature" + } + }, + "edges": { + "e03": { + "subject": "n0", + "object": "n3" + } + } + } + } +}s \ No newline at end of file diff --git a/examples/v1.1/multiomics/clinical_risk_kp/query_drug_to_disease.json b/examples/v1.1/multiomics/clinical_risk_kp/query_drug_to_disease.json new file mode 100644 index 00000000..fd3fc869 --- /dev/null +++ b/examples/v1.1/multiomics/clinical_risk_kp/query_drug_to_disease.json @@ -0,0 +1,21 @@ +{ + "message": { + "query_graph": { + "nodes": { + "n0": { + "categories": "biolink:Drug", + "ids": "CHEBI:86990" + }, + "n3": { + "categories": "biolink:Disease" + } + }, + "edges": { + "e03": { + "subject": "n0", + "object": "n3" + } + } + } + } +} \ No newline at end of file diff --git a/examples/v1.1/multiomics/clinical_risk_kp/query_observation_to_disease.json b/examples/v1.1/multiomics/clinical_risk_kp/query_observation_to_disease.json new file mode 100644 index 00000000..2ebc70b1 --- /dev/null +++ b/examples/v1.1/multiomics/clinical_risk_kp/query_observation_to_disease.json @@ -0,0 +1,21 @@ +{ + "message": { + "query_graph": { + "nodes": { + "n0": { + "categories": "biolink:Observation", + "ids": "NCIT:C110935" + }, + "n3": { + "categories": "biolink:DiseaseOrPhenotypicFeature" + } + }, + "edges": { + "e03": { + "subject": "n0", + "object": "n3" + } + } + } + } +} \ No newline at end of file diff --git a/examples/v1.1/query_chemicals_physically_interacts_with_genes.json b/examples/v1.1/query_chemicals_physically_interacts_with_genes.json new file mode 100644 index 00000000..8a8c5186 --- /dev/null +++ b/examples/v1.1/query_chemicals_physically_interacts_with_genes.json @@ -0,0 +1,22 @@ +{ + "message": { + "query_graph": { + "nodes": { + "n0": { + "categories": "biolink:Gene", + "ids": "NCBIGene:1017" + }, + "n1": { + "categories": "biolink:ChemicalSubstance" + } + }, + "edges": { + "e01": { + "subject": "n0", + "object": "n1", + "predicates": "biolink:physically_interacts_with" + } + } + } + } +} \ No newline at end of file diff --git a/examples/v1.1/query_disease_has_phenotype.json b/examples/v1.1/query_disease_has_phenotype.json new file mode 100644 index 00000000..dfb2f4b9 --- /dev/null +++ b/examples/v1.1/query_disease_has_phenotype.json @@ -0,0 +1,22 @@ +{ + "message": { + "query_graph": { + "nodes": { + "n0": { + "categories": "biolink:Disease", + "ids": "MONDO:0016575" + }, + "n1": { + "categories": "biolink:PhenotypicFeature" + } + }, + "edges": { + "e01": { + "subject": "n0", + "object": "n1", + "predicates": "biolink:has_phenotype" + } + } + } + } +} \ No newline at end of file diff --git a/examples/v1.1/query_genes_relate_to_disease.json b/examples/v1.1/query_genes_relate_to_disease.json new file mode 100644 index 00000000..90d2e88f --- /dev/null +++ b/examples/v1.1/query_genes_relate_to_disease.json @@ -0,0 +1,21 @@ +{ + "message": { + "query_graph": { + "nodes": { + "n0": { + "categories": "biolink:Disease", + "ids": "MONDO:0005737" + }, + "n1": { + "categories": "biolink:Gene" + } + }, + "edges": { + "e01": { + "subject": "n0", + "object": "n1" + } + } + } + } +} \ No newline at end of file diff --git a/examples/v1.1/query_multihop_disease_gene_chemical.json b/examples/v1.1/query_multihop_disease_gene_chemical.json new file mode 100644 index 00000000..4f7120f5 --- /dev/null +++ b/examples/v1.1/query_multihop_disease_gene_chemical.json @@ -0,0 +1,28 @@ +{ + "message": { + "query_graph": { + "nodes": { + "n0": { + "categories": "biolink:Disease", + "ids": "MONDO:0005737" + }, + "n1": { + "categories": "biolink:Gene" + }, + "n2": { + "categories": "biolink:ChemicalSubstance" + } + }, + "edges": { + "e01": { + "subject": "n0", + "object": "n1" + }, + "e02": { + "subject": "n1", + "object": "n2" + } + } + } + } +} \ No newline at end of file diff --git a/examples/v1.1/query_with_category_as_list.json b/examples/v1.1/query_with_category_as_list.json new file mode 100644 index 00000000..00f9f4f6 --- /dev/null +++ b/examples/v1.1/query_with_category_as_list.json @@ -0,0 +1,25 @@ +{ + "message": { + "query_graph": { + "nodes": { + "n0": { + "ids": "UMLS:C0008780", + "categories": "biolink:PhenotypicFeature" + }, + "n1": { + "categories": [ + "biolink:Disease", + "biolink:BiologicalProcess", + "biolink:Pathway" + ] + } + }, + "edges": { + "e01": { + "subject": "n0", + "object": "n1" + } + } + } + } +} \ No newline at end of file diff --git a/examples/v1.1/query_with_node_to_be_expanded.json b/examples/v1.1/query_with_node_to_be_expanded.json new file mode 100644 index 00000000..23844d1d --- /dev/null +++ b/examples/v1.1/query_with_node_to_be_expanded.json @@ -0,0 +1,22 @@ +{ + "message": { + "query_graph": { + "nodes": { + "n0": { + "ids": "NCBIGene:1017", + "categories": "biolink:Gene" + }, + "n1": { + "categories": "biolink:NamedThing" + } + }, + "edges": { + "e01": { + "subject": "n0", + "object": "n1", + "predicates": "biolink:participates_in" + } + } + } + } +} \ No newline at end of file diff --git a/examples/v1.1/query_without_input_category.json b/examples/v1.1/query_without_input_category.json new file mode 100644 index 00000000..722dc067 --- /dev/null +++ b/examples/v1.1/query_without_input_category.json @@ -0,0 +1,20 @@ +{ + "message": { + "query_graph": { + "nodes": { + "n0": { + "ids": "UMLS:C0008780" + }, + "n1": { + "categories": "biolink:Gene" + } + }, + "edges": { + "e01": { + "subject": "n0", + "object": "n1" + } + } + } + } +} \ No newline at end of file diff --git a/examples/v1.1/serviceprovider/mychem.json b/examples/v1.1/serviceprovider/mychem.json new file mode 100644 index 00000000..1ebc4110 --- /dev/null +++ b/examples/v1.1/serviceprovider/mychem.json @@ -0,0 +1,22 @@ +{ + "message": { + "query_graph": { + "edges": { + "e00": { + "object": "n01", + "subject": "n00", + "predicates": "biolink:physically_interacts_with" + } + }, + "nodes": { + "n00": { + "categories": "biolink:ChemicalSubstance", + "ids": "CHEMBL.COMPOUND:CHEMBL744" + }, + "n01": { + "categories": "biolink:Gene" + } + } + } + } +} \ No newline at end of file diff --git a/examples/v1.1/serviceprovider/mygene.json b/examples/v1.1/serviceprovider/mygene.json new file mode 100644 index 00000000..e10b9884 --- /dev/null +++ b/examples/v1.1/serviceprovider/mygene.json @@ -0,0 +1,22 @@ +{ + "message": { + "query_graph": { + "edges": { + "e00": { + "object": "n01", + "subject": "n00", + "predicates": "biolink:functional_association" + } + }, + "nodes": { + "n00": { + "categories": "biolink:Gene", + "ids": "ENSEMBL:ENSG00000123374" + }, + "n01": { + "categories": "biolink:BiologicalProcess" + } + } + } + } +} \ No newline at end of file diff --git a/examples/v1.1/textmining/query_chemicals_related_to_disease.json b/examples/v1.1/textmining/query_chemicals_related_to_disease.json new file mode 100644 index 00000000..a984e18f --- /dev/null +++ b/examples/v1.1/textmining/query_chemicals_related_to_disease.json @@ -0,0 +1,21 @@ +{ + "message": { + "query_graph": { + "nodes": { + "n0": { + "categories": "biolink:Disease", + "ids": "MONDO:0005252" + }, + "n3": { + "categories": "biolink:ChemicalSubstance" + } + }, + "edges": { + "e03": { + "subject": "n0", + "object": "n3" + } + } + } + } +} \ No newline at end of file diff --git a/examples/v1.1/textmining/query_chemicals_related_to_gene_or_gene_product.json b/examples/v1.1/textmining/query_chemicals_related_to_gene_or_gene_product.json new file mode 100644 index 00000000..279ae9f7 --- /dev/null +++ b/examples/v1.1/textmining/query_chemicals_related_to_gene_or_gene_product.json @@ -0,0 +1,21 @@ +{ + "message": { + "query_graph": { + "nodes": { + "n0": { + "categories": "biolink:GeneOrGeneProduct", + "ids": "PR:000008790" + }, + "n1": { + "categories": "biolink:ChemicalSubstance" + } + }, + "edges": { + "e01": { + "subject": "n0", + "object": "n1" + } + } + } + } +} \ No newline at end of file From 8882df487e7348918e437fa6f971fadd7b24cb3f Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Wed, 19 May 2021 20:50:17 -0700 Subject: [PATCH 30/75] feat: :sparkles: added meta_knowledge_graph endpoints by team and ip --- src/routes/index.js | 4 ++++ .../v1/meta_knowledge_graph_v1_by_api.js | 18 ++++++++++++++++++ .../v1/meta_knowledge_graph_v1_by_team.js | 18 ++++++++++++++++++ src/routes/v1/predicates_v1.js | 2 +- src/routes/v1/predicates_v1_by_api.js | 2 +- src/routes/v1/predicates_v1_by_team.js | 2 +- 6 files changed, 43 insertions(+), 3 deletions(-) create mode 100644 src/routes/v1/meta_knowledge_graph_v1_by_api.js create mode 100644 src/routes/v1/meta_knowledge_graph_v1_by_team.js diff --git a/src/routes/index.js b/src/routes/index.js index d2711639..7453d4e8 100644 --- a/src/routes/index.js +++ b/src/routes/index.js @@ -9,6 +9,8 @@ const routesV1QueryByTeam = require("./v1/query_v1_by_team"); const routesQueryTest = require("./v1/query_test"); const routesV1Query = require("./v1/query_v1"); const routesV1MetaKG = require("./v1/meta_knowledge_graph_v1") +const routesV1MetaKGByAPI = require("./v1/meta_knowledge_graph_v1_by_api"); +const routesV1MetaKGByTeam = require("./v1/meta_knowledge_graph_v1_by_team"); const ErrorHandler = require("../middlewares/error"); const LoggingHandler = require("../middlewares/logging"); @@ -17,6 +19,8 @@ class Routes { routesMetaKG.setRoutes(app); routesV1Predicates.setRoutes(app); routesV1MetaKG.setRoutes(app); + routesV1MetaKGByAPI.setRoutes(app); + routesV1MetaKGByTeam.setRoutes(app); routesV1PredicatesByAPI.setRoutes(app); routesV1PredicatesByTeam.setRoutes(app); routesFrontPage.setRoutes(app); diff --git a/src/routes/v1/meta_knowledge_graph_v1_by_api.js b/src/routes/v1/meta_knowledge_graph_v1_by_api.js new file mode 100644 index 00000000..3f7a3d60 --- /dev/null +++ b/src/routes/v1/meta_knowledge_graph_v1_by_api.js @@ -0,0 +1,18 @@ +const handler = require("../../controllers/meta_knowledge_graph"); + +class RouteMetaKGByAPI { + setRoutes(app) { + app.get('/v1/smartapi/:smartapiID/meta_knowledge_graph', async (req, res, next) => { + try { + const metaKGHandler = new handler(undefined, req.params.smartapiID); + const kg = await metaKGHandler.getKG(); + res.setHeader('Content-Type', 'application/json'); + res.end(JSON.stringify(kg)); + } catch (error) { + next(error) + } + }) + } +} + +module.exports = new RouteMetaKGByAPI(); \ No newline at end of file diff --git a/src/routes/v1/meta_knowledge_graph_v1_by_team.js b/src/routes/v1/meta_knowledge_graph_v1_by_team.js new file mode 100644 index 00000000..6f3d34f0 --- /dev/null +++ b/src/routes/v1/meta_knowledge_graph_v1_by_team.js @@ -0,0 +1,18 @@ +const handler = require("../../controllers/meta_knowledge_graph"); + +class RouteMetaKGByTeam { + setRoutes(app) { + app.get('/v1/team/:teamName/meta_knowledge_graph', async (req, res, next) => { + try { + const metaKGHandler = new handler(undefined, req.params.teamName); + const kg = await metaKGHandler.getKG(); + res.setHeader('Content-Type', 'application/json'); + res.end(JSON.stringify(kg)); + } catch (error) { + next(error) + } + }) + } +} + +module.exports = new RouteMetaKGByTeam(); \ No newline at end of file diff --git a/src/routes/v1/predicates_v1.js b/src/routes/v1/predicates_v1.js index c59981d0..b672bba9 100644 --- a/src/routes/v1/predicates_v1.js +++ b/src/routes/v1/predicates_v1.js @@ -2,7 +2,7 @@ const handler = require("../../controllers/predicates"); class RoutePredicates { setRoutes(app) { - app.get('/v1/meta_knowledge_graph', async (req, res, next) => { + app.get('/v1/predicates', async (req, res, next) => { try { const predicateHandler = new handler(undefined); const predicates = await predicateHandler.getPredicates(); diff --git a/src/routes/v1/predicates_v1_by_api.js b/src/routes/v1/predicates_v1_by_api.js index a13a4088..7d659451 100644 --- a/src/routes/v1/predicates_v1_by_api.js +++ b/src/routes/v1/predicates_v1_by_api.js @@ -2,7 +2,7 @@ const PredicatesHandler = require("../../controllers/predicates"); class RoutePredicatesByAPI { setRoutes(app) { - app.get('/v1/smartapi/:smartapiID/meta_knowledge_graph', async (req, res, next) => { + app.get('/v1/smartapi/:smartapiID/predicates', async (req, res, next) => { try { const handler = new PredicatesHandler(req.params.smartapiID); const predicates = await handler.getPredicates(); diff --git a/src/routes/v1/predicates_v1_by_team.js b/src/routes/v1/predicates_v1_by_team.js index 2ad86fcf..6d218989 100644 --- a/src/routes/v1/predicates_v1_by_team.js +++ b/src/routes/v1/predicates_v1_by_team.js @@ -2,7 +2,7 @@ const PredicatesHandler = require("../../controllers/predicates"); class RoutePredicatesByTeam { setRoutes(app) { - app.get('/v1/team/:teamName/meta_knowledge_graph', async (req, res, next) => { + app.get('/v1/team/:teamName/predicates', async (req, res, next) => { try { const handler = new PredicatesHandler(undefined, req.params.teamName); const predicates = await handler.getPredicates(); From 8ee7ec2519943c23d1f05197392cd29fb645ff78 Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Sat, 22 May 2021 13:09:10 -0700 Subject: [PATCH 31/75] docs: :memo: add RELEASE.md --- RELEASE.md | 54 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 RELEASE.md diff --git a/RELEASE.md b/RELEASE.md new file mode 100644 index 00000000..1f86262e --- /dev/null +++ b/RELEASE.md @@ -0,0 +1,54 @@ +### The procedure to make a release and deployment + +#### Before the release + +1. Work on a bug fix or a new feature at a separate branch + +2. Follow commitlint commit msg convention + + * the msg pattern: [optional scope]: + ``` + feat: add a new helper function + fix: add a type check + ``` + * More details and examples [here](https://www.conventionalcommits.org/en/v1.0.0/#summary) + * This commit msg pattern will be auto-checked by husky commit hooks + * If using VSCode, it's recommended to use this vscode plugin: **Conventional Commits** + * This will help auto-generate CHANGELOGS.md file upon a new release + + Note: by default, only bugfix and feature commit logs will be put in CHANGELOGS.md automatically + +2. Test to make sure all test pass + +#### Deploy and test on dev instance + +1. When ready, merge your code to the "**development**" branch + +2. A github action will trigger the deployment to the dev instance + + Monitor to make sure everything works as expected. Then test on the dev instance. + +#### Make a release + +1. When ready, merge the code from "**development**" branch to the master branch + +2. Run one of these commands to make a new release: + + ```bash + npm run release:patch + + (use "release:patch", "release:minor" or "release:major" based on the release types) + ``` + + This will do the version tagging (follow semver pattern) and auto-update CHANGELOGS.md + +2. Push changes to GitHub: + + ```bash + git push --follow-tags origin master + ``` + +3. GitHub Actions will take care the rest of release steps + + Double check to make sure everything works as expected: + https://github.com/biothings/BioThings_Explorer_TRAPI/actions \ No newline at end of file From 042e162a26fb3daf005c23d2f7a652eea737ff1a Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Sat, 22 May 2021 14:36:02 -0700 Subject: [PATCH 32/75] test: :white_check_mark: skip v1 tests --- __test__/integration/TRAPIv1.test.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/__test__/integration/TRAPIv1.test.js b/__test__/integration/TRAPIv1.test.js index ed41e0e8..9e056c98 100644 --- a/__test__/integration/TRAPIv1.test.js +++ b/__test__/integration/TRAPIv1.test.js @@ -3,8 +3,8 @@ const request = require('supertest'); const fs = require("fs"); var path = require('path'); - -describe("Testing endpoints", () => { +//V1 tests are now skipped. +describe.skip("Testing v1 endpoints", () => { const example_foler = path.resolve(__dirname, '../../examples/v1'); const clinical_risk_kp_folder = path.resolve(__dirname, '../../examples/v1/multiomics/clinical_risk_kp'); const old_spec_folder = path.resolve(__dirname, "../../examples/v0.9.2"); From dee3d5134f594061b7d45d46b4fb389b15fc52fa Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Sat, 22 May 2021 14:37:12 -0700 Subject: [PATCH 33/75] test: :white_check_mark: add v1.1 tests --- __test__/integration/TRAPIv1.1.test.js | 107 ++++++++++++++++++++++--- 1 file changed, 97 insertions(+), 10 deletions(-) diff --git a/__test__/integration/TRAPIv1.1.test.js b/__test__/integration/TRAPIv1.1.test.js index 496809cd..6ae17044 100644 --- a/__test__/integration/TRAPIv1.1.test.js +++ b/__test__/integration/TRAPIv1.1.test.js @@ -4,11 +4,11 @@ const fs = require("fs"); var path = require('path'); -describe("Testing endpoints", () => { - const example_foler = path.resolve(__dirname, '../../examples/v1'); - const clinical_risk_kp_folder = path.resolve(__dirname, '../../examples/v1/multiomics/clinical_risk_kp'); +describe("Testing v1.1 endpoints", () => { + const example_foler = path.resolve(__dirname, '../../examples/v1.1'); + const clinical_risk_kp_folder = path.resolve(__dirname, '../../examples/v1.1/multiomics/clinical_risk_kp'); const old_spec_folder = path.resolve(__dirname, "../../examples/v0.9.2"); - const invalid_example_folder = path.resolve(__dirname, "../../examples/v1/invalid"); + const invalid_example_folder = path.resolve(__dirname, "../../examples/v1.1/invalid"); const drug2disease_query = JSON.parse(fs.readFileSync(path.join(clinical_risk_kp_folder, 'query_drug_to_disease.json'))); const gene2chemical_query = JSON.parse(fs.readFileSync(path.join(example_foler, 'query_chemicals_physically_interacts_with_genes.json'))); const disease2gene_query = JSON.parse(fs.readFileSync(path.join(example_foler, 'query_genes_relate_to_disease.json'))); @@ -22,20 +22,106 @@ describe("Testing endpoints", () => { .expect(200) .expect('Content-Type', /json/) .then((response) => { - expect(response.body).toHaveProperty("biolink:Gene"); - expect(response.body["biolink:Gene"]).toHaveProperty("biolink:ChemicalSubstance"); - expect(response.body["biolink:Gene"]["biolink:ChemicalSubstance"]).toContain("biolink:related_to"); + expect(response.body).toHaveProperty("nodes"); + expect(response.body).toHaveProperty("nodes.biolink:Gene"); + expect(response.body).toHaveProperty("nodes.biolink:Gene.id_prefixes"); + + expect(response.body).toHaveProperty("edges"); + expect(response.body.edges).toEqual( + expect.arrayContaining([ + expect.objectContaining({ + "subject": "biolink:ChemicalSubstance", + "predicate": "biolink:entity_positively_regulates_entity", + "object": "biolink:Gene" + }) + ]) + ); + }) + }) + + test("GET /v1/team/{team_name}/meta_knowledge_graph", async () => { + await request(app) + .get("/v1/team/Service Provider/meta_knowledge_graph") + .expect(200) + .expect('Content-Type', /json/) + .then((response) => { + expect(response.body).toHaveProperty("nodes"); + expect(response.body).toHaveProperty("nodes.biolink:Gene"); + expect(response.body).toHaveProperty("nodes.biolink:Gene.id_prefixes"); + + expect(response.body).toHaveProperty("edges"); + expect(response.body.edges).toEqual( + expect.arrayContaining([ + expect.objectContaining({ + "subject": "biolink:SequenceVariant", + "predicate": "biolink:located_in", + "object": "biolink:Gene", + }) + ]) + ); + }) + }) + + test("Query to Text Mining team Should return 200 with valid response", async () => { + await request(app) + .get("/v1/team/Text Mining Provider/meta_knowledge_graph") + .expect(200) + .expect('Content-Type', /json/) + .then((response) => { + expect(response.body).toHaveProperty("nodes.biolink:Gene"); + expect(response.body.edges).toEqual( + expect.arrayContaining([ + expect.objectContaining({ + "subject": "biolink:ChemicalSubstance", + "predicate": "biolink:entity_positively_regulates_entity", + "object": "biolink:Gene", + }) + ]) + ); + }) + }) + + test("Query to Invalid team Should return 200 with empty response", async () => { + await request(app) + .get("/v1/team/wrong team/meta_knowledge_graph") + .expect(404) + .expect('Content-Type', /json/) + .then((response) => { + expect(response.body).toEqual({ + "error": "Unable to load predicates", + "more_info": "Failed to Load MetaKG", + }); }) }) test("GET /v1/smartapi/{smartapi_id}/meta_knowledge_graph", async () => { await request(app) + // testing with "Text Mining Targeted Association API" .get("/v1/smartapi/978fe380a147a8641caf72320862697b/meta_knowledge_graph") .expect(200) .expect('Content-Type', /json/) .then((response) => { - expect(response.body).toHaveProperty("biolink:Gene"); - expect(response.body["biolink:Gene"]).toHaveProperty("biolink:ChemicalSubstance"); + expect(response.body).toHaveProperty("nodes.biolink:Protein"); + expect(response.body.edges).toEqual( + expect.arrayContaining([ + expect.objectContaining({ + "subject": "biolink:ChemicalSubstance", + "predicate": "biolink:entity_positively_regulates_entity", + "object": "biolink:Gene" + }) + ]) + ); + }) + }) + + test("Query to Invalid API Should return 404 with error message included", async () => { + await request(app) + .get("/v1/smartapi/78fe380a147a8641caf72320862697b/meta_knowledge_graph") + .expect(404) + .expect('Content-Type', /json/) + .then((response) => { + expect(response.body).toHaveProperty("error", "Unable to load predicates"); + expect(response.body).toHaveProperty("more_info", "Failed to Load MetaKG"); }) }) @@ -55,7 +141,8 @@ describe("Testing endpoints", () => { }) }) - test("POST /v1/query with clinical risk kp query", async () => { + //Skip this test for now, need to check the actual API data + test.skip("POST /v1/query with clinical risk kp query", async () => { await request(app) .post("/v1/query") .send(drug2disease_query) From bbd71bb79650870c85f4e2428433e3ea573641e6 Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Sat, 22 May 2021 14:39:52 -0700 Subject: [PATCH 34/75] test: :white_check_mark: updated query examples --- .../multiomics/clinical_risk_kp/query_drug_to_disease.json | 6 +++--- .../clinical_risk_kp/query_disease_to_disease.json | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/examples/v1.1/multiomics/clinical_risk_kp/query_drug_to_disease.json b/examples/v1.1/multiomics/clinical_risk_kp/query_drug_to_disease.json index fd3fc869..9158c553 100644 --- a/examples/v1.1/multiomics/clinical_risk_kp/query_drug_to_disease.json +++ b/examples/v1.1/multiomics/clinical_risk_kp/query_drug_to_disease.json @@ -3,11 +3,11 @@ "query_graph": { "nodes": { "n0": { - "categories": "biolink:Drug", - "ids": "CHEBI:86990" + "categories": ["biolink:Drug"], + "ids": ["CHEBI:86990"] }, "n3": { - "categories": "biolink:Disease" + "categories": ["biolink:Disease"] } }, "edges": { diff --git a/examples/v1/multiomics/clinical_risk_kp/query_disease_to_disease.json b/examples/v1/multiomics/clinical_risk_kp/query_disease_to_disease.json index 048ff5fd..9964bcad 100644 --- a/examples/v1/multiomics/clinical_risk_kp/query_disease_to_disease.json +++ b/examples/v1/multiomics/clinical_risk_kp/query_disease_to_disease.json @@ -18,4 +18,4 @@ } } } -}s \ No newline at end of file +} \ No newline at end of file From 623fc1659a81bd6093c3d1aa1958c19bea712ca0 Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Sat, 22 May 2021 14:45:16 -0700 Subject: [PATCH 35/75] test: :white_check_mark: skip tests for /v1/predicates --- __test__/integration/routes/v1predicates.test.js | 4 ++-- __test__/integration/routes/v1predicates_by_api.test.js | 6 +++--- __test__/integration/routes/v1predicates_by_team.test.js | 6 +++--- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/__test__/integration/routes/v1predicates.test.js b/__test__/integration/routes/v1predicates.test.js index 54ef33c5..5f2226fe 100644 --- a/__test__/integration/routes/v1predicates.test.js +++ b/__test__/integration/routes/v1predicates.test.js @@ -1,10 +1,10 @@ const app = require("../../../src/app"); const request = require('supertest'); -describe("Test /v1/meta_knowledge_graph endpoint", () => { +describe.skip("Test /v1/predicates endpoint", () => { test("Should return 200 with valid response", async () => { await request(app) - .get("/v1/meta_knowledge_graph") + .get("/v1/predicates") .expect(200) .expect('Content-Type', /json/) .then((response) => { diff --git a/__test__/integration/routes/v1predicates_by_api.test.js b/__test__/integration/routes/v1predicates_by_api.test.js index 2212836f..d92e2102 100644 --- a/__test__/integration/routes/v1predicates_by_api.test.js +++ b/__test__/integration/routes/v1predicates_by_api.test.js @@ -1,10 +1,10 @@ const app = require("../../../src/app"); const request = require('supertest'); -describe("Test /v1/smartapi/{smartapi_id}/meta_knowledge_graph endpoint", () => { +describe.skip("Test /v1/smartapi/{smartapi_id}/predicates endpoint", () => { test("Query to Text Mining Targeted Association API Should return 200 with valid response", async () => { await request(app) - .get("/v1/smartapi/978fe380a147a8641caf72320862697b/meta_knowledge_graph") + .get("/v1/smartapi/978fe380a147a8641caf72320862697b/predicates") .expect(200) .expect('Content-Type', /json/) .then((response) => { @@ -15,7 +15,7 @@ describe("Test /v1/smartapi/{smartapi_id}/meta_knowledge_graph endpoint", () => test("Query to Invalid API Should return 404 with error message included", async () => { await request(app) - .get("/v1/smartapi/78fe380a147a8641caf72320862697b/meta_knowledge_graph") + .get("/v1/smartapi/78fe380a147a8641caf72320862697b/predicates") .expect(404) .expect('Content-Type', /json/) .then((response) => { diff --git a/__test__/integration/routes/v1predicates_by_team.test.js b/__test__/integration/routes/v1predicates_by_team.test.js index c25176c0..93fbf513 100644 --- a/__test__/integration/routes/v1predicates_by_team.test.js +++ b/__test__/integration/routes/v1predicates_by_team.test.js @@ -1,10 +1,10 @@ const app = require("../../../src/app"); const request = require('supertest'); -describe("Test /v1/team/{team_name}/meta_knowledge_graph endpoint", () => { +describe.skip("Test /v1/team/{team_name}/predicates endpoint", () => { test("Query to Text Mining team Should return 200 with valid response", async () => { await request(app) - .get("/v1/team/Text Mining Provider/meta_knowledge_graph") + .get("/v1/team/Text Mining Provider/predicates") .expect(200) .expect('Content-Type', /json/) .then((response) => { @@ -15,7 +15,7 @@ describe("Test /v1/team/{team_name}/meta_knowledge_graph endpoint", () => { test("Query to Invalid team Should return 200 with empty response", async () => { await request(app) - .get("/v1/team/wrong team/meta_knowledge_graph") + .get("/v1/team/wrong team/predicates") .expect(404) .expect('Content-Type', /json/) .then((response) => { From daea4d0166c16498baa1e5c05f0b043ce670e4ff Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Sat, 22 May 2021 14:48:21 -0700 Subject: [PATCH 36/75] test: :white_check_mark: updated to use v1.1 examples --- __test__/integration/routes/v1query.test.js | 2 +- __test__/integration/routes/v1query_by_api.test.js | 4 ++-- __test__/integration/routes/v1query_by_team.test.js | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/__test__/integration/routes/v1query.test.js b/__test__/integration/routes/v1query.test.js index 0452e134..4e9afde6 100644 --- a/__test__/integration/routes/v1query.test.js +++ b/__test__/integration/routes/v1query.test.js @@ -4,7 +4,7 @@ const fs = require("fs"); var path = require('path'); describe("Testing /v1/query endpoints", () => { - const invalid_example_folder = path.resolve(__dirname, "../../../examples/v1/invalid"); + const invalid_example_folder = path.resolve(__dirname, "../../../examples/v1.1/invalid"); test("Input query graph that doesn't pass Swagger Validation should return 400 error", async () => { const InvalidInputQueryGraph = { message1: 1 diff --git a/__test__/integration/routes/v1query_by_api.test.js b/__test__/integration/routes/v1query_by_api.test.js index 0a9501d2..55db666d 100644 --- a/__test__/integration/routes/v1query_by_api.test.js +++ b/__test__/integration/routes/v1query_by_api.test.js @@ -5,8 +5,8 @@ const axios = require("axios"); var path = require('path'); describe("Testing /v1/smartapi/{smartapi_id}/query endpoints", () => { - const invalid_example_folder = path.resolve(__dirname, "../../../examples/v1/invalid"); - const example_foler = path.resolve(__dirname, '../../../examples/v1'); + const invalid_example_folder = path.resolve(__dirname, "../../../examples/v1.1/invalid"); + const example_foler = path.resolve(__dirname, '../../../examples/v1.1'); test("Input query graph that doesn't pass Swagger Validation should return 400 error", async () => { const InvalidInputQueryGraph = { message1: 1 diff --git a/__test__/integration/routes/v1query_by_team.test.js b/__test__/integration/routes/v1query_by_team.test.js index e4aae853..f1a7b329 100644 --- a/__test__/integration/routes/v1query_by_team.test.js +++ b/__test__/integration/routes/v1query_by_team.test.js @@ -5,8 +5,8 @@ const axios = require("axios"); var path = require('path'); describe("Testing /v1/team/{team_name}/query endpoints", () => { - const invalid_example_folder = path.resolve(__dirname, "../../../examples/v1/invalid"); - const example_foler = path.resolve(__dirname, '../../../examples/v1'); + const invalid_example_folder = path.resolve(__dirname, "../../../examples/v1.1/invalid"); + const example_foler = path.resolve(__dirname, '../../../examples/v1.1'); test("Input query graph that doesn't pass Swagger Validation should return 400 error", async () => { const InvalidInputQueryGraph = { message1: 1 From a9ffbf96f7a896f077bbedcc95c7ebb97eccda8b Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Sat, 22 May 2021 14:49:40 -0700 Subject: [PATCH 37/75] test: :white_check_mark: fix more tests --- __test__/unittest/routes/predicates.test.js | 4 ++-- __test__/unittest/routes/predicates_team.test.js | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/__test__/unittest/routes/predicates.test.js b/__test__/unittest/routes/predicates.test.js index 77ea2422..1657d34c 100644 --- a/__test__/unittest/routes/predicates.test.js +++ b/__test__/unittest/routes/predicates.test.js @@ -1,9 +1,9 @@ const app = require("../../../src/app"); const request = require('supertest'); -const pred = require("../../../src/controllers/predicates"); +const pred = require("../../../src/controllers/meta_knowledge_graph"); const PredicateLoadingError = require("../../../src/utils/errors/predicates_error"); const PredicatesLoadingError = require("../../../src/utils/errors/predicates_error"); -jest.mock('../../../src/controllers/predicates'); +jest.mock('../../../src/controllers/meta_knowledge_graph'); diff --git a/__test__/unittest/routes/predicates_team.test.js b/__test__/unittest/routes/predicates_team.test.js index 07c94b96..0c38b13f 100644 --- a/__test__/unittest/routes/predicates_team.test.js +++ b/__test__/unittest/routes/predicates_team.test.js @@ -1,9 +1,9 @@ const app = require("../../../src/app"); const request = require('supertest'); -const pred = require("../../../src/controllers/predicates"); +const pred = require("../../../src/controllers/meta_knowledge_graph"); const PredicateLoadingError = require("../../../src/utils/errors/predicates_error"); const PredicatesLoadingError = require("../../../src/utils/errors/predicates_error"); -jest.mock('../../../src/controllers/predicates'); +jest.mock('../../../src/controllers/meta_knowledge_graph'); From 85ff733bbaefec91c55d36b9bf62bc4bc16259de Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Sat, 22 May 2021 14:52:50 -0700 Subject: [PATCH 38/75] fix: :bug: fix meta_kg endpoint for a given API --- src/routes/v1/meta_knowledge_graph_v1_by_api.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/routes/v1/meta_knowledge_graph_v1_by_api.js b/src/routes/v1/meta_knowledge_graph_v1_by_api.js index 3f7a3d60..f12cfdd2 100644 --- a/src/routes/v1/meta_knowledge_graph_v1_by_api.js +++ b/src/routes/v1/meta_knowledge_graph_v1_by_api.js @@ -4,7 +4,7 @@ class RouteMetaKGByAPI { setRoutes(app) { app.get('/v1/smartapi/:smartapiID/meta_knowledge_graph', async (req, res, next) => { try { - const metaKGHandler = new handler(undefined, req.params.smartapiID); + const metaKGHandler = new handler(req.params.smartapiID); const kg = await metaKGHandler.getKG(); res.setHeader('Content-Type', 'application/json'); res.end(JSON.stringify(kg)); From a4a95328861c1e10f63b2137a4e0b45a12922566 Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Sat, 22 May 2021 15:03:40 -0700 Subject: [PATCH 39/75] chore: update local cache files --- data/predicates.json | 16721 +------------------------------------ data/smartapi_specs.json | 2 +- 2 files changed, 2 insertions(+), 16721 deletions(-) diff --git a/data/predicates.json b/data/predicates.json index bde4526d..30bba2db 100644 --- a/data/predicates.json +++ b/data/predicates.json @@ -1,16720 +1 @@ -[ - { - "association": { - "api_name": "SRI Reference Knowledge Graph API", - "smartapi": { - "id": "b0c489ea3a4d5aacfd833616d07a037a", - "meta": { - "date_created": "2021-01-30T16:08:43.224448+00:00", - "last_updated": "2021-03-29T07:01:41.169400+00:00", - "url": "https://monarch-sandbox.cgrb.oregonstate.edu/openapi.json", - "username": "kshefchek" - } - }, - "x-translator": { - "component": "KP", - "team": [ - "Standards Reference Implementation Team" - ] - } - }, - "tags": [ - "translator" - ], - "query_operation": { - "path": "/query", - "server": "https://monarch-sandbox.cgrb.oregonstate.edu", - "method": "post" - }, - "predicates": { - "biolink:Gene": { - "biolink:BiologicalProcess": [ - "biolink:actively_involved_in", - "biolink:enables" - ], - "biolink:Occurrent": [ - "biolink:actively_involved_in", - "biolink:enables" - ], - "biolink:CellularComponent": [ - "biolink:part_of" - ], - "biolink:Gene": [ - "biolink:same_as", - "biolink:subclass_of", - "biolink:superclass_of", - "biolink:related_to", - "biolink:orthologous_to", - "biolink:has_gene_product", - "biolink:interacts_with", - "biolink:genetically_interacts_with", - "biolink:contributes_to", - "biolink:biomarker_for", - "biolink:has_biomarker" - ], - "biolink:SequenceFeature": [ - "biolink:subclass_of", - "biolink:related_to", - "biolink:superclass_of" - ], - "biolink:MolecularActivity": [ - "biolink:enables" - ], - "biolink:Pathway": [ - "biolink:actively_involved_in" - ], - "biolink:OrganismalEntity": [ - "biolink:related_to" - ], - "biolink:OntologyClass": [ - "biolink:has_phenotype", - "biolink:subclass_of", - "biolink:expressed_in", - "biolink:superclass_of", - "biolink:related_to" - ], - "biolink:PhenotypicFeature": [ - "biolink:has_phenotype", - "biolink:related_to", - "biolink:model_of", - "biolink:expressed_in" - ], - "biolink:Disease": [ - "biolink:has_phenotype", - "biolink:related_to", - "biolink:same_as", - "biolink:biomarker_for", - "biolink:contributes_to", - "biolink:model_of", - "biolink:superclass_of", - "biolink:subclass_of" - ], - "biolink:GenomicEntity": [ - "biolink:related_to", - "biolink:subclass_of", - "biolink:same_as", - "biolink:has_sequence_location", - "biolink:interacts_with", - "biolink:genetically_interacts_with", - "biolink:has_gene_product", - "biolink:has_part", - "biolink:condition_associated_with_gene" - ], - "biolink:Transcript": [ - "biolink:same_as", - "biolink:interacts_with", - "biolink:related_to", - "biolink:subclass_of", - "biolink:superclass_of", - "biolink:orthologous_to" - ], - "biolink:RNAProduct": [ - "biolink:same_as", - "biolink:interacts_with", - "biolink:related_to", - "biolink:subclass_of", - "biolink:superclass_of", - "biolink:orthologous_to" - ], - "biolink:Inheritance": [ - "biolink:related_to" - ], - "biolink:GrossAnatomicalStructure": [ - "biolink:expressed_in" - ], - "biolink:AnatomicalEntity": [ - "biolink:expressed_in" - ], - "biolink:Cell": [ - "biolink:expressed_in" - ], - "biolink:InformationContentEntity": [ - "biolink:actively_involved_in", - "biolink:related_to" - ], - "biolink:SequenceVariant": [ - "biolink:has_part", - "biolink:related_to", - "biolink:same_as", - "biolink:condition_associated_with_gene", - "biolink:part_of", - "biolink:superclass_of" - ], - "biolink:Publication": [ - "biolink:related_to" - ], - "biolink:Protein": [ - "biolink:related_to" - ], - "biolink:GeneFamily": [ - "biolink:related_to" - ], - "biolink:Snv": [ - "biolink:related_to", - "biolink:has_part", - "biolink:condition_associated_with_gene" - ], - "biolink:Zygosity": [ - "biolink:related_to" - ], - "biolink:Haplotype": [ - "biolink:has_part", - "biolink:related_to" - ], - "biolink:ReagentTargetedGene": [ - "biolink:related_to" - ], - "biolink:Genotype": [ - "biolink:related_to" - ] - }, - "biolink:CellularComponent": { - "biolink:Gene": [ - "biolink:has_part" - ], - "biolink:Transcript": [ - "biolink:has_part" - ], - "biolink:RNAProduct": [ - "biolink:has_part" - ], - "biolink:OrganismalEntity": [ - "biolink:superclass_of", - "biolink:related_to", - "biolink:subclass_of" - ], - "biolink:OntologyClass": [ - "biolink:affected_by", - "biolink:superclass_of", - "biolink:related_to", - "biolink:participates_in", - "biolink:subclass_of", - "biolink:part_of", - "biolink:has_attribute", - "biolink:has_phenotype" - ], - "biolink:AnatomicalEntity": [ - "biolink:part_of", - "biolink:related_to", - "biolink:subclass_of" - ], - "biolink:PhenotypicFeature": [ - "biolink:affected_by", - "biolink:has_phenotype" - ], - "biolink:Cell": [ - "biolink:superclass_of", - "biolink:part_of", - "biolink:related_to", - "biolink:produced_by", - "biolink:overlaps", - "biolink:subclass_of" - ], - "biolink:BiologicalProcess": [ - "biolink:related_to", - "biolink:participates_in", - "biolink:capable_of" - ], - "biolink:Occurrent": [ - "biolink:related_to", - "biolink:participates_in", - "biolink:capable_of" - ], - "biolink:MolecularActivity": [ - "biolink:related_to", - "biolink:capable_of" - ], - "biolink:Protein": [ - "biolink:superclass_of", - "biolink:has_part" - ], - "biolink:CellularComponent": [ - "biolink:subclass_of", - "biolink:superclass_of", - "biolink:related_to", - "biolink:part_of", - "biolink:has_part", - "biolink:overlaps" - ], - "biolink:ChemicalSubstance": [ - "biolink:has_part" - ], - "biolink:SequenceFeature": [ - "biolink:related_to" - ], - "biolink:Pathway": [ - "biolink:related_to" - ], - "biolink:GenomicEntity": [ - "biolink:related_to" - ], - "biolink:Disease": [ - "biolink:related_to" - ], - "biolink:GrossAnatomicalStructure": [ - "biolink:part_of", - "biolink:related_to" - ] - }, - "biolink:SequenceFeature": { - "biolink:Gene": [ - "biolink:superclass_of", - "biolink:related_to", - "biolink:subclass_of" - ], - "biolink:GenomicEntity": [ - "biolink:superclass_of", - "biolink:subclass_of", - "biolink:related_to", - "biolink:part_of", - "biolink:has_part" - ], - "biolink:SequenceFeature": [ - "biolink:subclass_of", - "biolink:superclass_of", - "biolink:related_to", - "biolink:part_of", - "biolink:has_part" - ], - "biolink:OntologyClass": [ - "biolink:subclass_of", - "biolink:related_to", - "biolink:superclass_of", - "biolink:has_part", - "biolink:part_of" - ], - "biolink:Genome": [ - "biolink:superclass_of", - "biolink:related_to", - "biolink:subclass_of" - ], - "biolink:Transcript": [ - "biolink:superclass_of", - "biolink:subclass_of", - "biolink:related_to" - ], - "biolink:RNAProduct": [ - "biolink:superclass_of", - "biolink:subclass_of", - "biolink:related_to" - ], - "biolink:Disease": [ - "biolink:superclass_of", - "biolink:related_to" - ], - "biolink:BiologicalProcess": [ - "biolink:related_to", - "biolink:participates_in" - ], - "biolink:Occurrent": [ - "biolink:related_to", - "biolink:participates_in" - ], - "biolink:Protein": [ - "biolink:related_to", - "biolink:subclass_of" - ], - "biolink:ChemicalSubstance": [ - "biolink:superclass_of", - "biolink:subclass_of" - ], - "biolink:CellularComponent": [ - "biolink:related_to" - ], - "biolink:Snv": [ - "biolink:subclass_of", - "biolink:superclass_of" - ], - "biolink:SequenceVariant": [ - "biolink:related_to", - "biolink:subclass_of", - "biolink:superclass_of" - ], - "biolink:Haplotype": [ - "biolink:related_to", - "biolink:superclass_of" - ], - "biolink:GenomeBuild": [ - "biolink:superclass_of" - ] - }, - "biolink:MolecularActivity": { - "biolink:Gene": [ - "biolink:enabled_by" - ], - "biolink:Transcript": [ - "biolink:enabled_by", - "biolink:has_input", - "biolink:related_to" - ], - "biolink:RNAProduct": [ - "biolink:enabled_by", - "biolink:related_to", - "biolink:has_input" - ], - "biolink:OntologyClass": [ - "biolink:affected_by", - "biolink:related_to", - "biolink:superclass_of", - "biolink:has_input", - "biolink:subclass_of", - "biolink:has_phenotype" - ], - "biolink:AnatomicalEntity": [ - "biolink:part_of", - "biolink:occurs_in" - ], - "biolink:PhenotypicFeature": [ - "biolink:affected_by", - "biolink:has_phenotype" - ], - "biolink:BiologicalProcess": [ - "biolink:related_to", - "biolink:part_of", - "biolink:participates_in", - "biolink:has_part", - "biolink:regulates_process_to_process", - "biolink:negatively_regulates_process_to_process", - "biolink:superclass_of", - "biolink:subclass_of" - ], - "biolink:Occurrent": [ - "biolink:related_to", - "biolink:part_of", - "biolink:participates_in", - "biolink:has_part", - "biolink:subclass_of", - "biolink:superclass_of", - "biolink:regulates_process_to_process", - "biolink:negatively_regulates_process_to_process", - "biolink:has_input" - ], - "biolink:MolecularActivity": [ - "biolink:has_part", - "biolink:part_of", - "biolink:subclass_of", - "biolink:superclass_of", - "biolink:related_to", - "biolink:regulates_process_to_process", - "biolink:negatively_regulates_process_to_process", - "biolink:has_input" - ], - "biolink:ChemicalSubstance": [ - "biolink:related_to", - "biolink:has_input", - "biolink:has_output", - "biolink:has_participant" - ], - "biolink:CellularComponent": [ - "biolink:related_to", - "biolink:has_input", - "biolink:occurs_in" - ], - "biolink:Protein": [ - "biolink:has_input", - "biolink:related_to", - "biolink:has_participant" - ], - "biolink:Pathway": [ - "biolink:part_of", - "biolink:related_to" - ], - "biolink:OrganismalEntity": [ - "biolink:related_to" - ], - "biolink:SequenceFeature": [ - "biolink:has_input" - ], - "biolink:GrossAnatomicalStructure": [ - "biolink:occurs_in" - ], - "biolink:Disease": [ - "biolink:related_to" - ], - "biolink:EvidenceType": [ - "biolink:related_to" - ] - }, - "biolink:Occurrent": { - "biolink:Gene": [ - "biolink:enabled_by" - ], - "biolink:EvidenceType": [ - "biolink:related_to" - ], - "biolink:Transcript": [ - "biolink:enabled_by", - "biolink:related_to", - "biolink:has_input", - "biolink:has_output" - ], - "biolink:RNAProduct": [ - "biolink:enabled_by", - "biolink:related_to", - 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s","biolink:part_of","biolink:located_in","biolink:occurs_in","biolink:causes","biolink:quantifier_qualifier","biolink:biomarker_for","biolink:predisposes","biolink:interacts_with","biolink:disrupts","biolink:manifestation_of","biolink:derives_into"],"biolink:GeographicLocation":["biolink:has_input","biolink:subclass_of"],"biolink:GrossAnatomicalStructure":["biolink:located_in","biolink:part_of","biolink:subclass_of","biolink:affects","biolink:related_to","biolink:disrupts","biolink:has_input","biolink:causes","biolink:treats","biolink:prevents"],"biolink:IndividualOrganism":["biolink:part_of","biolink:treats","biolink:located_in","biolink:related_to","biolink:affects","biolink:biomarker_for","biolink:occurs_in","biolink:subclass_of","biolink:has_quantitative_value","biolink:has_input","biolink:causes"],"biolink:InformationContentEntity":["biolink:subclass_of","biolink:treats","biolink:has_attribute","biolink:physically_interacts_with","biolink:related_to","biolink:affects","biolink:located_in","biolink:precedes","biolink:has_input","biolink:biomarker_for","biolink:quantifier_qualifier","biolink:positively_regulates_entity_to_entity","biolink:interacts_with","biolink:prevents","biolink:close_match","biolink:coexists_with","biolink:causes","biolink:disrupts","biolink:predisposes","biolink:has_route","biolink:part_of","biolink:has_quantitative_value"],"biolink:MaterialSample":["biolink:subclass_of","biolink:has_attribute"],"biolink:Metabolite":["biolink:physically_interacts_with","biolink:related_to"],"biolink:MolecularActivity":["biolink:affects","biolink:positively_regulates","biolink:has_input"],"biolink:MolecularEntity":["biolink:has_input","biolink:related_to","biolink:physically_interacts_with","biolink:close_match","biolink:quantifier_qualifier","biolink:positively_regulates_entity_to_entity","biolink:subclass_of","biolink:coexists_with","biolink:negatively_regulates_entity_to_entity","biolink:precedes","biolink:produces","biolink:derives_into","biolink:treats","biolink:affects","biolink:prevents","biolink:part_of","biolink:located_in","biolink:occurs_in","biolink:causes","biolink:biomarker_for","biolink:predisposes","biolink:interacts_with","biolink:disrupts","biolink:has_unit","biolink:manifestation_of","biolink:has_attribute"],"biolink:NamedThing":["biolink:treats","biolink:has_input","biolink:related_to","biolink:physically_interacts_with","biolink:close_match","biolink:quantifier_qualifier","biolink:positively_regulates_entity_to_entity","biolink:subclass_of","biolink:coexists_with","biolink:causes","biolink:negatively_regulates_entity_to_entity","biolink:precedes","biolink:participates_in","biolink:affects","biolink:produces","biolink:biomarker_for","biolink:interacts_with","biolink:prevents","biolink:predisposes","biolink:part_of","biolink:located_in","biolink:derives_into","biolink:has_attribute","biolink:positively_regulates","biolink:has_route","biolink:occurs_in","biolink:disrupts","biolink:manifestation_of","biolink:correlated_with","biolink:has_unit","biolink:has_quantitative_value","biolink:derives_from"],"biolink:OntologyClass":["biolink:affects","biolink:located_in","biolink:treats","biolink:has_input","biolink:subclass_of","biolink:related_to","biolink:physically_interacts_with","biolink:close_match","biolink:part_of","biolink:produces","biolink:quantifier_qualifier","biolink:disrupts","biolink:causes","biolink:biomarker_for","biolink:occurs_in","biolink:positively_regulates_entity_to_entity","biolink:coexists_with"],"biolink:OrganismTaxon":["biolink:part_of","biolink:located_in","biolink:biomarker_for","biolink:affects","biolink:occurs_in","biolink:treats"],"biolink:OrganismalEntity":["biolink:has_input","biolink:physically_interacts_with","biolink:related_to","biolink:quantifier_qualifier","biolink:close_match","biolink:subclass_of","biolink:located_in","biolink:coexists_with","biolink:precedes","biolink:causes","biolink:treats","biolink:part_of","biolink:produces","biolink:positively_regulates_entity_to_entity","biolink:prevents","biolink:affects","biolink:has_route","biolink:negatively_regulates_entity_to_entity","biolink:positively_regulates","biolink:biomarker_for","biolink:predisposes","biolink:occurs_in","biolink:has_quantitative_value","biolink:disrupts","biolink:derives_from"],"biolink:PathologicalProcess":["biolink:related_to","biolink:treats","biolink:affects","biolink:causes","biolink:positively_regulates","biolink:prevents","biolink:biomarker_for","biolink:predisposes","biolink:correlated_with","biolink:disrupts","biolink:precedes","biolink:coexists_with","biolink:subclass_of","biolink:quantifier_qualifier"],"biolink:Phenomenon":["biolink:affects","biolink:positively_regulates_entity_to_entity","biolink:treats","biolink:prevents","biolink:causes","biolink:biomarker_for","biolink:related_to","biolink:has_input","biolink:correlated_with","biolink:subclass_of","biolink:physically_interacts_with","biolink:quantifier_qualifier"],"biolink:PhenotypicFeature":["biolink:has_input"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Block Groups are aggregates of an average of 39 Blocks each, each of which is delineated by visible and invisible geographic boundaries. Block groups, in turn, are aggregated into Census Tracts, which generally have a population size between 1,200 and 8,000 people, with an optimum size of 4,000 people. Census Tracts aggregate into counties and counties into states. Metropolitan and micropolitan areas are aggregates of counties. See https://www2.census.gov/geo/pdfs/reference/geodiagram.pdf for further detail. Census geography, even Block Groups, may cross municipal lines and may include both urbanized and rural areas. Because population is a large factor in determining Census geography, some Block Groups may cover an extensive rural or wilderness area while others are quite compact. Census Block, Block Group, and Tract boundaries may change somewhat with each decennial Census, but remain stable in between Censuses.\n\nThe US Census Bureau is mandated to preserve the confidentiality of individual-level data. Therefore, data are often summarized, coarsened into categories, or suppressed by complex secret algorithms (especially, but not limited to household income data). In addition, because the variables of interest may only apply to a small subset of Block Group missing data can occur. In some versions of the data, calculated values are suppressed in Block Groups with less than 50 residents.\n\nStandard errors for the socio-demographic variables are provided. Because each of the values in the ACS data files are summary statistics calculated from sample survey data for each Block Group, different samples yield somewhat different values. Therefore, the Census Bureau generates 80 replicate values for selected variables. These provide the basis for the estimated standard errors of the estimates.\n\nThe currently available variables are listed here:\n\n **(2007-2011 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **EstResidentialDensity** - block group population density\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\n **(2012-2016 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **EstTotalPopulation_SE** - standard error of total population in block group\n - 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WGS84 is the World Geodetic System for expressing latitude and longitude. For example, Raleigh, North Carolina is at latitude 35.7796 and longitude -78.6382.\n\nAdditional details on the data can be found in this documentation: (https://github.com/lstillwe/socio-economic-api/blob/master/docs/CensusData.md)\n","license":{"name":"MIT","url":"http://opensource.org/licenses/MIT"},"title":"Socio-Environmental Exposures API","version":"1.0.1","x-translator":{"component":"KP","team":["Exposures Provider"]}},"paths":{"/values":{"get":{"description":"By passing in a location specification (lat, lon) and a year range, you can retrieve the the ACS Values for that location and year range\n","operationId":"get_values","parameters":[{"description":"latitude in decimal degrees format, ie: 32.47","in":"query","name":"latitude","required":true,"schema":{"type":"string"}},{"description":"longitude in decimal degrees format, ie: -86.5","in":"query","name":"longitude","required":true,"schema":{"type":"string"}},{"description":"ACS data year range 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Multiple results may be returned representing possible conceptual matches, but all of the identifiers have been correctly normalized using the NodeNormalization service.","termsOfService":"robokop.renci.org:7055/tos?service_long=Name+Resolver&provider_long=the+Translator+Consortium","title":"Name Resolver","version":"1.0.0","x-translator":{"component":"Utility","team":["Standards Reference Implementation Team"]}},"paths":{"/reverse_lookup":{"post":{"description":"Look up curies from name or fragment.","operationId":"lookup_names_reverse_lookup_post","requestBody":{"content":{"application/json":{"schema":{"allOf":[{"$ref":"#/components/schemas/Request"}],"example":{"curies":["MONDO:0005737","MONDO:0009757"]},"title":"Request"}}},"required":true},"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"items":{"type":"string"},"type":"array"},"title":"Response Lookup Names Reverse Lookup Post","type":"object"}}},"description":"Successful Response"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":"Lookup Names","tags":["lookup"]}},"/lookup":{"post":{"description":"Look up curies from name or fragment.","operationId":"lookup_curies_lookup_post","parameters":[{"in":"query","name":"string","required":true,"schema":{"title":"String","type":"string"}},{"in":"query","name":"offset","required":false,"schema":{"default":0,"title":"Offset","type":"integer"}},{"in":"query","name":"limit","required":false,"schema":{"default":10,"maximum":1000,"title":"Limit","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"items":{"type":"string"},"type":"array"},"title":"Response Lookup Curies Lookup Post","type":"object"}}},"description":"Successful Response"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":"Lookup Curies","tags":["lookup"]}}},"servers":[{"description":"Default server","url":"https://name-resolution-sri.renci.org/"}],"tags":[{"name":"translator"}]},{"_id":"b0c489ea3a4d5aacfd833616d07a037a","_meta":{"date_created":"2021-01-30T16:08:43.224448+00:00","last_updated":"2021-03-31T07:02:07.266784+00:00","url":"https://monarch-sandbox.cgrb.oregonstate.edu/openapi.json","username":"kshefchek"},"_score":0.75804067,"info":{"contact":{"email":"shefchek@oregonstate.edu","name":"Kent Shefchek","x-id":"https://github.com/kshefchek","x-role":"responsible developer"},"description":"The SRI reference KG aims to aggregate knowledge sources across translator using KGX. 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versiontable content
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This appears at the top level of the results payload"}},"summary":"Returns genes associated with a phenotype","tags":["phenotype"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/phenotype-gene"}]}},"/bioentity/phenotype/{phenotype_id}/pathways":{"get":{"parameters":[{"description":"CURIE identifier of phenotype IDs can be used with same results","example":"HP:0012265","in":"path","name":"phenotype_id","required":true,"schema":{"type":"string"}},{"description":"number of rows","example":100,"in":"query","name":"rows","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"A distinct set of association.objects (typically ontology terms). 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This appears at the top level of the results payload"}},"summary":"Returns pathways associated with a phenotype","tags":["phenotype"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/phenotype-variant"}]}},"/bioentity/phenotype/{phenotype_id}/diseases":{"get":{"parameters":[{"description":"CURIE identifier of phenotype IDs can be used with same results","example":"HP:0012265","in":"path","name":"phenotype_id","required":true,"schema":{"type":"string"}},{"description":"number of rows","example":100,"in":"query","name":"rows","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"A distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload"}},"summary":"Returns diseases associated with a phenotype","tags":["phenotype"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/phenotype-disease"}]}}},"servers":[{"description":"Production server","url":"https://api.monarchinitiative.org/api"}],"tags":[{"name":"anatomy"},{"name":"disease"},{"name":"gene"},{"name":"phenotype"},{"name":"pathway"},{"name":"annotation"},{"name":"query"},{"name":"translator"},{"name":"biolink"}]},{"_id":"9ee398a738916a98b612068cc022454f","_meta":{"date_created":"2020-12-11T23:57:12.070157+00:00","last_updated":"2021-03-31T07:03:06.189200+00:00","url":"https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/LINCS/smartapi.yml","username":"kevinxin90"},"_score":0.37009162,"components":{"x-bte-kgs-operations":{"drug-indication":[{"inputs":[{"id":"LINCS","semantic":"ChemicalSubstance"}],"method":"get","outputs":[{"id":"MESH","semantic":"Disease"}],"parameters":{"id":"{inputs[0]}"},"path":"/query","predicate":"treats","response_mapping":{"$ref":"#/components/x-bte-response-mapping/drug-indication"},"source":"LINCS","supportBatch":false}]},"x-bte-response-mapping":{"drug-indication":{"MESH":"documents.mesh_id","name":"documents.mesh_heading"}}},"info":{"contact":{"email":"akoleti@med.miami.edu","name":"UM BD2K-LINCS DCIC","x-id":"http://lincsportal.ccs.miami.edu/","x-role":"responsible organization"},"description":"Documentation of the LINCS Data Portal web services. Learn more about [LINCS Data Portal](http://lincsportal.ccs.miami.edu/dcic-portal/)","termsOfService":"http://lincsportal.ccs.miami.edu/dcic-portal/#/terms","title":"LINCS Data Portal API","version":"1.0","x-translator":{"component":"KP","team":["Service Provider"]}},"paths":{"/fetchmolecules":{"get":{"parameters":[{"description":"Parameter used for searching small molecule metadata fields. Syntax is \"field name:\"value\"\" Do Not include outer quotes. 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Parameter 'searchTerm' allows querying by specific metadata fields within small molecule records.","tags":["small molecule","query","LINCS","SchuererLab"]}},"/fetchcells":{"get":{"parameters":[{"description":"Parameter used for searching cell line metadata fields. Syntax is \"field name:\"value\"\" Do Not include outer quotes. Example; Name:\"MCF7\", lincsidentifier:\"LSM-1028\", etc. Setting search term equal to the wildcard charachter, \"*\", will query for all fields of all records up to the specified limit.","in":"query","name":"searchTerm","required":true,"schema":{"type":"string"},"x-valueType":[" http://identifiers.org/lincs.cell"]},{"description":"limit the number of records returned, default is 10","in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"A query response object with 'documents' property, each document corresponds to a cell line that matched the query criteria.","x-responseValueType":[{"path":"lincs.cell","valueType":"http://identifiers.org/'"}]}},"summary":"Get LINCS cell lines records, which contain both LINCS-based and general metadata about the cell lines tested in the NIH LINCS program. Parameter 'searchTerm' allows querying by specific metadata fields within the cell line records.","tags":["diseases","cells","query","LINCS","SchuererLab"]}},"/fetchdata":{"get":{"parameters":[{"description":"Parameter used for searching data set metadata fields. Syntax is \"field name:\"value\"\" Do Not include outer quotes. 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Parameter 'searchTerm' allows querying by specific metadata fields within the assay metadata records.","tags":["signature","query","LINCS","SchuererLab"]}},"/mechanismOfAction":{"get":{"parameters":[{"description":"Parameter used to search by LINCS small molecule identifier. Syntax is \"id=LSM-#\" Do Not use quotes. Example; id=LSM-1008.","in":"query","name":"id","required":false,"schema":{"type":"string"},"x-valueType":["http://identifiers.org/lincs.smallmolecule"]},{"description":"Parameter used to search by the full name of the mechanism of action. Syntax is \"moa=Mechanism name\" Do Not use quotes. 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Examples; uniprto=O15264; uniprot=P15056; etc..","in":"query","name":"uniprot","required":false,"schema":{"type":"string"}},{"description":"limit the number of records returned, default is 10","in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"A query response object with 'documents' property, each document corresponds to a bioactivity that matched the query criteria.","x-responseValueType":[{"path":"lincs.smallmolecule","valueType":"http://identifiers.org/"}]}},"summary":"Get known bioactivities for LINCS small molecules, these data are aggregated values resourced from the ChEMBL ver 23 database . The ChEMBL values were mined from numerous sources.","tags":["signature","query","LINCS","SchuererLab","small molecule"]}},"/drugindication":{"get":{"parameters":[{"description":"Parameter used to search by LINCS small molecule identifier. Syntax is \"id=LSM-#\" Do Not use quotes. Example; id=LSM-1008.","in":"query","name":"id","required":false,"schema":{"type":"string"},"x-valueType":["http://identifiers.org/lincs.smallmolecule"]},{"description":"Parameter used to search by the EFO drug indication. Syntax is \"efo=Drug Indication\" Do Not use quotes. Example; efo=renal carcinoma","in":"query","name":"efo","required":false,"schema":{"type":"string"}},{"description":"Parameter used to search by the MeSH drug indication. Syntax is \"efo=Drug Indication\" Do Not use quotes. Example; mesh=carcinoma, renal cell","in":"query","name":"mesh","required":false,"schema":{"type":"string"}},{"description":"limit the number of records returned, default is 10","in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"A query response object with 'documents' property, each document corresponds to a drug indication that matched the query criteria.","x-responseValueType":[{"path":"lincs.smallmolecule","valueType":"http://identifiers.org/"}]}},"summary":"Get known drug indications for LINCS small molecules, the indications are captured from both the Experimental Factor Ontology (EFO) and the Medical Subject Headings (MeSH) vocabularies.","tags":["signature","query","LINCS","SchuererLab","small molecule"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/drug-indication"}]}},"/disease":{"get":{"parameters":[{"description":"Parameter used to search by the DO disease name. Syntax is \"disease=disease name\" Do Not use quotes. Example; disease=breast carcinoma","in":"query","name":"disease","required":false,"schema":{"type":"string"}},{"description":"Parameter used to search by the DO identifier. Syntax is \"doid=DOID:#\" Do Not use quotes. Example; doid=DOID:3459","in":"query","name":"doid","required":false,"schema":{"type":"string"}},{"description":"limit the number of records returned, default is 10","in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"A query response object with 'documents' property, each document corresponds to a disease that matched the query criteria.","x-responseValueType":[{"path":"lincs.cell","valueType":"http://identifiers.org/"}]}},"summary":"Query for LINCS cell line identifiers by disease, the diseases are captured from the Disease Ontology (DO) vocabulary.","tags":["diseases","query","LINCS","SchuererLab","cells"]}}},"servers":[{"description":"Production server","url":"http://lincsportal.ccs.miami.edu/dcic/api/"}],"tags":[{"name":"small molecule"},{"name":"query"},{"name":"cells"},{"name":"gene"},{"name":"diseases"},{"name":"LINCS"},{"name":"SchuererLab"},{"name":"signature"},{"name":"translator"}]},{"_id":"70117385218edc9bc01633829011dfcf","_meta":{"date_created":"2021-02-03T00:00:11.872122+00:00","last_updated":"2021-03-31T07:01:02.897302+00:00","slug":"cohd","url":"https://raw.githubusercontent.com/WengLab-InformaticsResearch/cohd_api/master/cohd/cohd_oas3.yaml","username":"CaseyTa"},"_score":0.3501789,"components":{"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)","version":"3.0.0","x-accessRestriction":"none","x-implementationLanguage":"Python","x-translator":{"component":"KP","team":["Clinical Data Provider"]},"x-trapi":{"version":"1.0.0"}},"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":{"description":"Attempts 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":{"description":"Attempts 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":0.000005585247351056813,"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. \n \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"]}},"/predicates":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"additionalProperties":{"description":"Array of predicates","items":{"type":"string"},"type":"array"},"description":"Target map","type":"object"},"description":"Source map","example":{"biolink:ChemicalSubstance":{"biolink:Gene":["biolink:directly_interacts_with","biolink:decreases_activity_of"]}},"type":"object"}}},"description":"Predicates by source and target"}},"summary":"Get supported relationships by source and target","tags":["translator","trapi"]}},"/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.\n \nFor the subject node, the id must be specified (category is ignored).\n \nFor the object node, both the id and category are optional. If id is specified for the object node, then the association between the two identified concepts is returned. If id is not specified and category is specified, the associations between the subject node and all concepts with the specified category are returned. If neither are specified, then the associations between the subject node and all concepts are returned.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.\nAdditional behavior options can be controlled using the optional parameters in query_options.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"id\": \"DOID:9053\",\n \"category\": \"biolink:Disease\"\n },\n \"n01\": {\n \"category\": \"biolink:Procedure\"\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicate\": \"biolink:correlated_with\",\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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)."},"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","tags":["translator","trapi"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false}],"x-swagger-router-controller":"swagger_server.controllers.query_controller"}},"/0.9.3/query":{"post":{"description":"This endpoint is temporarily provided to support TRAPI 0.9.3 queries\nQuery 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.\nFor the source node, the curie must be specified (type is ignored).\nFor the target node, both the curie and type are optional. If curie is specified for the target node, then the association between the two identified concepts is returned. If curie is not specified and type is specified, the associations between the source node and all concepts with the specified type are returned. If neither are specified, then the associations between the source node and all concepts are returned.\nCOHD will attempt to map the CURIE to an OMOP concept and the node type to an OMOP domain.","operationId":"query093","requestBody":{"content":{"application/json":{"example":"{\n \"max_results\": 50,\n \"message\": {\n \"query_graph\": {\n \"nodes\": [\n {\n \"id\": \"n00\",\n \"curie\": \"DOID:9053\",\n \"type\": \"biolink:Disease\"\n },\n {\n \"id\": \"n01\",\n \"type\": \"biolink:Procedure\"\n }\n ],\n \"edges\": [\n {\n \"id\": \"e00\",\n \"type\": \"biolink:correlated_with\",\n \"source_id\": \"n00\",\n \"target_id\": \"n01\"\n }\n ]\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\n \"dataset_id\": 3,\n \"confidence_interval\": 0.99,\n \"min_cooccurrence\": 50,\n \"threshold\": 0.5,\n \"local_oxo\": true,\n \"ontology_targets\": {\n \"biolink:Disease\": [\"ICD9\", \"SNOMEDCT\", \"DOID\"],\n \"biolink:Drug\": [\"RxNorm\"],\n \"biolink:Procedure\": [\"ICD10PCS\", \"SNOMEDCT\"],\n \"_DEFAULT\": []\n },\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/Message"}}},"description":"successful operation"},"400":{"description":"Invalid status value"}},"summary":"Query COHD following NCATS Translator Reasoner Standard API version 0.9.3","tags":["translator","trapi"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false}],"x-swagger-router-controller":"swagger_server.controllers.query_controller"}},"/translator/biolink_to_omop":{"post":{"description":"Map Biolink CURIEs to OMOP concepts","operationId":"biolink_to_omop","requestBody":{"content":{"application/json":{"example":"{\n \"curies\": [\n \"HP:0002907\",\n \"MONDO:0001187\"\n ]\n}","schema":{"$ref":"#/components/schemas/CurieList"}}},"description":"List of CURIEs","required":true},"responses":{"200":{"content":{"application/json":{"example":"{\n \"MONDO:0001187\": {\n \"distance\": 2,\n \"omop_concept_id\": 197508,\n \"omop_concept_name\": \"Malignant tumor of urinary bladder\"\n }\n}","schema":{"additionalProperties":{"description":"Mapping from OMOP concept to Biolink","properties":{"distance":{"description":"mapping distance","type":"integer"},"omop_concept_id":{"type":"integer"},"omop_concept_name":{"type":"string"}},"type":"object"}}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from Biolink to OMOP","tags":["translator"]}},"/translator/omop_to_biolink":{"post":{"description":"Map OMOP concepts to normalized Biolink nodes using SRI Node Normalizer.","operationId":"omop_to_biolink","requestBody":{"content":{"application/json":{"example":"{\n \"omop_ids\": [\n 78472,\n 197508\n ]\n}","schema":{"$ref":"#/components/schemas/OmopList"}}},"description":"List of OMOP IDs","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"type":"object"},"example":"{\n \"197508\": {\n \"equivalent_identifiers\": [\n {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n {\n \"identifier\": \"DOID:11054\"\n },\n {\n \"identifier\": \"OMIM:109800\"\n },\n {\n \"identifier\": \"UMLS:C0005684\"\n },\n {\n \"identifier\": \"NCIT:C9334\"\n },\n {\n \"identifier\": \"SNOMEDCT:399326009\"\n }\n ],\n \"id\": {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n \"type\": [\n \"biolink:Disease\",\n \"biolink:DiseaseOrPhenotypicFeature\",\n \"biolink:BiologicalEntity\",\n \"biolink:NamedThing\"\n ]\n }\n}","type":"object"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized. Mapping from OMOP concept to Biolink normalized nodes. See [SRI Node Normalizer](https://nodenormalization-sri.renci.org/docs#/) for response format"},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from OMOP to Biolink","tags":["translator"]}}},"servers":[{"url":"http://tr-kp-clinical.ncats.io/api/"},{"url":"http://cohd.io/api/"}],"tags":[{"description":"COHD metadata","name":"Metadata"},{"description":"OMOP Common Data Model concepts","name":"OMOP"},{"description":"Clinical frequency data","name":"Clinical Frequencies"},{"description":"Estimated association between concepts","name":"Concept Associations"},{"description":"Concept-age distributions, concept-pair delta distributions, and temporal analyses","name":"Temporal Clinical Data"},{"description":"NCATS Biomedical Data Translator APIs","name":"translator"},{"description":"Implements the NCATS Translator Reasoner API standards","name":"trapi"}]},{"_id":"fc8245e92c970298449294fc04211869","_meta":{"date_created":"2021-02-04T00:00:10.655676+00:00","last_updated":"2021-03-31T07:01:04.079587+00:00","slug":"cohdcovid","url":"https://raw.githubusercontent.com/WengLab-InformaticsResearch/cohd_api/cohd_covid/cohd/cohd_oas3.yaml","username":"CaseyTa"},"_score":0.3501789,"components":{"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) for COVID-19 Research API provides access to counts and frequencies (i.e., EHR visit prevalence) of conditions, procedures, drug exposures, and the co-occurrence frequencies between them for a cohort of hospitalized COVID-19 patients and two comparator cohorts of hospitalized influenza patients and hospitalized patients. Count and frequency data were derived from the [Columbia University Medical Center's](http://www.cumc.columbia.edu/) [OHDSI](https://www.ohdsi.org/) database including inpatient. Counts are the number of inpatient visits associated with the concept, e.g., diagnosed with a condition, exposed to a drug, or a procedure was performed. Frequencies are the number of unique visits associated with the concept divided by the total number of visits in the dataset, i.e., prevalence in the electronic health records. To protect patient privacy, all concepts and pairs of concepts where the count <= 10 were excluded, and counts were randomized by the Poisson distribution. \n\nDatasets from three primary cohorts are available: \n1) COVID-19: Hospitalized patients aged 18 or older with a COVID-19 related condition diagnosis and/or a confirmed positive COVID-19 test during their hospitalization period or within the prior 21 days. Date range: March 1, 2020 to September 1, 2020. This cohort is also further stratified by sex (male and female) and age (adult: 18-64, senior: 65+).\n2) General inpatient: All hospitalized patients aged 18 or older. Date range: January 1, 2014 to December 31, 2019.\n3) Influenza: Hospitalized patients aged 18 or older who had at least one occurrence of influenza conditions or pre-coordinated positive measurements or positive influenza testing in the prior 21 days or during their hospitalization period. Date range: January 1, 2014 to December 31, 2019.\n\nBoth hierarchical and non-hierarchical datasets are available for each cohort. In the hierarchical datasets, the counts for each concept include the visits from all descendant concepts. For example, the count for ibuprofen (ID 1177480) includes visits with Ibuprofen 600 MG Oral Tablet (ID 19019073), Ibuprofen 400 MG Oral Tablet (ID 19019072), Ibuprofen 20 MG/ML Oral Suspension (ID 19019050), etc. \n\nClinical concepts (e.g., conditions, procedures, drugs) are coded by their standard concept ID in the [OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki). API methods are provided to map to/from other vocabularies supported in OMOP and other ontologies using the EMBL-EBI Ontology Xref Service (OxO). \n\n\nThe following resources are available through this API: \n\n\n1. Metadata: Metadata on the COHD database, including dataset descriptions, number of concepts, etc. \n\n\n2. OMOP: Access to the common vocabulary for name and concept identifier mapping\n\n\n3. Clinical Frequencies: Access to the counts and frequencies of conditions, procedures, and drug exposures, and the associations between them. Frequency was determined as the number of visits with the code(s) / total number of visits. \n\n\n4. Concept Associations: Inferred associations between concepts using chi-square analysis, ratio between observed to expected frequency, and relative frequency. \n\n\nA [Python notebook](https://github.com/WengLab-InformaticsResearch/cohd_api/blob/master/notebooks/COHD_API_Example.ipynb) demonstrates simple examples of how to use the COHD API.\n\n\nCOHD was developed at the [Columbia University Department of Biomedical Informatics](https://www.dbmi.columbia.edu/) as a collaboration between the [Weng Lab](http://people.dbmi.columbia.edu/~chw7007/), [Tatonetti Lab](http://tatonettilab.org/), and the [NCATS Biomedical Data Translator](https://ncats.nih.gov/translator) program (TReK Team). This work was supported in part by grants: NCATS 1OT2TR003434, NLM R01LM012895, NCATS OT3TR002027, NLM R01LM009886-08A1, and NIGMS R01GM107145.\n\nThe following external resources may be useful: \n[OHDSI](https://www.ohdsi.org/) \n[OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki) \n[Athena](http://athena.ohdsi.org) (OMOP vocabularies, search, concept relationships, concept hierarchy) \n[Atlas](http://www.ohdsi.org/web/atlas/) (OMOP vocabularies, search, concept relationships, concept hierarchy, concept sets) \n[NCATS Biomedical Data Translator](https://sites.google.com/ncats.nih.gov/translator-io/home) \n","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"termsOfService":"http://cohd.io/terms/","title":"Columbia Open Health Data (COHD) for COVID-19 Research","version":"3.0.0","x-accessRestriction":"none","x-implementationLanguage":"Python","x-translator":{"component":"KP","team":["Clinical Data Provider"]},"x-trapi":{"version":"1.0.0"}},"paths":{"/metadata/datasets":{"get":{"description":"Returns a list of datasets, including dataset ID, name, and description.","operationId":"datasets","responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"dataset_description":{"example":"Hospitalized patients with a COVID-19 condition and/or positive lab test (non-hierarchical)","type":"string"},"dataset_id":{"example":1,"type":"integer"},"dataset_name":{"example":"COVID Cohort (non-hierarchical)","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of dataset descriptions."},"default":{"description":"Unexpected error"}},"summary":"Enumerates the datasets available in COHD","tags":["Metadata"]}},"/metadata/domainCounts":{"get":{"description":"Returns a list of domains and the number of concepts in each domain.","operationId":"domainCounts","parameters":[{"description":"The dataset_id of the dataset to query. 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/visitCount":{"get":{"description":"Returns the number of visits in the dataset.","operationId":"visitCount","parameters":[{"description":"The dataset_id of the dataset to query.","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 visit counts."},"default":{"description":"Unexpected error"}},"summary":"The number of visits 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":{"description":"Attempts 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":{"description":"Attempts 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":0.000005585247351056813,"type":"integer"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2008271,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequency of a pair of concepts","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id. Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"q","required":true,"schema":{"type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":19041324,"type":"integer"},"associated_concept_name":{"example":"Acetaminophen 325 MG Oral Tablet [Tylenol]","type":"string"},"associated_domain_id":{"example":"Drug","type":"string"},"concept_count":{"example":277,"type":"integer"},"concept_frequency":{"example":0.0001547113516242737,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptDomainFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id restricted by domain of the associated concept_id. Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptDomainFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id","required":true,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc. See /metadata/domainCounts for a list of valid domain IDs.","example":"Procedure","in":"query","name":"domain","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":2211361,"type":"integer"},"associated_concept_name":{"example":"Radiologic examination, chest, 2 views, frontal and lateral","type":"string"},"associated_domain_id":{"example":"Procedure","type":"string"},"concept_count":{"example":257,"type":"integer"},"concept_frequency":{"example":0.00014354085692216007,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/mostFrequentConcepts":{"get":{"description":"Retrieves the most frequent concepts.","operationId":"mostFrequentConcepts","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The number of concepts to retreieve, e.g., 100. 0 or unspecified will return all matching concepts.","example":100,"in":"query","name":"q","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The domain_id to restrict to, e.g., \"Condition\", \"Drug\", \"Procedure\". See /metadata/domainCounts for a list of valid domain IDs.","example":"Condition","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"(Optional) The vocabulary_id(s) to restrict to, e.g., \"SNOMED\", \"MedDRA\", \"RxNorm\", \"ATC\" etc. Comma separated to include multiple vocabularies, e.g., \"SNOMED,MedDRA\". Default: unrestricted","example":null,"in":"query","name":"vocabulary_id","required":false,"schema":{"type":"string"}},{"description":"(Optional) The concept_class_id(s) to restrict to. concept_class_ids are specific to each vocabulary, e.g.,: [ATC](https://en.wikipedia.org/wiki/Anatomical_Therapeutic_Chemical_Classification_System) {ATC 1st, ATC 2nd, ATC 3rd, ATC 4th, ATC 5th}; [MedDRA](https://en.wikipedia.org/wiki/MedDRA) {PT, HLT, HLGT, SOC}; [RxNorm](https://www.nlm.nih.gov/research/umls/rxnorm/docs/2015/appendix5.html) {Ingredient, Clinical Drug Form, Clinical Drug Comp, Clinical Drug}. Comma separated to include multiple concept_class_ids, e.g., \"PT,HLT\". Default: unrestricted","example":null,"in":"query","name":"concept_class_id","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_class_id":{"example":"Clinical Finding","type":"string"},"concept_count":{"example":233790,"type":"integer"},"concept_frequency":{"example":0.1305774978203572,"type":"integer"},"concept_id":{"example":320128,"type":"integer"},"concept_name":{"example":"Essential hypertension","type":"string"},"dataset_id":{"example":1,"type":"integer"},"domain_id":{"example":"Condition","type":"string"},"vocabulary_id":{"example":"SNOMED","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of most frequent concepts."},"default":{"description":"Unexpected error"}},"summary":"Most frequent concepts [by domain]","tags":["Clinical Frequencies"]}},"/association/chiSquare":{"get":{"description":"Returns the chi-square statistic and p-value between pairs of concepts. Results are returned in descending order of the chi-square statistic. Note that due to large sample sizes, the chi-square can become very large. \n\nThe expected frequencies for the chi-square analysis are calculated based on the single concept frequencies and assuming independence between concepts. P-value is calculated with 1 DOF. \n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"chiSquare","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If this parameter is specified, then the chi-square between concept_id_1 and concept_id_2 is returned. If this parameter is not specified, then a list of chi-squared results between concept_id_1 and other concepts is returned.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"adj_p-value":{"description":"Bonferonni adjusted p-value, adjusted with the total number of pairs of concepts in the dataset.","example":0.0314,"type":"number"},"chi_square":{"example":370026.1780081638,"type":"integer"},"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Instillation of therapeutic substance into bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":4021588,"type":"integer"},"dataset_id":{"example":3,"type":"integer"},"p-value":{"example":0.0314,"type":"number"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of concept pairs and chi-squared values."},"default":{"description":"Unexpected error"}},"summary":"Chi-square analysis on pairs of concepts","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/obsExpRatio":{"get":{"description":"Returns the natural logarithm of the ratio between the observed count and expected count. Expected count is calculated from the single concept frequencies and assuming independence between the concepts. Results are returned in descending order of ln_ratio.\n\nexpected_count = Count_1_and_2 * num_visits / (Count_1 * Count_2)\n\nln_ratio = ln(expected_count)\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Results for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"obsExpRatio","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}},{"description":"The confidence level used for calculating confidence intervals (default 0.99).","example":0.99,"in":"query","name":"confidence","required":false,"schema":{"type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Closed [transurethral] biopsy of bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2003784,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"expected_count":{"example":0.060838982345591645,"type":"integer"},"ln_ratio":{"example":7.561698473261244,"type":"integer"},"observed_count":{"example":117,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concepts and observed-expected frequency ratio."},"default":{"description":"Unexpected error"}},"summary":"Observed Count / Expected Count","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/relativeFrequency":{"get":{"description":"Calculates the relative frequency (i.e., conditional probability) between pairs of concepts. Results are returned in descending order of relative frequency. Note that due to the randomization of the counts, the calculated relative frequencies can exceed the limit of 1.0.\n\nRelative Frequency = Count_1_and_2 / Count_2\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"relativeFrequency","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict concept_id_2 (the base concept) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. 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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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query terms separated by comma (also \"+\" or whitespace). Does not support wildcard queries","type":"string"},"scopes":{"description":"a comma-separated list of fields as the search \"scopes\" (fields to search through for query term). The available \"fields\" that can be passed to the \"scopes\" parameter are listed in the **/metadata/fields** endpoint.string Default: \"scopes=_id\".","type":"string"}}}}}},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/QueryPOSTResult"}}},"description":"Query response objects with the \"hits\" property"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorResult"}}},"description":"A response indicating an improperly formatted query"}},"summary":"Make batch disease queries and return matching disease hits","tags":["query"]}}},"servers":[{"description":"Encrypted Production server","url":"https://biothings.ncats.io/clinical_risk_kp"},{"description":"Production server","url":"http://biothings.ncats.io/clinical_risk_kp"}],"tags":[{"name":"disease"},{"name":"drug"},{"name":"chemical_substance"},{"name":"phenotypic_feature"},{"name":"clinical_finding"},{"name":"association"},{"name":"annotation"},{"name":"query"},{"name":"translator"},{"name":"biothings"},{"name":"biothings_graph"}]}]} \ No newline at end of file +{"took":165,"total":134,"max_score":0.53398204,"hits":[{"_id":"04f42ae00c8e5991b98d0e681dbdc596","_meta":{"date_created":"2021-03-04T18:27:43.614727+00:00","last_updated":"2021-05-22T07:00:53.068357+00:00","url":"http://bdt-social.renci.org:8080/socio_environmental_exposures_api/v1/openapi.json","username":"lstillwe"},"_score":0.53398204,"info":{"contact":{"email":"lisa@renci.org","name":"Lisa Stillwell"},"description":"\nThis API returns data from the US Census Bureau American Community Survey (ACS) for a given spatial location of interest.\n\nThe API returns estimated values for socio-economic variables and related variables for small geographic areas that may act as indirect indicators of relevant health behaviors and outcomes. The data are collected by the US Census Bureau and are publicly available.\n\nThe variables are taken from the five-year summary data file of the US Census Bureau ACS, which is constructed from five annual waves of the bureau’s largest household survey. Approximately, two million households have completed the survey annually since calendar year 2005. (Five waves of the survey before 2005 sampled approximately 500,000 households each.) See https://www.census.gov/acs/www/methodology/sample-size-and-data-quality/sample-size/ for more detail. Microdata are available, but small-area data are only available in summary tabulations.\n\nValues are provided at the US Census Block Group level, representing the 2007-2011 and 2012-2016 calendar-year periods for locations within the continental USA. Block groups, the smallest geographic area for which sample survey data are released, generally contain 600 to 3,000 people (e.g., the size of a single city apartment building). Block Groups are aggregates of an average of 39 Blocks each, each of which is delineated by visible and invisible geographic boundaries. Block groups, in turn, are aggregated into Census Tracts, which generally have a population size between 1,200 and 8,000 people, with an optimum size of 4,000 people. Census Tracts aggregate into counties and counties into states. Metropolitan and micropolitan areas are aggregates of counties. See https://www2.census.gov/geo/pdfs/reference/geodiagram.pdf for further detail. Census geography, even Block Groups, may cross municipal lines and may include both urbanized and rural areas. Because population is a large factor in determining Census geography, some Block Groups may cover an extensive rural or wilderness area while others are quite compact. Census Block, Block Group, and Tract boundaries may change somewhat with each decennial Census, but remain stable in between Censuses.\n\nThe US Census Bureau is mandated to preserve the confidentiality of individual-level data. Therefore, data are often summarized, coarsened into categories, or suppressed by complex secret algorithms (especially, but not limited to household income data). In addition, because the variables of interest may only apply to a small subset of Block Group missing data can occur. In some versions of the data, calculated values are suppressed in Block Groups with less than 50 residents.\n\nStandard errors for the socio-demographic variables are provided. Because each of the values in the ACS data files are summary statistics calculated from sample survey data for each Block Group, different samples yield somewhat different values. Therefore, the Census Bureau generates 80 replicate values for selected variables. These provide the basis for the estimated standard errors of the estimates.\n\nThe currently available variables are listed here:\n\n **(2007-2011 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **EstResidentialDensity** - block group population density\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\n **(2012-2016 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **EstTotalPopulation_SE** - standard error of total population in block group\n - **EstResidentialDensity** - block group population density\n- **EstResidentialDensity_SE** - standard error of residential population density in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **MedianHouseholdIncome_SE** - standard error of median household income\n- **EstPropPersonsNoHealthIns** - proportion of the block group population with no health insurance - **EstPropPersonsNoHealthIns_SE** - standard error of proportion of the block group population with no health insurance\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropNonHispWhite_SE** - standard error of proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropPersons5PlusNoEnglish_SE** - standard error of proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdsNoAuto_SE** - standard error of proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdSSI_SE** - standard error of proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHouseholdPA_SE** - standard error of proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolMaxEducation_SE** - standard error of proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdNoSpouse_SE** - standard error of proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild_SE** - standard error of proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n- **EstPropFemaleHouseholdAnyChild_SE** - standard error of proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. 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These data sets provide 8-hour ozone daily maximums (in ppbV) and daily PM2.5 daily averages (in µg/m3). The US EPA provides estimates at the resolution of US Census tract centroids for the continental US. For a given location, the API returns the estimated exposure for the census tract the location occurs in.\n\nThe API provides exposure estimates for calendar years 2002-2016. Resolution for model estimates is 12 km-squared, provisioned at a resolution of the US Census track centroid. The US census tract definition is from the calendar year 2010 definition of the US Census Bureau, for all years of CMAQ data.\n\nThe data sets sources are derived from air quality monitoring data from the National Air Monitoring Stations and Local Air Monitoring Stations (NAMS/LAMS) and numerical output from the Models-3/Community Multiscale Air Quality (CMAQ - https://www.epa.gov/cmaq).\n\nThe API currently provides the following exposure variables:\n- O3: provides estimated O3 concentration levels. Estimated values are for daily maximums in units of ppbV.\n- PM2.5: provides estimated pm2.5 concentration levels. Estimated values are for daily averages in units of µg/m3.\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. For example, Raleigh, North Carolina is at latitude 35.7796 and longitude -78.6382.\n","license":{"name":"MIT","url":"http://opensource.org/licenses/MIT"},"title":"CMAQ Exposures API","version":"1.0.0-oas3","x-translator":{"component":"KP","team":["Exposures Provider"]}},"paths":{"/values":{"get":{"description":"Get estimated air pollutant exposure levels based on time and location\n","operationId":"get_values","parameters":[{"description":"start date of range, ie: MM-DD-YYYY","in":"query","name":"start_date","required":true,"schema":{"format":"date","type":"string"}},{"description":"end date of range, ie: MM-DD-YYYY","in":"query","name":"end_date","required":true,"schema":{"format":"date","type":"string"}},{"description":"latitude in decimal degrees format, ie: 35.7","in":"query","name":"latitude","required":true,"schema":{"type":"string"}},{"description":"longitude in decimal degrees format, ie: -80.33","in":"query","name":"longitude","required":true,"schema":{"type":"string"}},{"description":"timezone offset from UTC (utc, eastern, central, mountain, pacific) - default is utc","in":"query","name":"utc_offset","required":false,"schema":{"default":"utc","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"values":{"items":{"$ref":"#/components/schemas/inline_response_200_values"},"type":"array"}},"type":"object"}}},"description":"OK"},"400":{"description":"Invalid parameter"},"404":{"description":"No values found"},"500":{"description":"Server error"}},"summary":"Retrieves air pollutant exposure levels","x-openapi-router-controller":"swagger_server.controllers.default_controller"}}},"servers":[{"url":"/cmaq_exposures_api/v1"}],"tags":[{"name":"translator"}]},{"_id":"d76f7d70f98b3ef124df0553d70490f7","_meta":{"date_created":"2021-05-08T22:19:34.401242+00:00","last_updated":"2021-05-22T07:01:37.932030+00:00","url":"https://cam-kp-api-dev.renci.org/docs/docs.yaml","username":"jdr0887"},"_score":0.53398204,"info":{"contact":{"email":"balhoff@renci.org","name":"Jim Balhoff"},"description":"TRAPI interface to database of Causal Activity Models","license":{"name":"MIT License","url":"https://opensource.org/licenses/MIT"},"termsOfService":"https://opensource.org/licenses/MIT","title":"CAM-KP API","version":"0.1","x-translator":{"component":"KP","team":["Exposures Provider"]}},"paths":{"/query":{"post":{"operationId":"postQuery","parameters":[{"in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e0":{"object":"n0","predicates":["biolink:has_participant"],"subject":"n1"}},"nodes":{"n0":{"categories":["biolink:Gene","biolink:GeneOrGeneProduct"]},"n1":{"categories":["biolink:BiologicalProcess"]}}}}},"schema":{"$ref":"#/components/schemas/TRAPIQuery"}}},"required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/TRAPIResponse"}}},"description":""},"default":{"content":{"text/plain":{"schema":{"type":"string"}}},"description":""}},"summary":"Submit a TRAPI question graph and retrieve matching solutions"}},"/meta_knowledge_graph":{"get":{"operationId":"getMeta_knowledge_graph","responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":""},"default":{"content":{"text/plain":{"schema":{"type":"string"}}},"description":""}},"summary":"Get MetaKnowledgeGraph used at this service"}}},"servers":[{"url":"https://cam-kp-api-dev.renci.org"}],"tags":[{"name":"translator"}]},{"_id":"1a41e3cd15f2b3bfa21c99900bfa1720","_meta":{"date_created":"2021-04-07T14:48:12.706214+00:00","last_updated":"2021-05-22T07:01:27.465172+00:00","url":"https://trapi.monarchinitiative.org/openapi.json","username":"kshefchek"},"_score":0.53398204,"info":{"contact":{"email":"shefchek@oregonstate.edu","name":"Kent Shefchek","x-id":"https://github.com/kshefchek","x-role":"responsible developer"},"description":"The SRI reference KG aims to aggregate knowledge sources across translator using KGX. 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[ICEES Overview page](https://researchsoftwareinstitute.github.io/data-translator/apps/icees)\n
[documentation](https://github.com/NCATS-Tangerine/icees-api/tree/master/docs) \n
[source](https://github.com/NCATS-Tangerine/icees-api/tree/master/) \n
[ICEES API example queries](https://github.com/NCATS-Tangerine/icees-api/tree/master/#examples)\n
dictionary for versioning of tables\n
\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
versiontable content
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2.0.0cdw in FHIR format, acs, nearest road, and cmaq from 2010
3.0.0cdw in FHIR format, acs, nearest road, cmaq, and EPR from 2010 to 2016
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[documentation](https://github.com/NCATS-Tangerine/icees-api/tree/master/docs) \n
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\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
versiontable content
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2.0.0cdw in FHIR format, acs, nearest road, and cmaq from 2010
3.0.0cdw in FHIR format, acs, nearest road, cmaq, and EPR from 2010 to 2016
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The value format should match the regular expression UP[0-9]{9}."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get gene centric proteins by proteome UPID is deprecated, please use new /genecentric?upid= endpoint","tags":["proteomes"]}},"/proteomes/proteins/{upid}":{"get":{"description":"","operationId":"getProteinsByUpid","parameters":[{"description":"UniProt Proteome UPID","in":"path","name":"upid","required":true,"schema":{"type":"string"}},{"description":"Reviewed(true) or not Reviewed (false)","in":"query","name":"reviewed","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Proteome"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Proteome"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid upid parameter. 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Values can be true or false.","in":"query","name":"unique","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"text/x-gff":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Search proteomics peptides in UniProt","tags":["proteomics"]}},"/proteomics/{accession}":{"get":{"description":"","operationId":"getProteomicsByAccession","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. 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Comma separated values accepted up to 20.","in":"query","name":"ipr","required":false,"schema":{"type":"string"}},{"description":"Search by signature database type, e.g. SMART, SUPFAM, Pfam, PIRSF, PROSITE, etc. Comma separated values accepted up to 20.","in":"query","name":"signaturetype","required":false,"schema":{"type":"string"}},{"description":"Search by signature database id, e.g. SM00044, SSF55073, PF00211, PIRSF039050, PS00452, etc. Comma separated values accepted up to 20.","in":"query","name":"signatureid","required":false,"schema":{"type":"string"}},{"description":"UniProt proteome UPID(s). Comma separated values accepted up to 100.","in":"query","name":"upid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."}},"summary":"Search UniParc entries","tags":["uniparc"]}},"/uniparc/accession/{accession}":{"get":{"description":"","operationId":"getUniParcEntryByUniprotAccession","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. The values's format should be a valid UniProtKB accession."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entry only by UniProt accession","tags":["uniparc"]}},"/uniparc/bestguess":{"get":{"description":"For a given user input (request parameters), Best Guess returns the UniParcEntry with a cross-reference to the longest active UniProtKB sequence (preferably from Swiss-Prot and if not then TrEMBL). It also returns the sequence and related information. If it finds more than one longest active UniProtKB sequence it returns 400 (Bad Request) error response with the list of cross references found.","operationId":"getUniParcBestGuess","parameters":[{"description":"UniParc ID (UPI). Comma separated values accepted up to 100","in":"query","name":"upi","required":false,"schema":{"type":"string"}},{"description":"UniProt accession(s). Comma separated values accepted up to 100.","in":"query","name":"accession","required":false,"schema":{"type":"string"}},{"description":"All UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted up to 100.","in":"query","name":"dbid","required":false,"schema":{"type":"string"}},{"description":"UniProt gene name. Comma separated values accepted up to 20.","in":"query","name":"gene","required":false,"schema":{"type":"string"}},{"description":"Organism taxon ID. 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AAC02967 (EMBL) or XP_006524055 (RefSeq).","in":"path","name":"dbid","required":true,"schema":{"type":"string"}},{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). 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Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entries by all UniParc cross reference accessions","tags":["uniparc"]}},"/uniparc/proteome/{upid}":{"get":{"description":"","operationId":"getByProteomeId","parameters":[{"description":"UniProt Proteome UPID","in":"path","name":"upid","required":true,"schema":{"type":"string"}},{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entries by Proteome UPID","tags":["uniparc"]}},"/uniparc/sequence":{"post":{"description":"","operationId":"getBySequence","parameters":[{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. 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AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid upid parameter. The value format should match the regular expression UPI[\\w]{10}."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entry by UniParc UPI","tags":["uniparc"]}},"/variation":{"get":{"description":"Among the available response content types, PEFF format (PSI Extended FASTA Format from the Human Proteome Organisation - Proteomics Standards Initiative, HUPO-PSI) is provided with only variants reported in the output.","operationId":"searchVariation","parameters":[{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. 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Any valid amino acid range position within the length of the protein sequence such as 10-60 (start position to end position)","in":"query","name":"location","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"text/x-gff":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get natural variants in UniProt by NIH-NCBI SNP database identifier","tags":["variation"]}},"/variation/hgvs/{hgvs}":{"get":{"description":"","operationId":"searchByHGVS","parameters":[{"description":"Human Genome Variation Society representation, e.g. NC_000017.11:g.58219213C>T","in":"path","name":"hgvs","required":true,"schema":{"type":"string"}},{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. 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Any valid amino acid range position within the length of the protein sequence such as 10-60 (start position to end position)","in":"query","name":"location","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"text/x-gff":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get natural variants in UniProt by HGVS expression","tags":["variation"]}},"/variation/{accession}":{"get":{"description":"","operationId":"getVariation","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}},{"description":"Filter by the sourceType for variants: uniprot, large scale study and mixed. 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Count and frequency data were derived from the [Columbia University Medical Center's](http://www.cumc.columbia.edu/) [OHDSI](https://www.ohdsi.org/) database including inpatient. Counts are the number of inpatient visits associated with the concept, e.g., diagnosed with a condition, exposed to a drug, or a procedure was performed. Frequencies are the number of unique visits associated with the concept divided by the total number of visits in the dataset, i.e., prevalence in the electronic health records. To protect patient privacy, all concepts and pairs of concepts where the count <= 10 were excluded, and counts were randomized by the Poisson distribution. \n\nDatasets from three primary cohorts are available: \n1) COVID-19: Hospitalized patients aged 18 or older with a COVID-19 related condition diagnosis and/or a confirmed positive COVID-19 test during their hospitalization period or within the prior 21 days. Date range: March 1, 2020 to September 1, 2020. This cohort is also further stratified by sex (male and female) and age (adult: 18-64, senior: 65+).\n2) General inpatient: All hospitalized patients aged 18 or older. Date range: January 1, 2014 to December 31, 2019.\n3) Influenza: Hospitalized patients aged 18 or older who had at least one occurrence of influenza conditions or pre-coordinated positive measurements or positive influenza testing in the prior 21 days or during their hospitalization period. Date range: January 1, 2014 to December 31, 2019.\n\nBoth hierarchical and non-hierarchical datasets are available for each cohort. In the hierarchical datasets, the counts for each concept include the visits from all descendant concepts. For example, the count for ibuprofen (ID 1177480) includes visits with Ibuprofen 600 MG Oral Tablet (ID 19019073), Ibuprofen 400 MG Oral Tablet (ID 19019072), Ibuprofen 20 MG/ML Oral Suspension (ID 19019050), etc. \n\nClinical concepts (e.g., conditions, procedures, drugs) are coded by their standard concept ID in the [OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki). API methods are provided to map to/from other vocabularies supported in OMOP and other ontologies using the EMBL-EBI Ontology Xref Service (OxO). \n\n\nThe following resources are available through this API: \n\n\n1. Metadata: Metadata on the COHD database, including dataset descriptions, number of concepts, etc. \n\n\n2. OMOP: Access to the common vocabulary for name and concept identifier mapping\n\n\n3. Clinical Frequencies: Access to the counts and frequencies of conditions, procedures, and drug exposures, and the associations between them. Frequency was determined as the number of visits with the code(s) / total number of visits. \n\n\n4. Concept Associations: Inferred associations between concepts using chi-square analysis, ratio between observed to expected frequency, and relative frequency. \n\n\nA [Python notebook](https://github.com/WengLab-InformaticsResearch/cohd_api/blob/master/notebooks/COHD_API_Example.ipynb) demonstrates simple examples of how to use the COHD API.\n\n\nCOHD was developed at the [Columbia University Department of Biomedical Informatics](https://www.dbmi.columbia.edu/) as a collaboration between the [Weng Lab](http://people.dbmi.columbia.edu/~chw7007/), [Tatonetti Lab](http://tatonettilab.org/), and the [NCATS Biomedical Data Translator](https://ncats.nih.gov/translator) program (TReK Team). 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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":{"description":"Attempts 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":{"description":"Attempts 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":0.000005585247351056813,"type":"integer"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2008271,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequency of a pair of concepts","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id. Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"q","required":true,"schema":{"type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":19041324,"type":"integer"},"associated_concept_name":{"example":"Acetaminophen 325 MG Oral Tablet [Tylenol]","type":"string"},"associated_domain_id":{"example":"Drug","type":"string"},"concept_count":{"example":277,"type":"integer"},"concept_frequency":{"example":0.0001547113516242737,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptDomainFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id restricted by domain of the associated concept_id. Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptDomainFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id","required":true,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc. See /metadata/domainCounts for a list of valid domain IDs.","example":"Procedure","in":"query","name":"domain","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":2211361,"type":"integer"},"associated_concept_name":{"example":"Radiologic examination, chest, 2 views, frontal and lateral","type":"string"},"associated_domain_id":{"example":"Procedure","type":"string"},"concept_count":{"example":257,"type":"integer"},"concept_frequency":{"example":0.00014354085692216007,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/mostFrequentConcepts":{"get":{"description":"Retrieves the most frequent concepts.","operationId":"mostFrequentConcepts","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The number of concepts to retreieve, e.g., 100. 0 or unspecified will return all matching concepts.","example":100,"in":"query","name":"q","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The domain_id to restrict to, e.g., \"Condition\", \"Drug\", \"Procedure\". See /metadata/domainCounts for a list of valid domain IDs.","example":"Condition","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"(Optional) The vocabulary_id(s) to restrict to, e.g., \"SNOMED\", \"MedDRA\", \"RxNorm\", \"ATC\" etc. Comma separated to include multiple vocabularies, e.g., \"SNOMED,MedDRA\". Default: unrestricted","example":null,"in":"query","name":"vocabulary_id","required":false,"schema":{"type":"string"}},{"description":"(Optional) The concept_class_id(s) to restrict to. concept_class_ids are specific to each vocabulary, e.g.,: [ATC](https://en.wikipedia.org/wiki/Anatomical_Therapeutic_Chemical_Classification_System) {ATC 1st, ATC 2nd, ATC 3rd, ATC 4th, ATC 5th}; [MedDRA](https://en.wikipedia.org/wiki/MedDRA) {PT, HLT, HLGT, SOC}; [RxNorm](https://www.nlm.nih.gov/research/umls/rxnorm/docs/2015/appendix5.html) {Ingredient, Clinical Drug Form, Clinical Drug Comp, Clinical Drug}. Comma separated to include multiple concept_class_ids, e.g., \"PT,HLT\". Default: unrestricted","example":null,"in":"query","name":"concept_class_id","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_class_id":{"example":"Clinical Finding","type":"string"},"concept_count":{"example":233790,"type":"integer"},"concept_frequency":{"example":0.1305774978203572,"type":"integer"},"concept_id":{"example":320128,"type":"integer"},"concept_name":{"example":"Essential hypertension","type":"string"},"dataset_id":{"example":1,"type":"integer"},"domain_id":{"example":"Condition","type":"string"},"vocabulary_id":{"example":"SNOMED","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of most frequent concepts."},"default":{"description":"Unexpected error"}},"summary":"Most frequent concepts [by domain]","tags":["Clinical Frequencies"]}},"/association/chiSquare":{"get":{"description":"Returns the chi-square statistic and p-value between pairs of concepts. Results are returned in descending order of the chi-square statistic. Note that due to large sample sizes, the chi-square can become very large. \n\nThe expected frequencies for the chi-square analysis are calculated based on the single concept frequencies and assuming independence between concepts. P-value is calculated with 1 DOF. \n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"chiSquare","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If this parameter is specified, then the chi-square between concept_id_1 and concept_id_2 is returned. If this parameter is not specified, then a list of chi-squared results between concept_id_1 and other concepts is returned.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"adj_p-value":{"description":"Bonferonni adjusted p-value, adjusted with the total number of pairs of concepts in the dataset.","example":0.0314,"type":"number"},"chi_square":{"example":370026.1780081638,"type":"integer"},"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Instillation of therapeutic substance into bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":4021588,"type":"integer"},"dataset_id":{"example":3,"type":"integer"},"p-value":{"example":0.0314,"type":"number"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of concept pairs and chi-squared values."},"default":{"description":"Unexpected error"}},"summary":"Chi-square analysis on pairs of concepts","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/obsExpRatio":{"get":{"description":"Returns the natural logarithm of the ratio between the observed count and expected count. Expected count is calculated from the single concept frequencies and assuming independence between the concepts. Results are returned in descending order of ln_ratio.\n\nexpected_count = Count_1_and_2 * num_visits / (Count_1 * Count_2)\n\nln_ratio = ln(expected_count)\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Results for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"obsExpRatio","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}},{"description":"The confidence level used for calculating confidence intervals (default 0.99).","example":0.99,"in":"query","name":"confidence","required":false,"schema":{"type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Closed [transurethral] biopsy of bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2003784,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"expected_count":{"example":0.060838982345591645,"type":"integer"},"ln_ratio":{"example":7.561698473261244,"type":"integer"},"observed_count":{"example":117,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concepts and observed-expected frequency ratio."},"default":{"description":"Unexpected error"}},"summary":"Observed Count / Expected Count","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/relativeFrequency":{"get":{"description":"Calculates the relative frequency (i.e., conditional probability) between pairs of concepts. Results are returned in descending order of relative frequency. Note that due to the randomization of the counts, the calculated relative frequencies can exceed the limit of 1.0.\n\nRelative Frequency = Count_1_and_2 / Count_2\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"relativeFrequency","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict concept_id_2 (the base concept) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}},{"description":"The confidence level used for calculating confidence intervals (default 0.99).","example":0.99,"in":"query","name":"confidence","required":false,"schema":{"type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_2_count":{"example":82,"type":"integer"},"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Radical cystectomy","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2003805,"type":"integer"},"concept_pair_count":{"example":29,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"relative_frequency":{"example":0.35365853658536583,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concepts and relative frequency."},"default":{"description":"Unexpected error"}},"summary":"Relative frequency between pairs of concepts","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/predicates":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"additionalProperties":{"description":"Array of predicates","items":{"type":"string"},"type":"array"},"description":"Target map","type":"object"},"description":"Source map","example":{"biolink:ChemicalSubstance":{"biolink:Gene":["biolink:directly_interacts_with","biolink:decreases_activity_of"]}},"type":"object"}}},"description":"Predicates by source and target"}},"summary":"Get supported relationships by source and target","tags":["translator","trapi"]}},"/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.\n \nFor the subject node, the id must be specified (category is ignored).\n \nFor the object node, both the id and category are optional. If id is specified for the object node, then the association between the two identified concepts is returned. If id is not specified and category is specified, the associations between the subject node and all concepts with the specified category are returned. If neither are specified, then the associations between the subject node and all concepts are returned.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.\nAdditional behavior options can be controlled using the optional parameters in query_options.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"id\": \"MONDO:0021113\",\n \"category\": \"biolink:Disease\"\n },\n \"n01\": {\n \"category\": \"biolink:Procedure\"\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicate\": \"biolink:correlated_with\",\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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)."},"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","tags":["translator","trapi"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false}],"x-swagger-router-controller":"swagger_server.controllers.query_controller"}},"/0.9.3/query":{"post":{"description":"This endpoint is temporarily provided to support TRAPI 0.9.3 queries\nQuery 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.\nFor the source node, the curie must be specified (type is ignored).\nFor the target node, both the curie and type are optional. If curie is specified for the target node, then the association between the two identified concepts is returned. If curie is not specified and type is specified, the associations between the source node and all concepts with the specified type are returned. If neither are specified, then the associations between the source node and all concepts are returned.\nCOHD will attempt to map the CURIE to an OMOP concept and the node type to an OMOP domain.","operationId":"query093","requestBody":{"content":{"application/json":{"example":"{\n \"max_results\": 50,\n \"message\": {\n \"query_graph\": {\n \"nodes\": [\n {\n \"id\": \"n00\",\n \"curie\": \"MONDO:0021113\",\n \"type\": \"biolink:Disease\"\n },\n {\n \"id\": \"n01\",\n \"type\": \"biolink:Procedure\"\n }\n ],\n \"edges\": [\n {\n \"id\": \"e00\",\n \"type\": \"biolink:correlated_with\",\n \"source_id\": \"n00\",\n \"target_id\": \"n01\"\n }\n ]\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\n \"dataset_id\": 3,\n \"confidence_interval\": 0.99,\n \"min_cooccurrence\": 50,\n \"threshold\": 0.5,\n \"local_oxo\": true,\n \"ontology_targets\": {\n \"biolink:Disease\": [\"ICD9\", \"SNOMEDCT\", \"DOID\"],\n \"biolink:Drug\": [\"RxNorm\"],\n \"biolink:Procedure\": [\"ICD10PCS\", \"SNOMEDCT\"],\n \"_DEFAULT\": []\n },\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":{"$ref":"#/components/schemas/Message"}}},"description":"successful operation"},"400":{"description":"Invalid status value"}},"summary":"Query COHD following NCATS Translator Reasoner Standard API version 0.9.3","tags":["translator","trapi"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false}],"x-swagger-router-controller":"swagger_server.controllers.query_controller"}},"/translator/biolink_to_omop":{"post":{"description":"Map Biolink CURIEs to OMOP concepts","operationId":"biolink_to_omop","requestBody":{"content":{"application/json":{"example":"{\n \"curies\": [\n \"HP:0002907\",\n \"MONDO:0001187\"\n ]\n}","schema":{"$ref":"#/components/schemas/CurieList"}}},"description":"List of CURIEs","required":true},"responses":{"200":{"content":{"application/json":{"example":"{\n \"MONDO:0001187\": {\n \"distance\": 2,\n \"omop_concept_id\": 197508,\n \"omop_concept_name\": \"Malignant tumor of urinary bladder\"\n }\n}","schema":{"additionalProperties":{"description":"Mapping from OMOP concept to Biolink","properties":{"distance":{"description":"mapping distance","type":"integer"},"omop_concept_id":{"type":"integer"},"omop_concept_name":{"type":"string"}},"type":"object"}}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from Biolink to OMOP","tags":["translator"]}},"/translator/omop_to_biolink":{"post":{"description":"Map OMOP concepts to normalized Biolink nodes using SRI Node Normalizer.","operationId":"omop_to_biolink","requestBody":{"content":{"application/json":{"example":"{\n \"omop_ids\": [\n 78472,\n 197508\n ]\n}","schema":{"$ref":"#/components/schemas/OmopList"}}},"description":"List of OMOP IDs","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"type":"object"},"example":"{\n \"197508\": {\n \"equivalent_identifiers\": [\n {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n {\n \"identifier\": \"DOID:11054\"\n },\n {\n \"identifier\": \"OMIM:109800\"\n },\n {\n \"identifier\": \"UMLS:C0005684\"\n },\n {\n \"identifier\": \"NCIT:C9334\"\n },\n {\n \"identifier\": \"SNOMEDCT:399326009\"\n }\n ],\n \"id\": {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n \"type\": [\n \"biolink:Disease\",\n \"biolink:DiseaseOrPhenotypicFeature\",\n \"biolink:BiologicalEntity\",\n \"biolink:NamedThing\"\n ]\n }\n}","type":"object"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized. Mapping from OMOP concept to Biolink normalized nodes. See [SRI Node Normalizer](https://nodenormalization-sri.renci.org/docs#/) for response format"},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from OMOP to Biolink","tags":["translator"]}}},"servers":[{"url":"https://covid.cohd.io/api/"}],"tags":[{"description":"COHD metadata","name":"Metadata"},{"description":"OMOP Common Data Model concepts","name":"OMOP"},{"description":"Clinical frequency data","name":"Clinical Frequencies"},{"description":"Estimated association between concepts","name":"Concept Associations"},{"description":"Concept-age distributions, concept-pair delta distributions, and temporal analyses","name":"Temporal Clinical Data"},{"description":"NCATS Biomedical Data Translator APIs","name":"translator"},{"description":"Implements the NCATS Translator Reasoner API 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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)","version":"4.0.0","x-accessRestriction":"none","x-implementationLanguage":"Python","x-translator":{"biolink-version":"1.8.2","component":"KP","externalDocs":{"description":"The values for component and team are restricted according to this external JSON schema. 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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":{"description":"Attempts 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. 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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":{"description":"Attempts 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. 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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. 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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":0.000005585247351056813,"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. 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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. \n \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"]}},"/predicates":{"get":{"deprecated":true,"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"additionalProperties":{"description":"Array of predicates","items":{"type":"string"},"type":"array"},"description":"Target map","type":"object"},"description":"Source map","example":{"biolink:ChemicalSubstance":{"biolink:Gene":["biolink:directly_interacts_with","biolink:decreases_activity_of"]}},"type":"object"}}},"description":"Predicates by source and target"}},"summary":"Get supported relationships by source and target","tags":["predicates"]}},"/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 \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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)."},"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","tags":["query"]}},"/1.0.0/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.\nFor the subject node, the id must be specified (category is ignored).\nFor the object node, both the id and category are optional. If id is specified for the object node, then the association between the two identified concepts is returned. If id is not specified and category is specified, the associations between the subject node and all concepts with the specified category are returned. If neither are specified, then the associations between the subject node and all concepts are returned.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.\nAdditional behavior options can be controlled using the optional parameters in query_options.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"id\": \"DOID:9053\",\n \"category\": \"biolink:Disease\"\n },\n \"n01\": {\n \"category\": \"biolink:Procedure\"\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicate\": \"biolink:correlated_with\",\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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)."},"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 TRAPI 1.0","tags":["translator"]}},"/translator/biolink_to_omop":{"post":{"description":"Map Biolink CURIEs to OMOP concepts","operationId":"biolink_to_omop","requestBody":{"content":{"application/json":{"example":"{\n \"curies\": [\n \"HP:0002907\",\n \"MONDO:0001187\"\n ]\n}","schema":{"$ref":"#/components/schemas/CurieList"}}},"description":"List of CURIEs","required":true},"responses":{"200":{"content":{"application/json":{"example":"{\n \"MONDO:0001187\": {\n \"distance\": 2,\n \"omop_concept_id\": 197508,\n \"omop_concept_name\": \"Malignant tumor of urinary bladder\"\n }\n}","schema":{"additionalProperties":{"description":"Mapping from OMOP concept to Biolink","properties":{"distance":{"description":"mapping distance","type":"integer"},"omop_concept_id":{"type":"integer"},"omop_concept_name":{"type":"string"}},"type":"object"}}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from Biolink to OMOP","tags":["translator"]}},"/translator/omop_to_biolink":{"post":{"description":"Map OMOP concepts to normalized Biolink nodes using SRI Node Normalizer.","operationId":"omop_to_biolink","requestBody":{"content":{"application/json":{"example":"{\n \"omop_ids\": [\n 78472,\n 197508\n ]\n}","schema":{"$ref":"#/components/schemas/OmopList"}}},"description":"List of OMOP IDs","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"type":"object"},"example":"{\n \"197508\": {\n \"equivalent_identifiers\": [\n {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n {\n \"identifier\": \"DOID:11054\"\n },\n {\n \"identifier\": \"OMIM:109800\"\n },\n {\n \"identifier\": \"UMLS:C0005684\"\n },\n {\n \"identifier\": \"NCIT:C9334\"\n },\n {\n \"identifier\": \"SNOMEDCT:399326009\"\n }\n ],\n \"id\": {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n \"type\": [\n \"biolink:Disease\",\n \"biolink:DiseaseOrPhenotypicFeature\",\n \"biolink:BiologicalEntity\",\n \"biolink:NamedThing\"\n ]\n }\n}","type":"object"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized. Mapping from OMOP concept to Biolink normalized nodes. See [SRI Node Normalizer](https://nodenormalization-sri.renci.org/docs#/) for response format"},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from OMOP to Biolink","tags":["translator"]}}},"servers":[{"url":"https://cohd.io/api/"}],"tags":[{"description":"COHD metadata","name":"Metadata"},{"description":"OMOP Common Data Model concepts","name":"OMOP"},{"description":"Clinical frequency data","name":"Clinical Frequencies"},{"description":"Estimated association between concepts","name":"Concept Associations"},{"description":"Concept-age distributions, concept-pair delta distributions, and temporal analyses","name":"Temporal Clinical Data"},{"description":"Get supported relationships by source and target","name":"predicates"},{"description":"Query reasoner using a predefined question type","name":"query"},{"description":"Required for SmartAPI validation of x-translator","name":"translator"},{"description":"Required for SmartAPI validation of x-trapi","name":"trapi"}]}]} \ No newline at end of file From e3cba57d9a784a06dfd677ad506da24fd0ac9c9a Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Sat, 22 May 2021 15:06:49 -0700 Subject: [PATCH 40/75] build: :arrow_up: upgrade smartapi-kg to 3.8.1 --- package-lock.json | 295 +++++++++++++++++++++++++++------------------- package.json | 2 +- 2 files changed, 178 insertions(+), 119 deletions(-) diff --git a/package-lock.json b/package-lock.json index 9678f85b..9c5f53df 100644 --- a/package-lock.json +++ b/package-lock.json @@ -6,11 +6,11 @@ "packages": { "": { "name": "@biothings-explorer/single-hop-app", - "version": "2.5.0", + "version": "2.7.0", "license": "ISC", "dependencies": { "@biothings-explorer/query_graph_handler": "^1.16.1", - "@biothings-explorer/smartapi-kg": "^3.8.0", + "@biothings-explorer/smartapi-kg": "file:../smartapi-kg.js", "axios": "^0.21.1", "biothings-explorer-graphql": "2.1.1", "body-parser": "^1.19.0", @@ -44,6 +44,56 @@ "supertest": "^6.1.3" } }, + "../smartapi-kg.js": { + "version": "3.8.0", + "license": "ISC", + "dependencies": { + "@babel/runtime": "^7.13.10", + "@commitlint/cli": "^11.0.0", + "@commitlint/config-conventional": "^11.0.0", + "@types/jest": "^26.0.20", + "@types/load-json-file": "^5.1.0", + "@types/lodash": "^4.14.168", + "axios": "^0.21.1", + "camelcase": "^6.2.0", + "core-js": "^3.9.1", + "debug": "^4.3.1", + "husky": "^4.3.8", + "jsnetworkx": "^0.3.4", + "lodash": "^4.17.21" + }, + "devDependencies": { + "@babel/cli": "^7.13.10", + "@babel/core": "^7.13.10", + "@babel/plugin-proposal-class-properties": "^7.13.0", + "@babel/plugin-proposal-object-rest-spread": "^7.13.8", + "@babel/plugin-transform-runtime": "^7.13.10", + "@babel/preset-env": "^7.13.10", + "@babel/preset-typescript": "^7.13.0", + "@types/axios": "^0.14.0", + "@types/debug": "^4.1.5", + "@types/express": "^4.17.11", + "@types/node": "^14.14.22", + "babel-loader": "^8.2.2", + "coveralls": "^3.1.0", + "jest": "^26.6.3", + "jsdoc": "^3.6.6", + "nodemon": "^2.0.7", + "path-browserify": "^1.0.1", + "prettier": "^2.2.1", + "readme-md-generator": "^1.0.0", + "rollup": "^2.39.1", + "standard-version": "^9.1.0", + "ts-jest": "^26.5.3", + "ts-node": "^9.1.1", + "tslint": "^6.1.3", + "tslint-config-prettier": "^1.18.0", + "typescript": "^4.1.3", + "uglify-js": "^3.12.5", + "webpack": "^5.24.4", + "webpack-cli": "^4.5.0" + } + }, "node_modules/@apidevtools/json-schema-ref-parser": { "version": "9.0.7", "resolved": "https://registry.npmjs.org/@apidevtools/json-schema-ref-parser/-/json-schema-ref-parser-9.0.7.tgz", @@ -581,39 +631,8 @@ "integrity": "sha512-6FlzubTLZG3J2a/NVCAleEhjzq5oxgHyaCU9yYXvcLsvoVaHJq/s5xXI6/XXP6tz7R9xAOtHnSO/tXtF3WRTlA==" }, "node_modules/@biothings-explorer/smartapi-kg": { - "version": "3.8.0", - "resolved": "https://registry.npmjs.org/@biothings-explorer/smartapi-kg/-/smartapi-kg-3.8.0.tgz", - "integrity": 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"https://registry.npmjs.org/@types/istanbul-reports/-/istanbul-reports-3.0.0.tgz", "integrity": "sha512-nwKNbvnwJ2/mndE9ItP/zc2TCzw6uuodnF4EHYWD+gCQDVBuRQL5UzbZD0/ezy1iKsFU2ZQiDqg4M9dN4+wZgA==", + "dev": true, "dependencies": { "@types/istanbul-lib-report": "*" } }, - "node_modules/@types/jest": { - "version": "26.0.22", - "resolved": "https://registry.npmjs.org/@types/jest/-/jest-26.0.22.tgz", - "integrity": "sha512-eeWwWjlqxvBxc4oQdkueW5OF/gtfSceKk4OnOAGlUSwS/liBRtZppbJuz1YkgbrbfGOoeBHun9fOvXnjNwrSOw==", - "dependencies": { - "jest-diff": "^26.0.0", - "pretty-format": "^26.0.0" - } - }, "node_modules/@types/keygrip": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/@types/keygrip/-/keygrip-1.0.2.tgz", @@ -1905,19 +1924,6 @@ "@types/koa": "*" } }, - "node_modules/@types/load-json-file": { - "version": "5.1.0", - "resolved": "https://registry.npmjs.org/@types/load-json-file/-/load-json-file-5.1.0.tgz", - "integrity": 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"integrity": "sha512-FA/BWv8t8ZWJ+gEOnLLd8ygxH/2UFbAvgEonyfN6yWGLKc7zVjbpl2Y4CTjid9h2RfgPP6SEt6uHwEOply00yw==" + "integrity": "sha512-FA/BWv8t8ZWJ+gEOnLLd8ygxH/2UFbAvgEonyfN6yWGLKc7zVjbpl2Y4CTjid9h2RfgPP6SEt6uHwEOply00yw==", + "dev": true }, "node_modules/@wry/equality": { "version": "0.1.11", @@ -5708,6 +5716,7 @@ "version": "26.6.2", "resolved": "https://registry.npmjs.org/diff-sequences/-/diff-sequences-26.6.2.tgz", "integrity": "sha512-Mv/TDa3nZ9sbc5soK+OoA74BsS3mL37yixCvUAQkiuA4Wz6YtwP/K47n2rv2ovzHZvoiQeA5FTQOschKkEwB0Q==", + "dev": true, "engines": { "node": ">= 10.14.2" } @@ -8302,7 +8311,8 @@ "node_modules/is-utf8": { "version": "0.2.1", "resolved": "https://registry.npmjs.org/is-utf8/-/is-utf8-0.2.1.tgz", - "integrity": "sha1-Sw2hRCEE0bM2NA6AeX6GXPOffXI=" + "integrity": "sha1-Sw2hRCEE0bM2NA6AeX6GXPOffXI=", + "dev": true }, "node_modules/is-valid-path": { "version": "0.1.1", @@ -8708,6 +8718,7 @@ "version": "26.6.2", "resolved": 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"extraneous": true, "inBundle": true, "license": "MIT" }, "node_modules/npm/node_modules/lodash._cacheindexof": { "version": "3.0.2", + "extraneous": true, "inBundle": true, "license": "MIT" }, "node_modules/npm/node_modules/lodash._createcache": { "version": "3.1.2", + "extraneous": true, "inBundle": true, "license": "MIT", "dependencies": { @@ -13607,6 +13631,7 @@ }, "node_modules/npm/node_modules/lodash._getnative": { "version": "3.9.1", + "extraneous": true, "inBundle": true, "license": "MIT" }, @@ -13622,6 +13647,7 @@ }, "node_modules/npm/node_modules/lodash.restparam": { "version": "3.6.1", + "extraneous": true, "inBundle": true, "license": "MIT" }, @@ -16128,6 +16154,7 @@ "version": "2.3.0", "resolved": "https://registry.npmjs.org/pify/-/pify-2.3.0.tgz", "integrity": "sha1-7RQaasBDqEnqWISY59yosVMw6Qw=", + "dev": true, "engines": { "node": ">=0.10.0" } @@ -16136,6 +16163,7 @@ "version": "2.0.4", "resolved": "https://registry.npmjs.org/pinkie/-/pinkie-2.0.4.tgz", "integrity": 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"version": "3.0.2", - "bundled": true + "bundled": true, + "extraneous": true }, "lodash._createcache": { "version": "3.1.2", "bundled": true, + "extraneous": true, "requires": { "lodash._getnative": "^3.0.0" } @@ -30246,7 +30296,8 @@ }, "lodash._getnative": { "version": "3.9.1", - "bundled": true + "bundled": true, + "extraneous": true }, "lodash._root": { "version": "3.0.1", @@ -30258,7 +30309,8 @@ }, "lodash.restparam": { "version": "3.6.1", - "bundled": true + "bundled": true, + "extraneous": true }, "lodash.union": { "version": "4.6.0", @@ -32178,17 +32230,20 @@ "pify": { "version": "2.3.0", "resolved": "https://registry.npmjs.org/pify/-/pify-2.3.0.tgz", - "integrity": "sha1-7RQaasBDqEnqWISY59yosVMw6Qw=" + "integrity": "sha1-7RQaasBDqEnqWISY59yosVMw6Qw=", + "dev": true }, "pinkie": { "version": "2.0.4", "resolved": "https://registry.npmjs.org/pinkie/-/pinkie-2.0.4.tgz", - "integrity": "sha1-clVrgM+g1IqXToDnckjoDtT3+HA=" + "integrity": "sha1-clVrgM+g1IqXToDnckjoDtT3+HA=", + "dev": true }, "pinkie-promise": { "version": "2.0.1", "resolved": "https://registry.npmjs.org/pinkie-promise/-/pinkie-promise-2.0.1.tgz", "integrity": "sha1-ITXW36ejWMBprJsXh3YogihFD/o=", + "dev": true, "requires": { "pinkie": "^2.0.0" } @@ -32247,6 +32302,7 @@ "version": "26.6.2", "resolved": "https://registry.npmjs.org/pretty-format/-/pretty-format-26.6.2.tgz", "integrity": "sha512-7AeGuCYNGmycyQbCqd/3PWH4eOoX/OiCa0uphp57NVTeAGdJGaAliecxwBDHYQCIvrW7aDBZCYeNTP/WX69mkg==", + "dev": true, "requires": { "@jest/types": "^26.6.2", "ansi-regex": "^5.0.0", @@ -32258,6 +32314,7 @@ "version": "4.3.0", "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-4.3.0.tgz", "integrity": "sha512-zbB9rCJAT1rbjiVDb2hqKFHNYLxgtk8NURxZ3IZwD3F6NtxbXZQCnnSi1Lkx+IDohdPlFp222wVALIheZJQSEg==", + "dev": true, "requires": { "color-convert": "^2.0.1" } @@ -32266,6 +32323,7 @@ "version": "2.0.1", "resolved": "https://registry.npmjs.org/color-convert/-/color-convert-2.0.1.tgz", "integrity": 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17 00:00:00 2001 From: Chunlei Wu Date: Sat, 22 May 2021 16:00:40 -0700 Subject: [PATCH 41/75] build: :arrow_up: updated package-lock.json --- package-lock.json | 293 ++++++++++++++++++---------------------------- 1 file changed, 111 insertions(+), 182 deletions(-) diff --git a/package-lock.json b/package-lock.json index 9c5f53df..2de9d12f 100644 --- a/package-lock.json +++ b/package-lock.json @@ -10,7 +10,7 @@ "license": "ISC", "dependencies": { "@biothings-explorer/query_graph_handler": "^1.16.1", - "@biothings-explorer/smartapi-kg": "file:../smartapi-kg.js", + "@biothings-explorer/smartapi-kg": "^3.8.1", "axios": "^0.21.1", "biothings-explorer-graphql": "2.1.1", "body-parser": "^1.19.0", @@ -44,56 +44,6 @@ "supertest": "^6.1.3" } }, - "../smartapi-kg.js": { - "version": "3.8.0", - "license": "ISC", - "dependencies": { - "@babel/runtime": "^7.13.10", - "@commitlint/cli": "^11.0.0", - "@commitlint/config-conventional": "^11.0.0", - "@types/jest": "^26.0.20", - "@types/load-json-file": 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e09da547f159931ff4686b9c4a120014cfc2bd5b Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Sat, 22 May 2021 16:31:53 -0700 Subject: [PATCH 42/75] ci: updated github actions --- .github/workflows/deploy.yml | 14 +++++++------- .github/workflows/development-deploy-revert.yml | 15 ++++++++++----- .github/workflows/development-deploy.yml | 6 +++--- .github/workflows/test.yml | 6 +++--- 4 files changed, 23 insertions(+), 18 deletions(-) diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index 553c4f83..01b67ad0 100644 --- a/.github/workflows/deploy.yml +++ b/.github/workflows/deploy.yml @@ -1,4 +1,4 @@ -name: ci-cd +name: deploy to production on: push: @@ -12,7 +12,7 @@ jobs: strategy: matrix: - node-version: [12.x] + node-version: [14.x] steps: - uses: actions/checkout@v2 @@ -33,12 +33,12 @@ jobs: - name: Set up QEMU uses: docker/setup-qemu-action@v1 - - + - name: Set up Docker Buildx id: buildx uses: docker/setup-buildx-action@v1 - - + - name: Cache Docker layers uses: actions/cache@v2 with: @@ -52,7 +52,7 @@ jobs: with: username: ${{ secrets.DOCKER_HUB_USERNAME }} password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }} - - + - name: Get the version id: vars run: echo ::set-output name=tag::$(echo ${GITHUB_REF:10}) @@ -70,7 +70,7 @@ jobs: builder: ${{ steps.buildx.outputs.name }} cache-from: type=local,src=/tmp/.buildx-cache cache-to: type=local,dest=/tmp/.buildx-cache - - + - name: Image digest run: echo ${{ steps.docker_build.outputs.digest }} @@ -99,7 +99,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - node-version: [12.x] + node-version: [14.x] steps: - uses: actions/checkout@v2 diff --git a/.github/workflows/development-deploy-revert.yml b/.github/workflows/development-deploy-revert.yml index 658ee33a..9b2c890e 100644 --- a/.github/workflows/development-deploy-revert.yml +++ b/.github/workflows/development-deploy-revert.yml @@ -1,10 +1,10 @@ name: deploy to dev server with git ref -on: +on: workflow_dispatch: inputs: git-ref: - description: Git Ref (Optional) + description: Git Ref (Optional) required: false branches: - development @@ -22,7 +22,12 @@ jobs: key: ${{ secrets.SSH_KEY_DEV }} port: ${{ secrets.SSH_PORT }} script: | - cd opt/BioThings_Explorer_TRAPI + cd ~/opt/BioThings_Explorer_TRAPI git reset ${{ github.event.inputs.git-ref }} - npm i --production - pm2 restart all \ No newline at end of file + cp docker-compose-dev.yml docker-compose.yml + docker-compose up --force-recreate --build -d + docker image prune -f + + # alternative way to start the app: + # npm i --production + # pm2 restart all \ No newline at end of file diff --git a/.github/workflows/development-deploy.yml b/.github/workflows/development-deploy.yml index c34132a1..7bbfcb83 100644 --- a/.github/workflows/development-deploy.yml +++ b/.github/workflows/development-deploy.yml @@ -13,7 +13,7 @@ jobs: strategy: matrix: - node-version: [13.x] + node-version: [14.x] steps: - uses: actions/checkout@v2 @@ -37,7 +37,7 @@ jobs: key: ${{ secrets.SSH_KEY_DEV }} port: ${{ secrets.SSH_PORT }} script: | - cd opt/BioThings_Explorer_TRAPI + cd ~/opt/BioThings_Explorer_TRAPI rm docker-compose.yml git stash git pull @@ -50,7 +50,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - node-version: [12.x] + node-version: [14.x] steps: - uses: actions/checkout@v2 diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index e5008c67..56d2ed35 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -3,7 +3,7 @@ on: push: - branches: + branches: - "**" pull_request: branches: [ master ] @@ -19,10 +19,10 @@ jobs: - uses: actions/checkout@v1 - - name: Use Node.js 12.x + - name: Use Node.js 14.x uses: actions/setup-node@v1 with: - node-version: 12.x + node-version: 14.x - name: npm install, generate coverage report run: | From 0cc716d7c2dd44fa1681f061554ad65592020d4f Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Sat, 22 May 2021 16:31:53 -0700 Subject: [PATCH 43/75] ci: updated github actions --- .github/workflows/deploy.yml | 14 +++++++------- .github/workflows/development-deploy-revert.yml | 15 ++++++++++----- .github/workflows/development-deploy.yml | 6 +++--- .github/workflows/test.yml | 6 +++--- 4 files changed, 23 insertions(+), 18 deletions(-) diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index 553c4f83..01b67ad0 100644 --- a/.github/workflows/deploy.yml +++ b/.github/workflows/deploy.yml @@ -1,4 +1,4 @@ -name: ci-cd +name: deploy to production on: push: @@ -12,7 +12,7 @@ jobs: strategy: matrix: - node-version: [12.x] + node-version: [14.x] steps: - uses: actions/checkout@v2 @@ -33,12 +33,12 @@ jobs: - name: Set up QEMU uses: docker/setup-qemu-action@v1 - - + - name: Set up Docker Buildx id: buildx uses: docker/setup-buildx-action@v1 - - + - name: Cache Docker layers uses: actions/cache@v2 with: @@ -52,7 +52,7 @@ jobs: with: username: ${{ secrets.DOCKER_HUB_USERNAME }} password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }} - - + - name: Get the version id: vars run: echo ::set-output name=tag::$(echo ${GITHUB_REF:10}) @@ -70,7 +70,7 @@ jobs: builder: ${{ steps.buildx.outputs.name }} cache-from: type=local,src=/tmp/.buildx-cache cache-to: type=local,dest=/tmp/.buildx-cache - - + - name: Image digest run: echo ${{ steps.docker_build.outputs.digest }} @@ -99,7 +99,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - node-version: [12.x] + node-version: [14.x] steps: - uses: actions/checkout@v2 diff --git a/.github/workflows/development-deploy-revert.yml b/.github/workflows/development-deploy-revert.yml index 658ee33a..9b2c890e 100644 --- a/.github/workflows/development-deploy-revert.yml +++ b/.github/workflows/development-deploy-revert.yml @@ -1,10 +1,10 @@ name: deploy to dev server with git ref -on: +on: workflow_dispatch: inputs: git-ref: - description: Git Ref (Optional) + description: Git Ref (Optional) required: false branches: - development @@ -22,7 +22,12 @@ jobs: key: ${{ secrets.SSH_KEY_DEV }} port: ${{ secrets.SSH_PORT }} script: | - cd opt/BioThings_Explorer_TRAPI + cd ~/opt/BioThings_Explorer_TRAPI git reset ${{ github.event.inputs.git-ref }} - npm i --production - pm2 restart all \ No newline at end of file + cp docker-compose-dev.yml docker-compose.yml + docker-compose up --force-recreate --build -d + docker image prune -f + + # alternative way to start the app: + # npm i --production + # pm2 restart all \ No newline at end of file diff --git a/.github/workflows/development-deploy.yml b/.github/workflows/development-deploy.yml index c34132a1..7bbfcb83 100644 --- a/.github/workflows/development-deploy.yml +++ b/.github/workflows/development-deploy.yml @@ -13,7 +13,7 @@ jobs: strategy: matrix: - node-version: [13.x] + node-version: [14.x] steps: - uses: actions/checkout@v2 @@ -37,7 +37,7 @@ jobs: key: ${{ secrets.SSH_KEY_DEV }} port: ${{ secrets.SSH_PORT }} script: | - cd opt/BioThings_Explorer_TRAPI + cd ~/opt/BioThings_Explorer_TRAPI rm docker-compose.yml git stash git pull @@ -50,7 +50,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - node-version: [12.x] + node-version: [14.x] steps: - uses: actions/checkout@v2 diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index e5008c67..56d2ed35 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -3,7 +3,7 @@ on: push: - branches: + branches: - "**" pull_request: branches: [ master ] @@ -19,10 +19,10 @@ jobs: - uses: actions/checkout@v1 - - name: Use Node.js 12.x + - name: Use Node.js 14.x uses: actions/setup-node@v1 with: - node-version: 12.x + node-version: 14.x - name: npm install, generate coverage report run: | From 674b35f0606ee0f2710093b4aa3f25e11e0142ff Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Sat, 22 May 2021 16:47:33 -0700 Subject: [PATCH 44/75] ci: updated github actions --- .github/workflows/development-deploy-revert.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/development-deploy-revert.yml b/.github/workflows/development-deploy-revert.yml index 9b2c890e..17accdf8 100644 --- a/.github/workflows/development-deploy-revert.yml +++ b/.github/workflows/development-deploy-revert.yml @@ -23,6 +23,7 @@ jobs: port: ${{ secrets.SSH_PORT }} script: | cd ~/opt/BioThings_Explorer_TRAPI + git fetch git reset ${{ github.event.inputs.git-ref }} cp docker-compose-dev.yml docker-compose.yml docker-compose up --force-recreate --build -d From d4ca195520e67377381f38622c576698ed2f52b1 Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Tue, 25 May 2021 09:35:02 -0700 Subject: [PATCH 45/75] build: :hammer: update deploy script --- .github/workflows/deploy.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index 01b67ad0..a7d85a62 100644 --- a/.github/workflows/deploy.yml +++ b/.github/workflows/deploy.yml @@ -87,7 +87,7 @@ jobs: key: ${{ secrets.SSH_KEY }} port: ${{ secrets.SSH_PORT }} script: | - cd opt/single-hop-app.js + cd ~/opt/BioThings_Explorer_TRAPI git stash && git pull rm docker-compose.yml cp docker-compose-prod.yml docker-compose.yml @@ -122,5 +122,5 @@ jobs: key: ${{ secrets.SSH_KEY }} port: ${{ secrets.SSH_PORT }} source: "performance-test/report.html" - target: "opt/single-hop-app.js/performance-test" + target: "~/opt/BioThings_Explorer_TRAPI/performance-test" strip_components: 1 \ No newline at end of file From 9c1d9a08f7fa0b3c8b6bade3b452b876fe17a384 Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Tue, 25 May 2021 09:42:06 -0700 Subject: [PATCH 46/75] chore(release): 2.8.0 --- CHANGELOG.md | 12 ++++++++++++ package-lock.json | 2 +- package.json | 2 +- 3 files changed, 14 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a05c2940..2196b525 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,18 @@ All notable changes to this project will be documented in this file. See [standard-version](https://github.com/conventional-changelog/standard-version) for commit guidelines. +## [2.8.0](https://github.com/biothings/BioThings_Explorer_TRAPI/compare/v2.7.0...v2.8.0) (2021-05-25) + + +### Features + +* :sparkles: added meta_knowledge_graph endpoints by team and ip ([8882df4](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/8882df487e7348918e437fa6f971fadd7b24cb3f)) + + +### Bug Fixes + +* :bug: fix meta_kg endpoint for a given API ([85ff733](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/85ff733bbaefec91c55d36b9bf62bc4bc16259de)) + ## [2.7.0](https://github.com/biothings/BioThings_Explorer_TRAPI/compare/v2.6.0...v2.7.0) (2021-05-16) diff --git a/package-lock.json b/package-lock.json index 2de9d12f..6b5e1cd9 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/single-hop-app", - "version": "2.7.0", + "version": "2.8.0", "lockfileVersion": 2, "requires": true, "packages": { diff --git a/package.json b/package.json index 0175ac41..f7701de9 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/single-hop-app", - "version": "2.7.0", + "version": "2.8.0", "description": "App performing single hop query for BioThings Explorer", "main": "src/server.js", "scripts": { From 5b2f465483b7e817a0d75721ea16e6655b4bd215 Mon Sep 17 00:00:00 2001 From: Marco Cano Date: Tue, 25 May 2021 17:21:54 -0700 Subject: [PATCH 47/75] feat: :sparks: update to consume trapi v1.1 apis --- __test__/integration/routes/metakg.test.js | 2 +- data/predicates.json | 2 +- data/smartapi_specs.json | 2 +- src/controllers/cron/update_local_smartapi.js | 87 ++++++++++++++----- 4 files changed, 69 insertions(+), 24 deletions(-) diff --git a/__test__/integration/routes/metakg.test.js b/__test__/integration/routes/metakg.test.js index 832de86a..bd52573c 100644 --- a/__test__/integration/routes/metakg.test.js +++ b/__test__/integration/routes/metakg.test.js @@ -94,7 +94,7 @@ describe("Test /metakg endpoint", () => { .then((response) => { expect(response.body).toHaveProperty("associations"); const apis = Array.from(new Set(response.body.associations.map(item => item.api.name))); - expect(apis).toContain("Automat Pharos"); + expect(apis).toContain("BioLink API"); }) }) }) \ No newline at end of file diff --git a/data/predicates.json b/data/predicates.json index 30bba2db..89ab3cd2 100644 --- a/data/predicates.json +++ b/data/predicates.json @@ -1 +1 @@ -[{"association":{"api_name":"SRI Reference Knowledge Graph API","smartapi":{"id":"1a41e3cd15f2b3bfa21c99900bfa1720","meta":{"date_created":"2021-04-07T14:48:12.706214+00:00","last_updated":"2021-05-22T07:01:27.465172+00:00","url":"https://trapi.monarchinitiative.org/openapi.json","username":"kshefchek"}},"x-translator":{"component":"KP","team":["Standards Reference Implementation 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s","biolink:part_of","biolink:located_in","biolink:occurs_in","biolink:causes","biolink:quantifier_qualifier","biolink:biomarker_for","biolink:predisposes","biolink:interacts_with","biolink:disrupts","biolink:manifestation_of","biolink:derives_into"],"biolink:GeographicLocation":["biolink:has_input","biolink:subclass_of"],"biolink:GrossAnatomicalStructure":["biolink:located_in","biolink:part_of","biolink:subclass_of","biolink:affects","biolink:related_to","biolink:disrupts","biolink:has_input","biolink:causes","biolink:treats","biolink:prevents"],"biolink:IndividualOrganism":["biolink:part_of","biolink:treats","biolink:located_in","biolink:related_to","biolink:affects","biolink:biomarker_for","biolink:occurs_in","biolink:subclass_of","biolink:has_quantitative_value","biolink:has_input","biolink:causes"],"biolink:InformationContentEntity":["biolink:subclass_of","biolink:treats","biolink:has_attribute","biolink:physically_interacts_with","biolink:related_to","biolink:affects","biolink:located_in","biolink:precedes","biolink:has_input","biolink:biomarker_for","biolink:quantifier_qualifier","biolink:positively_regulates_entity_to_entity","biolink:interacts_with","biolink:prevents","biolink:close_match","biolink:coexists_with","biolink:causes","biolink:disrupts","biolink:predisposes","biolink:has_route","biolink:part_of","biolink:has_quantitative_value"],"biolink:MaterialSample":["biolink:subclass_of","biolink:has_attribute"],"biolink:Metabolite":["biolink:physically_interacts_with","biolink:related_to"],"biolink:MolecularActivity":["biolink:affects","biolink:positively_regulates","biolink:has_input"],"biolink:MolecularEntity":["biolink:has_input","biolink:related_to","biolink:physically_interacts_with","biolink:close_match","biolink:quantifier_qualifier","biolink:positively_regulates_entity_to_entity","biolink:subclass_of","biolink:coexists_with","biolink:negatively_regulates_entity_to_entity","biolink:precedes","biolink:produces","biolink:derives_into","biolink:treats","biolink:affects","biolink:prevents","biolink:part_of","biolink:located_in","biolink:occurs_in","biolink:causes","biolink:biomarker_for","biolink:predisposes","biolink:interacts_with","biolink:disrupts","biolink:has_unit","biolink:manifestation_of","biolink:has_attribute"],"biolink:NamedThing":["biolink:treats","biolink:has_input","biolink:related_to","biolink:physically_interacts_with","biolink:close_match","biolink:quantifier_qualifier","biolink:positively_regulates_entity_to_entity","biolink:subclass_of","biolink:coexists_with","biolink:causes","biolink:negatively_regulates_entity_to_entity","biolink:precedes","biolink:participates_in","biolink:affects","biolink:produces","biolink:biomarker_for","biolink:interacts_with","biolink:prevents","biolink:predisposes","biolink:part_of","biolink:located_in","biolink:derives_into","biolink:has_attribute","biolink:positively_regulates","biolink:has_route","biolink:occurs_in","biolink:disrupts","biolink:manifestation_of","biolink:correlated_with","biolink:has_unit","biolink:has_quantitative_value","biolink:derives_from"],"biolink:OntologyClass":["biolink:affects","biolink:located_in","biolink:treats","biolink:has_input","biolink:subclass_of","biolink:related_to","biolink:physically_interacts_with","biolink:close_match","biolink:part_of","biolink:produces","biolink:quantifier_qualifier","biolink:disrupts","biolink:causes","biolink:biomarker_for","biolink:occurs_in","biolink:positively_regulates_entity_to_entity","biolink:coexists_with"],"biolink:OrganismTaxon":["biolink:part_of","biolink:located_in","biolink:biomarker_for","biolink:affects","biolink:occurs_in","biolink:treats"],"biolink:OrganismalEntity":["biolink:has_input","biolink:physically_interacts_with","biolink:related_to","biolink:quantifier_qualifier","biolink:close_match","biolink:subclass_of","biolink:located_in","biolink:coexists_with","biolink:precedes","biolink:causes","biolink:treats","biolink:part_of","biolink:produces","biolink:positively_regulates_entity_to_entity","biolink:prevents","biolink:affects","biolink:has_route","biolink:negatively_regulates_entity_to_entity","biolink:positively_regulates","biolink:biomarker_for","biolink:predisposes","biolink:occurs_in","biolink:has_quantitative_value","biolink:disrupts","biolink:derives_from"],"biolink:PathologicalProcess":["biolink:related_to","biolink:treats","biolink:affects","biolink:causes","biolink:positively_regulates","biolink:prevents","biolink:biomarker_for","biolink:predisposes","biolink:correlated_with","biolink:disrupts","biolink:precedes","biolink:coexists_with","biolink:subclass_of","biolink:quantifier_qualifier"],"biolink:Phenomenon":["biolink:affects","biolink:positively_regulates_entity_to_entity","biolink:treats","biolink:prevents","biolink:causes","biolink:biomarker_for","biolink:related_to","biolink:has_input","biolink:correlated_with","biolink:subclass_of","biolink:physically_interacts_with","biolink:quantifier_qualifier"],"biolink:PhenotypicFeature":["biolink:has_input"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odingRNAProduct":"biolink:subclass_of","biolink:Transcript":"biolink:superclass_of","biolink:GenomicEntity":"biolink:has_participant","biolink:MolecularEntity":"biolink:has_participant","biolink:DiseaseOrPhenotypicFeature":"biolink:subclass_of","biolink:Gene":"biolink:related_to","biolink:Protein":"biolink:related_to","biolink:PhenotypicFeature":"biolink:caused_by","biolink:RNAProduct":"biolink:related_to"},"biolink:ClinicalModifier":{"biolink:NamedThing":"biolink:superclass_of","biolink:InformationContentEntity":"biolink:superclass_of","biolink:ClinicalModifier":"biolink:superclass_of"},"biolink:ExposureEvent":{"biolink:ExposureEvent":"biolink:subclass_of","biolink:NamedThing":"biolink:related_to","biolink:Disease":"biolink:related_to","biolink:PhenotypicFeature":"biolink:related_to","biolink:BiologicalEntity":"biolink:superclass_of","biolink:DiseaseOrPhenotypicFeature":"biolink:superclass_of","biolink:PathologicalProcess":"biolink:superclass_of","biolink:Phenomenon":"biolink:related_to","biolink:BiologicalProcess":"biolink:related_to","biolink:BiologicalProcessOrActivity":"biolink:subclass_of","biolink:InformationContentEntity":"biolink:superclass_of"},"biolink:FrequencyValue":{"biolink:FrequencyValue":"biolink:subclass_of","biolink:InformationContentEntity":"biolink:related_to","biolink:NamedThing":"biolink:superclass_of","biolink:AdministrativeEntity":"biolink:related_to","biolink:Agent":"biolink:superclass_of"},"biolink:Carbohydrate":{"biolink:ClinicalEntity":"biolink:related_to","biolink:NamedThing":"biolink:superclass_of","biolink:ClinicalIntervention":"biolink:related_to"}}},{"association":{"api_name":"Columbia 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\ No newline at end of file diff --git a/data/smartapi_specs.json b/data/smartapi_specs.json index 72dd6348..144bd098 100644 --- a/data/smartapi_specs.json +++ b/data/smartapi_specs.json @@ -1 +1 @@ -{"took":165,"total":134,"max_score":0.53398204,"hits":[{"_id":"04f42ae00c8e5991b98d0e681dbdc596","_meta":{"date_created":"2021-03-04T18:27:43.614727+00:00","last_updated":"2021-05-22T07:00:53.068357+00:00","url":"http://bdt-social.renci.org:8080/socio_environmental_exposures_api/v1/openapi.json","username":"lstillwe"},"_score":0.53398204,"info":{"contact":{"email":"lisa@renci.org","name":"Lisa Stillwell"},"description":"\nThis API returns data from the US Census Bureau American Community Survey (ACS) for a given spatial location of interest.\n\nThe API returns estimated values for socio-economic variables and related variables for small geographic areas that may act as indirect indicators of relevant health behaviors and outcomes. The data are collected by the US Census Bureau and are publicly available.\n\nThe variables are taken from the five-year summary data file of the US Census Bureau ACS, which is constructed from five annual waves of the bureau’s largest household survey. Approximately, two million households have completed the survey annually since calendar year 2005. (Five waves of the survey before 2005 sampled approximately 500,000 households each.) See https://www.census.gov/acs/www/methodology/sample-size-and-data-quality/sample-size/ for more detail. Microdata are available, but small-area data are only available in summary tabulations.\n\nValues are provided at the US Census Block Group level, representing the 2007-2011 and 2012-2016 calendar-year periods for locations within the continental USA. Block groups, the smallest geographic area for which sample survey data are released, generally contain 600 to 3,000 people (e.g., the size of a single city apartment building). Block Groups are aggregates of an average of 39 Blocks each, each of which is delineated by visible and invisible geographic boundaries. Block groups, in turn, are aggregated into Census Tracts, which generally have a population size between 1,200 and 8,000 people, with an optimum size of 4,000 people. Census Tracts aggregate into counties and counties into states. Metropolitan and micropolitan areas are aggregates of counties. See https://www2.census.gov/geo/pdfs/reference/geodiagram.pdf for further detail. Census geography, even Block Groups, may cross municipal lines and may include both urbanized and rural areas. Because population is a large factor in determining Census geography, some Block Groups may cover an extensive rural or wilderness area while others are quite compact. Census Block, Block Group, and Tract boundaries may change somewhat with each decennial Census, but remain stable in between Censuses.\n\nThe US Census Bureau is mandated to preserve the confidentiality of individual-level data. Therefore, data are often summarized, coarsened into categories, or suppressed by complex secret algorithms (especially, but not limited to household income data). In addition, because the variables of interest may only apply to a small subset of Block Group missing data can occur. In some versions of the data, calculated values are suppressed in Block Groups with less than 50 residents.\n\nStandard errors for the socio-demographic variables are provided. Because each of the values in the ACS data files are summary statistics calculated from sample survey data for each Block Group, different samples yield somewhat different values. Therefore, the Census Bureau generates 80 replicate values for selected variables. These provide the basis for the estimated standard errors of the estimates.\n\nThe currently available variables are listed here:\n\n **(2007-2011 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **EstResidentialDensity** - block group population density\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\n **(2012-2016 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **EstTotalPopulation_SE** - standard error of total population in block group\n - **EstResidentialDensity** - block group population density\n- **EstResidentialDensity_SE** - standard error of residential population density in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **MedianHouseholdIncome_SE** - standard error of median household income\n- **EstPropPersonsNoHealthIns** - proportion of the block group population with no health insurance - **EstPropPersonsNoHealthIns_SE** - standard error of proportion of the block group population with no health insurance\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropNonHispWhite_SE** - standard error of proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropPersons5PlusNoEnglish_SE** - standard error of proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdsNoAuto_SE** - standard error of proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdSSI_SE** - standard error of proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHouseholdPA_SE** - standard error of proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolMaxEducation_SE** - standard error of proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdNoSpouse_SE** - standard error of proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild_SE** - standard error of proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n- **EstPropFemaleHouseholdAnyChild_SE** - standard error of proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. For example, Raleigh, North Carolina is at latitude 35.7796 and longitude -78.6382.\n\nAdditional details on the data can be found in this documentation: (https://github.com/lstillwe/socio-economic-api/blob/master/docs/CensusData.md)\n","license":{"name":"MIT","url":"http://opensource.org/licenses/MIT"},"title":"Socio-Environmental Exposures API","version":"1.0.1","x-translator":{"component":"KP","team":["Exposures Provider"]}},"paths":{"/values":{"get":{"description":"By passing in a location specification (lat, lon) and a year range, you can retrieve the the ACS Values for that location and year range\n","operationId":"get_values","parameters":[{"description":"latitude in decimal degrees format, ie: 32.47","in":"query","name":"latitude","required":true,"schema":{"type":"string"}},{"description":"longitude in decimal degrees format, ie: -86.5","in":"query","name":"longitude","required":true,"schema":{"type":"string"}},{"description":"ACS data year range specification","in":"query","name":"years","required":true,"schema":{"enum":["All (2007-2016)","2007-2011","2012-2016"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"latitude":{"example":"32.47","type":"string"},"longitude":{"example":-86.5,"type":"string"},"values":{"items":{"properties":{"EstPropFemaleHouseholdAnyChild":{"example":"0.154929577","type":"string"},"EstPropFemaleHouseholdAnyChild_SE":{"example":"0.075973316","type":"string"},"EstPropFemaleHouseholdFamilyChild":{"example":"0.227979275","type":"string"},"EstPropFemaleHouseholdFamilyChild_SE":{"example":"0.151408698","type":"string"},"EstPropFemaleHouseholdNoSpouse":{"example":"0.362694301","type":"string"},"EstPropFemaleHouseholdNoSpouse_SE":{"example":"0.108321058","type":"string"},"EstPropHighSchoolDropout":{"example":"n/a","type":"string"},"EstPropHighSchoolDropoutNoWork":{"example":"n/a","type":"string"},"EstPropHighSchoolMaxEducation":{"example":"0.53164557","type":"string"},"EstPropHighSchoolMaxEducation_SE":{"example":"0.076480429","type":"string"},"EstPropHouseholdPA":{"example":"0","type":"string"},"EstPropHouseholdPA_SE":{"example":"0.060887293","type":"string"},"EstPropHouseholdSSI":{"example":"0.088028169","type":"string"},"EstPropHouseholdSSI_SE":{"example":"0.04974414","type":"string"},"EstPropHouseholdsNoAuto":{"example":"0.038732394","type":"string"},"EstPropHouseholdsNoAuto_SE":{"example":"0.039252128","type":"string"},"EstPropMaleLittleWork":{"example":"0.385245902","type":"string"},"EstPropNonHispWhite":{"example":"0.763758389","type":"string"},"EstPropNonHispWhite_SE":{"example":"0.105181283","type":"string"},"EstPropPersons5PlusNoEnglish":{"example":"0.075070822","type":"string"},"EstPropPersons5PlusNoEnglish_SE":{"example":"0.040387049","type":"string"},"EstPropPersonsNoHealthIns":{"example":"0.183892617","type":"string"},"EstPropPersonsNoHealthIns_SE":{"example":"0.063328335","type":"string"},"EstResidentialDensity":{"example":"175.1077206","type":"string"},"EstResidentialDensity_SE":{"example":"32.32567504","type":"string"},"EstTotalPopulation":{"example":"745","type":"string"},"EstTotalPopulation_SE":{"example":"137.5303603","type":"string"},"MedianHouseholdIncome":{"example":"n/a","type":"string"},"MedianHouseholdIncome_SE":{"example":"9888","type":"string"},"geoid":{"example":"15000US010010201001","type":"string"},"years":{"example":"2012-2016","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"OK"},"400":{"content":{},"description":"Invalid parameter"},"404":{"content":{},"description":"No values found"},"500":{"content":{},"description":"Server error"}},"summary":"provides ACS values","x-openapi-router-controller":"swagger_server.controllers.default_controller"}}},"servers":[{"url":"/socio_environmental_exposures_api/v1"}],"tags":[{"name":"translator"}]},{"_id":"34e351cb4eac8bc7dbacf55f1b5ce44b","_meta":{"date_created":"2021-03-04T18:17:41.093656+00:00","last_updated":"2021-05-22T07:01:44.352151+00:00","url":"http://bdt-cmaq.renci.org:8080/cmaq_exposures_api/v1/openapi.json","username":"lstillwe"},"_score":0.53398204,"info":{"contact":{"email":"lisa@renci.org","name":"Lisa Stillwell"},"description":"This API returns estimated measurements of airborne particulate exposures for a given time period and spatial location of interest.\n\nEstimates are derived from the US EPA CONUS estimates of air quality available at https://www.epa.gov/hesc/rsig-related-downloadable-data-files. These data sets provide 8-hour ozone daily maximums (in ppbV) and daily PM2.5 daily averages (in µg/m3). The US EPA provides estimates at the resolution of US Census tract centroids for the continental US. For a given location, the API returns the estimated exposure for the census tract the location occurs in.\n\nThe API provides exposure estimates for calendar years 2002-2016. Resolution for model estimates is 12 km-squared, provisioned at a resolution of the US Census track centroid. The US census tract definition is from the calendar year 2010 definition of the US Census Bureau, for all years of CMAQ data.\n\nThe data sets sources are derived from air quality monitoring data from the National Air Monitoring Stations and Local Air Monitoring Stations (NAMS/LAMS) and numerical output from the Models-3/Community Multiscale Air Quality (CMAQ - https://www.epa.gov/cmaq).\n\nThe API currently provides the following exposure variables:\n- O3: provides estimated O3 concentration levels. Estimated values are for daily maximums in units of ppbV.\n- PM2.5: provides estimated pm2.5 concentration levels. Estimated values are for daily averages in units of µg/m3.\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. For example, Raleigh, North Carolina is at latitude 35.7796 and longitude -78.6382.\n","license":{"name":"MIT","url":"http://opensource.org/licenses/MIT"},"title":"CMAQ Exposures API","version":"1.0.0-oas3","x-translator":{"component":"KP","team":["Exposures Provider"]}},"paths":{"/values":{"get":{"description":"Get estimated air pollutant exposure levels based on time and location\n","operationId":"get_values","parameters":[{"description":"start date of range, ie: MM-DD-YYYY","in":"query","name":"start_date","required":true,"schema":{"format":"date","type":"string"}},{"description":"end date of range, ie: MM-DD-YYYY","in":"query","name":"end_date","required":true,"schema":{"format":"date","type":"string"}},{"description":"latitude in decimal degrees format, ie: 35.7","in":"query","name":"latitude","required":true,"schema":{"type":"string"}},{"description":"longitude in decimal degrees format, ie: -80.33","in":"query","name":"longitude","required":true,"schema":{"type":"string"}},{"description":"timezone offset from UTC (utc, eastern, central, mountain, pacific) - default is utc","in":"query","name":"utc_offset","required":false,"schema":{"default":"utc","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"values":{"items":{"$ref":"#/components/schemas/inline_response_200_values"},"type":"array"}},"type":"object"}}},"description":"OK"},"400":{"description":"Invalid parameter"},"404":{"description":"No values found"},"500":{"description":"Server error"}},"summary":"Retrieves air pollutant exposure levels","x-openapi-router-controller":"swagger_server.controllers.default_controller"}}},"servers":[{"url":"/cmaq_exposures_api/v1"}],"tags":[{"name":"translator"}]},{"_id":"d76f7d70f98b3ef124df0553d70490f7","_meta":{"date_created":"2021-05-08T22:19:34.401242+00:00","last_updated":"2021-05-22T07:01:37.932030+00:00","url":"https://cam-kp-api-dev.renci.org/docs/docs.yaml","username":"jdr0887"},"_score":0.53398204,"info":{"contact":{"email":"balhoff@renci.org","name":"Jim Balhoff"},"description":"TRAPI interface to database of Causal Activity Models","license":{"name":"MIT License","url":"https://opensource.org/licenses/MIT"},"termsOfService":"https://opensource.org/licenses/MIT","title":"CAM-KP API","version":"0.1","x-translator":{"component":"KP","team":["Exposures Provider"]}},"paths":{"/query":{"post":{"operationId":"postQuery","parameters":[{"in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e0":{"object":"n0","predicates":["biolink:has_participant"],"subject":"n1"}},"nodes":{"n0":{"categories":["biolink:Gene","biolink:GeneOrGeneProduct"]},"n1":{"categories":["biolink:BiologicalProcess"]}}}}},"schema":{"$ref":"#/components/schemas/TRAPIQuery"}}},"required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/TRAPIResponse"}}},"description":""},"default":{"content":{"text/plain":{"schema":{"type":"string"}}},"description":""}},"summary":"Submit a TRAPI question graph and retrieve matching solutions"}},"/meta_knowledge_graph":{"get":{"operationId":"getMeta_knowledge_graph","responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":""},"default":{"content":{"text/plain":{"schema":{"type":"string"}}},"description":""}},"summary":"Get MetaKnowledgeGraph used at this service"}}},"servers":[{"url":"https://cam-kp-api-dev.renci.org"}],"tags":[{"name":"translator"}]},{"_id":"1a41e3cd15f2b3bfa21c99900bfa1720","_meta":{"date_created":"2021-04-07T14:48:12.706214+00:00","last_updated":"2021-05-22T07:01:27.465172+00:00","url":"https://trapi.monarchinitiative.org/openapi.json","username":"kshefchek"},"_score":0.53398204,"info":{"contact":{"email":"shefchek@oregonstate.edu","name":"Kent Shefchek","x-id":"https://github.com/kshefchek","x-role":"responsible developer"},"description":"The SRI reference KG aims to aggregate knowledge sources across translator using KGX. 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[ICEES Overview page](https://researchsoftwareinstitute.github.io/data-translator/apps/icees)\n
[documentation](https://github.com/NCATS-Tangerine/icees-api/tree/master/docs) \n
[source](https://github.com/NCATS-Tangerine/icees-api/tree/master/) \n
[ICEES API example queries](https://github.com/NCATS-Tangerine/icees-api/tree/master/#examples)\n
dictionary for versioning of tables\n
\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
versiontable content
1.0.0cdw, acs, nearest road, and cmaq from 2010
2.0.0cdw in FHIR format, acs, nearest road, and cmaq from 2010
3.0.0cdw in FHIR format, acs, nearest road, cmaq, and EPR from 2010 to 2016
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[documentation](https://github.com/NCATS-Tangerine/icees-api/tree/master/docs) \n
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\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
versiontable content
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2.0.0cdw in FHIR format, acs, nearest road, and cmaq from 2010
3.0.0cdw in FHIR format, acs, nearest road, cmaq, and EPR from 2010 to 2016
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The value format should match the regular expression UP[0-9]{9}."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get gene centric proteins by proteome UPID is deprecated, please use new /genecentric?upid= endpoint","tags":["proteomes"]}},"/proteomes/proteins/{upid}":{"get":{"description":"","operationId":"getProteinsByUpid","parameters":[{"description":"UniProt Proteome UPID","in":"path","name":"upid","required":true,"schema":{"type":"string"}},{"description":"Reviewed(true) or not Reviewed (false)","in":"query","name":"reviewed","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Proteome"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Proteome"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid upid parameter. 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Values can be true or false.","in":"query","name":"unique","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"text/x-gff":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Search proteomics peptides in UniProt","tags":["proteomics"]}},"/proteomics/{accession}":{"get":{"description":"","operationId":"getProteomicsByAccession","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. 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Comma separated values accepted up to 20.","in":"query","name":"ipr","required":false,"schema":{"type":"string"}},{"description":"Search by signature database type, e.g. SMART, SUPFAM, Pfam, PIRSF, PROSITE, etc. Comma separated values accepted up to 20.","in":"query","name":"signaturetype","required":false,"schema":{"type":"string"}},{"description":"Search by signature database id, e.g. SM00044, SSF55073, PF00211, PIRSF039050, PS00452, etc. Comma separated values accepted up to 20.","in":"query","name":"signatureid","required":false,"schema":{"type":"string"}},{"description":"UniProt proteome UPID(s). Comma separated values accepted up to 100.","in":"query","name":"upid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."}},"summary":"Search UniParc entries","tags":["uniparc"]}},"/uniparc/accession/{accession}":{"get":{"description":"","operationId":"getUniParcEntryByUniprotAccession","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. The values's format should be a valid UniProtKB accession."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entry only by UniProt accession","tags":["uniparc"]}},"/uniparc/bestguess":{"get":{"description":"For a given user input (request parameters), Best Guess returns the UniParcEntry with a cross-reference to the longest active UniProtKB sequence (preferably from Swiss-Prot and if not then TrEMBL). It also returns the sequence and related information. If it finds more than one longest active UniProtKB sequence it returns 400 (Bad Request) error response with the list of cross references found.","operationId":"getUniParcBestGuess","parameters":[{"description":"UniParc ID (UPI). Comma separated values accepted up to 100","in":"query","name":"upi","required":false,"schema":{"type":"string"}},{"description":"UniProt accession(s). Comma separated values accepted up to 100.","in":"query","name":"accession","required":false,"schema":{"type":"string"}},{"description":"All UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted up to 100.","in":"query","name":"dbid","required":false,"schema":{"type":"string"}},{"description":"UniProt gene name. Comma separated values accepted up to 20.","in":"query","name":"gene","required":false,"schema":{"type":"string"}},{"description":"Organism taxon ID. 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AAC02967 (EMBL) or XP_006524055 (RefSeq).","in":"path","name":"dbid","required":true,"schema":{"type":"string"}},{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). 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Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entries by all UniParc cross reference accessions","tags":["uniparc"]}},"/uniparc/proteome/{upid}":{"get":{"description":"","operationId":"getByProteomeId","parameters":[{"description":"UniProt Proteome UPID","in":"path","name":"upid","required":true,"schema":{"type":"string"}},{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entries by Proteome UPID","tags":["uniparc"]}},"/uniparc/sequence":{"post":{"description":"","operationId":"getBySequence","parameters":[{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. 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AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid upid parameter. The value format should match the regular expression UPI[\\w]{10}."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entry by UniParc UPI","tags":["uniparc"]}},"/variation":{"get":{"description":"Among the available response content types, PEFF format (PSI Extended FASTA Format from the Human Proteome Organisation - Proteomics Standards Initiative, HUPO-PSI) is provided with only variants reported in the output.","operationId":"searchVariation","parameters":[{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. 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Any valid amino acid range position within the length of the protein sequence such as 10-60 (start position to end position)","in":"query","name":"location","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"text/x-gff":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get natural variants in UniProt by NIH-NCBI SNP database identifier","tags":["variation"]}},"/variation/hgvs/{hgvs}":{"get":{"description":"","operationId":"searchByHGVS","parameters":[{"description":"Human Genome Variation Society representation, e.g. NC_000017.11:g.58219213C>T","in":"path","name":"hgvs","required":true,"schema":{"type":"string"}},{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. 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Any valid amino acid range position within the length of the protein sequence such as 10-60 (start position to end position)","in":"query","name":"location","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"text/x-gff":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get natural variants in UniProt by HGVS expression","tags":["variation"]}},"/variation/{accession}":{"get":{"description":"","operationId":"getVariation","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}},{"description":"Filter by the sourceType for variants: uniprot, large scale study and mixed. 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Count and frequency data were derived from the [Columbia University Medical Center's](http://www.cumc.columbia.edu/) [OHDSI](https://www.ohdsi.org/) database including inpatient. Counts are the number of inpatient visits associated with the concept, e.g., diagnosed with a condition, exposed to a drug, or a procedure was performed. Frequencies are the number of unique visits associated with the concept divided by the total number of visits in the dataset, i.e., prevalence in the electronic health records. To protect patient privacy, all concepts and pairs of concepts where the count <= 10 were excluded, and counts were randomized by the Poisson distribution. \n\nDatasets from three primary cohorts are available: \n1) COVID-19: Hospitalized patients aged 18 or older with a COVID-19 related condition diagnosis and/or a confirmed positive COVID-19 test during their hospitalization period or within the prior 21 days. Date range: March 1, 2020 to September 1, 2020. This cohort is also further stratified by sex (male and female) and age (adult: 18-64, senior: 65+).\n2) General inpatient: All hospitalized patients aged 18 or older. Date range: January 1, 2014 to December 31, 2019.\n3) Influenza: Hospitalized patients aged 18 or older who had at least one occurrence of influenza conditions or pre-coordinated positive measurements or positive influenza testing in the prior 21 days or during their hospitalization period. Date range: January 1, 2014 to December 31, 2019.\n\nBoth hierarchical and non-hierarchical datasets are available for each cohort. In the hierarchical datasets, the counts for each concept include the visits from all descendant concepts. For example, the count for ibuprofen (ID 1177480) includes visits with Ibuprofen 600 MG Oral Tablet (ID 19019073), Ibuprofen 400 MG Oral Tablet (ID 19019072), Ibuprofen 20 MG/ML Oral Suspension (ID 19019050), etc. \n\nClinical concepts (e.g., conditions, procedures, drugs) are coded by their standard concept ID in the [OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki). API methods are provided to map to/from other vocabularies supported in OMOP and other ontologies using the EMBL-EBI Ontology Xref Service (OxO). \n\n\nThe following resources are available through this API: \n\n\n1. Metadata: Metadata on the COHD database, including dataset descriptions, number of concepts, etc. \n\n\n2. OMOP: Access to the common vocabulary for name and concept identifier mapping\n\n\n3. Clinical Frequencies: Access to the counts and frequencies of conditions, procedures, and drug exposures, and the associations between them. Frequency was determined as the number of visits with the code(s) / total number of visits. \n\n\n4. Concept Associations: Inferred associations between concepts using chi-square analysis, ratio between observed to expected frequency, and relative frequency. \n\n\nA [Python notebook](https://github.com/WengLab-InformaticsResearch/cohd_api/blob/master/notebooks/COHD_API_Example.ipynb) demonstrates simple examples of how to use the COHD API.\n\n\nCOHD was developed at the [Columbia University Department of Biomedical Informatics](https://www.dbmi.columbia.edu/) as a collaboration between the [Weng Lab](http://people.dbmi.columbia.edu/~chw7007/), [Tatonetti Lab](http://tatonettilab.org/), and the [NCATS Biomedical Data Translator](https://ncats.nih.gov/translator) program (TReK Team). 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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":{"description":"Attempts 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":{"description":"Attempts 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":0.000005585247351056813,"type":"integer"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2008271,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequency of a pair of concepts","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id. Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"q","required":true,"schema":{"type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":19041324,"type":"integer"},"associated_concept_name":{"example":"Acetaminophen 325 MG Oral Tablet [Tylenol]","type":"string"},"associated_domain_id":{"example":"Drug","type":"string"},"concept_count":{"example":277,"type":"integer"},"concept_frequency":{"example":0.0001547113516242737,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptDomainFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id restricted by domain of the associated concept_id. Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptDomainFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id","required":true,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc. See /metadata/domainCounts for a list of valid domain IDs.","example":"Procedure","in":"query","name":"domain","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":2211361,"type":"integer"},"associated_concept_name":{"example":"Radiologic examination, chest, 2 views, frontal and lateral","type":"string"},"associated_domain_id":{"example":"Procedure","type":"string"},"concept_count":{"example":257,"type":"integer"},"concept_frequency":{"example":0.00014354085692216007,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/mostFrequentConcepts":{"get":{"description":"Retrieves the most frequent concepts.","operationId":"mostFrequentConcepts","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The number of concepts to retreieve, e.g., 100. 0 or unspecified will return all matching concepts.","example":100,"in":"query","name":"q","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The domain_id to restrict to, e.g., \"Condition\", \"Drug\", \"Procedure\". See /metadata/domainCounts for a list of valid domain IDs.","example":"Condition","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"(Optional) The vocabulary_id(s) to restrict to, e.g., \"SNOMED\", \"MedDRA\", \"RxNorm\", \"ATC\" etc. Comma separated to include multiple vocabularies, e.g., \"SNOMED,MedDRA\". Default: unrestricted","example":null,"in":"query","name":"vocabulary_id","required":false,"schema":{"type":"string"}},{"description":"(Optional) The concept_class_id(s) to restrict to. concept_class_ids are specific to each vocabulary, e.g.,: [ATC](https://en.wikipedia.org/wiki/Anatomical_Therapeutic_Chemical_Classification_System) {ATC 1st, ATC 2nd, ATC 3rd, ATC 4th, ATC 5th}; [MedDRA](https://en.wikipedia.org/wiki/MedDRA) {PT, HLT, HLGT, SOC}; [RxNorm](https://www.nlm.nih.gov/research/umls/rxnorm/docs/2015/appendix5.html) {Ingredient, Clinical Drug Form, Clinical Drug Comp, Clinical Drug}. Comma separated to include multiple concept_class_ids, e.g., \"PT,HLT\". Default: unrestricted","example":null,"in":"query","name":"concept_class_id","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_class_id":{"example":"Clinical Finding","type":"string"},"concept_count":{"example":233790,"type":"integer"},"concept_frequency":{"example":0.1305774978203572,"type":"integer"},"concept_id":{"example":320128,"type":"integer"},"concept_name":{"example":"Essential hypertension","type":"string"},"dataset_id":{"example":1,"type":"integer"},"domain_id":{"example":"Condition","type":"string"},"vocabulary_id":{"example":"SNOMED","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of most frequent concepts."},"default":{"description":"Unexpected error"}},"summary":"Most frequent concepts [by domain]","tags":["Clinical Frequencies"]}},"/association/chiSquare":{"get":{"description":"Returns the chi-square statistic and p-value between pairs of concepts. Results are returned in descending order of the chi-square statistic. Note that due to large sample sizes, the chi-square can become very large. \n\nThe expected frequencies for the chi-square analysis are calculated based on the single concept frequencies and assuming independence between concepts. P-value is calculated with 1 DOF. \n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"chiSquare","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If this parameter is specified, then the chi-square between concept_id_1 and concept_id_2 is returned. If this parameter is not specified, then a list of chi-squared results between concept_id_1 and other concepts is returned.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"adj_p-value":{"description":"Bonferonni adjusted p-value, adjusted with the total number of pairs of concepts in the dataset.","example":0.0314,"type":"number"},"chi_square":{"example":370026.1780081638,"type":"integer"},"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Instillation of therapeutic substance into bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":4021588,"type":"integer"},"dataset_id":{"example":3,"type":"integer"},"p-value":{"example":0.0314,"type":"number"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of concept pairs and chi-squared values."},"default":{"description":"Unexpected error"}},"summary":"Chi-square analysis on pairs of concepts","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/obsExpRatio":{"get":{"description":"Returns the natural logarithm of the ratio between the observed count and expected count. Expected count is calculated from the single concept frequencies and assuming independence between the concepts. Results are returned in descending order of ln_ratio.\n\nexpected_count = Count_1_and_2 * num_visits / (Count_1 * Count_2)\n\nln_ratio = ln(expected_count)\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Results for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"obsExpRatio","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}},{"description":"The confidence level used for calculating confidence intervals (default 0.99).","example":0.99,"in":"query","name":"confidence","required":false,"schema":{"type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Closed [transurethral] biopsy of bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2003784,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"expected_count":{"example":0.060838982345591645,"type":"integer"},"ln_ratio":{"example":7.561698473261244,"type":"integer"},"observed_count":{"example":117,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concepts and observed-expected frequency ratio."},"default":{"description":"Unexpected error"}},"summary":"Observed Count / Expected Count","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/relativeFrequency":{"get":{"description":"Calculates the relative frequency (i.e., conditional probability) between pairs of concepts. Results are returned in descending order of relative frequency. Note that due to the randomization of the counts, the calculated relative frequencies can exceed the limit of 1.0.\n\nRelative Frequency = Count_1_and_2 / Count_2\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"relativeFrequency","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict concept_id_2 (the base concept) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}},{"description":"The confidence level used for calculating confidence intervals (default 0.99).","example":0.99,"in":"query","name":"confidence","required":false,"schema":{"type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_2_count":{"example":82,"type":"integer"},"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Radical cystectomy","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2003805,"type":"integer"},"concept_pair_count":{"example":29,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"relative_frequency":{"example":0.35365853658536583,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concepts and relative frequency."},"default":{"description":"Unexpected error"}},"summary":"Relative frequency between pairs of concepts","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/predicates":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"additionalProperties":{"description":"Array of predicates","items":{"type":"string"},"type":"array"},"description":"Target map","type":"object"},"description":"Source map","example":{"biolink:ChemicalSubstance":{"biolink:Gene":["biolink:directly_interacts_with","biolink:decreases_activity_of"]}},"type":"object"}}},"description":"Predicates by source and target"}},"summary":"Get supported relationships by source and target","tags":["translator","trapi"]}},"/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.\n \nFor the subject node, the id must be specified (category is ignored).\n \nFor the object node, both the id and category are optional. If id is specified for the object node, then the association between the two identified concepts is returned. If id is not specified and category is specified, the associations between the subject node and all concepts with the specified category are returned. If neither are specified, then the associations between the subject node and all concepts are returned.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.\nAdditional behavior options can be controlled using the optional parameters in query_options.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"id\": \"MONDO:0021113\",\n \"category\": \"biolink:Disease\"\n },\n \"n01\": {\n \"category\": \"biolink:Procedure\"\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicate\": \"biolink:correlated_with\",\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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)."},"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","tags":["translator","trapi"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false}],"x-swagger-router-controller":"swagger_server.controllers.query_controller"}},"/0.9.3/query":{"post":{"description":"This endpoint is temporarily provided to support TRAPI 0.9.3 queries\nQuery 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.\nFor the source node, the curie must be specified (type is ignored).\nFor the target node, both the curie and type are optional. If curie is specified for the target node, then the association between the two identified concepts is returned. If curie is not specified and type is specified, the associations between the source node and all concepts with the specified type are returned. If neither are specified, then the associations between the source node and all concepts are returned.\nCOHD will attempt to map the CURIE to an OMOP concept and the node type to an OMOP domain.","operationId":"query093","requestBody":{"content":{"application/json":{"example":"{\n \"max_results\": 50,\n \"message\": {\n \"query_graph\": {\n \"nodes\": [\n {\n \"id\": \"n00\",\n \"curie\": \"MONDO:0021113\",\n \"type\": \"biolink:Disease\"\n },\n {\n \"id\": \"n01\",\n \"type\": \"biolink:Procedure\"\n }\n ],\n \"edges\": [\n {\n \"id\": \"e00\",\n \"type\": \"biolink:correlated_with\",\n \"source_id\": \"n00\",\n \"target_id\": \"n01\"\n }\n ]\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\n \"dataset_id\": 3,\n \"confidence_interval\": 0.99,\n \"min_cooccurrence\": 50,\n \"threshold\": 0.5,\n \"local_oxo\": true,\n \"ontology_targets\": {\n \"biolink:Disease\": [\"ICD9\", \"SNOMEDCT\", \"DOID\"],\n \"biolink:Drug\": [\"RxNorm\"],\n \"biolink:Procedure\": [\"ICD10PCS\", \"SNOMEDCT\"],\n \"_DEFAULT\": []\n },\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/Message"}}},"description":"successful operation"},"400":{"description":"Invalid status value"}},"summary":"Query COHD following NCATS Translator Reasoner Standard API version 0.9.3","tags":["translator","trapi"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false}],"x-swagger-router-controller":"swagger_server.controllers.query_controller"}},"/translator/biolink_to_omop":{"post":{"description":"Map Biolink CURIEs to OMOP concepts","operationId":"biolink_to_omop","requestBody":{"content":{"application/json":{"example":"{\n \"curies\": [\n \"HP:0002907\",\n \"MONDO:0001187\"\n ]\n}","schema":{"$ref":"#/components/schemas/CurieList"}}},"description":"List of CURIEs","required":true},"responses":{"200":{"content":{"application/json":{"example":"{\n \"MONDO:0001187\": {\n \"distance\": 2,\n \"omop_concept_id\": 197508,\n \"omop_concept_name\": \"Malignant tumor of urinary bladder\"\n }\n}","schema":{"additionalProperties":{"description":"Mapping from OMOP concept to Biolink","properties":{"distance":{"description":"mapping distance","type":"integer"},"omop_concept_id":{"type":"integer"},"omop_concept_name":{"type":"string"}},"type":"object"}}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from Biolink to OMOP","tags":["translator"]}},"/translator/omop_to_biolink":{"post":{"description":"Map OMOP concepts to normalized Biolink nodes using SRI Node Normalizer.","operationId":"omop_to_biolink","requestBody":{"content":{"application/json":{"example":"{\n \"omop_ids\": [\n 78472,\n 197508\n ]\n}","schema":{"$ref":"#/components/schemas/OmopList"}}},"description":"List of OMOP IDs","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"type":"object"},"example":"{\n \"197508\": {\n \"equivalent_identifiers\": [\n {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n {\n \"identifier\": \"DOID:11054\"\n },\n {\n \"identifier\": \"OMIM:109800\"\n },\n {\n \"identifier\": \"UMLS:C0005684\"\n },\n {\n \"identifier\": \"NCIT:C9334\"\n },\n {\n \"identifier\": \"SNOMEDCT:399326009\"\n }\n ],\n \"id\": {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n \"type\": [\n \"biolink:Disease\",\n \"biolink:DiseaseOrPhenotypicFeature\",\n \"biolink:BiologicalEntity\",\n \"biolink:NamedThing\"\n ]\n }\n}","type":"object"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized. Mapping from OMOP concept to Biolink normalized nodes. See [SRI Node Normalizer](https://nodenormalization-sri.renci.org/docs#/) for response format"},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from OMOP to Biolink","tags":["translator"]}}},"servers":[{"url":"https://covid.cohd.io/api/"}],"tags":[{"description":"COHD metadata","name":"Metadata"},{"description":"OMOP Common Data Model concepts","name":"OMOP"},{"description":"Clinical frequency data","name":"Clinical Frequencies"},{"description":"Estimated association between concepts","name":"Concept Associations"},{"description":"Concept-age distributions, concept-pair delta distributions, and temporal analyses","name":"Temporal Clinical Data"},{"description":"NCATS Biomedical Data Translator APIs","name":"translator"},{"description":"Implements the NCATS Translator Reasoner API 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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)","version":"4.0.0","x-accessRestriction":"none","x-implementationLanguage":"Python","x-translator":{"biolink-version":"1.8.2","component":"KP","externalDocs":{"description":"The values for component and team are restricted according to this external JSON schema. 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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":{"description":"Attempts 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. 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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":{"description":"Attempts 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. 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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. 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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":0.000005585247351056813,"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. 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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. \n \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"]}},"/predicates":{"get":{"deprecated":true,"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"additionalProperties":{"description":"Array of predicates","items":{"type":"string"},"type":"array"},"description":"Target map","type":"object"},"description":"Source map","example":{"biolink:ChemicalSubstance":{"biolink:Gene":["biolink:directly_interacts_with","biolink:decreases_activity_of"]}},"type":"object"}}},"description":"Predicates by source and target"}},"summary":"Get supported relationships by source and target","tags":["predicates"]}},"/meta_knowledge_graph":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns meta knowledge graph representation of this TRAPI web service."}},"summary":"Meta knowledge graph representation of this TRAPI web service.","tags":["meta_knowledge_graph"]}},"/query":{"post":{"description":"Query the COHD API following the [NCATS Translator Reasoner Standard API](https://github.com/NCATSTranslator/ReasonerAPI). Only single hop queries are supported. See the example query_graph.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"ids\": [\"DOID:9053\"],\n \"categories\": [\"biolink:Disease\"]\n },\n \"n01\": {\n \"categories\": [\"biolink:Procedure\"]\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicates\": [\"biolink:correlated_with\"],\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\n \"dataset_id\": 3,\n \"confidence_interval\": 0.99,\n \"min_cooccurrence\": 50,\n \"threshold\": 0.5,\n \"local_oxo\": true,\n \"max_results\": 50,\n \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\n \"biolink_only\": true\n }\n}","schema":{"$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)."},"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","tags":["query"]}},"/1.0.0/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.\nFor the subject node, the id must be specified (category is ignored).\nFor the object node, both the id and category are optional. If id is specified for the object node, then the association between the two identified concepts is returned. If id is not specified and category is specified, the associations between the subject node and all concepts with the specified category are returned. If neither are specified, then the associations between the subject node and all concepts are returned.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.\nAdditional behavior options can be controlled using the optional parameters in query_options.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"id\": \"DOID:9053\",\n \"category\": \"biolink:Disease\"\n },\n \"n01\": {\n \"category\": \"biolink:Procedure\"\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicate\": \"biolink:correlated_with\",\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Query COHD following NCATS TRAPI 1.0","tags":["translator"]}},"/translator/biolink_to_omop":{"post":{"description":"Map Biolink CURIEs to OMOP concepts","operationId":"biolink_to_omop","requestBody":{"content":{"application/json":{"example":"{\n \"curies\": [\n \"HP:0002907\",\n \"MONDO:0001187\"\n ]\n}","schema":{"$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. 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The data are collected by the US Census Bureau and are publicly available.\n\nThe variables are taken from the five-year summary data file of the US Census Bureau ACS, which is constructed from five annual waves of the bureau’s largest household survey. Approximately, two million households have completed the survey annually since calendar year 2005. (Five waves of the survey before 2005 sampled approximately 500,000 households each.) See https://www.census.gov/acs/www/methodology/sample-size-and-data-quality/sample-size/ for more detail. Microdata are available, but small-area data are only available in summary tabulations.\n\nValues are provided at the US Census Block Group level, representing the 2007-2011 and 2012-2016 calendar-year periods for locations within the continental USA. Block groups, the smallest geographic area for which sample survey data are released, generally contain 600 to 3,000 people (e.g., the size of a single city apartment building). Block Groups are aggregates of an average of 39 Blocks each, each of which is delineated by visible and invisible geographic boundaries. Block groups, in turn, are aggregated into Census Tracts, which generally have a population size between 1,200 and 8,000 people, with an optimum size of 4,000 people. Census Tracts aggregate into counties and counties into states. Metropolitan and micropolitan areas are aggregates of counties. See https://www2.census.gov/geo/pdfs/reference/geodiagram.pdf for further detail. Census geography, even Block Groups, may cross municipal lines and may include both urbanized and rural areas. Because population is a large factor in determining Census geography, some Block Groups may cover an extensive rural or wilderness area while others are quite compact. Census Block, Block Group, and Tract boundaries may change somewhat with each decennial Census, but remain stable in between Censuses.\n\nThe US Census Bureau is mandated to preserve the confidentiality of individual-level data. Therefore, data are often summarized, coarsened into categories, or suppressed by complex secret algorithms (especially, but not limited to household income data). In addition, because the variables of interest may only apply to a small subset of Block Group missing data can occur. In some versions of the data, calculated values are suppressed in Block Groups with less than 50 residents.\n\nStandard errors for the socio-demographic variables are provided. Because each of the values in the ACS data files are summary statistics calculated from sample survey data for each Block Group, different samples yield somewhat different values. Therefore, the Census Bureau generates 80 replicate values for selected variables. These provide the basis for the estimated standard errors of the estimates.\n\nThe currently available variables are listed here:\n\n **(2007-2011 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **EstResidentialDensity** - block group population density\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\n **(2012-2016 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **EstTotalPopulation_SE** - standard error of total population in block group\n - **EstResidentialDensity** - block group population density\n- **EstResidentialDensity_SE** - standard error of residential population density in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **MedianHouseholdIncome_SE** - standard error of median household income\n- **EstPropPersonsNoHealthIns** - proportion of the block group population with no health insurance - **EstPropPersonsNoHealthIns_SE** - standard error of proportion of the block group population with no health insurance\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropNonHispWhite_SE** - standard error of proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropPersons5PlusNoEnglish_SE** - standard error of proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdsNoAuto_SE** - standard error of proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdSSI_SE** - standard error of proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHouseholdPA_SE** - standard error of proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolMaxEducation_SE** - standard error of proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdNoSpouse_SE** - standard error of proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild_SE** - standard error of proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n- **EstPropFemaleHouseholdAnyChild_SE** - standard error of proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. For example, Raleigh, North Carolina is at latitude 35.7796 and longitude -78.6382.\n\nAdditional details on the data can be found in this documentation: (https://github.com/lstillwe/socio-economic-api/blob/master/docs/CensusData.md)\n","license":{"name":"MIT","url":"http://opensource.org/licenses/MIT"},"title":"Socio-Environmental Exposures API","version":"1.0.1","x-translator":{"component":"KP","team":["Exposures Provider"]}},"paths":{"/values":{"get":{"description":"By passing in a location specification (lat, lon) and a year range, you can retrieve the the ACS Values for that location and year range\n","operationId":"get_values","parameters":[{"description":"latitude in decimal degrees format, ie: 32.47","in":"query","name":"latitude","required":true,"schema":{"type":"string"}},{"description":"longitude in decimal degrees format, ie: -86.5","in":"query","name":"longitude","required":true,"schema":{"type":"string"}},{"description":"ACS data year range specification","in":"query","name":"years","required":true,"schema":{"enum":["All (2007-2016)","2007-2011","2012-2016"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"latitude":{"example":"32.47","type":"string"},"longitude":{"example":-86.5,"type":"string"},"values":{"items":{"properties":{"EstPropFemaleHouseholdAnyChild":{"example":"0.154929577","type":"string"},"EstPropFemaleHouseholdAnyChild_SE":{"example":"0.075973316","type":"string"},"EstPropFemaleHouseholdFamilyChild":{"example":"0.227979275","type":"string"},"EstPropFemaleHouseholdFamilyChild_SE":{"example":"0.151408698","type":"string"},"EstPropFemaleHouseholdNoSpouse":{"example":"0.362694301","type":"string"},"EstPropFemaleHouseholdNoSpouse_SE":{"example":"0.108321058","type":"string"},"EstPropHighSchoolDropout":{"example":"n/a","type":"string"},"EstPropHighSchoolDropoutNoWork":{"example":"n/a","type":"string"},"EstPropHighSchoolMaxEducation":{"example":"0.53164557","type":"string"},"EstPropHighSchoolMaxEducation_SE":{"example":"0.076480429","type":"string"},"EstPropHouseholdPA":{"example":"0","type":"string"},"EstPropHouseholdPA_SE":{"example":"0.060887293","type":"string"},"EstPropHouseholdSSI":{"example":"0.088028169","type":"string"},"EstPropHouseholdSSI_SE":{"example":"0.04974414","type":"string"},"EstPropHouseholdsNoAuto":{"example":"0.038732394","type":"string"},"EstPropHouseholdsNoAuto_SE":{"example":"0.039252128","type":"string"},"EstPropMaleLittleWork":{"example":"0.385245902","type":"string"},"EstPropNonHispWhite":{"example":"0.763758389","type":"string"},"EstPropNonHispWhite_SE":{"example":"0.105181283","type":"string"},"EstPropPersons5PlusNoEnglish":{"example":"0.075070822","type":"string"},"EstPropPersons5PlusNoEnglish_SE":{"example":"0.040387049","type":"string"},"EstPropPersonsNoHealthIns":{"example":"0.183892617","type":"string"},"EstPropPersonsNoHealthIns_SE":{"example":"0.063328335","type":"string"},"EstResidentialDensity":{"example":"175.1077206","type":"string"},"EstResidentialDensity_SE":{"example":"32.32567504","type":"string"},"EstTotalPopulation":{"example":"745","type":"string"},"EstTotalPopulation_SE":{"example":"137.5303603","type":"string"},"MedianHouseholdIncome":{"example":"n/a","type":"string"},"MedianHouseholdIncome_SE":{"example":"9888","type":"string"},"geoid":{"example":"15000US010010201001","type":"string"},"years":{"example":"2012-2016","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"OK"},"400":{"content":{},"description":"Invalid parameter"},"404":{"content":{},"description":"No values found"},"500":{"content":{},"description":"Server error"}},"summary":"provides ACS values","x-openapi-router-controller":"swagger_server.controllers.default_controller"}}},"servers":[{"url":"/socio_environmental_exposures_api/v1"}],"tags":[{"name":"translator"}]},{"_id":"34e351cb4eac8bc7dbacf55f1b5ce44b","_meta":{"date_created":"2021-03-04T18:17:41.093656+00:00","last_updated":"2021-05-25T07:01:50.826242+00:00","url":"http://bdt-cmaq.renci.org:8080/cmaq_exposures_api/v1/openapi.json","username":"lstillwe"},"_score":0.5181118,"info":{"contact":{"email":"lisa@renci.org","name":"Lisa Stillwell"},"description":"This API returns estimated measurements of airborne particulate exposures for a given time period and spatial location of interest.\n\nEstimates are derived from the US EPA CONUS estimates of air quality available at https://www.epa.gov/hesc/rsig-related-downloadable-data-files. These data sets provide 8-hour ozone daily maximums (in ppbV) and daily PM2.5 daily averages (in µg/m3). The US EPA provides estimates at the resolution of US Census tract centroids for the continental US. For a given location, the API returns the estimated exposure for the census tract the location occurs in.\n\nThe API provides exposure estimates for calendar years 2002-2016. Resolution for model estimates is 12 km-squared, provisioned at a resolution of the US Census track centroid. The US census tract definition is from the calendar year 2010 definition of the US Census Bureau, for all years of CMAQ data.\n\nThe data sets sources are derived from air quality monitoring data from the National Air Monitoring Stations and Local Air Monitoring Stations (NAMS/LAMS) and numerical output from the Models-3/Community Multiscale Air Quality (CMAQ - https://www.epa.gov/cmaq).\n\nThe API currently provides the following exposure variables:\n- O3: provides estimated O3 concentration levels. Estimated values are for daily maximums in units of ppbV.\n- PM2.5: provides estimated pm2.5 concentration levels. Estimated values are for daily averages in units of µg/m3.\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. For example, Raleigh, North Carolina is at latitude 35.7796 and longitude -78.6382.\n","license":{"name":"MIT","url":"http://opensource.org/licenses/MIT"},"title":"CMAQ Exposures API","version":"1.0.0-oas3","x-translator":{"component":"KP","team":["Exposures Provider"]}},"paths":{"/values":{"get":{"description":"Get estimated air pollutant exposure levels based on time and location\n","operationId":"get_values","parameters":[{"description":"start date of range, ie: MM-DD-YYYY","in":"query","name":"start_date","required":true,"schema":{"format":"date","type":"string"}},{"description":"end date of range, ie: MM-DD-YYYY","in":"query","name":"end_date","required":true,"schema":{"format":"date","type":"string"}},{"description":"latitude in decimal degrees format, ie: 35.7","in":"query","name":"latitude","required":true,"schema":{"type":"string"}},{"description":"longitude in decimal degrees format, ie: -80.33","in":"query","name":"longitude","required":true,"schema":{"type":"string"}},{"description":"timezone offset from UTC (utc, eastern, central, mountain, pacific) - default is utc","in":"query","name":"utc_offset","required":false,"schema":{"default":"utc","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"values":{"items":{"$ref":"#/components/schemas/inline_response_200_values"},"type":"array"}},"type":"object"}}},"description":"OK"},"400":{"description":"Invalid parameter"},"404":{"description":"No values found"},"500":{"description":"Server error"}},"summary":"Retrieves air pollutant exposure levels","x-openapi-router-controller":"swagger_server.controllers.default_controller"}}},"servers":[{"url":"/cmaq_exposures_api/v1"}],"tags":[{"name":"translator"}]},{"_id":"ec1f4b0cfc37d7c2b9534591767e0c5a","_meta":{"date_created":"2021-03-30T20:24:25.461575+00:00","last_updated":"2021-05-25T07:01:52.321270+00:00","url":"https://stars-app.renci.org/sparql-kp/docs/docs.yaml","username":"balhoff"},"_score":0.5181118,"info":{"contact":{"email":"balhoff@renci.org","name":"Jim Balhoff"},"description":"TRAPI interface to integrated ontology knowledgebase","license":{"name":"MIT License","url":"https://opensource.org/licenses/MIT"},"termsOfService":"https://opensource.org/licenses/MIT","title":"Ontology-KP API","version":"0.1","x-translator":{"component":"KP","team":["Standards Reference Implementation Team"]}},"paths":{"/query":{"post":{"operationId":"postQuery","parameters":[{"in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/TRAPIQueryRequestBody"}}},"required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/TRAPIResponse"}}},"description":""},"default":{"content":{"text/plain":{"schema":{"type":"string"}}},"description":""}},"summary":"Submit a TRAPI question graph and retrieve matching solutions"}},"/predicates":{"get":{"operationId":"getPredicates","responses":{"200":{"content":{"application/json":{"schema":{"items":{"items":{"items":{"$ref":"#/components/schemas/BiolinkTerm"},"type":"array"},"type":"array"},"type":"array"}}},"description":""},"default":{"content":{"text/plain":{"schema":{"type":"string"}}},"description":""}},"summary":"Get predicates used at this service"}}},"servers":[{"url":"https://stars-app.renci.org/sparql-kp"}],"tags":[{"name":"translator"}]},{"_id":"219ac6646d0e2db862b533fb618db5b4","_meta":{"date_created":"2021-03-04T18:22:55.853241+00:00","last_updated":"2021-05-25T07:01:56.541658+00:00","url":"http://bdt-proximity.renci.org:8080/roadway_proximity_api/v1/openapi.json","username":"lstillwe"},"_score":0.5181118,"info":{"contact":{"email":"lisa@renci.org","name":"Lisa Stillwell"},"description":"This API returns the distance in meters from a location of interest to the nearest roadway.\n\nRoadway data are derived from GIS shapefiles provided by the US Federal Highway Administration's Highway Performance Monitoring System (HPMS). See the HPMS Field Manual (https://www.fhwa.dot.gov/policyinformation/hpms/fieldmanual/) for detailed explanation of methods and fields.\n\nResults are limited to major (or primary) roadway types, including interstates, principal arteries, minor arteries, and major collectors, in the United States.\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. For example, Raleigh, North Carolina is at latitude 35.7796 and longitude -78.6382.\n\nIn addition to distance, the API retrieves additional information, including the roadway type, the maximum speed limit, the annual average daily traffic (AADT), and the total number of lanes. See https://www.fhwa.dot.gov/policyinformation/travel_monitoring/pubs/aadt/ for information on how AADT is computed.\n\nThe following roadway types are supported:\n* Off-Network\n* Rural Restricted Access\n* Rural Unrestricted Access\n* Urban Restricted Access\n* Urban Unrestricted Access\n\nIn some cases, roadway type, AADT, and speed are not available in the HPMS data set. In this case, data from the US Census Bureau TIGER (Topologically Integrated Geographic Encoding and Referencing) data set (available at census.gov) was used to obtain roadway type. Roadway segments without roadway type were dropped from the dataset; this amounted to approximately 5% of roadways, many of which had not yet been built. Missing AADT and speeds were populated using a variety of methods. First, a lookup table was built with county averages by roadway type and facility type and populated with values from segments that already had AADT and/or speed. 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Sequence length can be a single length value such as 123 or range 123-234","in":"query","name":"seqLength","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Sequence md5 value.","in":"query","name":"md5","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Search UniProt entries","tags":["proteins"]}},"/proteins/covid-19/entries":{"get":{"description":"","operationId":"covidProteins","responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniProt entries by UniProt cross reference and its ID","tags":["proteins"]}},"/proteins/interaction/{accession}":{"get":{"description":"","operationId":"getAllInteractionEntries","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/UPInteraction"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/UPInteraction"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. The values's format should be a valid UniProtKB accession."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniProt interactions by accession","tags":["proteins"]}},"/proteins/{accession}":{"get":{"description":"","operationId":"getProteinsByAccession","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. 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Comma separated values accepted up to 20.","in":"query","name":"xref","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Genome accession. Comma separated values accepted up to 20.","in":"query","name":"genome_acc","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Reference Proteome(true) or not reference proteome (false)","in":"query","name":"is_ref_proteome","required":false,"schema":{"type":"string"}},{"description":"Redundant Proteome(true) or non redundant proteome (false)","in":"query","name":"is_redundant","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Proteome"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Proteome"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Search proteomes in UniProt","tags":["proteomes"]}},"/proteomes/genecentric/{upid}":{"get":{"deprecated":true,"description":"","operationId":"getGeneCentricByUpidDeprecated","parameters":[{"description":"UniProt Proteome UPID","in":"path","name":"upid","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Proteome"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Proteome"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid upid parameter. The value format should match the regular expression UP[0-9]{9}."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get gene centric proteins by proteome UPID is deprecated, please use new /genecentric?upid= endpoint","tags":["proteomes"]}},"/proteomes/proteins/{upid}":{"get":{"description":"","operationId":"getProteinsByUpid","parameters":[{"description":"UniProt Proteome UPID","in":"path","name":"upid","required":true,"schema":{"type":"string"}},{"description":"Reviewed(true) or not Reviewed (false)","in":"query","name":"reviewed","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Proteome"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Proteome"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid upid parameter. 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Values can be true or false.","in":"query","name":"unique","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"text/x-gff":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Search proteomics peptides in UniProt","tags":["proteomics"]}},"/proteomics/{accession}":{"get":{"description":"","operationId":"getProteomicsByAccession","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. 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Comma separated values accepted up to 20.","in":"query","name":"ipr","required":false,"schema":{"type":"string"}},{"description":"Search by signature database type, e.g. SMART, SUPFAM, Pfam, PIRSF, PROSITE, etc. Comma separated values accepted up to 20.","in":"query","name":"signaturetype","required":false,"schema":{"type":"string"}},{"description":"Search by signature database id, e.g. SM00044, SSF55073, PF00211, PIRSF039050, PS00452, etc. Comma separated values accepted up to 20.","in":"query","name":"signatureid","required":false,"schema":{"type":"string"}},{"description":"UniProt proteome UPID(s). Comma separated values accepted up to 100.","in":"query","name":"upid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."}},"summary":"Search UniParc entries","tags":["uniparc"]}},"/uniparc/accession/{accession}":{"get":{"description":"","operationId":"getUniParcEntryByUniprotAccession","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. The values's format should be a valid UniProtKB accession."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entry only by UniProt accession","tags":["uniparc"]}},"/uniparc/bestguess":{"get":{"description":"For a given user input (request parameters), Best Guess returns the UniParcEntry with a cross-reference to the longest active UniProtKB sequence (preferably from Swiss-Prot and if not then TrEMBL). It also returns the sequence and related information. If it finds more than one longest active UniProtKB sequence it returns 400 (Bad Request) error response with the list of cross references found.","operationId":"getUniParcBestGuess","parameters":[{"description":"UniParc ID (UPI). Comma separated values accepted up to 100","in":"query","name":"upi","required":false,"schema":{"type":"string"}},{"description":"UniProt accession(s). Comma separated values accepted up to 100.","in":"query","name":"accession","required":false,"schema":{"type":"string"}},{"description":"All UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted up to 100.","in":"query","name":"dbid","required":false,"schema":{"type":"string"}},{"description":"UniProt gene name. Comma separated values accepted up to 20.","in":"query","name":"gene","required":false,"schema":{"type":"string"}},{"description":"Organism taxon ID. Comma separated values accepted up to 20.","in":"query","name":"taxid","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Could not find best guess for the requested filter"}},"summary":"Get UniParc longest sequence for entries.","tags":["uniparc"]}},"/uniparc/dbreference/{dbid}":{"get":{"description":"","operationId":"getUniParcByUniparcAccessions","parameters":[{"description":"All UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq).","in":"path","name":"dbid","required":true,"schema":{"type":"string"}},{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entries by all UniParc cross reference accessions","tags":["uniparc"]}},"/uniparc/proteome/{upid}":{"get":{"description":"","operationId":"getByProteomeId","parameters":[{"description":"UniProt Proteome UPID","in":"path","name":"upid","required":true,"schema":{"type":"string"}},{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entries by Proteome UPID","tags":["uniparc"]}},"/uniparc/sequence":{"post":{"description":"","operationId":"getBySequence","parameters":[{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/UniparcSequenceParam"}},"application/xml":{"schema":{"$ref":"#/components/schemas/UniparcSequenceParam"}},"text/plain":{"schema":{"$ref":"#/components/schemas/UniparcSequenceParam"}}},"description":"Post uniparc Sequence in text, json or xml content type. Look the expected model in Data Type column","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entries by sequence","tags":["uniparc"]}},"/uniparc/upi/{upi}":{"get":{"description":"","operationId":"getUniParcEntryByUpId","parameters":[{"description":"UniParc ID (UPI)","in":"path","name":"upi","required":true,"schema":{"type":"string"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid upid parameter. The value format should match the regular expression UPI[\\w]{10}."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entry by UniParc UPI","tags":["uniparc"]}},"/variation":{"get":{"description":"Among the available response content types, PEFF format (PSI Extended FASTA Format from the Human Proteome Organisation - Proteomics Standards Initiative, HUPO-PSI) is provided with only variants reported in the output.","operationId":"searchVariation","parameters":[{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"Filter by the sourceType for variants: uniprot, large scale study and mixed. Comma separated values accepted up to 2.","in":"query","name":"sourcetype","required":false,"schema":{"type":"string"}},{"description":"Filter by consequenceType for variants: missense, stop gained or stop lost. Comma separated values accepted up to 2.","in":"query","name":"consequencetype","required":false,"schema":{"type":"string"}},{"description":"Search by specific wildType amino acid. Options: Any single letter amino acid and * for stop codon. Comma separated values accepted up to 20.","in":"query","name":"wildtype","required":false,"schema":{"type":"string"}},{"description":"Filter by the alternativeSequence amino acid. Any single letter amino acid and * for stopcodon and - for deletions. Comma separated values accepted up to 20.","in":"query","name":"alternativesequence","required":false,"schema":{"type":"string"}},{"description":"Filter by the amino acid range position in the sequence(s). Any valid amino acid range position within the length of the protein sequence such as 10-60 (start position to end position)","in":"query","name":"location","required":false,"schema":{"type":"string"}},{"description":"UniProt accession(s). Comma separated values accepted up to 100.","in":"query","name":"accession","required":false,"schema":{"type":"string"}},{"description":"Search by disease name/ acronym for associated variants , e.g. alzheimer disease 1 or AD1. Partial names allowed.","in":"query","name":"disease","required":false,"schema":{"maxItems":60,"minItems":2,"type":"string"}},{"description":"Search by MIM ID, e.g. 104300. Comma separated values accepted up to 20.","in":"query","name":"omim","required":false,"schema":{"type":"string"}},{"description":"Search by PubMed ID, e.g. 22472873. Comma separated values accepted up to 20.","in":"query","name":"evidence","required":false,"schema":{"type":"string"}},{"description":"Organism taxon ID. Comma separated values accepted up to 20.","in":"query","name":"taxid","required":false,"schema":{"type":"string"}},{"description":"Cross reference database type, e.g, dbSNP, cosmic curate or ClinVar. Comma separated values accepted up to 2.","in":"query","name":"dbtype","required":false,"schema":{"type":"string"}},{"description":"Cross-reference database ID, e.g. rs121918508 for dbSNP, COSM29836 for cosmic curated, rcv61200 for ClinVar. Comma separated values accepted up to 20.","in":"query","name":"dbid","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"text/x-gff":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Search natural variants in UniProt","tags":["variation"]}},"/variation/dbsnp/{dbid}":{"get":{"description":"","operationId":"searchByDbSNP","parameters":[{"description":"Cross-reference NIH-NCBI SNP database identifier, e.g. rs121918508","in":"path","name":"dbid","required":true,"schema":{"type":"string"}},{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"Filter by the sourceType for variants: uniprot, large scale study and mixed. Comma separated values accepted up to 2.","in":"query","name":"sourcetype","required":false,"schema":{"type":"string"}},{"description":"Filter by consequenceType for variants: missense, stop gained or stop lost. Comma separated values accepted up to 2.","in":"query","name":"consequencetype","required":false,"schema":{"type":"string"}},{"description":"Search by specific wildType amino acid. Options: Any single letter amino acid and * for stop codon. Comma separated values accepted up to 20.","in":"query","name":"wildtype","required":false,"schema":{"type":"string"}},{"description":"Filter by the alternativeSequence amino acid. Any single letter amino acid and * for stopcodon and - for deletions. Comma separated values accepted up to 20.","in":"query","name":"alternativesequence","required":false,"schema":{"type":"string"}},{"description":"Filter by the amino acid range position in the sequence(s). Any valid amino acid range position within the length of the protein sequence such as 10-60 (start position to end position)","in":"query","name":"location","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"text/x-gff":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get natural variants in UniProt by NIH-NCBI SNP database identifier","tags":["variation"]}},"/variation/hgvs/{hgvs}":{"get":{"description":"","operationId":"searchByHGVS","parameters":[{"description":"Human Genome Variation Society representation, e.g. NC_000017.11:g.58219213C>T","in":"path","name":"hgvs","required":true,"schema":{"type":"string"}},{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"Filter by the sourceType for variants: uniprot, large scale study and mixed. Comma separated values accepted up to 2.","in":"query","name":"sourcetype","required":false,"schema":{"type":"string"}},{"description":"Filter by consequenceType for variants: missense, stop gained or stop lost. Comma separated values accepted up to 2.","in":"query","name":"consequencetype","required":false,"schema":{"type":"string"}},{"description":"Search by specific wildType amino acid. Options: Any single letter amino acid and * for stop codon. Comma separated values accepted up to 20.","in":"query","name":"wildtype","required":false,"schema":{"type":"string"}},{"description":"Filter by the alternativeSequence amino acid. Any single letter amino acid and * for stopcodon and - for deletions. Comma separated values accepted up to 20.","in":"query","name":"alternativesequence","required":false,"schema":{"type":"string"}},{"description":"Filter by the amino acid range position in the sequence(s). Any valid amino acid range position within the length of the protein sequence such as 10-60 (start position to end position)","in":"query","name":"location","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"text/x-gff":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get natural variants in UniProt by HGVS expression","tags":["variation"]}},"/variation/{accession}":{"get":{"description":"","operationId":"getVariation","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}},{"description":"Filter by the sourceType for variants: uniprot, large scale study and mixed. Comma separated values accepted up to 2.","in":"query","name":"sourcetype","required":false,"schema":{"type":"string"}},{"description":"Filter by consequenceType for variants: missense, stop gained or stop lost. Comma separated values accepted up to 2.","in":"query","name":"consequencetype","required":false,"schema":{"type":"string"}},{"description":"Search by specific wildType amino acid. Options: Any single letter amino acid and * for stop codon. Comma separated values accepted up to 20.","in":"query","name":"wildtype","required":false,"schema":{"type":"string"}},{"description":"Filter by the alternativeSequence amino acid. Any single letter amino acid and * for stopcodon and - for deletions. Comma separated values accepted up to 20.","in":"query","name":"alternativesequence","required":false,"schema":{"type":"string"}},{"description":"Filter by the amino acid range position in the sequence(s). Any valid amino acid range position within the length of the protein sequence such as 10-60 (start position to end position)","in":"query","name":"location","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. The values's format should be a valid UniProtKB accession."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get natural variants by UniProt accession","tags":["variation"]}}},"servers":[{"url":"https://www.ebi.ac.uk/proteins/api"}],"tags":[{"name":"coordinates"},{"name":"antigen"},{"name":"uniparc"},{"name":"proteomics"},{"name":"features"},{"name":"proteomes"},{"name":"variation"},{"name":"genecentric"},{"name":"proteins"},{"name":"translator"}]},{"_id":"9ee398a738916a98b612068cc022454f","_meta":{"date_created":"2020-12-11T23:57:12.070157+00:00","last_updated":"2021-05-25T07:05:10.117829+00:00","url":"https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/LINCS/smartapi.yml","username":"kevinxin90"},"_score":0.24302328,"components":{"x-bte-kgs-operations":{"drug-indication":[{"inputs":[{"id":"LINCS","semantic":"ChemicalSubstance"}],"method":"get","outputs":[{"id":"MESH","semantic":"Disease"}],"parameters":{"id":"{inputs[0]}"},"path":"/query","predicate":"treats","response_mapping":{"$ref":"#/components/x-bte-response-mapping/drug-indication"},"source":"LINCS","supportBatch":false}]},"x-bte-response-mapping":{"drug-indication":{"MESH":"documents.mesh_id","name":"documents.mesh_heading"}}},"info":{"contact":{"email":"akoleti@med.miami.edu","name":"UM BD2K-LINCS DCIC","x-id":"http://lincsportal.ccs.miami.edu/","x-role":"responsible organization"},"description":"Documentation of the LINCS Data Portal web services. Learn more about [LINCS Data Portal](http://lincsportal.ccs.miami.edu/dcic-portal/)","termsOfService":"http://lincsportal.ccs.miami.edu/dcic-portal/#/terms","title":"LINCS Data Portal API","version":"1.0","x-translator":{"component":"KP","team":["Service Provider"]}},"paths":{"/fetchmolecules":{"get":{"parameters":[{"description":"Parameter used for searching small molecule metadata fields. Syntax is \"field name:\"value\"\" Do Not include outer quotes. Example; Name:\"Imatinib\", lincsidentifier:\"LSM-1028\", etc. Setting search term equal to the wildcard charachter, \"*\", will query for all fields of all records up to the specified limit.","in":"query","name":"searchTerm","required":true,"schema":{"type":"string"},"x-valueType":["http://identifiers.org/lincs.smallmolecule"]},{"description":"limit the number of records returned, default is 10","in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"A query response object with 'documents' property, each document corresponds to a small molecule that matched the query criteria.","x-responseValueType":[{"path":"lincs.smallmolecule","valueType":" http://identifiers.org/"}]}},"summary":"Get LINCS small molecule records, which contain both LINCS-based and general metadata about the small molecules tested in the NIH LINCS program. Parameter 'searchTerm' allows querying by specific metadata fields within small molecule records.","tags":["small molecule","query","LINCS","SchuererLab"]}},"/fetchcells":{"get":{"parameters":[{"description":"Parameter used for searching cell line metadata fields. Syntax is \"field name:\"value\"\" Do Not include outer quotes. Example; Name:\"MCF7\", lincsidentifier:\"LSM-1028\", etc. Setting search term equal to the wildcard charachter, \"*\", will query for all fields of all records up to the specified limit.","in":"query","name":"searchTerm","required":true,"schema":{"type":"string"},"x-valueType":[" http://identifiers.org/lincs.cell"]},{"description":"limit the number of records returned, default is 10","in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"A query response object with 'documents' property, each document corresponds to a cell line that matched the query criteria.","x-responseValueType":[{"path":"lincs.cell","valueType":"http://identifiers.org/'"}]}},"summary":"Get LINCS cell lines records, which contain both LINCS-based and general metadata about the cell lines tested in the NIH LINCS program. Parameter 'searchTerm' allows querying by specific metadata fields within the cell line records.","tags":["diseases","cells","query","LINCS","SchuererLab"]}},"/fetchdata":{"get":{"parameters":[{"description":"Parameter used for searching data set metadata fields. Syntax is \"field name:\"value\"\" Do Not include outer quotes. Example; centerfullname:\"HMS LINCS (Harvard Medical School)\", technologies:\"Fluorescence imaging\", etc. Setting search term equal to the wildcard charachter, \"*\", will query for all fields of all records up to the specified limit.","in":"query","name":"searchTerm","required":true,"schema":{"type":"string"},"x-valueType":["http://identifiers.org/lincs.data"]},{"description":"limit the number of records returned, default is 10","in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"A query response object with 'documents' property, each document corresponds to a dataset that matched the query criteria.","x-responseValueType":[{"path":"lincs.data","valueType":"http://identifiers.org/"}]}},"summary":"Get metadata for LINCS assay data sets (DOES NOT RETURN ASSAY ENDPOINT DATA). Parameter 'searchTerm' allows querying by specific metadata fields within the assay metadata records.","tags":["signature","query","LINCS","SchuererLab"]}},"/mechanismOfAction":{"get":{"parameters":[{"description":"Parameter used to search by LINCS small molecule identifier. Syntax is \"id=LSM-#\" Do Not use quotes. Example; id=LSM-1008.","in":"query","name":"id","required":false,"schema":{"type":"string"},"x-valueType":["http://identifiers.org/lincs.smallmolecule"]},{"description":"Parameter used to search by the full name of the mechanism of action. Syntax is \"moa=Mechanism name\" Do Not use quotes. Example; moa=Stem cell growth factor receptor inhibitor.","in":"query","name":"moa","required":false,"schema":{"type":"string"}},{"description":"limit the number of records returned, default is 10","in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"A query response object with 'documents' property, each document corresponds to a mechanism of action that matched the query criteria.","x-responseValueType":[{"path":"lincs.smallmolecule","valueType":"http://identifiers.org/"}]}},"summary":"Get known mechanisms of action for LINCS small molecules.","tags":["query","LINCS","SchuererLab","small molecule"]}},"/bioactivity":{"get":{"parameters":[{"description":"Parameter used to search by LINCS small molecule identifier. Syntax is \"id=LSM-#\" Do Not use quotes. Example; id=LSM-1008.","in":"query","name":"id","required":false,"schema":{"type":"string"},"x-valueType":["http://identifiers.org/lincs.smallmolecule"]},{"description":"Parameter used to search by the biochemical assay target using the target's preferred gene symbol from UniProt. Syntax is \"target=GENE SYMBOL\" Do Not use quotes. Examples; target=BRAF; target=MAPK13; etc..","in":"query","name":"target","required":false,"schema":{"type":"string"}},{"description":"Parameter used to search by the biochemical assay target using the target's UniProt accession number. Syntax is \"uniprot=accession number\" Do Not use quotes. Examples; uniprto=O15264; uniprot=P15056; etc..","in":"query","name":"uniprot","required":false,"schema":{"type":"string"}},{"description":"limit the number of records returned, default is 10","in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"A query response object with 'documents' property, each document corresponds to a bioactivity that matched the query criteria.","x-responseValueType":[{"path":"lincs.smallmolecule","valueType":"http://identifiers.org/"}]}},"summary":"Get known bioactivities for LINCS small molecules, these data are aggregated values resourced from the ChEMBL ver 23 database . The ChEMBL values were mined from numerous sources.","tags":["signature","query","LINCS","SchuererLab","small molecule"]}},"/drugindication":{"get":{"parameters":[{"description":"Parameter used to search by LINCS small molecule identifier. Syntax is \"id=LSM-#\" Do Not use quotes. Example; id=LSM-1008.","in":"query","name":"id","required":false,"schema":{"type":"string"},"x-valueType":["http://identifiers.org/lincs.smallmolecule"]},{"description":"Parameter used to search by the EFO drug indication. Syntax is \"efo=Drug Indication\" Do Not use quotes. Example; efo=renal carcinoma","in":"query","name":"efo","required":false,"schema":{"type":"string"}},{"description":"Parameter used to search by the MeSH drug indication. Syntax is \"efo=Drug Indication\" Do Not use quotes. Example; mesh=carcinoma, renal cell","in":"query","name":"mesh","required":false,"schema":{"type":"string"}},{"description":"limit the number of records returned, default is 10","in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"A query response object with 'documents' property, each document corresponds to a drug indication that matched the query criteria.","x-responseValueType":[{"path":"lincs.smallmolecule","valueType":"http://identifiers.org/"}]}},"summary":"Get known drug indications for LINCS small molecules, the indications are captured from both the Experimental Factor Ontology (EFO) and the Medical Subject Headings (MeSH) vocabularies.","tags":["signature","query","LINCS","SchuererLab","small molecule"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/drug-indication"}]}},"/disease":{"get":{"parameters":[{"description":"Parameter used to search by the DO disease name. Syntax is \"disease=disease name\" Do Not use quotes. Example; disease=breast carcinoma","in":"query","name":"disease","required":false,"schema":{"type":"string"}},{"description":"Parameter used to search by the DO identifier. Syntax is \"doid=DOID:#\" Do Not use quotes. Example; doid=DOID:3459","in":"query","name":"doid","required":false,"schema":{"type":"string"}},{"description":"limit the number of records returned, default is 10","in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"A query response object with 'documents' property, each document corresponds to a disease that matched the query criteria.","x-responseValueType":[{"path":"lincs.cell","valueType":"http://identifiers.org/"}]}},"summary":"Query for LINCS cell line identifiers by disease, the diseases are captured from the Disease Ontology (DO) vocabulary.","tags":["diseases","query","LINCS","SchuererLab","cells"]}}},"servers":[{"description":"Production server","url":"http://lincsportal.ccs.miami.edu/dcic/api/"}],"tags":[{"name":"small molecule"},{"name":"query"},{"name":"cells"},{"name":"gene"},{"name":"diseases"},{"name":"LINCS"},{"name":"SchuererLab"},{"name":"signature"},{"name":"translator"}]},{"_id":"fc8245e92c970298449294fc04211869","_meta":{"date_created":"2021-02-04T00:00:10.655676+00:00","last_updated":"2021-05-25T07:01:18.112693+00:00","slug":"cohdcovid","url":"https://raw.githubusercontent.com/WengLab-InformaticsResearch/cohd_api/cohd_covid/cohd/cohd_oas3.yaml","username":"CaseyTa"},"_score":0.2294851,"components":{"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) for COVID-19 Research API provides access to counts and frequencies (i.e., EHR visit prevalence) of conditions, procedures, drug exposures, and the co-occurrence frequencies between them for a cohort of hospitalized COVID-19 patients and two comparator cohorts of hospitalized influenza patients and hospitalized patients. Count and frequency data were derived from the [Columbia University Medical Center's](http://www.cumc.columbia.edu/) [OHDSI](https://www.ohdsi.org/) database including inpatient. Counts are the number of inpatient visits associated with the concept, e.g., diagnosed with a condition, exposed to a drug, or a procedure was performed. Frequencies are the number of unique visits associated with the concept divided by the total number of visits in the dataset, i.e., prevalence in the electronic health records. To protect patient privacy, all concepts and pairs of concepts where the count <= 10 were excluded, and counts were randomized by the Poisson distribution. \n\nDatasets from three primary cohorts are available: \n1) COVID-19: Hospitalized patients aged 18 or older with a COVID-19 related condition diagnosis and/or a confirmed positive COVID-19 test during their hospitalization period or within the prior 21 days. Date range: March 1, 2020 to September 1, 2020. This cohort is also further stratified by sex (male and female) and age (adult: 18-64, senior: 65+).\n2) General inpatient: All hospitalized patients aged 18 or older. Date range: January 1, 2014 to December 31, 2019.\n3) Influenza: Hospitalized patients aged 18 or older who had at least one occurrence of influenza conditions or pre-coordinated positive measurements or positive influenza testing in the prior 21 days or during their hospitalization period. Date range: January 1, 2014 to December 31, 2019.\n\nBoth hierarchical and non-hierarchical datasets are available for each cohort. In the hierarchical datasets, the counts for each concept include the visits from all descendant concepts. For example, the count for ibuprofen (ID 1177480) includes visits with Ibuprofen 600 MG Oral Tablet (ID 19019073), Ibuprofen 400 MG Oral Tablet (ID 19019072), Ibuprofen 20 MG/ML Oral Suspension (ID 19019050), etc. \n\nClinical concepts (e.g., conditions, procedures, drugs) are coded by their standard concept ID in the [OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki). API methods are provided to map to/from other vocabularies supported in OMOP and other ontologies using the EMBL-EBI Ontology Xref Service (OxO). \n\n\nThe following resources are available through this API: \n\n\n1. Metadata: Metadata on the COHD database, including dataset descriptions, number of concepts, etc. \n\n\n2. OMOP: Access to the common vocabulary for name and concept identifier mapping\n\n\n3. Clinical Frequencies: Access to the counts and frequencies of conditions, procedures, and drug exposures, and the associations between them. Frequency was determined as the number of visits with the code(s) / total number of visits. \n\n\n4. Concept Associations: Inferred associations between concepts using chi-square analysis, ratio between observed to expected frequency, and relative frequency. \n\n\nA [Python notebook](https://github.com/WengLab-InformaticsResearch/cohd_api/blob/master/notebooks/COHD_API_Example.ipynb) demonstrates simple examples of how to use the COHD API.\n\n\nCOHD was developed at the [Columbia University Department of Biomedical Informatics](https://www.dbmi.columbia.edu/) as a collaboration between the [Weng Lab](http://people.dbmi.columbia.edu/~chw7007/), [Tatonetti Lab](http://tatonettilab.org/), and the [NCATS Biomedical Data Translator](https://ncats.nih.gov/translator) program (TReK Team). This work was supported in part by grants: NCATS 1OT2TR003434, NLM R01LM012895, NCATS OT3TR002027, NLM R01LM009886-08A1, and NIGMS R01GM107145.\n\nThe following external resources may be useful: \n[OHDSI](https://www.ohdsi.org/) \n[OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki) \n[Athena](http://athena.ohdsi.org) (OMOP vocabularies, search, concept relationships, concept hierarchy) \n[Atlas](http://www.ohdsi.org/web/atlas/) (OMOP vocabularies, search, concept relationships, concept hierarchy, concept sets) \n[NCATS Biomedical Data Translator](https://sites.google.com/ncats.nih.gov/translator-io/home) \n","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"termsOfService":"http://cohd.io/terms/","title":"Columbia Open Health Data (COHD) for COVID-19 Research","version":"3.0.0","x-accessRestriction":"none","x-implementationLanguage":"Python","x-translator":{"component":"KP","team":["Clinical Data Provider"]},"x-trapi":{"version":"1.0.0"}},"paths":{"/metadata/datasets":{"get":{"description":"Returns a list of datasets, including dataset ID, name, and description.","operationId":"datasets","responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"dataset_description":{"example":"Hospitalized patients with a COVID-19 condition and/or positive lab test (non-hierarchical)","type":"string"},"dataset_id":{"example":1,"type":"integer"},"dataset_name":{"example":"COVID Cohort (non-hierarchical)","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of dataset descriptions."},"default":{"description":"Unexpected error"}},"summary":"Enumerates the datasets available in COHD","tags":["Metadata"]}},"/metadata/domainCounts":{"get":{"description":"Returns a list of domains and the number of concepts in each domain.","operationId":"domainCounts","parameters":[{"description":"The dataset_id of the dataset to query. 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. 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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. 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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":{"description":"Attempts 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":{"description":"Attempts 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":0.000005585247351056813,"type":"integer"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2008271,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequency of a pair of concepts","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id. Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"q","required":true,"schema":{"type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":19041324,"type":"integer"},"associated_concept_name":{"example":"Acetaminophen 325 MG Oral Tablet [Tylenol]","type":"string"},"associated_domain_id":{"example":"Drug","type":"string"},"concept_count":{"example":277,"type":"integer"},"concept_frequency":{"example":0.0001547113516242737,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptDomainFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id restricted by domain of the associated concept_id. Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptDomainFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id","required":true,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc. See /metadata/domainCounts for a list of valid domain IDs.","example":"Procedure","in":"query","name":"domain","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":2211361,"type":"integer"},"associated_concept_name":{"example":"Radiologic examination, chest, 2 views, frontal and lateral","type":"string"},"associated_domain_id":{"example":"Procedure","type":"string"},"concept_count":{"example":257,"type":"integer"},"concept_frequency":{"example":0.00014354085692216007,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/mostFrequentConcepts":{"get":{"description":"Retrieves the most frequent concepts.","operationId":"mostFrequentConcepts","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The number of concepts to retreieve, e.g., 100. 0 or unspecified will return all matching concepts.","example":100,"in":"query","name":"q","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The domain_id to restrict to, e.g., \"Condition\", \"Drug\", \"Procedure\". See /metadata/domainCounts for a list of valid domain IDs.","example":"Condition","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"(Optional) The vocabulary_id(s) to restrict to, e.g., \"SNOMED\", \"MedDRA\", \"RxNorm\", \"ATC\" etc. Comma separated to include multiple vocabularies, e.g., \"SNOMED,MedDRA\". Default: unrestricted","example":null,"in":"query","name":"vocabulary_id","required":false,"schema":{"type":"string"}},{"description":"(Optional) The concept_class_id(s) to restrict to. concept_class_ids are specific to each vocabulary, e.g.,: [ATC](https://en.wikipedia.org/wiki/Anatomical_Therapeutic_Chemical_Classification_System) {ATC 1st, ATC 2nd, ATC 3rd, ATC 4th, ATC 5th}; [MedDRA](https://en.wikipedia.org/wiki/MedDRA) {PT, HLT, HLGT, SOC}; [RxNorm](https://www.nlm.nih.gov/research/umls/rxnorm/docs/2015/appendix5.html) {Ingredient, Clinical Drug Form, Clinical Drug Comp, Clinical Drug}. Comma separated to include multiple concept_class_ids, e.g., \"PT,HLT\". Default: unrestricted","example":null,"in":"query","name":"concept_class_id","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_class_id":{"example":"Clinical Finding","type":"string"},"concept_count":{"example":233790,"type":"integer"},"concept_frequency":{"example":0.1305774978203572,"type":"integer"},"concept_id":{"example":320128,"type":"integer"},"concept_name":{"example":"Essential hypertension","type":"string"},"dataset_id":{"example":1,"type":"integer"},"domain_id":{"example":"Condition","type":"string"},"vocabulary_id":{"example":"SNOMED","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of most frequent concepts."},"default":{"description":"Unexpected error"}},"summary":"Most frequent concepts [by domain]","tags":["Clinical Frequencies"]}},"/association/chiSquare":{"get":{"description":"Returns the chi-square statistic and p-value between pairs of concepts. Results are returned in descending order of the chi-square statistic. Note that due to large sample sizes, the chi-square can become very large. \n\nThe expected frequencies for the chi-square analysis are calculated based on the single concept frequencies and assuming independence between concepts. P-value is calculated with 1 DOF. \n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"chiSquare","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If this parameter is specified, then the chi-square between concept_id_1 and concept_id_2 is returned. If this parameter is not specified, then a list of chi-squared results between concept_id_1 and other concepts is returned.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"adj_p-value":{"description":"Bonferonni adjusted p-value, adjusted with the total number of pairs of concepts in the dataset.","example":0.0314,"type":"number"},"chi_square":{"example":370026.1780081638,"type":"integer"},"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Instillation of therapeutic substance into bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":4021588,"type":"integer"},"dataset_id":{"example":3,"type":"integer"},"p-value":{"example":0.0314,"type":"number"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of concept pairs and chi-squared values."},"default":{"description":"Unexpected error"}},"summary":"Chi-square analysis on pairs of concepts","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/obsExpRatio":{"get":{"description":"Returns the natural logarithm of the ratio between the observed count and expected count. Expected count is calculated from the single concept frequencies and assuming independence between the concepts. Results are returned in descending order of ln_ratio.\n\nexpected_count = Count_1_and_2 * num_visits / (Count_1 * Count_2)\n\nln_ratio = ln(expected_count)\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Results for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"obsExpRatio","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}},{"description":"The confidence level used for calculating confidence intervals (default 0.99).","example":0.99,"in":"query","name":"confidence","required":false,"schema":{"type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Closed [transurethral] biopsy of bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2003784,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"expected_count":{"example":0.060838982345591645,"type":"integer"},"ln_ratio":{"example":7.561698473261244,"type":"integer"},"observed_count":{"example":117,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concepts and observed-expected frequency ratio."},"default":{"description":"Unexpected error"}},"summary":"Observed Count / Expected Count","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/relativeFrequency":{"get":{"description":"Calculates the relative frequency (i.e., conditional probability) between pairs of concepts. Results are returned in descending order of relative frequency. Note that due to the randomization of the counts, the calculated relative frequencies can exceed the limit of 1.0.\n\nRelative Frequency = Count_1_and_2 / Count_2\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"relativeFrequency","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict concept_id_2 (the base concept) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}},{"description":"The confidence level used for calculating confidence intervals (default 0.99).","example":0.99,"in":"query","name":"confidence","required":false,"schema":{"type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_2_count":{"example":82,"type":"integer"},"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Radical cystectomy","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2003805,"type":"integer"},"concept_pair_count":{"example":29,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"relative_frequency":{"example":0.35365853658536583,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concepts and relative frequency."},"default":{"description":"Unexpected error"}},"summary":"Relative frequency between pairs of concepts","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/predicates":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"additionalProperties":{"description":"Array of predicates","items":{"type":"string"},"type":"array"},"description":"Target map","type":"object"},"description":"Source map","example":{"biolink:ChemicalSubstance":{"biolink:Gene":["biolink:directly_interacts_with","biolink:decreases_activity_of"]}},"type":"object"}}},"description":"Predicates by source and target"}},"summary":"Get supported relationships by source and target","tags":["translator","trapi"]}},"/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.\n \nFor the subject node, the id must be specified (category is ignored).\n \nFor the object node, both the id and category are optional. If id is specified for the object node, then the association between the two identified concepts is returned. If id is not specified and category is specified, the associations between the subject node and all concepts with the specified category are returned. If neither are specified, then the associations between the subject node and all concepts are returned.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.\nAdditional behavior options can be controlled using the optional parameters in query_options.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"id\": \"MONDO:0021113\",\n \"category\": \"biolink:Disease\"\n },\n \"n01\": {\n \"category\": \"biolink:Procedure\"\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicate\": \"biolink:correlated_with\",\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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. 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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)","version":"4.0.0","x-accessRestriction":"none","x-implementationLanguage":"Python","x-translator":{"biolink-version":"1.8.2","component":"KP","externalDocs":{"description":"The values for component and team are restricted according to this external JSON schema. 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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":{"description":"Attempts 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. 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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":{"description":"Attempts 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. 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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. 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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":0.000005585247351056813,"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. 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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. \n \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"]}},"/predicates":{"get":{"deprecated":true,"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"additionalProperties":{"description":"Array of predicates","items":{"type":"string"},"type":"array"},"description":"Target map","type":"object"},"description":"Source map","example":{"biolink:ChemicalSubstance":{"biolink:Gene":["biolink:directly_interacts_with","biolink:decreases_activity_of"]}},"type":"object"}}},"description":"Predicates by source and target"}},"summary":"Get supported relationships by source and target","tags":["predicates"]}},"/meta_knowledge_graph":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns meta knowledge graph representation of this TRAPI web service."}},"summary":"Meta knowledge graph representation of this TRAPI web service.","tags":["meta_knowledge_graph"]}},"/query":{"post":{"description":"Query the COHD API following the [NCATS Translator Reasoner Standard API](https://github.com/NCATSTranslator/ReasonerAPI). Only single hop queries are supported. See the example query_graph.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"ids\": [\"DOID:9053\"],\n \"categories\": [\"biolink:Disease\"]\n },\n \"n01\": {\n \"categories\": [\"biolink:Procedure\"]\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicates\": [\"biolink:correlated_with\"],\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\n \"dataset_id\": 3,\n \"confidence_interval\": 0.99,\n \"min_cooccurrence\": 50,\n \"threshold\": 0.5,\n \"local_oxo\": true,\n \"max_results\": 50,\n \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\n \"biolink_only\": true\n }\n}","schema":{"$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)."},"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","tags":["query"]}},"/1.0.0/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.\nFor the subject node, the id must be specified (category is ignored).\nFor the object node, both the id and category are optional. If id is specified for the object node, then the association between the two identified concepts is returned. If id is not specified and category is specified, the associations between the subject node and all concepts with the specified category are returned. If neither are specified, then the associations between the subject node and all concepts are returned.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.\nAdditional behavior options can be controlled using the optional parameters in query_options.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"id\": \"DOID:9053\",\n \"category\": \"biolink:Disease\"\n },\n \"n01\": {\n \"category\": \"biolink:Procedure\"\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicate\": \"biolink:correlated_with\",\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Query COHD following NCATS TRAPI 1.0","tags":["translator"]}},"/translator/biolink_to_omop":{"post":{"description":"Map Biolink CURIEs to OMOP concepts","operationId":"biolink_to_omop","requestBody":{"content":{"application/json":{"example":"{\n \"curies\": [\n \"HP:0002907\",\n \"MONDO:0001187\"\n ]\n}","schema":{"$ref":"#/components/schemas/CurieList"}}},"description":"List of CURIEs","required":true},"responses":{"200":{"content":{"application/json":{"example":"{\n \"MONDO:0001187\": {\n \"distance\": 2,\n \"omop_concept_id\": 197508,\n \"omop_concept_name\": \"Malignant tumor of urinary bladder\"\n }\n}","schema":{"additionalProperties":{"description":"Mapping from OMOP concept to Biolink","properties":{"distance":{"description":"mapping distance","type":"integer"},"omop_concept_id":{"type":"integer"},"omop_concept_name":{"type":"string"}},"type":"object"}}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from Biolink to OMOP","tags":["translator"]}},"/translator/omop_to_biolink":{"post":{"description":"Map OMOP concepts to normalized Biolink nodes using SRI Node Normalizer.","operationId":"omop_to_biolink","requestBody":{"content":{"application/json":{"example":"{\n \"omop_ids\": [\n 78472,\n 197508\n ]\n}","schema":{"$ref":"#/components/schemas/OmopList"}}},"description":"List of OMOP IDs","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"type":"object"},"example":"{\n \"197508\": {\n \"equivalent_identifiers\": [\n {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n {\n \"identifier\": \"DOID:11054\"\n },\n {\n \"identifier\": \"OMIM:109800\"\n },\n {\n \"identifier\": \"UMLS:C0005684\"\n },\n {\n \"identifier\": \"NCIT:C9334\"\n },\n {\n \"identifier\": \"SNOMEDCT:399326009\"\n }\n ],\n \"id\": {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n \"type\": [\n \"biolink:Disease\",\n \"biolink:DiseaseOrPhenotypicFeature\",\n \"biolink:BiologicalEntity\",\n \"biolink:NamedThing\"\n ]\n }\n}","type":"object"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized. Mapping from OMOP concept to Biolink normalized nodes. See [SRI Node Normalizer](https://nodenormalization-sri.renci.org/docs#/) for response format"},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from OMOP to Biolink","tags":["translator"]}}},"servers":[{"url":"https://cohd.io/api/"}],"tags":[{"description":"COHD metadata","name":"Metadata"},{"description":"OMOP Common Data Model concepts","name":"OMOP"},{"description":"Clinical frequency data","name":"Clinical Frequencies"},{"description":"Estimated association between concepts","name":"Concept Associations"},{"description":"Concept-age distributions, concept-pair delta distributions, and temporal analyses","name":"Temporal Clinical Data"},{"description":"Get supported relationships by source and target","name":"predicates"},{"description":"Query reasoner using a predefined question type","name":"query"},{"description":"Required for SmartAPI validation of x-translator","name":"translator"},{"description":"Required for SmartAPI validation of x-trapi","name":"trapi"}]}]} \ No newline at end of file diff --git a/src/controllers/cron/update_local_smartapi.js b/src/controllers/cron/update_local_smartapi.js index 10d39b23..0e964e23 100644 --- a/src/controllers/cron/update_local_smartapi.js +++ b/src/controllers/cron/update_local_smartapi.js @@ -13,10 +13,12 @@ const getTRAPIWithPredicatesEndpoint = (specs) => { "x-translator" in spec.info && spec.info["x-translator"].component === "KP" && "paths" in spec && - "/predicates" in spec.paths && - "/query" in spec.paths + "/query" in spec.paths && + "x-trapi" in spec.info && + spec.servers.length && + "/predicates" in spec.paths || "/meta_knowledge_graph" in spec.paths ) { - trapi.push({ + let api = { association: { api_name: spec.info.title, smartapi: { @@ -34,7 +36,21 @@ const getTRAPIWithPredicatesEndpoint = (specs) => { server: spec.servers[0].url, method: 'post' } - }); + } + // check trapi 1.1 or 1.0 + if ( + "/meta_knowledge_graph" in spec.paths && + Object.prototype.hasOwnProperty.call(spec.info["x-trapi"], "version") && + spec.info["x-trapi"].version.includes("1.1") + ) { + //1.1 + api['predicates_path'] = "/meta_knowledge_graph"; + trapi.push(api); + }else if("/predicates" in spec.paths ){ + //1.0 + api['predicates_path'] = "/predicates"; + trapi.push(api); + } } } catch (err) { debug( @@ -46,58 +62,87 @@ const getTRAPIWithPredicatesEndpoint = (specs) => { return trapi; } -const constructQueryUrl = (serverUrl) => { +const constructQueryUrl = (serverUrl, path) => { if (serverUrl.endsWith("/")) { serverUrl = serverUrl.slice(0, -1); } - return serverUrl + "/predicates"; + return serverUrl + path; } -const getOpsFromPredicatesEndpoint = async (metadata) => { +const getPredicatesFromGraphData = (predicate_endpoint, data) => { + //if /predicates just return normal response + if (predicate_endpoint !== '/meta_knowledge_graph') { + return data + } + // transform graph data to legacy format > object.subject : predicates + const predicates = {} + + const addNewPredicates= (edge) => { + if (Object.prototype.hasOwnProperty.call(predicates, edge.object)) { + predicates[edge.object][edge.subject] = edge.predicate + } else { + predicates[edge.object] = {} + predicates[edge.object][edge.subject] = edge.predicate + } + } + + if (Object.prototype.hasOwnProperty.call(data, "edges")){ + data.edges.forEach(edge => addNewPredicates(edge)) + }else{ + //some apis still redirect to previous format + return data + } + return predicates +} + +const getOpsFromEndpoint = async (metadata) => { return axios - .get(constructQueryUrl(metadata.query_operation.server), { timeout: 5000 }) + .get(constructQueryUrl(metadata.query_operation.server, metadata.predicates_path), { timeout: 5000 }) .then((res) => { if (res.status === 200) { - debug(`Successfully get /predicates for ${metadata.query_operation.server}`) - return { ...metadata, ...{ predicates: res.data } }; + debug(`Successfully got ${metadata.predicates_path} for ${metadata.query_operation.server}`) + return { ...metadata, ...{ predicates: getPredicatesFromGraphData(metadata.predicates_path, res.data) } }; } debug( - `[error]: Unable to get /predicates for ${metadata.query_operation.server} due to query failure with status code ${res.status}` + `[error]: API "${metadata.association.api_name}" Unable to get ${metadata.predicates_path}` + + ` for ${metadata.query_operation.server} due to query failure with status code ${res.status}` ); - return []; + return false; }) .catch((err) => { debug( - `[error]: Unable to get /predicates for ${metadata.url + `[error]: API "${metadata.association.api_name}" failed to get ${metadata.predicates_path} for ${metadata.query_operation.server } due to error ${err.toString()}` ); - return []; + return false; }); } const getOpsFromPredicatesEndpoints = async (specs) => { const metadatas = getTRAPIWithPredicatesEndpoint(specs); let res = []; + debug(`Lining up ${metadatas.length} items to get predicates from`); await Promise.allSettled( - metadatas.map((metadata) => getOpsFromPredicatesEndpoint(metadata)) + metadatas.map((metadata) => getOpsFromEndpoint(metadata)) ).then((results) => { results.map((rec) => { - if (rec.status === "fulfilled") { + if (rec.status === "fulfilled" && rec.value) { res.push(rec.value); } }); }); + debug(`Got ${res.length} successful requests`); return res; } const updateSmartAPISpecs = async () => { const SMARTAPI_URL = 'https://smart-api.info/api/query?q=tags.name:translator&size=150&fields=paths,servers,tags,components.x-bte*,info,_meta'; const res = await axios.get(SMARTAPI_URL); - const localFilePath = path.resolve(__dirname, '../../../data/smartapi_specs.json'); + // const localFilePath = path.resolve(__dirname, '../../../data/smartapi_specs.json'); const predicatesFilePath = path.resolve(__dirname, '../../../data/predicates.json'); - fs.writeFile(localFilePath, JSON.stringify(res.data), (err) => { - if (err) throw err; - }); + // fs.writeFile(localFilePath, JSON.stringify(res.data), (err) => { + // if (err) throw err; + // }); const predicatesInfo = await getOpsFromPredicatesEndpoints(res.data.hits); fs.writeFile(predicatesFilePath, JSON.stringify(predicatesInfo), (err) => { if (err) throw err; @@ -108,7 +153,7 @@ module.exports = () => { debug(`Updating local copy of SmartAPI specs now at ${new Date().toUTCString()}!`); try { await updateSmartAPISpecs(); - debug("Successfull updated the local copy of SmartAPI specs.") + debug("Successfully updated the local copy of SmartAPI specs.") } catch (err) { debug(`Updating local copy of SmartAPI specs failed! The error message is ${err.toString()}`) } From b1d24135c7831041a17eda277bfb6264959d957a Mon Sep 17 00:00:00 2001 From: Marco Cano Date: Tue, 25 May 2021 17:25:33 -0700 Subject: [PATCH 48/75] feat: transform graph data from v1.1 to legacy format, uncomment code --- src/controllers/cron/update_local_smartapi.js | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/controllers/cron/update_local_smartapi.js b/src/controllers/cron/update_local_smartapi.js index 0e964e23..753b5826 100644 --- a/src/controllers/cron/update_local_smartapi.js +++ b/src/controllers/cron/update_local_smartapi.js @@ -138,11 +138,11 @@ const getOpsFromPredicatesEndpoints = async (specs) => { const updateSmartAPISpecs = async () => { const SMARTAPI_URL = 'https://smart-api.info/api/query?q=tags.name:translator&size=150&fields=paths,servers,tags,components.x-bte*,info,_meta'; const res = await axios.get(SMARTAPI_URL); - // const localFilePath = path.resolve(__dirname, '../../../data/smartapi_specs.json'); + const localFilePath = path.resolve(__dirname, '../../../data/smartapi_specs.json'); const predicatesFilePath = path.resolve(__dirname, '../../../data/predicates.json'); - // fs.writeFile(localFilePath, JSON.stringify(res.data), (err) => { - // if (err) throw err; - // }); + fs.writeFile(localFilePath, JSON.stringify(res.data), (err) => { + if (err) throw err; + }); const predicatesInfo = await getOpsFromPredicatesEndpoints(res.data.hits); fs.writeFile(predicatesFilePath, JSON.stringify(predicatesInfo), (err) => { if (err) throw err; From 0bd4e3f38efe518e202a975dc3f6d8b9119e401c Mon Sep 17 00:00:00 2001 From: Andrew Su Date: Thu, 27 May 2021 09:42:19 -0700 Subject: [PATCH 49/75] revise and update README --- README.md | 63 +++++++++++++++++++++++++------------------------------ 1 file changed, 28 insertions(+), 35 deletions(-) diff --git a/README.md b/README.md index 5d682ed3..84769bea 100644 --- a/README.md +++ b/README.md @@ -5,44 +5,29 @@ ## Introduction -This GitHub repo serves as the development repo for the TRAPI API implementation of BioThings Explorer. +This GitHub repo serves as the development repo for the TRAPI API implementation of **BioThings Explorer (BTE)**. BTE is an engine for autonomously querying a distributed knowledge graph. The distributed knowledge graph is made up of biomedical APIs that have been annotated with semantically-precise descriptions of their inputs and outputs in the [SmartAPI registry](https://smart-api.info/). This project is primarily funded by the [NCATS Translator project](https://ncats.nih.gov/translator). There is also an older [python version of BioThings Explorer](https://github.com/biothings/biothings_explorer) that is currently not being actively developed. -### What's BioThings Explorer +An older version of the meta knowledge graph that is consumed by BTE is in this figure (which, although older, gives a nice conceptual visualization of API interoperability): -BioThings Explorer aims at helping users querying and linking results from a variety of biomedical relevant APIs through one interface. The project is funded by the [NCATS Translator project](https://ncats.nih.gov/translator). +![BTE Meta-KG](diagrams/smartapi_metagraph.png "BioThings Explorer metagraph") -### What's TRAPI +### What's TRAPI? -TRAPI stands for [Translator Reasoner API](https://github.com/NCATSTranslator/ReasonerAPI). It is a standard defined for APIs developed within NCATS Biomedical Translator project to allow easy information exchange among them. +TRAPI stands for [Translator Reasoner API](https://github.com/NCATSTranslator/ReasonerAPI). It is a standard defined for APIs developed within NCATS Biomedical Translator project to facilitate information exchange between resources. BTE exports results via TRAPI to maintain interoperability with other Translator tools. BTE can also _consume_ knowledge resources that expose the TRAPI interface, but it also can consume APIs that have been annotated in the [SmartAPI registry](https://smart-api.info/) using the [x-bte extension](https://x-bte-extension.readthedocs.io/en/latest/index.html) to the OpenAPI specification. -### Our TRAPI Interface +### Live TRAPI Instance -Please visit our TRAPI API landing page [here](http://bte_trapi.smart-api.info/). +We maintain a live instance of this application at https://api.bte.ncats.io/ that can be used for testing. Query Examples can be found [here](/examples). -### Some Query Examples - -Query Examples can be found [here](https://github.com/kevinxin90/BioThings_Explorer_TRAPI/tree/master/examples). - ---- - - -## Current Development Status - -Currently, the BioThings Explorer TRAPI API implements TRAPI v1.0.0 standard, and can be queried at https://api.bte.ncats.io/v1/query endpoint. - - -The TRAPI v0.9.2 standard is deprecated. But it can still be tested using https://api.bte.ncats.io/query endpoint. - --- -## Requirements -For development, you will only need Node.js and a node global package, e.g. npm, installed in your environment. +## Local installations -### Node +### Requirements -NOTE: Node version must be higher than v12. +For development, you will only need Node.js and a node global package, e.g. npm, installed in your environment. Your Node version must be higher than v12. - #### Node installation on Windows @@ -75,14 +60,14 @@ If you need to update `npm`, you can make it using `npm`! Cool right? After runn --- -## Install +### Installation - $ git clone https://github.com/biothings/BioThings_Explorer_TRAPI` - $ cd BioThings_Explorer_TRAPI` - $ npm install` + $ git clone https://github.com/biothings/BioThings_Explorer_TRAPI + $ cd BioThings_Explorer_TRAPI + $ npm install -## Running the project +### Running the project $ npm start @@ -96,11 +81,11 @@ By default, the `/v1/query` endpoint only supports 3 queries per min, you could `$ MAX_QUERIES_PER_MIN=5 npm start` -## Simple build for production +### Simple build for production $ npm build -## Deploy +### Deploy A docker file is included in the base directory and can be used to build the customized container @@ -116,11 +101,14 @@ docker-compose up Public Docker image located at [link](https://hub.docker.com/repository/docker/biothings/bte_reasoner_api) -## Usage +### Usage + +You now can POST queries to `http://:3000/v1/query`. + +Query Examples can be found [here](/examples). -`http://:3000` -## Test with local SmartAPI spec +### Test with local SmartAPI spec The TRAPI interface has `/test/query` endpoint which uses a SmartAPI spec stored at **test** folder named **smartapi.json** @@ -138,3 +126,8 @@ Then, Run the image and mount your local smartapi spec folder Now, you should be able to test your local smartapi using POST queries at: `http://localhost:3000/test/query` + +### Testing on a specific SmartAPI API + +By default, BTE queries all APIs specified in the the[ config.js file](https://github.com/biothings/BioThings_Explorer_TRAPI/blob/master/src/routes/v1/config.js). In some cases, you may want to override that default to specifically query a single API. For example, the SmartAPI record for the "EBI Proteins API) is [43af91b3d7cae43591083bff9d75c6dd](https://smart-api.info/registry?q=43af91b3d7cae43591083bff9d75c6dd). To instruct BTE to query that API only, you can POST your query to http://localhost:3000/v1/smartapi/43af91b3d7cae43591083bff9d75c6dd/query + From d82a4f9f732fb0641a0a1726cdf4547a98d119c1 Mon Sep 17 00:00:00 2001 From: Andrew Su Date: Thu, 27 May 2021 09:43:39 -0700 Subject: [PATCH 50/75] upload metagraph image --- diagrams/smartapi_metagraph.png | Bin 0 -> 25893 bytes 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 diagrams/smartapi_metagraph.png diff --git a/diagrams/smartapi_metagraph.png b/diagrams/smartapi_metagraph.png new file mode 100644 index 0000000000000000000000000000000000000000..a3b03a7c326a53e06b868ff7334ab057a22e01a6 GIT binary patch literal 25893 zcmdSAcT`i~_aJ%`5(z{hGy@120!Baxy$cdLO0S}n(0lKw7y?oRA)p{2A|TSFNk>#V z1{6h5snSGxQvs18bMf=}eb>yadGqGYe=iGG_Bm&_v(Mi9+?;)GyrI6<33^U?002(t zXsa6o01Sko{RkSc2hV8l1vcmnbxk!64-dU1H~{&=?&D&I4jka<;ai~I7*N0iloVhr z1#rd#3IPBG50U|6Zvjdra99Z_0Kgd782~s30QHpsU<@3Bm?=R0Tfi9{ss!p&01C*& z7;rWQ>H`3v@&Z5t0Jo?@T~w8)srjh 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zt(}3CBSwZF$hF2ELA|yLd=tUXpnx-IQ(wSHhyAcBfI>crUOva|9_)`?Vq zf*pi2Ce0v8OQ7LckDSj^nnGS){KG|RaqjK+i!6i)F2g8e6&k|7?qVP=1{y+es4<#@ zsKES)a!SI>#YbZd7WqwO$2(WF* z0V|lh(5%-Ul1Y|mVhPn-#bht}4eM_rJJ{3G)ILWz$VW{=_tKf^Vi3k$009RDn2x9c z8vXb78J0BE01dGix5w{P@LB0v@;&h|!Oe%zC91Dn4Bdp{dE|sURq1PEBpSy21&1A0 zqyr^)LEiH^Bx<%J+zc@QCyzw+X(u-WNf^*ld0q$f0WA-0mja* Date: Thu, 27 May 2021 15:22:39 -0700 Subject: [PATCH 51/75] Add EBI Proteins to APIs BTE uses Add smartapi registration title for EBI Proteins API to this list (see entry here http://smart-api.info/registry?q=43af91b3d7cae43591083bff9d75c6dd) --- src/routes/v1/config.js | 1 + 1 file changed, 1 insertion(+) diff --git a/src/routes/v1/config.js b/src/routes/v1/config.js index 4df63bb4..25174ff4 100644 --- a/src/routes/v1/config.js +++ b/src/routes/v1/config.js @@ -29,6 +29,7 @@ exports.API_LIST = [ 'Multiomics Wellness KP API', 'BioLink API', 'LINCS Data Portal API', + 'EBI Proteins API' 'Automat IntAct', 'Automat Cord19 Scibite', 'Automat Gtopdb', From 1e180d2bc926b2257507c0e36db7d3bc88b701d3 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Fri, 28 May 2021 11:38:16 -0700 Subject: [PATCH 52/75] add trailing comma --- src/routes/v1/config.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/routes/v1/config.js b/src/routes/v1/config.js index 25174ff4..b63853a4 100644 --- a/src/routes/v1/config.js +++ b/src/routes/v1/config.js @@ -29,7 +29,7 @@ exports.API_LIST = [ 'Multiomics Wellness KP API', 'BioLink API', 'LINCS Data Portal API', - 'EBI Proteins API' + 'EBI Proteins API', 'Automat IntAct', 'Automat Cord19 Scibite', 'Automat Gtopdb', From 1d36a18694e4ca291afda8d25ddc878e33bf1b16 Mon Sep 17 00:00:00 2001 From: Marco Cano Date: Thu, 3 Jun 2021 15:06:40 -0700 Subject: [PATCH 53/75] fix: add details to meta graph error --- data/smartapi_specs.json | 2 +- package-lock.json | 244 ------------------------ src/controllers/meta_knowledge_graph.js | 10 +- 3 files changed, 9 insertions(+), 247 deletions(-) diff --git a/data/smartapi_specs.json b/data/smartapi_specs.json index 144bd098..b642d53a 100644 --- a/data/smartapi_specs.json +++ b/data/smartapi_specs.json @@ -1 +1 @@ -{"took":1089,"total":134,"max_score":0.5181118,"hits":[{"_id":"04f42ae00c8e5991b98d0e681dbdc596","_meta":{"date_created":"2021-03-04T18:27:43.614727+00:00","last_updated":"2021-05-25T07:01:10.186039+00:00","url":"http://bdt-social.renci.org:8080/socio_environmental_exposures_api/v1/openapi.json","username":"lstillwe"},"_score":0.5181118,"info":{"contact":{"email":"lisa@renci.org","name":"Lisa Stillwell"},"description":"\nThis API returns data from the US Census Bureau American Community Survey (ACS) for a given spatial location of interest.\n\nThe API returns estimated values for socio-economic variables and related variables for small geographic areas that may act as indirect indicators of relevant health behaviors and outcomes. The data are collected by the US Census Bureau and are publicly available.\n\nThe variables are taken from the five-year summary data file of the US Census Bureau ACS, which is constructed from five annual waves of the bureau’s largest household survey. Approximately, two million households have completed the survey annually since calendar year 2005. (Five waves of the survey before 2005 sampled approximately 500,000 households each.) See https://www.census.gov/acs/www/methodology/sample-size-and-data-quality/sample-size/ for more detail. Microdata are available, but small-area data are only available in summary tabulations.\n\nValues are provided at the US Census Block Group level, representing the 2007-2011 and 2012-2016 calendar-year periods for locations within the continental USA. Block groups, the smallest geographic area for which sample survey data are released, generally contain 600 to 3,000 people (e.g., the size of a single city apartment building). Block Groups are aggregates of an average of 39 Blocks each, each of which is delineated by visible and invisible geographic boundaries. Block groups, in turn, are aggregated into Census Tracts, which generally have a population size between 1,200 and 8,000 people, with an optimum size of 4,000 people. Census Tracts aggregate into counties and counties into states. Metropolitan and micropolitan areas are aggregates of counties. See https://www2.census.gov/geo/pdfs/reference/geodiagram.pdf for further detail. Census geography, even Block Groups, may cross municipal lines and may include both urbanized and rural areas. Because population is a large factor in determining Census geography, some Block Groups may cover an extensive rural or wilderness area while others are quite compact. Census Block, Block Group, and Tract boundaries may change somewhat with each decennial Census, but remain stable in between Censuses.\n\nThe US Census Bureau is mandated to preserve the confidentiality of individual-level data. Therefore, data are often summarized, coarsened into categories, or suppressed by complex secret algorithms (especially, but not limited to household income data). In addition, because the variables of interest may only apply to a small subset of Block Group missing data can occur. In some versions of the data, calculated values are suppressed in Block Groups with less than 50 residents.\n\nStandard errors for the socio-demographic variables are provided. Because each of the values in the ACS data files are summary statistics calculated from sample survey data for each Block Group, different samples yield somewhat different values. Therefore, the Census Bureau generates 80 replicate values for selected variables. These provide the basis for the estimated standard errors of the estimates.\n\nThe currently available variables are listed here:\n\n **(2007-2011 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **EstResidentialDensity** - block group population density\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\n **(2012-2016 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **EstTotalPopulation_SE** - standard error of total population in block group\n - **EstResidentialDensity** - block group population density\n- **EstResidentialDensity_SE** - standard error of residential population density in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **MedianHouseholdIncome_SE** - standard error of median household income\n- **EstPropPersonsNoHealthIns** - proportion of the block group population with no health insurance - **EstPropPersonsNoHealthIns_SE** - standard error of proportion of the block group population with no health insurance\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropNonHispWhite_SE** - standard error of proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropPersons5PlusNoEnglish_SE** - standard error of proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdsNoAuto_SE** - standard error of proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdSSI_SE** - standard error of proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHouseholdPA_SE** - standard error of proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolMaxEducation_SE** - standard error of proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdNoSpouse_SE** - standard error of proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild_SE** - standard error of proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n- **EstPropFemaleHouseholdAnyChild_SE** - standard error of proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. For example, Raleigh, North Carolina is at latitude 35.7796 and longitude -78.6382.\n\nAdditional details on the data can be found in this documentation: (https://github.com/lstillwe/socio-economic-api/blob/master/docs/CensusData.md)\n","license":{"name":"MIT","url":"http://opensource.org/licenses/MIT"},"title":"Socio-Environmental Exposures API","version":"1.0.1","x-translator":{"component":"KP","team":["Exposures Provider"]}},"paths":{"/values":{"get":{"description":"By passing in a location specification (lat, lon) and a year range, you can retrieve the the ACS Values for that location and year range\n","operationId":"get_values","parameters":[{"description":"latitude in decimal degrees format, ie: 32.47","in":"query","name":"latitude","required":true,"schema":{"type":"string"}},{"description":"longitude in decimal degrees format, ie: -86.5","in":"query","name":"longitude","required":true,"schema":{"type":"string"}},{"description":"ACS data year range specification","in":"query","name":"years","required":true,"schema":{"enum":["All (2007-2016)","2007-2011","2012-2016"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"latitude":{"example":"32.47","type":"string"},"longitude":{"example":-86.5,"type":"string"},"values":{"items":{"properties":{"EstPropFemaleHouseholdAnyChild":{"example":"0.154929577","type":"string"},"EstPropFemaleHouseholdAnyChild_SE":{"example":"0.075973316","type":"string"},"EstPropFemaleHouseholdFamilyChild":{"example":"0.227979275","type":"string"},"EstPropFemaleHouseholdFamilyChild_SE":{"example":"0.151408698","type":"string"},"EstPropFemaleHouseholdNoSpouse":{"example":"0.362694301","type":"string"},"EstPropFemaleHouseholdNoSpouse_SE":{"example":"0.108321058","type":"string"},"EstPropHighSchoolDropout":{"example":"n/a","type":"string"},"EstPropHighSchoolDropoutNoWork":{"example":"n/a","type":"string"},"EstPropHighSchoolMaxEducation":{"example":"0.53164557","type":"string"},"EstPropHighSchoolMaxEducation_SE":{"example":"0.076480429","type":"string"},"EstPropHouseholdPA":{"example":"0","type":"string"},"EstPropHouseholdPA_SE":{"example":"0.060887293","type":"string"},"EstPropHouseholdSSI":{"example":"0.088028169","type":"string"},"EstPropHouseholdSSI_SE":{"example":"0.04974414","type":"string"},"EstPropHouseholdsNoAuto":{"example":"0.038732394","type":"string"},"EstPropHouseholdsNoAuto_SE":{"example":"0.039252128","type":"string"},"EstPropMaleLittleWork":{"example":"0.385245902","type":"string"},"EstPropNonHispWhite":{"example":"0.763758389","type":"string"},"EstPropNonHispWhite_SE":{"example":"0.105181283","type":"string"},"EstPropPersons5PlusNoEnglish":{"example":"0.075070822","type":"string"},"EstPropPersons5PlusNoEnglish_SE":{"example":"0.040387049","type":"string"},"EstPropPersonsNoHealthIns":{"example":"0.183892617","type":"string"},"EstPropPersonsNoHealthIns_SE":{"example":"0.063328335","type":"string"},"EstResidentialDensity":{"example":"175.1077206","type":"string"},"EstResidentialDensity_SE":{"example":"32.32567504","type":"string"},"EstTotalPopulation":{"example":"745","type":"string"},"EstTotalPopulation_SE":{"example":"137.5303603","type":"string"},"MedianHouseholdIncome":{"example":"n/a","type":"string"},"MedianHouseholdIncome_SE":{"example":"9888","type":"string"},"geoid":{"example":"15000US010010201001","type":"string"},"years":{"example":"2012-2016","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"OK"},"400":{"content":{},"description":"Invalid parameter"},"404":{"content":{},"description":"No values found"},"500":{"content":{},"description":"Server error"}},"summary":"provides ACS values","x-openapi-router-controller":"swagger_server.controllers.default_controller"}}},"servers":[{"url":"/socio_environmental_exposures_api/v1"}],"tags":[{"name":"translator"}]},{"_id":"34e351cb4eac8bc7dbacf55f1b5ce44b","_meta":{"date_created":"2021-03-04T18:17:41.093656+00:00","last_updated":"2021-05-25T07:01:50.826242+00:00","url":"http://bdt-cmaq.renci.org:8080/cmaq_exposures_api/v1/openapi.json","username":"lstillwe"},"_score":0.5181118,"info":{"contact":{"email":"lisa@renci.org","name":"Lisa Stillwell"},"description":"This API returns estimated measurements of airborne particulate exposures for a given time period and spatial location of interest.\n\nEstimates are derived from the US EPA CONUS estimates of air quality available at https://www.epa.gov/hesc/rsig-related-downloadable-data-files. These data sets provide 8-hour ozone daily maximums (in ppbV) and daily PM2.5 daily averages (in µg/m3). The US EPA provides estimates at the resolution of US Census tract centroids for the continental US. For a given location, the API returns the estimated exposure for the census tract the location occurs in.\n\nThe API provides exposure estimates for calendar years 2002-2016. Resolution for model estimates is 12 km-squared, provisioned at a resolution of the US Census track centroid. The US census tract definition is from the calendar year 2010 definition of the US Census Bureau, for all years of CMAQ data.\n\nThe data sets sources are derived from air quality monitoring data from the National Air Monitoring Stations and Local Air Monitoring Stations (NAMS/LAMS) and numerical output from the Models-3/Community Multiscale Air Quality (CMAQ - https://www.epa.gov/cmaq).\n\nThe API currently provides the following exposure variables:\n- O3: provides estimated O3 concentration levels. Estimated values are for daily maximums in units of ppbV.\n- PM2.5: provides estimated pm2.5 concentration levels. Estimated values are for daily averages in units of µg/m3.\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. 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Sequence length can be a single length value such as 123 or range 123-234","in":"query","name":"seqLength","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Sequence md5 value.","in":"query","name":"md5","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Search UniProt entries","tags":["proteins"]}},"/proteins/covid-19/entries":{"get":{"description":"","operationId":"covidProteins","responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniProt entries by UniProt cross reference and its ID","tags":["proteins"]}},"/proteins/interaction/{accession}":{"get":{"description":"","operationId":"getAllInteractionEntries","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/UPInteraction"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/UPInteraction"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. The values's format should be a valid UniProtKB accession."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniProt interactions by accession","tags":["proteins"]}},"/proteins/{accession}":{"get":{"description":"","operationId":"getProteinsByAccession","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. 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Comma separated values accepted up to 20.","in":"query","name":"xref","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Genome accession. Comma separated values accepted up to 20.","in":"query","name":"genome_acc","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Reference Proteome(true) or not reference proteome (false)","in":"query","name":"is_ref_proteome","required":false,"schema":{"type":"string"}},{"description":"Redundant Proteome(true) or non redundant proteome (false)","in":"query","name":"is_redundant","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Proteome"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Proteome"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Search proteomes in UniProt","tags":["proteomes"]}},"/proteomes/genecentric/{upid}":{"get":{"deprecated":true,"description":"","operationId":"getGeneCentricByUpidDeprecated","parameters":[{"description":"UniProt Proteome UPID","in":"path","name":"upid","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Proteome"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Proteome"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid upid parameter. The value format should match the regular expression UP[0-9]{9}."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get gene centric proteins by proteome UPID is deprecated, please use new /genecentric?upid= endpoint","tags":["proteomes"]}},"/proteomes/proteins/{upid}":{"get":{"description":"","operationId":"getProteinsByUpid","parameters":[{"description":"UniProt Proteome UPID","in":"path","name":"upid","required":true,"schema":{"type":"string"}},{"description":"Reviewed(true) or not Reviewed (false)","in":"query","name":"reviewed","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Proteome"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Proteome"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid upid parameter. 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Values can be true or false.","in":"query","name":"unique","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"text/x-gff":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Search proteomics peptides in UniProt","tags":["proteomics"]}},"/proteomics/{accession}":{"get":{"description":"","operationId":"getProteomicsByAccession","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. 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Comma separated values accepted up to 20.","in":"query","name":"ipr","required":false,"schema":{"type":"string"}},{"description":"Search by signature database type, e.g. SMART, SUPFAM, Pfam, PIRSF, PROSITE, etc. Comma separated values accepted up to 20.","in":"query","name":"signaturetype","required":false,"schema":{"type":"string"}},{"description":"Search by signature database id, e.g. SM00044, SSF55073, PF00211, PIRSF039050, PS00452, etc. Comma separated values accepted up to 20.","in":"query","name":"signatureid","required":false,"schema":{"type":"string"}},{"description":"UniProt proteome UPID(s). Comma separated values accepted up to 100.","in":"query","name":"upid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."}},"summary":"Search UniParc entries","tags":["uniparc"]}},"/uniparc/accession/{accession}":{"get":{"description":"","operationId":"getUniParcEntryByUniprotAccession","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. The values's format should be a valid UniProtKB accession."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entry only by UniProt accession","tags":["uniparc"]}},"/uniparc/bestguess":{"get":{"description":"For a given user input (request parameters), Best Guess returns the UniParcEntry with a cross-reference to the longest active UniProtKB sequence (preferably from Swiss-Prot and if not then TrEMBL). It also returns the sequence and related information. If it finds more than one longest active UniProtKB sequence it returns 400 (Bad Request) error response with the list of cross references found.","operationId":"getUniParcBestGuess","parameters":[{"description":"UniParc ID (UPI). Comma separated values accepted up to 100","in":"query","name":"upi","required":false,"schema":{"type":"string"}},{"description":"UniProt accession(s). Comma separated values accepted up to 100.","in":"query","name":"accession","required":false,"schema":{"type":"string"}},{"description":"All UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted up to 100.","in":"query","name":"dbid","required":false,"schema":{"type":"string"}},{"description":"UniProt gene name. Comma separated values accepted up to 20.","in":"query","name":"gene","required":false,"schema":{"type":"string"}},{"description":"Organism taxon ID. Comma separated values accepted up to 20.","in":"query","name":"taxid","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Could not find best guess for the requested filter"}},"summary":"Get UniParc longest sequence for entries.","tags":["uniparc"]}},"/uniparc/dbreference/{dbid}":{"get":{"description":"","operationId":"getUniParcByUniparcAccessions","parameters":[{"description":"All UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq).","in":"path","name":"dbid","required":true,"schema":{"type":"string"}},{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entries by all UniParc cross reference accessions","tags":["uniparc"]}},"/uniparc/proteome/{upid}":{"get":{"description":"","operationId":"getByProteomeId","parameters":[{"description":"UniProt Proteome UPID","in":"path","name":"upid","required":true,"schema":{"type":"string"}},{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entries by Proteome UPID","tags":["uniparc"]}},"/uniparc/sequence":{"post":{"description":"","operationId":"getBySequence","parameters":[{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/UniparcSequenceParam"}},"application/xml":{"schema":{"$ref":"#/components/schemas/UniparcSequenceParam"}},"text/plain":{"schema":{"$ref":"#/components/schemas/UniparcSequenceParam"}}},"description":"Post uniparc Sequence in text, json or xml content type. Look the expected model in Data Type column","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entries by sequence","tags":["uniparc"]}},"/uniparc/upi/{upi}":{"get":{"description":"","operationId":"getUniParcEntryByUpId","parameters":[{"description":"UniParc ID (UPI)","in":"path","name":"upi","required":true,"schema":{"type":"string"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid upid parameter. The value format should match the regular expression UPI[\\w]{10}."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entry by UniParc UPI","tags":["uniparc"]}},"/variation":{"get":{"description":"Among the available response content types, PEFF format (PSI Extended FASTA Format from the Human Proteome Organisation - Proteomics Standards Initiative, HUPO-PSI) is provided with only variants reported in the output.","operationId":"searchVariation","parameters":[{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"Filter by the sourceType for variants: uniprot, large scale study and mixed. Comma separated values accepted up to 2.","in":"query","name":"sourcetype","required":false,"schema":{"type":"string"}},{"description":"Filter by consequenceType for variants: missense, stop gained or stop lost. Comma separated values accepted up to 2.","in":"query","name":"consequencetype","required":false,"schema":{"type":"string"}},{"description":"Search by specific wildType amino acid. Options: Any single letter amino acid and * for stop codon. Comma separated values accepted up to 20.","in":"query","name":"wildtype","required":false,"schema":{"type":"string"}},{"description":"Filter by the alternativeSequence amino acid. Any single letter amino acid and * for stopcodon and - for deletions. Comma separated values accepted up to 20.","in":"query","name":"alternativesequence","required":false,"schema":{"type":"string"}},{"description":"Filter by the amino acid range position in the sequence(s). Any valid amino acid range position within the length of the protein sequence such as 10-60 (start position to end position)","in":"query","name":"location","required":false,"schema":{"type":"string"}},{"description":"UniProt accession(s). Comma separated values accepted up to 100.","in":"query","name":"accession","required":false,"schema":{"type":"string"}},{"description":"Search by disease name/ acronym for associated variants , e.g. alzheimer disease 1 or AD1. Partial names allowed.","in":"query","name":"disease","required":false,"schema":{"maxItems":60,"minItems":2,"type":"string"}},{"description":"Search by MIM ID, e.g. 104300. Comma separated values accepted up to 20.","in":"query","name":"omim","required":false,"schema":{"type":"string"}},{"description":"Search by PubMed ID, e.g. 22472873. Comma separated values accepted up to 20.","in":"query","name":"evidence","required":false,"schema":{"type":"string"}},{"description":"Organism taxon ID. Comma separated values accepted up to 20.","in":"query","name":"taxid","required":false,"schema":{"type":"string"}},{"description":"Cross reference database type, e.g, dbSNP, cosmic curate or ClinVar. Comma separated values accepted up to 2.","in":"query","name":"dbtype","required":false,"schema":{"type":"string"}},{"description":"Cross-reference database ID, e.g. rs121918508 for dbSNP, COSM29836 for cosmic curated, rcv61200 for ClinVar. Comma separated values accepted up to 20.","in":"query","name":"dbid","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"text/x-gff":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Search natural variants in UniProt","tags":["variation"]}},"/variation/dbsnp/{dbid}":{"get":{"description":"","operationId":"searchByDbSNP","parameters":[{"description":"Cross-reference NIH-NCBI SNP database identifier, e.g. rs121918508","in":"path","name":"dbid","required":true,"schema":{"type":"string"}},{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"Filter by the sourceType for variants: uniprot, large scale study and mixed. Comma separated values accepted up to 2.","in":"query","name":"sourcetype","required":false,"schema":{"type":"string"}},{"description":"Filter by consequenceType for variants: missense, stop gained or stop lost. Comma separated values accepted up to 2.","in":"query","name":"consequencetype","required":false,"schema":{"type":"string"}},{"description":"Search by specific wildType amino acid. Options: Any single letter amino acid and * for stop codon. Comma separated values accepted up to 20.","in":"query","name":"wildtype","required":false,"schema":{"type":"string"}},{"description":"Filter by the alternativeSequence amino acid. Any single letter amino acid and * for stopcodon and - for deletions. Comma separated values accepted up to 20.","in":"query","name":"alternativesequence","required":false,"schema":{"type":"string"}},{"description":"Filter by the amino acid range position in the sequence(s). Any valid amino acid range position within the length of the protein sequence such as 10-60 (start position to end position)","in":"query","name":"location","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"text/x-gff":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get natural variants in UniProt by NIH-NCBI SNP database identifier","tags":["variation"]}},"/variation/hgvs/{hgvs}":{"get":{"description":"","operationId":"searchByHGVS","parameters":[{"description":"Human Genome Variation Society representation, e.g. NC_000017.11:g.58219213C>T","in":"path","name":"hgvs","required":true,"schema":{"type":"string"}},{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"Filter by the sourceType for variants: uniprot, large scale study and mixed. Comma separated values accepted up to 2.","in":"query","name":"sourcetype","required":false,"schema":{"type":"string"}},{"description":"Filter by consequenceType for variants: missense, stop gained or stop lost. Comma separated values accepted up to 2.","in":"query","name":"consequencetype","required":false,"schema":{"type":"string"}},{"description":"Search by specific wildType amino acid. Options: Any single letter amino acid and * for stop codon. Comma separated values accepted up to 20.","in":"query","name":"wildtype","required":false,"schema":{"type":"string"}},{"description":"Filter by the alternativeSequence amino acid. Any single letter amino acid and * for stopcodon and - for deletions. Comma separated values accepted up to 20.","in":"query","name":"alternativesequence","required":false,"schema":{"type":"string"}},{"description":"Filter by the amino acid range position in the sequence(s). Any valid amino acid range position within the length of the protein sequence such as 10-60 (start position to end position)","in":"query","name":"location","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"text/x-gff":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get natural variants in UniProt by HGVS expression","tags":["variation"]}},"/variation/{accession}":{"get":{"description":"","operationId":"getVariation","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}},{"description":"Filter by the sourceType for variants: uniprot, large scale study and mixed. Comma separated values accepted up to 2.","in":"query","name":"sourcetype","required":false,"schema":{"type":"string"}},{"description":"Filter by consequenceType for variants: missense, stop gained or stop lost. Comma separated values accepted up to 2.","in":"query","name":"consequencetype","required":false,"schema":{"type":"string"}},{"description":"Search by specific wildType amino acid. Options: Any single letter amino acid and * for stop codon. Comma separated values accepted up to 20.","in":"query","name":"wildtype","required":false,"schema":{"type":"string"}},{"description":"Filter by the alternativeSequence amino acid. Any single letter amino acid and * for stopcodon and - for deletions. Comma separated values accepted up to 20.","in":"query","name":"alternativesequence","required":false,"schema":{"type":"string"}},{"description":"Filter by the amino acid range position in the sequence(s). Any valid amino acid range position within the length of the protein sequence such as 10-60 (start position to end position)","in":"query","name":"location","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. The values's format should be a valid UniProtKB accession."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get natural variants by UniProt accession","tags":["variation"]}}},"servers":[{"url":"https://www.ebi.ac.uk/proteins/api"}],"tags":[{"name":"coordinates"},{"name":"antigen"},{"name":"uniparc"},{"name":"proteomics"},{"name":"features"},{"name":"proteomes"},{"name":"variation"},{"name":"genecentric"},{"name":"proteins"},{"name":"translator"}]},{"_id":"9ee398a738916a98b612068cc022454f","_meta":{"date_created":"2020-12-11T23:57:12.070157+00:00","last_updated":"2021-05-25T07:05:10.117829+00:00","url":"https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/LINCS/smartapi.yml","username":"kevinxin90"},"_score":0.24302328,"components":{"x-bte-kgs-operations":{"drug-indication":[{"inputs":[{"id":"LINCS","semantic":"ChemicalSubstance"}],"method":"get","outputs":[{"id":"MESH","semantic":"Disease"}],"parameters":{"id":"{inputs[0]}"},"path":"/query","predicate":"treats","response_mapping":{"$ref":"#/components/x-bte-response-mapping/drug-indication"},"source":"LINCS","supportBatch":false}]},"x-bte-response-mapping":{"drug-indication":{"MESH":"documents.mesh_id","name":"documents.mesh_heading"}}},"info":{"contact":{"email":"akoleti@med.miami.edu","name":"UM BD2K-LINCS DCIC","x-id":"http://lincsportal.ccs.miami.edu/","x-role":"responsible organization"},"description":"Documentation of the LINCS Data Portal web services. Learn more about [LINCS Data Portal](http://lincsportal.ccs.miami.edu/dcic-portal/)","termsOfService":"http://lincsportal.ccs.miami.edu/dcic-portal/#/terms","title":"LINCS Data Portal API","version":"1.0","x-translator":{"component":"KP","team":["Service Provider"]}},"paths":{"/fetchmolecules":{"get":{"parameters":[{"description":"Parameter used for searching small molecule metadata fields. Syntax is \"field name:\"value\"\" Do Not include outer quotes. Example; Name:\"Imatinib\", lincsidentifier:\"LSM-1028\", etc. Setting search term equal to the wildcard charachter, \"*\", will query for all fields of all records up to the specified limit.","in":"query","name":"searchTerm","required":true,"schema":{"type":"string"},"x-valueType":["http://identifiers.org/lincs.smallmolecule"]},{"description":"limit the number of records returned, default is 10","in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"A query response object with 'documents' property, each document corresponds to a small molecule that matched the query criteria.","x-responseValueType":[{"path":"lincs.smallmolecule","valueType":" http://identifiers.org/"}]}},"summary":"Get LINCS small molecule records, which contain both LINCS-based and general metadata about the small molecules tested in the NIH LINCS program. Parameter 'searchTerm' allows querying by specific metadata fields within small molecule records.","tags":["small molecule","query","LINCS","SchuererLab"]}},"/fetchcells":{"get":{"parameters":[{"description":"Parameter used for searching cell line metadata fields. Syntax is \"field name:\"value\"\" Do Not include outer quotes. Example; Name:\"MCF7\", lincsidentifier:\"LSM-1028\", etc. Setting search term equal to the wildcard charachter, \"*\", will query for all fields of all records up to the specified limit.","in":"query","name":"searchTerm","required":true,"schema":{"type":"string"},"x-valueType":[" http://identifiers.org/lincs.cell"]},{"description":"limit the number of records returned, default is 10","in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"A query response object with 'documents' property, each document corresponds to a cell line that matched the query criteria.","x-responseValueType":[{"path":"lincs.cell","valueType":"http://identifiers.org/'"}]}},"summary":"Get LINCS cell lines records, which contain both LINCS-based and general metadata about the cell lines tested in the NIH LINCS program. Parameter 'searchTerm' allows querying by specific metadata fields within the cell line records.","tags":["diseases","cells","query","LINCS","SchuererLab"]}},"/fetchdata":{"get":{"parameters":[{"description":"Parameter used for searching data set metadata fields. Syntax is \"field name:\"value\"\" Do Not include outer quotes. Example; centerfullname:\"HMS LINCS (Harvard Medical School)\", technologies:\"Fluorescence imaging\", etc. Setting search term equal to the wildcard charachter, \"*\", will query for all fields of all records up to the specified limit.","in":"query","name":"searchTerm","required":true,"schema":{"type":"string"},"x-valueType":["http://identifiers.org/lincs.data"]},{"description":"limit the number of records returned, default is 10","in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"A query response object with 'documents' property, each document corresponds to a dataset that matched the query criteria.","x-responseValueType":[{"path":"lincs.data","valueType":"http://identifiers.org/"}]}},"summary":"Get metadata for LINCS assay data sets (DOES NOT RETURN ASSAY ENDPOINT DATA). Parameter 'searchTerm' allows querying by specific metadata fields within the assay metadata records.","tags":["signature","query","LINCS","SchuererLab"]}},"/mechanismOfAction":{"get":{"parameters":[{"description":"Parameter used to search by LINCS small molecule identifier. Syntax is \"id=LSM-#\" Do Not use quotes. Example; id=LSM-1008.","in":"query","name":"id","required":false,"schema":{"type":"string"},"x-valueType":["http://identifiers.org/lincs.smallmolecule"]},{"description":"Parameter used to search by the full name of the mechanism of action. Syntax is \"moa=Mechanism name\" Do Not use quotes. Example; moa=Stem cell growth factor receptor inhibitor.","in":"query","name":"moa","required":false,"schema":{"type":"string"}},{"description":"limit the number of records returned, default is 10","in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"A query response object with 'documents' property, each document corresponds to a mechanism of action that matched the query criteria.","x-responseValueType":[{"path":"lincs.smallmolecule","valueType":"http://identifiers.org/"}]}},"summary":"Get known mechanisms of action for LINCS small molecules.","tags":["query","LINCS","SchuererLab","small molecule"]}},"/bioactivity":{"get":{"parameters":[{"description":"Parameter used to search by LINCS small molecule identifier. Syntax is \"id=LSM-#\" Do Not use quotes. Example; id=LSM-1008.","in":"query","name":"id","required":false,"schema":{"type":"string"},"x-valueType":["http://identifiers.org/lincs.smallmolecule"]},{"description":"Parameter used to search by the biochemical assay target using the target's preferred gene symbol from UniProt. Syntax is \"target=GENE SYMBOL\" Do Not use quotes. Examples; target=BRAF; target=MAPK13; etc..","in":"query","name":"target","required":false,"schema":{"type":"string"}},{"description":"Parameter used to search by the biochemical assay target using the target's UniProt accession number. Syntax is \"uniprot=accession number\" Do Not use quotes. Examples; uniprto=O15264; uniprot=P15056; etc..","in":"query","name":"uniprot","required":false,"schema":{"type":"string"}},{"description":"limit the number of records returned, default is 10","in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"A query response object with 'documents' property, each document corresponds to a bioactivity that matched the query criteria.","x-responseValueType":[{"path":"lincs.smallmolecule","valueType":"http://identifiers.org/"}]}},"summary":"Get known bioactivities for LINCS small molecules, these data are aggregated values resourced from the ChEMBL ver 23 database . The ChEMBL values were mined from numerous sources.","tags":["signature","query","LINCS","SchuererLab","small molecule"]}},"/drugindication":{"get":{"parameters":[{"description":"Parameter used to search by LINCS small molecule identifier. Syntax is \"id=LSM-#\" Do Not use quotes. Example; id=LSM-1008.","in":"query","name":"id","required":false,"schema":{"type":"string"},"x-valueType":["http://identifiers.org/lincs.smallmolecule"]},{"description":"Parameter used to search by the EFO drug indication. Syntax is \"efo=Drug Indication\" Do Not use quotes. Example; efo=renal carcinoma","in":"query","name":"efo","required":false,"schema":{"type":"string"}},{"description":"Parameter used to search by the MeSH drug indication. Syntax is \"efo=Drug Indication\" Do Not use quotes. Example; mesh=carcinoma, renal cell","in":"query","name":"mesh","required":false,"schema":{"type":"string"}},{"description":"limit the number of records returned, default is 10","in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"A query response object with 'documents' property, each document corresponds to a drug indication that matched the query criteria.","x-responseValueType":[{"path":"lincs.smallmolecule","valueType":"http://identifiers.org/"}]}},"summary":"Get known drug indications for LINCS small molecules, the indications are captured from both the Experimental Factor Ontology (EFO) and the Medical Subject Headings (MeSH) vocabularies.","tags":["signature","query","LINCS","SchuererLab","small molecule"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/drug-indication"}]}},"/disease":{"get":{"parameters":[{"description":"Parameter used to search by the DO disease name. Syntax is \"disease=disease name\" Do Not use quotes. Example; disease=breast carcinoma","in":"query","name":"disease","required":false,"schema":{"type":"string"}},{"description":"Parameter used to search by the DO identifier. Syntax is \"doid=DOID:#\" Do Not use quotes. Example; doid=DOID:3459","in":"query","name":"doid","required":false,"schema":{"type":"string"}},{"description":"limit the number of records returned, default is 10","in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"A query response object with 'documents' property, each document corresponds to a disease that matched the query criteria.","x-responseValueType":[{"path":"lincs.cell","valueType":"http://identifiers.org/"}]}},"summary":"Query for LINCS cell line identifiers by disease, the diseases are captured from the Disease Ontology (DO) vocabulary.","tags":["diseases","query","LINCS","SchuererLab","cells"]}}},"servers":[{"description":"Production server","url":"http://lincsportal.ccs.miami.edu/dcic/api/"}],"tags":[{"name":"small molecule"},{"name":"query"},{"name":"cells"},{"name":"gene"},{"name":"diseases"},{"name":"LINCS"},{"name":"SchuererLab"},{"name":"signature"},{"name":"translator"}]},{"_id":"fc8245e92c970298449294fc04211869","_meta":{"date_created":"2021-02-04T00:00:10.655676+00:00","last_updated":"2021-05-25T07:01:18.112693+00:00","slug":"cohdcovid","url":"https://raw.githubusercontent.com/WengLab-InformaticsResearch/cohd_api/cohd_covid/cohd/cohd_oas3.yaml","username":"CaseyTa"},"_score":0.2294851,"components":{"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) for COVID-19 Research API provides access to counts and frequencies (i.e., EHR visit prevalence) of conditions, procedures, drug exposures, and the co-occurrence frequencies between them for a cohort of hospitalized COVID-19 patients and two comparator cohorts of hospitalized influenza patients and hospitalized patients. Count and frequency data were derived from the [Columbia University Medical Center's](http://www.cumc.columbia.edu/) [OHDSI](https://www.ohdsi.org/) database including inpatient. Counts are the number of inpatient visits associated with the concept, e.g., diagnosed with a condition, exposed to a drug, or a procedure was performed. Frequencies are the number of unique visits associated with the concept divided by the total number of visits in the dataset, i.e., prevalence in the electronic health records. To protect patient privacy, all concepts and pairs of concepts where the count <= 10 were excluded, and counts were randomized by the Poisson distribution. \n\nDatasets from three primary cohorts are available: \n1) COVID-19: Hospitalized patients aged 18 or older with a COVID-19 related condition diagnosis and/or a confirmed positive COVID-19 test during their hospitalization period or within the prior 21 days. Date range: March 1, 2020 to September 1, 2020. This cohort is also further stratified by sex (male and female) and age (adult: 18-64, senior: 65+).\n2) General inpatient: All hospitalized patients aged 18 or older. Date range: January 1, 2014 to December 31, 2019.\n3) Influenza: Hospitalized patients aged 18 or older who had at least one occurrence of influenza conditions or pre-coordinated positive measurements or positive influenza testing in the prior 21 days or during their hospitalization period. Date range: January 1, 2014 to December 31, 2019.\n\nBoth hierarchical and non-hierarchical datasets are available for each cohort. In the hierarchical datasets, the counts for each concept include the visits from all descendant concepts. For example, the count for ibuprofen (ID 1177480) includes visits with Ibuprofen 600 MG Oral Tablet (ID 19019073), Ibuprofen 400 MG Oral Tablet (ID 19019072), Ibuprofen 20 MG/ML Oral Suspension (ID 19019050), etc. \n\nClinical concepts (e.g., conditions, procedures, drugs) are coded by their standard concept ID in the [OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki). API methods are provided to map to/from other vocabularies supported in OMOP and other ontologies using the EMBL-EBI Ontology Xref Service (OxO). \n\n\nThe following resources are available through this API: \n\n\n1. Metadata: Metadata on the COHD database, including dataset descriptions, number of concepts, etc. \n\n\n2. OMOP: Access to the common vocabulary for name and concept identifier mapping\n\n\n3. Clinical Frequencies: Access to the counts and frequencies of conditions, procedures, and drug exposures, and the associations between them. Frequency was determined as the number of visits with the code(s) / total number of visits. \n\n\n4. Concept Associations: Inferred associations between concepts using chi-square analysis, ratio between observed to expected frequency, and relative frequency. \n\n\nA [Python notebook](https://github.com/WengLab-InformaticsResearch/cohd_api/blob/master/notebooks/COHD_API_Example.ipynb) demonstrates simple examples of how to use the COHD API.\n\n\nCOHD was developed at the [Columbia University Department of Biomedical Informatics](https://www.dbmi.columbia.edu/) as a collaboration between the [Weng Lab](http://people.dbmi.columbia.edu/~chw7007/), [Tatonetti Lab](http://tatonettilab.org/), and the [NCATS Biomedical Data Translator](https://ncats.nih.gov/translator) program (TReK Team). This work was supported in part by grants: NCATS 1OT2TR003434, NLM R01LM012895, NCATS OT3TR002027, NLM R01LM009886-08A1, and NIGMS R01GM107145.\n\nThe following external resources may be useful: \n[OHDSI](https://www.ohdsi.org/) \n[OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki) \n[Athena](http://athena.ohdsi.org) (OMOP vocabularies, search, concept relationships, concept hierarchy) \n[Atlas](http://www.ohdsi.org/web/atlas/) (OMOP vocabularies, search, concept relationships, concept hierarchy, concept sets) \n[NCATS Biomedical Data Translator](https://sites.google.com/ncats.nih.gov/translator-io/home) \n","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"termsOfService":"http://cohd.io/terms/","title":"Columbia Open Health Data (COHD) for COVID-19 Research","version":"3.0.0","x-accessRestriction":"none","x-implementationLanguage":"Python","x-translator":{"component":"KP","team":["Clinical Data Provider"]},"x-trapi":{"version":"1.0.0"}},"paths":{"/metadata/datasets":{"get":{"description":"Returns a list of datasets, including dataset ID, name, and description.","operationId":"datasets","responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"dataset_description":{"example":"Hospitalized patients with a COVID-19 condition and/or positive lab test (non-hierarchical)","type":"string"},"dataset_id":{"example":1,"type":"integer"},"dataset_name":{"example":"COVID Cohort (non-hierarchical)","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of dataset descriptions."},"default":{"description":"Unexpected error"}},"summary":"Enumerates the datasets available in COHD","tags":["Metadata"]}},"/metadata/domainCounts":{"get":{"description":"Returns a list of domains and the number of concepts in each domain.","operationId":"domainCounts","parameters":[{"description":"The dataset_id of the dataset to query. 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. 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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. 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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":{"description":"Attempts 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":{"description":"Attempts 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":0.000005585247351056813,"type":"integer"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2008271,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequency of a pair of concepts","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id. Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"q","required":true,"schema":{"type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":19041324,"type":"integer"},"associated_concept_name":{"example":"Acetaminophen 325 MG Oral Tablet [Tylenol]","type":"string"},"associated_domain_id":{"example":"Drug","type":"string"},"concept_count":{"example":277,"type":"integer"},"concept_frequency":{"example":0.0001547113516242737,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptDomainFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id restricted by domain of the associated concept_id. Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptDomainFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id","required":true,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc. See /metadata/domainCounts for a list of valid domain IDs.","example":"Procedure","in":"query","name":"domain","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":2211361,"type":"integer"},"associated_concept_name":{"example":"Radiologic examination, chest, 2 views, frontal and lateral","type":"string"},"associated_domain_id":{"example":"Procedure","type":"string"},"concept_count":{"example":257,"type":"integer"},"concept_frequency":{"example":0.00014354085692216007,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/mostFrequentConcepts":{"get":{"description":"Retrieves the most frequent concepts.","operationId":"mostFrequentConcepts","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The number of concepts to retreieve, e.g., 100. 0 or unspecified will return all matching concepts.","example":100,"in":"query","name":"q","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The domain_id to restrict to, e.g., \"Condition\", \"Drug\", \"Procedure\". See /metadata/domainCounts for a list of valid domain IDs.","example":"Condition","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"(Optional) The vocabulary_id(s) to restrict to, e.g., \"SNOMED\", \"MedDRA\", \"RxNorm\", \"ATC\" etc. Comma separated to include multiple vocabularies, e.g., \"SNOMED,MedDRA\". Default: unrestricted","example":null,"in":"query","name":"vocabulary_id","required":false,"schema":{"type":"string"}},{"description":"(Optional) The concept_class_id(s) to restrict to. concept_class_ids are specific to each vocabulary, e.g.,: [ATC](https://en.wikipedia.org/wiki/Anatomical_Therapeutic_Chemical_Classification_System) {ATC 1st, ATC 2nd, ATC 3rd, ATC 4th, ATC 5th}; [MedDRA](https://en.wikipedia.org/wiki/MedDRA) {PT, HLT, HLGT, SOC}; [RxNorm](https://www.nlm.nih.gov/research/umls/rxnorm/docs/2015/appendix5.html) {Ingredient, Clinical Drug Form, Clinical Drug Comp, Clinical Drug}. Comma separated to include multiple concept_class_ids, e.g., \"PT,HLT\". Default: unrestricted","example":null,"in":"query","name":"concept_class_id","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_class_id":{"example":"Clinical Finding","type":"string"},"concept_count":{"example":233790,"type":"integer"},"concept_frequency":{"example":0.1305774978203572,"type":"integer"},"concept_id":{"example":320128,"type":"integer"},"concept_name":{"example":"Essential hypertension","type":"string"},"dataset_id":{"example":1,"type":"integer"},"domain_id":{"example":"Condition","type":"string"},"vocabulary_id":{"example":"SNOMED","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of most frequent concepts."},"default":{"description":"Unexpected error"}},"summary":"Most frequent concepts [by domain]","tags":["Clinical Frequencies"]}},"/association/chiSquare":{"get":{"description":"Returns the chi-square statistic and p-value between pairs of concepts. Results are returned in descending order of the chi-square statistic. Note that due to large sample sizes, the chi-square can become very large. \n\nThe expected frequencies for the chi-square analysis are calculated based on the single concept frequencies and assuming independence between concepts. P-value is calculated with 1 DOF. \n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"chiSquare","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If this parameter is specified, then the chi-square between concept_id_1 and concept_id_2 is returned. If this parameter is not specified, then a list of chi-squared results between concept_id_1 and other concepts is returned.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"adj_p-value":{"description":"Bonferonni adjusted p-value, adjusted with the total number of pairs of concepts in the dataset.","example":0.0314,"type":"number"},"chi_square":{"example":370026.1780081638,"type":"integer"},"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Instillation of therapeutic substance into bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":4021588,"type":"integer"},"dataset_id":{"example":3,"type":"integer"},"p-value":{"example":0.0314,"type":"number"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of concept pairs and chi-squared values."},"default":{"description":"Unexpected error"}},"summary":"Chi-square analysis on pairs of concepts","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/obsExpRatio":{"get":{"description":"Returns the natural logarithm of the ratio between the observed count and expected count. Expected count is calculated from the single concept frequencies and assuming independence between the concepts. Results are returned in descending order of ln_ratio.\n\nexpected_count = Count_1_and_2 * num_visits / (Count_1 * Count_2)\n\nln_ratio = ln(expected_count)\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Results for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"obsExpRatio","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}},{"description":"The confidence level used for calculating confidence intervals (default 0.99).","example":0.99,"in":"query","name":"confidence","required":false,"schema":{"type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Closed [transurethral] biopsy of bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2003784,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"expected_count":{"example":0.060838982345591645,"type":"integer"},"ln_ratio":{"example":7.561698473261244,"type":"integer"},"observed_count":{"example":117,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concepts and observed-expected frequency ratio."},"default":{"description":"Unexpected error"}},"summary":"Observed Count / Expected Count","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/relativeFrequency":{"get":{"description":"Calculates the relative frequency (i.e., conditional probability) between pairs of concepts. Results are returned in descending order of relative frequency. Note that due to the randomization of the counts, the calculated relative frequencies can exceed the limit of 1.0.\n\nRelative Frequency = Count_1_and_2 / Count_2\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"relativeFrequency","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict concept_id_2 (the base concept) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}},{"description":"The confidence level used for calculating confidence intervals (default 0.99).","example":0.99,"in":"query","name":"confidence","required":false,"schema":{"type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_2_count":{"example":82,"type":"integer"},"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Radical cystectomy","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2003805,"type":"integer"},"concept_pair_count":{"example":29,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"relative_frequency":{"example":0.35365853658536583,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concepts and relative frequency."},"default":{"description":"Unexpected error"}},"summary":"Relative frequency between pairs of concepts","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/predicates":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"additionalProperties":{"description":"Array of predicates","items":{"type":"string"},"type":"array"},"description":"Target map","type":"object"},"description":"Source map","example":{"biolink:ChemicalSubstance":{"biolink:Gene":["biolink:directly_interacts_with","biolink:decreases_activity_of"]}},"type":"object"}}},"description":"Predicates by source and target"}},"summary":"Get supported relationships by source and target","tags":["translator","trapi"]}},"/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.\n \nFor the subject node, the id must be specified (category is ignored).\n \nFor the object node, both the id and category are optional. If id is specified for the object node, then the association between the two identified concepts is returned. If id is not specified and category is specified, the associations between the subject node and all concepts with the specified category are returned. If neither are specified, then the associations between the subject node and all concepts are returned.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.\nAdditional behavior options can be controlled using the optional parameters in query_options.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"id\": \"MONDO:0021113\",\n \"category\": \"biolink:Disease\"\n },\n \"n01\": {\n \"category\": \"biolink:Procedure\"\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicate\": \"biolink:correlated_with\",\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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. 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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)","version":"4.0.0","x-accessRestriction":"none","x-implementationLanguage":"Python","x-translator":{"biolink-version":"1.8.2","component":"KP","externalDocs":{"description":"The values for component and team are restricted according to this external JSON schema. 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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":{"description":"Attempts 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. 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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":{"description":"Attempts 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. 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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. 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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":0.000005585247351056813,"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. 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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. \n \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"]}},"/predicates":{"get":{"deprecated":true,"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"additionalProperties":{"description":"Array of predicates","items":{"type":"string"},"type":"array"},"description":"Target map","type":"object"},"description":"Source map","example":{"biolink:ChemicalSubstance":{"biolink:Gene":["biolink:directly_interacts_with","biolink:decreases_activity_of"]}},"type":"object"}}},"description":"Predicates by source and target"}},"summary":"Get supported relationships by source and target","tags":["predicates"]}},"/meta_knowledge_graph":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns meta knowledge graph representation of this TRAPI web service."}},"summary":"Meta knowledge graph representation of this TRAPI web service.","tags":["meta_knowledge_graph"]}},"/query":{"post":{"description":"Query the COHD API following the [NCATS Translator Reasoner Standard API](https://github.com/NCATSTranslator/ReasonerAPI). Only single hop queries are supported. See the example query_graph.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"ids\": [\"DOID:9053\"],\n \"categories\": [\"biolink:Disease\"]\n },\n \"n01\": {\n \"categories\": [\"biolink:Procedure\"]\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicates\": [\"biolink:correlated_with\"],\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\n \"dataset_id\": 3,\n \"confidence_interval\": 0.99,\n \"min_cooccurrence\": 50,\n \"threshold\": 0.5,\n \"local_oxo\": true,\n \"max_results\": 50,\n \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\n \"biolink_only\": true\n }\n}","schema":{"$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)."},"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","tags":["query"]}},"/1.0.0/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.\nFor the subject node, the id must be specified (category is ignored).\nFor the object node, both the id and category are optional. If id is specified for the object node, then the association between the two identified concepts is returned. If id is not specified and category is specified, the associations between the subject node and all concepts with the specified category are returned. If neither are specified, then the associations between the subject node and all concepts are returned.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.\nAdditional behavior options can be controlled using the optional parameters in query_options.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"id\": \"DOID:9053\",\n \"category\": \"biolink:Disease\"\n },\n \"n01\": {\n \"category\": \"biolink:Procedure\"\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicate\": \"biolink:correlated_with\",\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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. 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Census Block, Block Group, and Tract boundaries may change somewhat with each decennial Census, but remain stable in between Censuses.\n\nThe US Census Bureau is mandated to preserve the confidentiality of individual-level data. Therefore, data are often summarized, coarsened into categories, or suppressed by complex secret algorithms (especially, but not limited to household income data). In addition, because the variables of interest may only apply to a small subset of Block Group missing data can occur. In some versions of the data, calculated values are suppressed in Block Groups with less than 50 residents.\n\nStandard errors for the socio-demographic variables are provided. Because each of the values in the ACS data files are summary statistics calculated from sample survey data for each Block Group, different samples yield somewhat different values. Therefore, the Census Bureau generates 80 replicate values for selected variables. 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These data sets provide 8-hour ozone daily maximums (in ppbV) and daily PM2.5 daily averages (in µg/m3). The US EPA provides estimates at the resolution of US Census tract centroids for the continental US. For a given location, the API returns the estimated exposure for the census tract the location occurs in.\n\nThe API provides exposure estimates for calendar years 2002-2016. Resolution for model estimates is 12 km-squared, provisioned at a resolution of the US Census track centroid. The US census tract definition is from the calendar year 2010 definition of the US Census Bureau, for all years of CMAQ data.\n\nThe data sets sources are derived from air quality monitoring data from the National Air Monitoring Stations and Local Air Monitoring Stations (NAMS/LAMS) and numerical output from the Models-3/Community Multiscale Air Quality (CMAQ - https://www.epa.gov/cmaq).\n\nThe API currently provides the following exposure variables:\n- O3: provides estimated O3 concentration levels. Estimated values are for daily maximums in units of ppbV.\n- PM2.5: provides estimated pm2.5 concentration levels. Estimated values are for daily averages in units of µg/m3.\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. 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See the HPMS Field Manual (https://www.fhwa.dot.gov/policyinformation/hpms/fieldmanual/) for detailed explanation of methods and fields.\n\nResults are limited to major (or primary) roadway types, including interstates, principal arteries, minor arteries, and major collectors, in the United States.\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. For example, Raleigh, North Carolina is at latitude 35.7796 and longitude -78.6382.\n\nIn addition to distance, the API retrieves additional information, including the roadway type, the maximum speed limit, the annual average daily traffic (AADT), and the total number of lanes. See https://www.fhwa.dot.gov/policyinformation/travel_monitoring/pubs/aadt/ for information on how AADT is computed.\n\nThe following roadway types are supported:\n* Off-Network\n* Rural Restricted Access\n* Rural Unrestricted Access\n* Urban Restricted Access\n* Urban Unrestricted Access\n\nIn some cases, roadway type, AADT, and speed are not available in the HPMS data set. In this case, data from the US Census Bureau TIGER (Topologically Integrated Geographic Encoding and Referencing) data set (available at census.gov) was used to obtain roadway type. Roadway segments without roadway type were dropped from the dataset; this amounted to approximately 5% of roadways, many of which had not yet been built. Missing AADT and speeds were populated using a variety of methods. First, a lookup table was built with county averages by roadway type and facility type and populated with values from segments that already had AADT and/or speed. Second, in cases in which the lookup table could not be used (e.g., ramps often didn’t match), speeds were assigned based on the function class of the roadway, state averages, or averages for a similar (but different) roadway type.\n\nThe API is currently restricted to calendar year 2016.\n","license":{"name":"MIT","url":"http://opensource.org/licenses/MIT"},"title":"Roadway Exposures API","version":"1.0.0","x-translator":{"component":"KP","team":["Exposures Provider"]}},"paths":{"/distance":{"get":{"description":"Get the distance to the nearest roadway in meters","operationId":"get_distance","parameters":[{"description":"latitude of the location of interest using decimal format (WGS84 datum)","in":"query","name":"latitude","required":true,"schema":{"format":"double","type":"number"}},{"description":"longitude of the location of interest using decimal format (WGS84 datum)","in":"query","name":"longitude","required":true,"schema":{"format":"double","type":"number"}},{"description":"the maximum search distance between the location of interest and nearest road (meters)","in":"query","name":"limit_distance","schema":{"default":500,"format":"double","type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/RoadwayData"}}},"description":"search results matching criteria"},"204":{"content":{},"description":"No content returned - nearest roadway is >500 meters from specified latitude/longitude"},"400":{"content":{},"description":"Bad input parameter"},"404":{"content":{},"description":"No values found"},"500":{"content":{},"description":"Server error"}},"summary":"retrieves distance in meters","x-openapi-router-controller":"swagger_server.controllers.default_controller"}}},"servers":[{"url":"/roadway_proximity_api/v1"}],"tags":[{"name":"translator"}]},{"_id":"55510544e95386a5a8ac3b88f9d00d21","_meta":{"date_created":"2021-01-30T20:45:51.489336+00:00","last_updated":"2021-06-03T07:02:59.510913+00:00","url":"https://name-resolution-sri.renci.org/openapi.json","username":"kshefchek"},"_score":0.5320405,"info":{"contact":{"email":"patrick@covar.com","name":"Patrick Wang","x-id":"https://github.com/patrickkwang","x-role":"responsible developer"},"description":"Name resolution service

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[ICEES Overview page](https://researchsoftwareinstitute.github.io/data-translator/apps/icees)\n
[documentation](https://github.com/NCATS-Tangerine/icees-api/tree/master/docs) \n
[source](https://github.com/NCATS-Tangerine/icees-api/tree/master/) \n
[ICEES API example queries](https://github.com/NCATS-Tangerine/icees-api/tree/master/#examples)\n
dictionary for versioning of tables\n
\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
versiontable content
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[ICEES Overview page](https://researchsoftwareinstitute.github.io/data-translator/apps/icees)\n
[documentation](https://github.com/NCATS-Tangerine/icees-api/tree/master/docs) \n
[source](https://github.com/NCATS-Tangerine/icees-api/tree/master/) \n
[ICEES API example queries](https://github.com/NCATS-Tangerine/icees-api/tree/master/#examples)\n
dictionary for versioning of tables\n
\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
versiontable content
1.0.0cdw, acs, nearest road, and cmaq from 2010
2.0.0cdw in FHIR format, acs, nearest road, and cmaq from 2010
3.0.0cdw in FHIR format, acs, nearest road, cmaq, and EPR from 2010 to 2016
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Comma separated values accepted up to 20.","in":"query","name":"ipr","required":false,"schema":{"type":"string"}},{"description":"Search by signature database type, e.g. SMART, SUPFAM, Pfam, PIRSF, PROSITE, etc. Comma separated values accepted up to 20.","in":"query","name":"signaturetype","required":false,"schema":{"type":"string"}},{"description":"Search by signature database id, e.g. SM00044, SSF55073, PF00211, PIRSF039050, PS00452, etc. Comma separated values accepted up to 20.","in":"query","name":"signatureid","required":false,"schema":{"type":"string"}},{"description":"UniProt proteome UPID(s). Comma separated values accepted up to 100.","in":"query","name":"upid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."}},"summary":"Search UniParc entries","tags":["uniparc"]}},"/uniparc/accession/{accession}":{"get":{"description":"","operationId":"getUniParcEntryByUniprotAccession","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. 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Count and frequency data were derived from the [Columbia University Medical Center's](http://www.cumc.columbia.edu/) [OHDSI](https://www.ohdsi.org/) database including inpatient. Counts are the number of inpatient visits associated with the concept, e.g., diagnosed with a condition, exposed to a drug, or a procedure was performed. Frequencies are the number of unique visits associated with the concept divided by the total number of visits in the dataset, i.e., prevalence in the electronic health records. To protect patient privacy, all concepts and pairs of concepts where the count <= 10 were excluded, and counts were randomized by the Poisson distribution. \n\nDatasets from three primary cohorts are available: \n1) COVID-19: Hospitalized patients aged 18 or older with a COVID-19 related condition diagnosis and/or a confirmed positive COVID-19 test during their hospitalization period or within the prior 21 days. Date range: March 1, 2020 to September 1, 2020. This cohort is also further stratified by sex (male and female) and age (adult: 18-64, senior: 65+).\n2) General inpatient: All hospitalized patients aged 18 or older. Date range: January 1, 2014 to December 31, 2019.\n3) Influenza: Hospitalized patients aged 18 or older who had at least one occurrence of influenza conditions or pre-coordinated positive measurements or positive influenza testing in the prior 21 days or during their hospitalization period. Date range: January 1, 2014 to December 31, 2019.\n\nBoth hierarchical and non-hierarchical datasets are available for each cohort. In the hierarchical datasets, the counts for each concept include the visits from all descendant concepts. For example, the count for ibuprofen (ID 1177480) includes visits with Ibuprofen 600 MG Oral Tablet (ID 19019073), Ibuprofen 400 MG Oral Tablet (ID 19019072), Ibuprofen 20 MG/ML Oral Suspension (ID 19019050), etc. \n\nClinical concepts (e.g., conditions, procedures, drugs) are coded by their standard concept ID in the [OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki). API methods are provided to map to/from other vocabularies supported in OMOP and other ontologies using the EMBL-EBI Ontology Xref Service (OxO). \n\n\nThe following resources are available through this API: \n\n\n1. Metadata: Metadata on the COHD database, including dataset descriptions, number of concepts, etc. \n\n\n2. OMOP: Access to the common vocabulary for name and concept identifier mapping\n\n\n3. Clinical Frequencies: Access to the counts and frequencies of conditions, procedures, and drug exposures, and the associations between them. Frequency was determined as the number of visits with the code(s) / total number of visits. \n\n\n4. Concept Associations: Inferred associations between concepts using chi-square analysis, ratio between observed to expected frequency, and relative frequency. \n\n\nA [Python notebook](https://github.com/WengLab-InformaticsResearch/cohd_api/blob/master/notebooks/COHD_API_Example.ipynb) demonstrates simple examples of how to use the COHD API.\n\n\nCOHD was developed at the [Columbia University Department of Biomedical Informatics](https://www.dbmi.columbia.edu/) as a collaboration between the [Weng Lab](http://people.dbmi.columbia.edu/~chw7007/), [Tatonetti Lab](http://tatonettilab.org/), and the [NCATS Biomedical Data Translator](https://ncats.nih.gov/translator) program (TReK Team). This work was supported in part by grants: NCATS 1OT2TR003434, NLM R01LM012895, NCATS OT3TR002027, NLM R01LM009886-08A1, and NIGMS R01GM107145.\n\nThe following external resources may be useful: \n[OHDSI](https://www.ohdsi.org/) \n[OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki) \n[Athena](http://athena.ohdsi.org) (OMOP vocabularies, search, concept relationships, concept hierarchy) \n[Atlas](http://www.ohdsi.org/web/atlas/) (OMOP vocabularies, search, concept relationships, concept hierarchy, concept sets) \n[NCATS Biomedical Data Translator](https://sites.google.com/ncats.nih.gov/translator-io/home) \n","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"termsOfService":"http://cohd.io/terms/","title":"Columbia Open Health Data (COHD) for COVID-19 Research","version":"3.0.0","x-accessRestriction":"none","x-implementationLanguage":"Python","x-translator":{"component":"KP","team":["Clinical Data Provider"]},"x-trapi":{"version":"1.0.0"}},"paths":{"/metadata/datasets":{"get":{"description":"Returns a list of datasets, including dataset ID, name, and description.","operationId":"datasets","responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"dataset_description":{"example":"Hospitalized patients with a COVID-19 condition and/or positive lab test (non-hierarchical)","type":"string"},"dataset_id":{"example":1,"type":"integer"},"dataset_name":{"example":"COVID Cohort (non-hierarchical)","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of dataset descriptions."},"default":{"description":"Unexpected error"}},"summary":"Enumerates the datasets available in COHD","tags":["Metadata"]}},"/metadata/domainCounts":{"get":{"description":"Returns a list of domains and the number of concepts in each domain.","operationId":"domainCounts","parameters":[{"description":"The dataset_id of the dataset to query. 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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":{"description":"Attempts 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":{"description":"Attempts 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":0.000005585247351056813,"type":"integer"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2008271,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequency of a pair of concepts","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id. Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"q","required":true,"schema":{"type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":19041324,"type":"integer"},"associated_concept_name":{"example":"Acetaminophen 325 MG Oral Tablet [Tylenol]","type":"string"},"associated_domain_id":{"example":"Drug","type":"string"},"concept_count":{"example":277,"type":"integer"},"concept_frequency":{"example":0.0001547113516242737,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptDomainFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id restricted by domain of the associated concept_id. Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptDomainFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id","required":true,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc. See /metadata/domainCounts for a list of valid domain IDs.","example":"Procedure","in":"query","name":"domain","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":2211361,"type":"integer"},"associated_concept_name":{"example":"Radiologic examination, chest, 2 views, frontal and lateral","type":"string"},"associated_domain_id":{"example":"Procedure","type":"string"},"concept_count":{"example":257,"type":"integer"},"concept_frequency":{"example":0.00014354085692216007,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/mostFrequentConcepts":{"get":{"description":"Retrieves the most frequent concepts.","operationId":"mostFrequentConcepts","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The number of concepts to retreieve, e.g., 100. 0 or unspecified will return all matching concepts.","example":100,"in":"query","name":"q","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The domain_id to restrict to, e.g., \"Condition\", \"Drug\", \"Procedure\". See /metadata/domainCounts for a list of valid domain IDs.","example":"Condition","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"(Optional) The vocabulary_id(s) to restrict to, e.g., \"SNOMED\", \"MedDRA\", \"RxNorm\", \"ATC\" etc. Comma separated to include multiple vocabularies, e.g., \"SNOMED,MedDRA\". Default: unrestricted","example":null,"in":"query","name":"vocabulary_id","required":false,"schema":{"type":"string"}},{"description":"(Optional) The concept_class_id(s) to restrict to. concept_class_ids are specific to each vocabulary, e.g.,: [ATC](https://en.wikipedia.org/wiki/Anatomical_Therapeutic_Chemical_Classification_System) {ATC 1st, ATC 2nd, ATC 3rd, ATC 4th, ATC 5th}; [MedDRA](https://en.wikipedia.org/wiki/MedDRA) {PT, HLT, HLGT, SOC}; [RxNorm](https://www.nlm.nih.gov/research/umls/rxnorm/docs/2015/appendix5.html) {Ingredient, Clinical Drug Form, Clinical Drug Comp, Clinical Drug}. Comma separated to include multiple concept_class_ids, e.g., \"PT,HLT\". Default: unrestricted","example":null,"in":"query","name":"concept_class_id","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_class_id":{"example":"Clinical Finding","type":"string"},"concept_count":{"example":233790,"type":"integer"},"concept_frequency":{"example":0.1305774978203572,"type":"integer"},"concept_id":{"example":320128,"type":"integer"},"concept_name":{"example":"Essential hypertension","type":"string"},"dataset_id":{"example":1,"type":"integer"},"domain_id":{"example":"Condition","type":"string"},"vocabulary_id":{"example":"SNOMED","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of most frequent concepts."},"default":{"description":"Unexpected error"}},"summary":"Most frequent concepts [by domain]","tags":["Clinical Frequencies"]}},"/association/chiSquare":{"get":{"description":"Returns the chi-square statistic and p-value between pairs of concepts. Results are returned in descending order of the chi-square statistic. Note that due to large sample sizes, the chi-square can become very large. \n\nThe expected frequencies for the chi-square analysis are calculated based on the single concept frequencies and assuming independence between concepts. P-value is calculated with 1 DOF. \n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"chiSquare","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If this parameter is specified, then the chi-square between concept_id_1 and concept_id_2 is returned. If this parameter is not specified, then a list of chi-squared results between concept_id_1 and other concepts is returned.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"adj_p-value":{"description":"Bonferonni adjusted p-value, adjusted with the total number of pairs of concepts in the dataset.","example":0.0314,"type":"number"},"chi_square":{"example":370026.1780081638,"type":"integer"},"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Instillation of therapeutic substance into bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":4021588,"type":"integer"},"dataset_id":{"example":3,"type":"integer"},"p-value":{"example":0.0314,"type":"number"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of concept pairs and chi-squared values."},"default":{"description":"Unexpected error"}},"summary":"Chi-square analysis on pairs of concepts","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/obsExpRatio":{"get":{"description":"Returns the natural logarithm of the ratio between the observed count and expected count. Expected count is calculated from the single concept frequencies and assuming independence between the concepts. Results are returned in descending order of ln_ratio.\n\nexpected_count = Count_1_and_2 * num_visits / (Count_1 * Count_2)\n\nln_ratio = ln(expected_count)\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Results for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"obsExpRatio","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}},{"description":"The confidence level used for calculating confidence intervals (default 0.99).","example":0.99,"in":"query","name":"confidence","required":false,"schema":{"type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Closed [transurethral] biopsy of bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2003784,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"expected_count":{"example":0.060838982345591645,"type":"integer"},"ln_ratio":{"example":7.561698473261244,"type":"integer"},"observed_count":{"example":117,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concepts and observed-expected frequency ratio."},"default":{"description":"Unexpected error"}},"summary":"Observed Count / Expected Count","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/relativeFrequency":{"get":{"description":"Calculates the relative frequency (i.e., conditional probability) between pairs of concepts. Results are returned in descending order of relative frequency. Note that due to the randomization of the counts, the calculated relative frequencies can exceed the limit of 1.0.\n\nRelative Frequency = Count_1_and_2 / Count_2\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"relativeFrequency","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict concept_id_2 (the base concept) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}},{"description":"The confidence level used for calculating confidence intervals (default 0.99).","example":0.99,"in":"query","name":"confidence","required":false,"schema":{"type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_2_count":{"example":82,"type":"integer"},"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Radical cystectomy","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2003805,"type":"integer"},"concept_pair_count":{"example":29,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"relative_frequency":{"example":0.35365853658536583,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concepts and relative frequency."},"default":{"description":"Unexpected error"}},"summary":"Relative frequency between pairs of concepts","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/predicates":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"additionalProperties":{"description":"Array of predicates","items":{"type":"string"},"type":"array"},"description":"Target map","type":"object"},"description":"Source map","example":{"biolink:ChemicalSubstance":{"biolink:Gene":["biolink:directly_interacts_with","biolink:decreases_activity_of"]}},"type":"object"}}},"description":"Predicates by source and target"}},"summary":"Get supported relationships by source and target","tags":["translator","trapi"]}},"/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.\n \nFor the subject node, the id must be specified (category is ignored).\n \nFor the object node, both the id and category are optional. If id is specified for the object node, then the association between the two identified concepts is returned. If id is not specified and category is specified, the associations between the subject node and all concepts with the specified category are returned. If neither are specified, then the associations between the subject node and all concepts are returned.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.\nAdditional behavior options can be controlled using the optional parameters in query_options.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"id\": \"MONDO:0021113\",\n \"category\": \"biolink:Disease\"\n },\n \"n01\": {\n \"category\": \"biolink:Procedure\"\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicate\": \"biolink:correlated_with\",\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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)."},"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","tags":["translator","trapi"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false}],"x-swagger-router-controller":"swagger_server.controllers.query_controller"}},"/0.9.3/query":{"post":{"description":"This endpoint is temporarily provided to support TRAPI 0.9.3 queries\nQuery 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.\nFor the source node, the curie must be specified (type is ignored).\nFor the target node, both the curie and type are optional. If curie is specified for the target node, then the association between the two identified concepts is returned. If curie is not specified and type is specified, the associations between the source node and all concepts with the specified type are returned. If neither are specified, then the associations between the source node and all concepts are returned.\nCOHD will attempt to map the CURIE to an OMOP concept and the node type to an OMOP domain.","operationId":"query093","requestBody":{"content":{"application/json":{"example":"{\n \"max_results\": 50,\n \"message\": {\n \"query_graph\": {\n \"nodes\": [\n {\n \"id\": \"n00\",\n \"curie\": \"MONDO:0021113\",\n \"type\": \"biolink:Disease\"\n },\n {\n \"id\": \"n01\",\n \"type\": \"biolink:Procedure\"\n }\n ],\n \"edges\": [\n {\n \"id\": \"e00\",\n \"type\": \"biolink:correlated_with\",\n \"source_id\": \"n00\",\n \"target_id\": \"n01\"\n }\n ]\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\n \"dataset_id\": 3,\n \"confidence_interval\": 0.99,\n \"min_cooccurrence\": 50,\n \"threshold\": 0.5,\n \"local_oxo\": true,\n \"ontology_targets\": {\n \"biolink:Disease\": [\"ICD9\", \"SNOMEDCT\", \"DOID\"],\n \"biolink:Drug\": [\"RxNorm\"],\n \"biolink:Procedure\": [\"ICD10PCS\", \"SNOMEDCT\"],\n \"_DEFAULT\": []\n },\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/Message"}}},"description":"successful operation"},"400":{"description":"Invalid status value"}},"summary":"Query COHD following NCATS Translator Reasoner Standard API version 0.9.3","tags":["translator","trapi"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false}],"x-swagger-router-controller":"swagger_server.controllers.query_controller"}},"/translator/biolink_to_omop":{"post":{"description":"Map Biolink CURIEs to OMOP concepts","operationId":"biolink_to_omop","requestBody":{"content":{"application/json":{"example":"{\n \"curies\": [\n \"HP:0002907\",\n \"MONDO:0001187\"\n ]\n}","schema":{"$ref":"#/components/schemas/CurieList"}}},"description":"List of CURIEs","required":true},"responses":{"200":{"content":{"application/json":{"example":"{\n \"MONDO:0001187\": {\n \"distance\": 2,\n \"omop_concept_id\": 197508,\n \"omop_concept_name\": \"Malignant tumor of urinary bladder\"\n }\n}","schema":{"additionalProperties":{"description":"Mapping from OMOP concept to Biolink","properties":{"distance":{"description":"mapping distance","type":"integer"},"omop_concept_id":{"type":"integer"},"omop_concept_name":{"type":"string"}},"type":"object"}}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from Biolink to OMOP","tags":["translator"]}},"/translator/omop_to_biolink":{"post":{"description":"Map OMOP concepts to normalized Biolink nodes using SRI Node Normalizer.","operationId":"omop_to_biolink","requestBody":{"content":{"application/json":{"example":"{\n \"omop_ids\": [\n 78472,\n 197508\n ]\n}","schema":{"$ref":"#/components/schemas/OmopList"}}},"description":"List of OMOP IDs","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"type":"object"},"example":"{\n \"197508\": {\n \"equivalent_identifiers\": [\n {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n {\n \"identifier\": \"DOID:11054\"\n },\n {\n \"identifier\": \"OMIM:109800\"\n },\n {\n \"identifier\": \"UMLS:C0005684\"\n },\n {\n \"identifier\": \"NCIT:C9334\"\n },\n {\n \"identifier\": \"SNOMEDCT:399326009\"\n }\n ],\n \"id\": {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n \"type\": [\n \"biolink:Disease\",\n \"biolink:DiseaseOrPhenotypicFeature\",\n \"biolink:BiologicalEntity\",\n \"biolink:NamedThing\"\n ]\n }\n}","type":"object"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized. Mapping from OMOP concept to Biolink normalized nodes. See [SRI Node Normalizer](https://nodenormalization-sri.renci.org/docs#/) for response format"},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from OMOP to Biolink","tags":["translator"]}}},"servers":[{"url":"https://covid.cohd.io/api/"}],"tags":[{"description":"COHD metadata","name":"Metadata"},{"description":"OMOP Common Data Model concepts","name":"OMOP"},{"description":"Clinical frequency data","name":"Clinical Frequencies"},{"description":"Estimated association between concepts","name":"Concept Associations"},{"description":"Concept-age distributions, concept-pair delta distributions, and temporal analyses","name":"Temporal Clinical Data"},{"description":"NCATS Biomedical Data Translator APIs","name":"translator"},{"description":"Implements the NCATS Translator Reasoner API 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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)","version":"4.0.0","x-accessRestriction":"none","x-implementationLanguage":"Python","x-translator":{"biolink-version":"1.8.2","component":"KP","externalDocs":{"description":"The values for component and team are restricted according to this external JSON schema. 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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":{"description":"Attempts 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. 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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":{"description":"Attempts 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. 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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. 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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":0.000005585247351056813,"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. 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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. \n \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"]}},"/predicates":{"get":{"deprecated":true,"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"additionalProperties":{"description":"Array of predicates","items":{"type":"string"},"type":"array"},"description":"Target map","type":"object"},"description":"Source map","example":{"biolink:ChemicalSubstance":{"biolink:Gene":["biolink:directly_interacts_with","biolink:decreases_activity_of"]}},"type":"object"}}},"description":"Predicates by source and target"}},"summary":"Get supported relationships by source and target","tags":["predicates"]}},"/meta_knowledge_graph":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns meta knowledge graph representation of this TRAPI web service."}},"summary":"Meta knowledge graph representation of this TRAPI web service.","tags":["meta_knowledge_graph"]}},"/query":{"post":{"description":"Query the COHD API following the [NCATS Translator Reasoner Standard API](https://github.com/NCATSTranslator/ReasonerAPI). Only single hop queries are supported. See the example query_graph.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"ids\": [\"DOID:9053\"],\n \"categories\": [\"biolink:Disease\"]\n },\n \"n01\": {\n \"categories\": [\"biolink:Procedure\"]\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicates\": [\"biolink:correlated_with\"],\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\n \"dataset_id\": 3,\n \"confidence_interval\": 0.99,\n \"min_cooccurrence\": 50,\n \"threshold\": 0.5,\n \"local_oxo\": true,\n \"max_results\": 50,\n \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\n \"biolink_only\": true\n }\n}","schema":{"$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)."},"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","tags":["query"]}},"/1.0.0/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.\nFor the subject node, the id must be specified (category is ignored).\nFor the object node, both the id and category are optional. If id is specified for the object node, then the association between the two identified concepts is returned. If id is not specified and category is specified, the associations between the subject node and all concepts with the specified category are returned. If neither are specified, then the associations between the subject node and all concepts are returned.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.\nAdditional behavior options can be controlled using the optional parameters in query_options.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"id\": \"DOID:9053\",\n \"category\": \"biolink:Disease\"\n },\n \"n01\": {\n \"category\": \"biolink:Procedure\"\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicate\": \"biolink:correlated_with\",\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Query COHD following NCATS TRAPI 1.0","tags":["translator"]}},"/translator/biolink_to_omop":{"post":{"description":"Map Biolink CURIEs to OMOP concepts","operationId":"biolink_to_omop","requestBody":{"content":{"application/json":{"example":"{\n \"curies\": [\n \"HP:0002907\",\n \"MONDO:0001187\"\n ]\n}","schema":{"$ref":"#/components/schemas/CurieList"}}},"description":"List of CURIEs","required":true},"responses":{"200":{"content":{"application/json":{"example":"{\n \"MONDO:0001187\": {\n \"distance\": 2,\n \"omop_concept_id\": 197508,\n \"omop_concept_name\": \"Malignant tumor of urinary bladder\"\n }\n}","schema":{"additionalProperties":{"description":"Mapping from OMOP concept to Biolink","properties":{"distance":{"description":"mapping distance","type":"integer"},"omop_concept_id":{"type":"integer"},"omop_concept_name":{"type":"string"}},"type":"object"}}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from Biolink to OMOP","tags":["translator"]}},"/translator/omop_to_biolink":{"post":{"description":"Map OMOP concepts to normalized Biolink nodes using SRI Node Normalizer.","operationId":"omop_to_biolink","requestBody":{"content":{"application/json":{"example":"{\n \"omop_ids\": [\n 78472,\n 197508\n ]\n}","schema":{"$ref":"#/components/schemas/OmopList"}}},"description":"List of OMOP IDs","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"type":"object"},"example":"{\n \"197508\": {\n \"equivalent_identifiers\": [\n {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n {\n \"identifier\": \"DOID:11054\"\n },\n {\n \"identifier\": \"OMIM:109800\"\n },\n {\n \"identifier\": \"UMLS:C0005684\"\n },\n {\n \"identifier\": \"NCIT:C9334\"\n },\n {\n \"identifier\": \"SNOMEDCT:399326009\"\n }\n ],\n \"id\": {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n \"type\": [\n \"biolink:Disease\",\n \"biolink:DiseaseOrPhenotypicFeature\",\n \"biolink:BiologicalEntity\",\n \"biolink:NamedThing\"\n ]\n }\n}","type":"object"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized. Mapping from OMOP concept to Biolink normalized nodes. See [SRI Node Normalizer](https://nodenormalization-sri.renci.org/docs#/) for response format"},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from OMOP to Biolink","tags":["translator"]}}},"servers":[{"url":"https://cohd.io/api/"}],"tags":[{"description":"COHD metadata","name":"Metadata"},{"description":"OMOP Common Data Model concepts","name":"OMOP"},{"description":"Clinical frequency data","name":"Clinical Frequencies"},{"description":"Estimated association between concepts","name":"Concept Associations"},{"description":"Concept-age distributions, concept-pair delta distributions, and temporal analyses","name":"Temporal Clinical Data"},{"description":"Get supported relationships by source and target","name":"predicates"},{"description":"Query reasoner using a predefined question type","name":"query"},{"description":"Required for SmartAPI validation of x-translator","name":"translator"},{"description":"Required for SmartAPI validation of x-trapi","name":"trapi"}]}]} \ No newline at end of file diff --git a/package-lock.json b/package-lock.json index 2de9d12f..f1329b5e 100644 --- a/package-lock.json +++ b/package-lock.json @@ -9,7 +9,6 @@ "version": "2.7.0", "license": "ISC", "dependencies": { - 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For more information, see https://github.com/axios/axios/pull/3410", - "dependencies": { - "follow-redirects": "1.5.10" - } - }, - "node_modules/biomedical_id_resolver/node_modules/follow-redirects": { - "version": "1.5.10", - "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.5.10.tgz", - "integrity": "sha512-0V5l4Cizzvqt5D44aTXbFZz+FtyXV1vrDN6qrelxtfYQKW0KO0W2T/hkE8xvGa/540LkZlkaUjO4ailYTFtHVQ==", - "dependencies": { - "debug": "=3.1.0" - }, - "engines": { - "node": ">=4.0" - } - }, - "node_modules/biomedical_id_resolver/node_modules/follow-redirects/node_modules/debug": { - "version": "3.1.0", - "resolved": "https://registry.npmjs.org/debug/-/debug-3.1.0.tgz", - "integrity": "sha512-OX8XqP7/1a9cqkxYw2yXss15f26NKWBpDXQd0/uK/KPqdQhxbPa994hnzjcE2VqQpDslf55723cKPUOGSmMY3g==", - "dependencies": { - "ms": "2.0.0" - } - }, - "node_modules/biomedical_id_resolver/node_modules/ms": { - "version": "2.0.0", - "resolved": "https://registry.npmjs.org/ms/-/ms-2.0.0.tgz", - "integrity": "sha1-VgiurfwAvmwpAd9fmGF4jeDVl8g=" - }, "node_modules/biothings-explorer-filters": { "version": "1.0.1", "resolved": "https://registry.npmjs.org/biothings-explorer-filters/-/biothings-explorer-filters-1.0.1.tgz", @@ -16023,20 +15916,6 @@ "node": ">= 0.8" } }, - "node_modules/pascal-case": { - "version": "3.1.2", - "resolved": "https://registry.npmjs.org/pascal-case/-/pascal-case-3.1.2.tgz", - "integrity": "sha512-uWlGT3YSnK9x3BQJaOdcZwrnV6hPpd8jFH1/ucpiLRPh/2zCVJKS19E4GvYHvaCcACn3foXZ0cLB9Wrx1KGe5g==", - "dependencies": { - "no-case": "^3.0.4", - "tslib": "^2.0.3" - } - }, - "node_modules/pascal-case/node_modules/tslib": { - "version": "2.2.0", - "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.2.0.tgz", - "integrity": "sha512-gS9GVHRU+RGn5KQM2rllAlR3dU6m7AcpJKdtH8gFvQiC4Otgk98XnmMU+nZenHt/+VhnBPWwgrJsyrdcw6i23w==" - }, "node_modules/pascalcase": { "version": "0.1.1", "resolved": "https://registry.npmjs.org/pascalcase/-/pascalcase-0.1.1.tgz", @@ -19940,18 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"requires": { - "@biothings-explorer/call-apis": "^1.23.0", - "@biothings-explorer/smartapi-kg": "^3.8.0", - "biolink-model": "^0.3.0", - "biomedical_id_resolver": "^3.9.0", - "debug": "^4.3.1", - "lodash": "^4.17.21", - "ms": "^2.1.3", - "redis": "^3.0.2" - }, - "dependencies": { - "ms": { - "version": "2.1.3", - "resolved": "https://registry.npmjs.org/ms/-/ms-2.1.3.tgz", - "integrity": "sha512-6FlzubTLZG3J2a/NVCAleEhjzq5oxgHyaCU9yYXvcLsvoVaHJq/s5xXI6/XXP6tz7R9xAOtHnSO/tXtF3WRTlA==" - } - } - }, "@biothings-explorer/smartapi-kg": { "version": "3.8.1", "resolved": "https://registry.npmjs.org/@biothings-explorer/smartapi-kg/-/smartapi-kg-3.8.1.tgz", @@ -22536,79 +22381,6 @@ "integrity": "sha512-jDctJ/IVQbZoJykoeHbhXpOlNBqGNcwXJKJog42E5HDPUwQTSdjCHdihjj0DlnheQ7blbT6dHOafNAiS8ooQKA==", "dev": true }, - "biolink-model": { - "version": "0.3.1", - "resolved": "https://registry.npmjs.org/biolink-model/-/biolink-model-0.3.1.tgz", - "integrity": 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"https://registry.npmjs.org/debug/-/debug-3.1.0.tgz", - "integrity": "sha512-OX8XqP7/1a9cqkxYw2yXss15f26NKWBpDXQd0/uK/KPqdQhxbPa994hnzjcE2VqQpDslf55723cKPUOGSmMY3g==", - "requires": { - "ms": "2.0.0" - } - } - } - }, - "ms": { - "version": "2.0.0", - "resolved": "https://registry.npmjs.org/ms/-/ms-2.0.0.tgz", - "integrity": "sha1-VgiurfwAvmwpAd9fmGF4jeDVl8g=" - } - } - }, "biothings-explorer-filters": { "version": "1.0.1", "resolved": "https://registry.npmjs.org/biothings-explorer-filters/-/biothings-explorer-filters-1.0.1.tgz", @@ -32085,22 +31857,6 @@ "resolved": "https://registry.npmjs.org/parseurl/-/parseurl-1.3.3.tgz", "integrity": "sha512-CiyeOxFT/JZyN5m0z9PfXw4SCBJ6Sygz1Dpl0wqjlhDEGGBP1GnsUVEL0p63hoG1fcj3fHynXi9NYO4nWOL+qQ==" }, - "pascal-case": { - "version": "3.1.2", - "resolved": "https://registry.npmjs.org/pascal-case/-/pascal-case-3.1.2.tgz", - "integrity": "sha512-uWlGT3YSnK9x3BQJaOdcZwrnV6hPpd8jFH1/ucpiLRPh/2zCVJKS19E4GvYHvaCcACn3foXZ0cLB9Wrx1KGe5g==", - "requires": { - "no-case": "^3.0.4", - "tslib": "^2.0.3" - }, - "dependencies": { - "tslib": { - "version": "2.2.0", - "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.2.0.tgz", - "integrity": "sha512-gS9GVHRU+RGn5KQM2rllAlR3dU6m7AcpJKdtH8gFvQiC4Otgk98XnmMU+nZenHt/+VhnBPWwgrJsyrdcw6i23w==" - } - } - }, "pascalcase": { "version": "0.1.1", "resolved": "https://registry.npmjs.org/pascalcase/-/pascalcase-0.1.1.tgz", diff --git a/src/controllers/meta_knowledge_graph.js b/src/controllers/meta_knowledge_graph.js index 53e926bf..e4337d9c 100644 --- a/src/controllers/meta_knowledge_graph.js +++ b/src/controllers/meta_knowledge_graph.js @@ -6,6 +6,7 @@ const util = require('util'); const PredicatesLoadingError = require("../utils/errors/predicates_error"); const ids = require("./ids"); const readFile = util.promisify(fs.readFile); +const debug = require("debug")("biothings-explorer-trapi:metakg"); module.exports = class MetaKnowledgeGraphHandler { constructor(smartapiID = undefined, team = undefined) { @@ -19,18 +20,23 @@ module.exports = class MetaKnowledgeGraphHandler { const kg = new meta_kg.default(smartapi_specs, predicates); try { if (smartapiID !== undefined) { + debug(`Constructing with SmartAPI ID ${smartapiID}`) kg.constructMetaKGSync(false, { smartAPIID: smartapiID }) } else if (team !== undefined) { + debug(`Constructing with team ${team}`) kg.constructMetaKGSync(false, { teamName: team }) } else { + debug(`Constructing with default`) kg.constructMetaKGSync(true, {}) } if (kg.ops.length === 0) { - throw new PredicatesLoadingError("Failed to Load MetaKG"); + debug(`Found 0 operations`) + throw new PredicatesLoadingError("Not Found - 0 operations"); } return kg; } catch (error) { - throw new PredicatesLoadingError("Failed to Load MetaKG"); + debug(`ERROR getting graph with ID:${smartapiID} team:${team} because ${error}`) + throw new PredicatesLoadingError(`Failed to Load MetaKG: ${error}`); } } From af36907ac0a0f9d4b0a2d5aecfc20bf355cefcfa Mon Sep 17 00:00:00 2001 From: Anders Riutta Date: Fri, 4 Jun 2021 16:43:21 -0700 Subject: [PATCH 54/75] chore: update URLs to biothings --- package.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/package.json b/package.json index f7701de9..d409cc96 100644 --- a/package.json +++ b/package.json @@ -17,7 +17,7 @@ }, "repository": { "type": "git", - "url": "git+https://github.com/kevinxin90/single-hop-app.js.git" + "url": "git+https://github.com/biothings/BioThings_Explorer_TRAPI.git" }, "keywords": [ "bte", @@ -29,9 +29,9 @@ "author": "jiwen xin", "license": "ISC", "bugs": { - "url": "https://github.com/kevinxin90/single-hop-app.js/issues" + "url": "https://github.com/biothings/BioThings_Explorer_TRAPI/issues" }, - "homepage": "https://github.com/kevinxin90/single-hop-app.js#readme", + "homepage": "https://github.com/biothings/BioThings_Explorer_TRAPI#readme", "devDependencies": { "artillery": "^1.6.2", "coveralls": "^3.1.0", From ef43b579e2dbe7b4dc968cef2b83c0efb34e5907 Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Fri, 4 Jun 2021 22:20:04 -0700 Subject: [PATCH 55/75] build: add debug command --- package.json | 1 + 1 file changed, 1 insertion(+) diff --git a/package.json b/package.json index f7701de9..61666634 100644 --- a/package.json +++ b/package.json @@ -5,6 +5,7 @@ "main": "src/server.js", "scripts": { "start": "nodemon src/server.js", + "debug": "DEBUG=* nodemon src/server.js", "test": "jest --forceExit", "test-cov": "jest --coverage", "coveralls": "jest --coverage --forceExit && cat ./coverage/lcov.info | ./node_modules/coveralls/bin/coveralls.js && rm -rf ./coverage", From 8014129d930525d2e8f58a355250b769d7a4560f Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Fri, 4 Jun 2021 22:21:01 -0700 Subject: [PATCH 56/75] build: expose redis port --- docker-compose-dev.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docker-compose-dev.yml b/docker-compose-dev.yml index bb54ba25..71a7af3e 100644 --- a/docker-compose-dev.yml +++ b/docker-compose-dev.yml @@ -16,5 +16,7 @@ services: container_name: bte_redis restart: always image: "redis:alpine" + ports: + - '6379:6379' volumes: - ./.redis.conf:/usr/local/etc/redis/redis.conf From 25159855a8e8bfef0dea6c033f06d4904425c1d5 Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Fri, 4 Jun 2021 22:21:59 -0700 Subject: [PATCH 57/75] build: updated query_graph_handler version --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 61666634..5f119d1b 100644 --- a/package.json +++ b/package.json @@ -42,7 +42,7 @@ "supertest": "^6.1.3" }, "dependencies": { - "@biothings-explorer/query_graph_handler": "^1.16.1", + "@biothings-explorer/query_graph_handler": "^1.17.1", "@biothings-explorer/smartapi-kg": "^3.8.1", "axios": "^0.21.1", "biothings-explorer-graphql": "2.1.1", From 40d91a9b74c7895d7bb0ee5c885bca8c4fea8855 Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Sat, 5 Jun 2021 14:57:08 -0700 Subject: [PATCH 58/75] build: remove unused packages --- package.json | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/package.json b/package.json index 760d7ca9..de9cb919 100644 --- a/package.json +++ b/package.json @@ -45,9 +45,7 @@ "@biothings-explorer/query_graph_handler": "^1.17.1", "@biothings-explorer/smartapi-kg": "^3.8.1", "axios": "^0.21.1", - "biothings-explorer-graphql": "2.1.1", "body-parser": "^1.19.0", - "camelcase": "^6.2.0", "compression": "^1.7.4", "cors": "^2.8.5", "debug": "^4.3.1", @@ -55,7 +53,6 @@ "express": "^4.17.1", "express-rate-limit": "^5.2.6", "express-winston": "^4.1.0", - "graphql-depth-limit": "^1.1.0", "helmet": "^4.4.1", "husky": "^4.3.8", "lodash": "^4.17.21", @@ -65,8 +62,7 @@ "redis": "^3.1.1", "snake-case": "^3.0.4", "winston": "^3.3.3", - "winston-daily-rotate-file": "^4.5.1", - "winston-elasticsearch": "^0.7.13" + "winston-daily-rotate-file": "^4.5.1" }, "husky": { "hooks": { From 686cc2dca7c19cceba8a5470af1653644c437375 Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Sat, 5 Jun 2021 14:57:52 -0700 Subject: [PATCH 59/75] test: updated expected values --- __test__/integration/TRAPIv1.1.test.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/__test__/integration/TRAPIv1.1.test.js b/__test__/integration/TRAPIv1.1.test.js index 6ae17044..e00f6312 100644 --- a/__test__/integration/TRAPIv1.1.test.js +++ b/__test__/integration/TRAPIv1.1.test.js @@ -89,7 +89,7 @@ describe("Testing v1.1 endpoints", () => { .then((response) => { expect(response.body).toEqual({ "error": "Unable to load predicates", - "more_info": "Failed to Load MetaKG", + "more_info": "Failed to Load MetaKG: PredicatesLoadingError: Not Found - 0 operations", }); }) }) @@ -121,7 +121,7 @@ describe("Testing v1.1 endpoints", () => { .expect('Content-Type', /json/) .then((response) => { expect(response.body).toHaveProperty("error", "Unable to load predicates"); - expect(response.body).toHaveProperty("more_info", "Failed to Load MetaKG"); + expect(response.body).toHaveProperty("more_info", "Failed to Load MetaKG: PredicatesLoadingError: Not Found - 0 operations"); }) }) From cd71ed1a81c0dd18aa132d48145c79e119983ef9 Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Sat, 5 Jun 2021 15:07:58 -0700 Subject: [PATCH 60/75] chore: update local cache files --- data/predicates.json | 2 +- data/smartapi_specs.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/data/predicates.json b/data/predicates.json index 89ab3cd2..bb610ed7 100644 --- a/data/predicates.json +++ b/data/predicates.json @@ -1 +1 @@ -[{"association":{"api_name":"ICEES API","smartapi":{"id":"0864c0912390d0876c3c34a00acb5c3b","meta":{"date_created":"2021-05-12T17:58:14.831380+00:00","last_updated":"2021-05-25T18:26:40.301395+00:00","url":"https://icees.renci.org:16339/openapi.json","username":"patrickkwang"}},"x-translator":{"component":"KP","team":["Exposures Provider"]}},"tags":["translator","trapi"],"query_operation":{"path":"/query","server":"https://icees.renci.org:16339","method":"post"},"predicates_path":"/meta_knowledge_graph","predicates":{"biolink:Environment":{"biolink:Environment":"biolink:correlated_with"}}},{"association":{"api_name":"CAM-KP API","smartapi":{"id":"d76f7d70f98b3ef124df0553d70490f7","meta":{"date_created":"2021-05-08T22:19:34.401242+00:00","last_updated":"2021-05-25T21:05:42.164983+00:00","url":"https://cam-kp-api-dev.renci.org/docs/docs.yaml","username":"jdr0887"}},"x-translator":{"component":"KP","team":["Exposures Provider"]}},"tags":["translator","trapi"],"query_operation":{"path":"/query","server":"https://cam-kp-api-dev.renci.org","method":"post"},"predicates_path":"/meta_knowledge_graph","predicates":{"biolink:NamedThing":{"biolink:DiseaseOrPhenotypicFeature":"biolink:has_part","biolink:PhysicalEssence":"biolink:derives_from","biolink:ChemicalOrDrugOrTreatment":"biolink:participates_in","biolink:Entity":"biolink:derives_from","biolink:Protein":"biolink:process_regulates_process","biolink:IndividualOrganism":"biolink:related_to","biolink:RNAProduct":"biolink:related_to","biolink:AnatomicalEntity":"biolink:derives_into","biolink:GrossAnatomicalStructure":"biolink:caused_by","biolink:NamedThing":"biolink:derives_into","biolink:PhysicalEssenceOrOccurrent":"biolink:derives_into","biolink:PlanetaryEntity":"biolink:has_attribute","biolink:ThingWithTaxon":"biolink:derives_into","biolink:MacromolecularMachineMixin":"biolink:has_attribute","biolink:OntologyClass":"biolink:has_attribute","biolink:Mixture":"biolink:participates_in","biolink:Occurrent":"biolink:derives_into","biolink:OrganismalEntity":"biolink:derives_into","biolink:ChemicalSubstance":"biolink:has_attribute","biolink:OrganismAttribute":"biolink:has_participant","biolink:Drug":"biolink:temporally_related_to","biolink:GeneOrGeneProduct":"biolink:has_attribute","biolink:BiologicalProcess":"biolink:derives_into","biolink:Behavior":"biolink:part_of","biolink:CellularComponent":"biolink:process_negatively_regulates_process","biolink:Cell":"biolink:derives_into","biolink:EnvironmentalProcess":"biolink:has_attribute","biolink:GeneProductMixin":"biolink:caused_by","biolink:GenomicEntity":"biolink:has_attribute","biolink:MacromolecularComplexMixin":"biolink:occurs_in","biolink:MolecularActivity":"biolink:produced_by","biolink:Pathway":"biolink:enabled_by","biolink:BiologicalEntity":"biolink:derives_into","biolink:PathologicalEntityMixin":"biolink:part_of","biolink:PhenotypicQuality":"biolink:has_participant","biolink:Attribute":"biolink:has_participant","biolink:Gene":"biolink:caused_by","biolink:MolecularEntity":"biolink:has_attribute","biolink:Transcript":"biolink:related_to","biolink:BiologicalProcessOrActivity":"biolink:has_attribute","biolink:Annotation":"biolink:affects","biolink:PhenotypicFeature":"biolink:part_of","biolink:NoncodingRNAProduct":"biolink:related_to"},"biolink:Occurrent":{"biolink:DiseaseOrPhenotypicFeature":"biolink:overlaps","biolink:PhysicalEssence":"biolink:derives_from","biolink:ChemicalOrDrugOrTreatment":"biolink:participates_in","biolink:Entity":"biolink:derives_from","biolink:Protein":"biolink:process_regulates_process","biolink:IndividualOrganism":"biolink:related_to","biolink:RNAProduct":"biolink:related_to","biolink:AnatomicalEntity":"biolink:affects_activity_of","biolink:GrossAnatomicalStructure":"biolink:participates_in","biolink:NamedThing":"biolink:affects_transport_of","biolink:PhysicalEssenceOrOccurrent":"biolink:derives_into","biolink:PlanetaryEntity":"biolink:contributes_to","biolink:ThingWithTaxon":"biolink:derives_into","biolink:MacromolecularMachineMixin":"biolink:affects_activity_of","biolink:OntologyClass":"biolink:affects_transport_of","biolink:Mixture":"biolink:participates_in","biolink:Occurrent":"biolink:affects_transport_of","biolink:OrganismalEntity":"biolink:affects_activity_of","biolink:ChemicalSubstance":"biolink:affects_activity_of","biolink:OrganismAttribute":"biolink:affects","biolink:Drug":"biolink:temporally_related_to","biolink:GeneOrGeneProduct":"biolink:affects_activity_of","biolink:BiologicalProcess":"biolink:affects_transport_of","biolink:Behavior":"biolink:part_of","biolink:CellularComponent":"biolink:affects_activity_of","biolink:Cell":"biolink:derives_into","biolink:EnvironmentalProcess":"biolink:contributes_to","biolink:GeneProductMixin":"biolink:caused_by","biolink:GenomicEntity":"biolink:caused_by","biolink:MacromolecularComplexMixin":"biolink:process_negatively_regulates_process","biolink:MolecularActivity":"biolink:enables","biolink:Pathway":"biolink:caused_by","biolink:BiologicalEntity":"biolink:causes","biolink:PathologicalEntityMixin":"biolink:overlaps","biolink:PhenotypicQuality":"biolink:part_of","biolink:Attribute":"biolink:part_of","biolink:Gene":"biolink:caused_by","biolink:MolecularEntity":"biolink:affects_activity_of","biolink:Transcript":"biolink:related_to","biolink:BiologicalProcessOrActivity":"biolink:has_output","biolink:Annotation":"biolink:part_of","biolink:PhenotypicFeature":"biolink:overlaps","biolink:NoncodingRNAProduct":"biolink:related_to"},"biolink:Entity":{"biolink:DiseaseOrPhenotypicFeature":"biolink:has_part","biolink:PhysicalEssence":"biolink:derives_from","biolink:ChemicalOrDrugOrTreatment":"biolink:participates_in","biolink:Entity":"biolink:derives_from","biolink:Protein":"biolink:process_regulates_process","biolink:IndividualOrganism":"biolink:related_to","biolink:RNAProduct":"biolink:related_to","biolink:AnatomicalEntity":"biolink:derives_into","biolink:GrossAnatomic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odingRNAProduct":"biolink:subclass_of","biolink:Transcript":"biolink:superclass_of","biolink:GenomicEntity":"biolink:has_participant","biolink:MolecularEntity":"biolink:has_participant","biolink:DiseaseOrPhenotypicFeature":"biolink:subclass_of","biolink:Gene":"biolink:related_to","biolink:Protein":"biolink:related_to","biolink:PhenotypicFeature":"biolink:caused_by","biolink:RNAProduct":"biolink:related_to"},"biolink:ClinicalModifier":{"biolink:NamedThing":"biolink:superclass_of","biolink:InformationContentEntity":"biolink:superclass_of","biolink:ClinicalModifier":"biolink:superclass_of"},"biolink:ExposureEvent":{"biolink:ExposureEvent":"biolink:subclass_of","biolink:NamedThing":"biolink:related_to","biolink:Disease":"biolink:related_to","biolink:PhenotypicFeature":"biolink:related_to","biolink:BiologicalEntity":"biolink:superclass_of","biolink:DiseaseOrPhenotypicFeature":"biolink:superclass_of","biolink:PathologicalProcess":"biolink:superclass_of","biolink:Phenomenon":"biolink:related_to","biolink:BiologicalProcess":"biolink:related_to","biolink:BiologicalProcessOrActivity":"biolink:subclass_of","biolink:InformationContentEntity":"biolink:superclass_of"},"biolink:FrequencyValue":{"biolink:FrequencyValue":"biolink:subclass_of","biolink:InformationContentEntity":"biolink:related_to","biolink:NamedThing":"biolink:superclass_of","biolink:AdministrativeEntity":"biolink:related_to","biolink:Agent":"biolink:superclass_of"},"biolink:Carbohydrate":{"biolink:ClinicalEntity":"biolink:related_to","biolink:NamedThing":"biolink:superclass_of","biolink:ClinicalIntervention":"biolink:related_to"}}},{"association":{"api_name":"Columbia 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odingRNAProduct":"biolink:subclass_of","biolink:Transcript":"biolink:superclass_of","biolink:GenomicEntity":"biolink:has_participant","biolink:MolecularEntity":"biolink:has_participant","biolink:DiseaseOrPhenotypicFeature":"biolink:subclass_of","biolink:Gene":"biolink:related_to","biolink:Protein":"biolink:related_to","biolink:PhenotypicFeature":"biolink:caused_by","biolink:RNAProduct":"biolink:related_to"},"biolink:ClinicalModifier":{"biolink:NamedThing":"biolink:superclass_of","biolink:InformationContentEntity":"biolink:superclass_of","biolink:ClinicalModifier":"biolink:superclass_of"},"biolink:ExposureEvent":{"biolink:ExposureEvent":"biolink:subclass_of","biolink:NamedThing":"biolink:related_to","biolink:Disease":"biolink:related_to","biolink:PhenotypicFeature":"biolink:related_to","biolink:BiologicalEntity":"biolink:superclass_of","biolink:DiseaseOrPhenotypicFeature":"biolink:superclass_of","biolink:PathologicalProcess":"biolink:superclass_of","biolink:Phenomenon":"biolink:related_to","biolink:BiologicalProcess":"biolink:related_to","biolink:BiologicalProcessOrActivity":"biolink:subclass_of","biolink:InformationContentEntity":"biolink:superclass_of"},"biolink:FrequencyValue":{"biolink:FrequencyValue":"biolink:subclass_of","biolink:InformationContentEntity":"biolink:related_to","biolink:NamedThing":"biolink:superclass_of","biolink:AdministrativeEntity":"biolink:related_to","biolink:Agent":"biolink:superclass_of"},"biolink:Carbohydrate":{"biolink:ClinicalEntity":"biolink:related_to","biolink:NamedThing":"biolink:superclass_of","biolink:ClinicalIntervention":"biolink:related_to"}}},{"association":{"api_name":"Genetics 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\ No newline at end of file diff --git a/data/smartapi_specs.json b/data/smartapi_specs.json index b642d53a..f199169b 100644 --- a/data/smartapi_specs.json +++ b/data/smartapi_specs.json @@ -1 +1 @@ -{"took":1024,"total":134,"max_score":0.5320405,"hits":[{"_id":"04f42ae00c8e5991b98d0e681dbdc596","_meta":{"date_created":"2021-03-04T18:27:43.614727+00:00","last_updated":"2021-06-03T07:01:42.864966+00:00","url":"http://bdt-social.renci.org:8080/socio_environmental_exposures_api/v1/openapi.json","username":"lstillwe"},"_score":0.5320405,"info":{"contact":{"email":"lisa@renci.org","name":"Lisa Stillwell"},"description":"\nThis API returns data from the US Census Bureau American Community Survey (ACS) for a given spatial location of interest.\n\nThe API returns estimated values for socio-economic variables and related variables for small geographic areas that may act as indirect indicators of relevant health behaviors and outcomes. The data are collected by the US Census Bureau and are publicly available.\n\nThe variables are taken from the five-year summary data file of the US Census Bureau ACS, which is constructed from five annual waves of the bureau’s largest household survey. Approximately, two million households have completed the survey annually since calendar year 2005. (Five waves of the survey before 2005 sampled approximately 500,000 households each.) See https://www.census.gov/acs/www/methodology/sample-size-and-data-quality/sample-size/ for more detail. Microdata are available, but small-area data are only available in summary tabulations.\n\nValues are provided at the US Census Block Group level, representing the 2007-2011 and 2012-2016 calendar-year periods for locations within the continental USA. Block groups, the smallest geographic area for which sample survey data are released, generally contain 600 to 3,000 people (e.g., the size of a single city apartment building). Block Groups are aggregates of an average of 39 Blocks each, each of which is delineated by visible and invisible geographic boundaries. Block groups, in turn, are aggregated into Census Tracts, which generally have a population size between 1,200 and 8,000 people, with an optimum size of 4,000 people. Census Tracts aggregate into counties and counties into states. Metropolitan and micropolitan areas are aggregates of counties. See https://www2.census.gov/geo/pdfs/reference/geodiagram.pdf for further detail. Census geography, even Block Groups, may cross municipal lines and may include both urbanized and rural areas. Because population is a large factor in determining Census geography, some Block Groups may cover an extensive rural or wilderness area while others are quite compact. Census Block, Block Group, and Tract boundaries may change somewhat with each decennial Census, but remain stable in between Censuses.\n\nThe US Census Bureau is mandated to preserve the confidentiality of individual-level data. Therefore, data are often summarized, coarsened into categories, or suppressed by complex secret algorithms (especially, but not limited to household income data). In addition, because the variables of interest may only apply to a small subset of Block Group missing data can occur. In some versions of the data, calculated values are suppressed in Block Groups with less than 50 residents.\n\nStandard errors for the socio-demographic variables are provided. Because each of the values in the ACS data files are summary statistics calculated from sample survey data for each Block Group, different samples yield somewhat different values. Therefore, the Census Bureau generates 80 replicate values for selected variables. These provide the basis for the estimated standard errors of the estimates.\n\nThe currently available variables are listed here:\n\n **(2007-2011 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **EstResidentialDensity** - block group population density\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\n **(2012-2016 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **EstTotalPopulation_SE** - standard error of total population in block group\n - **EstResidentialDensity** - block group population density\n- **EstResidentialDensity_SE** - standard error of residential population density in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **MedianHouseholdIncome_SE** - standard error of median household income\n- **EstPropPersonsNoHealthIns** - proportion of the block group population with no health insurance - **EstPropPersonsNoHealthIns_SE** - standard error of proportion of the block group population with no health insurance\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropNonHispWhite_SE** - standard error of proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropPersons5PlusNoEnglish_SE** - standard error of proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdsNoAuto_SE** - standard error of proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdSSI_SE** - standard error of proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHouseholdPA_SE** - standard error of proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolMaxEducation_SE** - standard error of proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdNoSpouse_SE** - standard error of proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild_SE** - standard error of proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n- **EstPropFemaleHouseholdAnyChild_SE** - standard error of proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. 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These data sets provide 8-hour ozone daily maximums (in ppbV) and daily PM2.5 daily averages (in µg/m3). The US EPA provides estimates at the resolution of US Census tract centroids for the continental US. For a given location, the API returns the estimated exposure for the census tract the location occurs in.\n\nThe API provides exposure estimates for calendar years 2002-2016. Resolution for model estimates is 12 km-squared, provisioned at a resolution of the US Census track centroid. The US census tract definition is from the calendar year 2010 definition of the US Census Bureau, for all years of CMAQ data.\n\nThe data sets sources are derived from air quality monitoring data from the National Air Monitoring Stations and Local Air Monitoring Stations (NAMS/LAMS) and numerical output from the Models-3/Community Multiscale Air Quality (CMAQ - https://www.epa.gov/cmaq).\n\nThe API currently provides the following exposure variables:\n- O3: provides estimated O3 concentration levels. Estimated values are for daily maximums in units of ppbV.\n- PM2.5: provides estimated pm2.5 concentration levels. Estimated values are for daily averages in units of µg/m3.\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. For example, Raleigh, North Carolina is at latitude 35.7796 and longitude -78.6382.\n","license":{"name":"MIT","url":"http://opensource.org/licenses/MIT"},"title":"CMAQ Exposures API","version":"1.0.0-oas3","x-translator":{"component":"KP","team":["Exposures Provider"]}},"paths":{"/values":{"get":{"description":"Get estimated air pollutant exposure levels based on time and location\n","operationId":"get_values","parameters":[{"description":"start date of range, ie: MM-DD-YYYY","in":"query","name":"start_date","required":true,"schema":{"format":"date","type":"string"}},{"description":"end date of range, ie: MM-DD-YYYY","in":"query","name":"end_date","required":true,"schema":{"format":"date","type":"string"}},{"description":"latitude in decimal degrees format, ie: 35.7","in":"query","name":"latitude","required":true,"schema":{"type":"string"}},{"description":"longitude in decimal degrees format, ie: -80.33","in":"query","name":"longitude","required":true,"schema":{"type":"string"}},{"description":"timezone offset from UTC (utc, eastern, central, mountain, pacific) - default is utc","in":"query","name":"utc_offset","required":false,"schema":{"default":"utc","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"values":{"items":{"$ref":"#/components/schemas/inline_response_200_values"},"type":"array"}},"type":"object"}}},"description":"OK"},"400":{"description":"Invalid parameter"},"404":{"description":"No values found"},"500":{"description":"Server error"}},"summary":"Retrieves air pollutant exposure levels","x-openapi-router-controller":"swagger_server.controllers.default_controller"}}},"servers":[{"url":"/cmaq_exposures_api/v1"}],"tags":[{"name":"translator"}]},{"_id":"219ac6646d0e2db862b533fb618db5b4","_meta":{"date_created":"2021-03-04T18:22:55.853241+00:00","last_updated":"2021-06-03T07:01:50.720582+00:00","url":"http://bdt-proximity.renci.org:8080/roadway_proximity_api/v1/openapi.json","username":"lstillwe"},"_score":0.5320405,"info":{"contact":{"email":"lisa@renci.org","name":"Lisa Stillwell"},"description":"This API returns the distance in meters from a location of interest to the nearest roadway.\n\nRoadway data are derived from GIS shapefiles provided by the US Federal Highway Administration's Highway Performance Monitoring System (HPMS). See the HPMS Field Manual (https://www.fhwa.dot.gov/policyinformation/hpms/fieldmanual/) for detailed explanation of methods and fields.\n\nResults are limited to major (or primary) roadway types, including interstates, principal arteries, minor arteries, and major collectors, in the United States.\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. For example, Raleigh, North Carolina is at latitude 35.7796 and longitude -78.6382.\n\nIn addition to distance, the API retrieves additional information, including the roadway type, the maximum speed limit, the annual average daily traffic (AADT), and the total number of lanes. See https://www.fhwa.dot.gov/policyinformation/travel_monitoring/pubs/aadt/ for information on how AADT is computed.\n\nThe following roadway types are supported:\n* Off-Network\n* Rural Restricted Access\n* Rural Unrestricted Access\n* Urban Restricted Access\n* Urban Unrestricted Access\n\nIn some cases, roadway type, AADT, and speed are not available in the HPMS data set. In this case, data from the US Census Bureau TIGER (Topologically Integrated Geographic Encoding and Referencing) data set (available at census.gov) was used to obtain roadway type. Roadway segments without roadway type were dropped from the dataset; this amounted to approximately 5% of roadways, many of which had not yet been built. Missing AADT and speeds were populated using a variety of methods. First, a lookup table was built with county averages by roadway type and facility type and populated with values from segments that already had AADT and/or speed. Second, in cases in which the lookup table could not be used (e.g., ramps often didn’t match), speeds were assigned based on the function class of the roadway, state averages, or averages for a similar (but different) roadway type.\n\nThe API is currently restricted to calendar year 2016.\n","license":{"name":"MIT","url":"http://opensource.org/licenses/MIT"},"title":"Roadway Exposures API","version":"1.0.0","x-translator":{"component":"KP","team":["Exposures Provider"]}},"paths":{"/distance":{"get":{"description":"Get the distance to the nearest roadway in meters","operationId":"get_distance","parameters":[{"description":"latitude of the location of interest using decimal format (WGS84 datum)","in":"query","name":"latitude","required":true,"schema":{"format":"double","type":"number"}},{"description":"longitude of the location of interest using decimal format (WGS84 datum)","in":"query","name":"longitude","required":true,"schema":{"format":"double","type":"number"}},{"description":"the maximum search distance between the location of interest and nearest road (meters)","in":"query","name":"limit_distance","schema":{"default":500,"format":"double","type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/RoadwayData"}}},"description":"search results matching criteria"},"204":{"content":{},"description":"No content returned - nearest roadway is >500 meters from specified latitude/longitude"},"400":{"content":{},"description":"Bad input parameter"},"404":{"content":{},"description":"No values found"},"500":{"content":{},"description":"Server error"}},"summary":"retrieves distance in meters","x-openapi-router-controller":"swagger_server.controllers.default_controller"}}},"servers":[{"url":"/roadway_proximity_api/v1"}],"tags":[{"name":"translator"}]},{"_id":"55510544e95386a5a8ac3b88f9d00d21","_meta":{"date_created":"2021-01-30T20:45:51.489336+00:00","last_updated":"2021-06-03T07:02:59.510913+00:00","url":"https://name-resolution-sri.renci.org/openapi.json","username":"kshefchek"},"_score":0.5320405,"info":{"contact":{"email":"patrick@covar.com","name":"Patrick Wang","x-id":"https://github.com/patrickkwang","x-role":"responsible developer"},"description":"Name resolution service

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Comma separated values accepted up to 20.","in":"query","name":"ipr","required":false,"schema":{"type":"string"}},{"description":"Search by signature database type, e.g. SMART, SUPFAM, Pfam, PIRSF, PROSITE, etc. Comma separated values accepted up to 20.","in":"query","name":"signaturetype","required":false,"schema":{"type":"string"}},{"description":"Search by signature database id, e.g. SM00044, SSF55073, PF00211, PIRSF039050, PS00452, etc. Comma separated values accepted up to 20.","in":"query","name":"signatureid","required":false,"schema":{"type":"string"}},{"description":"UniProt proteome UPID(s). Comma separated values accepted up to 100.","in":"query","name":"upid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."}},"summary":"Search UniParc entries","tags":["uniparc"]}},"/uniparc/accession/{accession}":{"get":{"description":"","operationId":"getUniParcEntryByUniprotAccession","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. 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Count and frequency data were derived from the [Columbia University Medical Center's](http://www.cumc.columbia.edu/) [OHDSI](https://www.ohdsi.org/) database including inpatient. Counts are the number of inpatient visits associated with the concept, e.g., diagnosed with a condition, exposed to a drug, or a procedure was performed. Frequencies are the number of unique visits associated with the concept divided by the total number of visits in the dataset, i.e., prevalence in the electronic health records. To protect patient privacy, all concepts and pairs of concepts where the count <= 10 were excluded, and counts were randomized by the Poisson distribution. \n\nDatasets from three primary cohorts are available: \n1) COVID-19: Hospitalized patients aged 18 or older with a COVID-19 related condition diagnosis and/or a confirmed positive COVID-19 test during their hospitalization period or within the prior 21 days. Date range: March 1, 2020 to September 1, 2020. This cohort is also further stratified by sex (male and female) and age (adult: 18-64, senior: 65+).\n2) General inpatient: All hospitalized patients aged 18 or older. Date range: January 1, 2014 to December 31, 2019.\n3) Influenza: Hospitalized patients aged 18 or older who had at least one occurrence of influenza conditions or pre-coordinated positive measurements or positive influenza testing in the prior 21 days or during their hospitalization period. Date range: January 1, 2014 to December 31, 2019.\n\nBoth hierarchical and non-hierarchical datasets are available for each cohort. In the hierarchical datasets, the counts for each concept include the visits from all descendant concepts. For example, the count for ibuprofen (ID 1177480) includes visits with Ibuprofen 600 MG Oral Tablet (ID 19019073), Ibuprofen 400 MG Oral Tablet (ID 19019072), Ibuprofen 20 MG/ML Oral Suspension (ID 19019050), etc. \n\nClinical concepts (e.g., conditions, procedures, drugs) are coded by their standard concept ID in the [OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki). API methods are provided to map to/from other vocabularies supported in OMOP and other ontologies using the EMBL-EBI Ontology Xref Service (OxO). \n\n\nThe following resources are available through this API: \n\n\n1. Metadata: Metadata on the COHD database, including dataset descriptions, number of concepts, etc. \n\n\n2. OMOP: Access to the common vocabulary for name and concept identifier mapping\n\n\n3. Clinical Frequencies: Access to the counts and frequencies of conditions, procedures, and drug exposures, and the associations between them. Frequency was determined as the number of visits with the code(s) / total number of visits. \n\n\n4. Concept Associations: Inferred associations between concepts using chi-square analysis, ratio between observed to expected frequency, and relative frequency. \n\n\nA [Python notebook](https://github.com/WengLab-InformaticsResearch/cohd_api/blob/master/notebooks/COHD_API_Example.ipynb) demonstrates simple examples of how to use the COHD API.\n\n\nCOHD was developed at the [Columbia University Department of Biomedical Informatics](https://www.dbmi.columbia.edu/) as a collaboration between the [Weng Lab](http://people.dbmi.columbia.edu/~chw7007/), [Tatonetti Lab](http://tatonettilab.org/), and the [NCATS Biomedical Data Translator](https://ncats.nih.gov/translator) program (TReK Team). This work was supported in part by grants: NCATS 1OT2TR003434, NLM R01LM012895, NCATS OT3TR002027, NLM R01LM009886-08A1, and NIGMS R01GM107145.\n\nThe following external resources may be useful: \n[OHDSI](https://www.ohdsi.org/) \n[OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki) \n[Athena](http://athena.ohdsi.org) (OMOP vocabularies, search, concept relationships, concept hierarchy) \n[Atlas](http://www.ohdsi.org/web/atlas/) (OMOP vocabularies, search, concept relationships, concept hierarchy, concept sets) \n[NCATS Biomedical Data Translator](https://sites.google.com/ncats.nih.gov/translator-io/home) \n","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"termsOfService":"http://cohd.io/terms/","title":"Columbia Open Health Data (COHD) for COVID-19 Research","version":"3.0.0","x-accessRestriction":"none","x-implementationLanguage":"Python","x-translator":{"component":"KP","team":["Clinical Data Provider"]},"x-trapi":{"version":"1.0.0"}},"paths":{"/metadata/datasets":{"get":{"description":"Returns a list of datasets, including dataset ID, name, and description.","operationId":"datasets","responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"dataset_description":{"example":"Hospitalized patients with a COVID-19 condition and/or positive lab test (non-hierarchical)","type":"string"},"dataset_id":{"example":1,"type":"integer"},"dataset_name":{"example":"COVID Cohort (non-hierarchical)","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of dataset descriptions."},"default":{"description":"Unexpected error"}},"summary":"Enumerates the datasets available in COHD","tags":["Metadata"]}},"/metadata/domainCounts":{"get":{"description":"Returns a list of domains and the number of concepts in each domain.","operationId":"domainCounts","parameters":[{"description":"The dataset_id of the dataset to query. 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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":{"description":"Attempts 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":{"description":"Attempts 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":0.000005585247351056813,"type":"integer"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2008271,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequency of a pair of concepts","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id. Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"q","required":true,"schema":{"type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":19041324,"type":"integer"},"associated_concept_name":{"example":"Acetaminophen 325 MG Oral Tablet [Tylenol]","type":"string"},"associated_domain_id":{"example":"Drug","type":"string"},"concept_count":{"example":277,"type":"integer"},"concept_frequency":{"example":0.0001547113516242737,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptDomainFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id restricted by domain of the associated concept_id. Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptDomainFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id","required":true,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc. See /metadata/domainCounts for a list of valid domain IDs.","example":"Procedure","in":"query","name":"domain","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":2211361,"type":"integer"},"associated_concept_name":{"example":"Radiologic examination, chest, 2 views, frontal and lateral","type":"string"},"associated_domain_id":{"example":"Procedure","type":"string"},"concept_count":{"example":257,"type":"integer"},"concept_frequency":{"example":0.00014354085692216007,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/mostFrequentConcepts":{"get":{"description":"Retrieves the most frequent concepts.","operationId":"mostFrequentConcepts","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The number of concepts to retreieve, e.g., 100. 0 or unspecified will return all matching concepts.","example":100,"in":"query","name":"q","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The domain_id to restrict to, e.g., \"Condition\", \"Drug\", \"Procedure\". See /metadata/domainCounts for a list of valid domain IDs.","example":"Condition","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"(Optional) The vocabulary_id(s) to restrict to, e.g., \"SNOMED\", \"MedDRA\", \"RxNorm\", \"ATC\" etc. Comma separated to include multiple vocabularies, e.g., \"SNOMED,MedDRA\". Default: unrestricted","example":null,"in":"query","name":"vocabulary_id","required":false,"schema":{"type":"string"}},{"description":"(Optional) The concept_class_id(s) to restrict to. concept_class_ids are specific to each vocabulary, e.g.,: [ATC](https://en.wikipedia.org/wiki/Anatomical_Therapeutic_Chemical_Classification_System) {ATC 1st, ATC 2nd, ATC 3rd, ATC 4th, ATC 5th}; [MedDRA](https://en.wikipedia.org/wiki/MedDRA) {PT, HLT, HLGT, SOC}; [RxNorm](https://www.nlm.nih.gov/research/umls/rxnorm/docs/2015/appendix5.html) {Ingredient, Clinical Drug Form, Clinical Drug Comp, Clinical Drug}. Comma separated to include multiple concept_class_ids, e.g., \"PT,HLT\". Default: unrestricted","example":null,"in":"query","name":"concept_class_id","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_class_id":{"example":"Clinical Finding","type":"string"},"concept_count":{"example":233790,"type":"integer"},"concept_frequency":{"example":0.1305774978203572,"type":"integer"},"concept_id":{"example":320128,"type":"integer"},"concept_name":{"example":"Essential hypertension","type":"string"},"dataset_id":{"example":1,"type":"integer"},"domain_id":{"example":"Condition","type":"string"},"vocabulary_id":{"example":"SNOMED","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of most frequent concepts."},"default":{"description":"Unexpected error"}},"summary":"Most frequent concepts [by domain]","tags":["Clinical Frequencies"]}},"/association/chiSquare":{"get":{"description":"Returns the chi-square statistic and p-value between pairs of concepts. Results are returned in descending order of the chi-square statistic. Note that due to large sample sizes, the chi-square can become very large. \n\nThe expected frequencies for the chi-square analysis are calculated based on the single concept frequencies and assuming independence between concepts. P-value is calculated with 1 DOF. \n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"chiSquare","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If this parameter is specified, then the chi-square between concept_id_1 and concept_id_2 is returned. If this parameter is not specified, then a list of chi-squared results between concept_id_1 and other concepts is returned.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"adj_p-value":{"description":"Bonferonni adjusted p-value, adjusted with the total number of pairs of concepts in the dataset.","example":0.0314,"type":"number"},"chi_square":{"example":370026.1780081638,"type":"integer"},"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Instillation of therapeutic substance into bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":4021588,"type":"integer"},"dataset_id":{"example":3,"type":"integer"},"p-value":{"example":0.0314,"type":"number"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of concept pairs and chi-squared values."},"default":{"description":"Unexpected error"}},"summary":"Chi-square analysis on pairs of concepts","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/obsExpRatio":{"get":{"description":"Returns the natural logarithm of the ratio between the observed count and expected count. Expected count is calculated from the single concept frequencies and assuming independence between the concepts. Results are returned in descending order of ln_ratio.\n\nexpected_count = Count_1_and_2 * num_visits / (Count_1 * Count_2)\n\nln_ratio = ln(expected_count)\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Results for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"obsExpRatio","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}},{"description":"The confidence level used for calculating confidence intervals (default 0.99).","example":0.99,"in":"query","name":"confidence","required":false,"schema":{"type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Closed [transurethral] biopsy of bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2003784,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"expected_count":{"example":0.060838982345591645,"type":"integer"},"ln_ratio":{"example":7.561698473261244,"type":"integer"},"observed_count":{"example":117,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concepts and observed-expected frequency ratio."},"default":{"description":"Unexpected error"}},"summary":"Observed Count / Expected Count","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/relativeFrequency":{"get":{"description":"Calculates the relative frequency (i.e., conditional probability) between pairs of concepts. Results are returned in descending order of relative frequency. Note that due to the randomization of the counts, the calculated relative frequencies can exceed the limit of 1.0.\n\nRelative Frequency = Count_1_and_2 / Count_2\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"relativeFrequency","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict concept_id_2 (the base concept) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}},{"description":"The confidence level used for calculating confidence intervals (default 0.99).","example":0.99,"in":"query","name":"confidence","required":false,"schema":{"type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_2_count":{"example":82,"type":"integer"},"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Radical cystectomy","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2003805,"type":"integer"},"concept_pair_count":{"example":29,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"relative_frequency":{"example":0.35365853658536583,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concepts and relative frequency."},"default":{"description":"Unexpected error"}},"summary":"Relative frequency between pairs of concepts","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/predicates":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"additionalProperties":{"description":"Array of predicates","items":{"type":"string"},"type":"array"},"description":"Target map","type":"object"},"description":"Source map","example":{"biolink:ChemicalSubstance":{"biolink:Gene":["biolink:directly_interacts_with","biolink:decreases_activity_of"]}},"type":"object"}}},"description":"Predicates by source and target"}},"summary":"Get supported relationships by source and target","tags":["translator","trapi"]}},"/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.\n \nFor the subject node, the id must be specified (category is ignored).\n \nFor the object node, both the id and category are optional. If id is specified for the object node, then the association between the two identified concepts is returned. If id is not specified and category is specified, the associations between the subject node and all concepts with the specified category are returned. If neither are specified, then the associations between the subject node and all concepts are returned.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.\nAdditional behavior options can be controlled using the optional parameters in query_options.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"id\": \"MONDO:0021113\",\n \"category\": \"biolink:Disease\"\n },\n \"n01\": {\n \"category\": \"biolink:Procedure\"\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicate\": \"biolink:correlated_with\",\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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)."},"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","tags":["translator","trapi"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false}],"x-swagger-router-controller":"swagger_server.controllers.query_controller"}},"/0.9.3/query":{"post":{"description":"This endpoint is temporarily provided to support TRAPI 0.9.3 queries\nQuery 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.\nFor the source node, the curie must be specified (type is ignored).\nFor the target node, both the curie and type are optional. If curie is specified for the target node, then the association between the two identified concepts is returned. If curie is not specified and type is specified, the associations between the source node and all concepts with the specified type are returned. If neither are specified, then the associations between the source node and all concepts are returned.\nCOHD will attempt to map the CURIE to an OMOP concept and the node type to an OMOP domain.","operationId":"query093","requestBody":{"content":{"application/json":{"example":"{\n \"max_results\": 50,\n \"message\": {\n \"query_graph\": {\n \"nodes\": [\n {\n \"id\": \"n00\",\n \"curie\": \"MONDO:0021113\",\n \"type\": \"biolink:Disease\"\n },\n {\n \"id\": \"n01\",\n \"type\": \"biolink:Procedure\"\n }\n ],\n \"edges\": [\n {\n \"id\": \"e00\",\n \"type\": \"biolink:correlated_with\",\n \"source_id\": \"n00\",\n \"target_id\": \"n01\"\n }\n ]\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\n \"dataset_id\": 3,\n \"confidence_interval\": 0.99,\n \"min_cooccurrence\": 50,\n \"threshold\": 0.5,\n \"local_oxo\": true,\n \"ontology_targets\": {\n \"biolink:Disease\": [\"ICD9\", \"SNOMEDCT\", \"DOID\"],\n \"biolink:Drug\": [\"RxNorm\"],\n \"biolink:Procedure\": [\"ICD10PCS\", \"SNOMEDCT\"],\n \"_DEFAULT\": []\n },\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/Message"}}},"description":"successful operation"},"400":{"description":"Invalid status value"}},"summary":"Query COHD following NCATS Translator Reasoner Standard API version 0.9.3","tags":["translator","trapi"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false}],"x-swagger-router-controller":"swagger_server.controllers.query_controller"}},"/translator/biolink_to_omop":{"post":{"description":"Map Biolink CURIEs to OMOP concepts","operationId":"biolink_to_omop","requestBody":{"content":{"application/json":{"example":"{\n \"curies\": [\n \"HP:0002907\",\n \"MONDO:0001187\"\n ]\n}","schema":{"$ref":"#/components/schemas/CurieList"}}},"description":"List of CURIEs","required":true},"responses":{"200":{"content":{"application/json":{"example":"{\n \"MONDO:0001187\": {\n \"distance\": 2,\n \"omop_concept_id\": 197508,\n \"omop_concept_name\": \"Malignant tumor of urinary bladder\"\n }\n}","schema":{"additionalProperties":{"description":"Mapping from OMOP concept to Biolink","properties":{"distance":{"description":"mapping distance","type":"integer"},"omop_concept_id":{"type":"integer"},"omop_concept_name":{"type":"string"}},"type":"object"}}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from Biolink to OMOP","tags":["translator"]}},"/translator/omop_to_biolink":{"post":{"description":"Map OMOP concepts to normalized Biolink nodes using SRI Node Normalizer.","operationId":"omop_to_biolink","requestBody":{"content":{"application/json":{"example":"{\n \"omop_ids\": [\n 78472,\n 197508\n ]\n}","schema":{"$ref":"#/components/schemas/OmopList"}}},"description":"List of OMOP IDs","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"type":"object"},"example":"{\n \"197508\": {\n \"equivalent_identifiers\": [\n {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n {\n \"identifier\": \"DOID:11054\"\n },\n {\n \"identifier\": \"OMIM:109800\"\n },\n {\n \"identifier\": \"UMLS:C0005684\"\n },\n {\n \"identifier\": \"NCIT:C9334\"\n },\n {\n \"identifier\": \"SNOMEDCT:399326009\"\n }\n ],\n \"id\": {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n \"type\": [\n \"biolink:Disease\",\n \"biolink:DiseaseOrPhenotypicFeature\",\n \"biolink:BiologicalEntity\",\n \"biolink:NamedThing\"\n ]\n }\n}","type":"object"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized. Mapping from OMOP concept to Biolink normalized nodes. See [SRI Node Normalizer](https://nodenormalization-sri.renci.org/docs#/) for response format"},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from OMOP to Biolink","tags":["translator"]}}},"servers":[{"url":"https://covid.cohd.io/api/"}],"tags":[{"description":"COHD metadata","name":"Metadata"},{"description":"OMOP Common Data Model concepts","name":"OMOP"},{"description":"Clinical frequency data","name":"Clinical Frequencies"},{"description":"Estimated association between concepts","name":"Concept Associations"},{"description":"Concept-age distributions, concept-pair delta distributions, and temporal analyses","name":"Temporal Clinical Data"},{"description":"NCATS Biomedical Data Translator APIs","name":"translator"},{"description":"Implements the NCATS Translator Reasoner API 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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)","version":"4.0.0","x-accessRestriction":"none","x-implementationLanguage":"Python","x-translator":{"biolink-version":"1.8.2","component":"KP","externalDocs":{"description":"The values for component and team are restricted according to this external JSON schema. 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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":{"description":"Attempts 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. 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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":{"description":"Attempts 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. 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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. 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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":0.000005585247351056813,"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. 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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. \n \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"]}},"/predicates":{"get":{"deprecated":true,"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"additionalProperties":{"description":"Array of predicates","items":{"type":"string"},"type":"array"},"description":"Target map","type":"object"},"description":"Source map","example":{"biolink:ChemicalSubstance":{"biolink:Gene":["biolink:directly_interacts_with","biolink:decreases_activity_of"]}},"type":"object"}}},"description":"Predicates by source and target"}},"summary":"Get supported relationships by source and target","tags":["predicates"]}},"/meta_knowledge_graph":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns meta knowledge graph representation of this TRAPI web service."}},"summary":"Meta knowledge graph representation of this TRAPI web service.","tags":["meta_knowledge_graph"]}},"/query":{"post":{"description":"Query the COHD API following the [NCATS Translator Reasoner Standard API](https://github.com/NCATSTranslator/ReasonerAPI). Only single hop queries are supported. See the example query_graph.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"ids\": [\"DOID:9053\"],\n \"categories\": [\"biolink:Disease\"]\n },\n \"n01\": {\n \"categories\": [\"biolink:Procedure\"]\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicates\": [\"biolink:correlated_with\"],\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\n \"dataset_id\": 3,\n \"confidence_interval\": 0.99,\n \"min_cooccurrence\": 50,\n \"threshold\": 0.5,\n \"local_oxo\": true,\n \"max_results\": 50,\n \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\n \"biolink_only\": true\n }\n}","schema":{"$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)."},"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","tags":["query"]}},"/1.0.0/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.\nFor the subject node, the id must be specified (category is ignored).\nFor the object node, both the id and category are optional. If id is specified for the object node, then the association between the two identified concepts is returned. If id is not specified and category is specified, the associations between the subject node and all concepts with the specified category are returned. If neither are specified, then the associations between the subject node and all concepts are returned.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.\nAdditional behavior options can be controlled using the optional parameters in query_options.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"id\": \"DOID:9053\",\n \"category\": \"biolink:Disease\"\n },\n \"n01\": {\n \"category\": \"biolink:Procedure\"\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicate\": \"biolink:correlated_with\",\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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. 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Block Groups are aggregates of an average of 39 Blocks each, each of which is delineated by visible and invisible geographic boundaries. Block groups, in turn, are aggregated into Census Tracts, which generally have a population size between 1,200 and 8,000 people, with an optimum size of 4,000 people. Census Tracts aggregate into counties and counties into states. Metropolitan and micropolitan areas are aggregates of counties. See https://www2.census.gov/geo/pdfs/reference/geodiagram.pdf for further detail. Census geography, even Block Groups, may cross municipal lines and may include both urbanized and rural areas. Because population is a large factor in determining Census geography, some Block Groups may cover an extensive rural or wilderness area while others are quite compact. Census Block, Block Group, and Tract boundaries may change somewhat with each decennial Census, but remain stable in between Censuses.\n\nThe US Census Bureau is mandated to preserve the confidentiality of individual-level data. Therefore, data are often summarized, coarsened into categories, or suppressed by complex secret algorithms (especially, but not limited to household income data). In addition, because the variables of interest may only apply to a small subset of Block Group missing data can occur. In some versions of the data, calculated values are suppressed in Block Groups with less than 50 residents.\n\nStandard errors for the socio-demographic variables are provided. Because each of the values in the ACS data files are summary statistics calculated from sample survey data for each Block Group, different samples yield somewhat different values. Therefore, the Census Bureau generates 80 replicate values for selected variables. These provide the basis for the estimated standard errors of the estimates.\n\nThe currently available variables are listed here:\n\n **(2007-2011 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **EstResidentialDensity** - block group population density\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\n **(2012-2016 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **EstTotalPopulation_SE** - standard error of total population in block group\n - 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These data sets provide 8-hour ozone daily maximums (in ppbV) and daily PM2.5 daily averages (in µg/m3). The US EPA provides estimates at the resolution of US Census tract centroids for the continental US. For a given location, the API returns the estimated exposure for the census tract the location occurs in.\n\nThe API provides exposure estimates for calendar years 2002-2016. Resolution for model estimates is 12 km-squared, provisioned at a resolution of the US Census track centroid. The US census tract definition is from the calendar year 2010 definition of the US Census Bureau, for all years of CMAQ data.\n\nThe data sets sources are derived from air quality monitoring data from the National Air Monitoring Stations and Local Air Monitoring Stations (NAMS/LAMS) and numerical output from the Models-3/Community Multiscale Air Quality (CMAQ - https://www.epa.gov/cmaq).\n\nThe API currently provides the following exposure variables:\n- O3: provides estimated O3 concentration levels. Estimated values are for daily maximums in units of ppbV.\n- PM2.5: provides estimated pm2.5 concentration levels. Estimated values are for daily averages in units of µg/m3.\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. For example, Raleigh, North Carolina is at latitude 35.7796 and longitude -78.6382.\n","license":{"name":"MIT","url":"http://opensource.org/licenses/MIT"},"title":"CMAQ Exposures API","version":"1.0.0-oas3","x-translator":{"component":"KP","team":["Exposures Provider"]}},"paths":{"/values":{"get":{"description":"Get estimated air pollutant exposure levels based on time and location\n","operationId":"get_values","parameters":[{"description":"start date of range, ie: MM-DD-YYYY","in":"query","name":"start_date","required":true,"schema":{"format":"date","type":"string"}},{"description":"end date of range, ie: MM-DD-YYYY","in":"query","name":"end_date","required":true,"schema":{"format":"date","type":"string"}},{"description":"latitude in decimal degrees format, ie: 35.7","in":"query","name":"latitude","required":true,"schema":{"type":"string"}},{"description":"longitude in decimal degrees format, ie: -80.33","in":"query","name":"longitude","required":true,"schema":{"type":"string"}},{"description":"timezone offset from UTC (utc, eastern, central, mountain, pacific) - default is utc","in":"query","name":"utc_offset","required":false,"schema":{"default":"utc","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"values":{"items":{"$ref":"#/components/schemas/inline_response_200_values"},"type":"array"}},"type":"object"}}},"description":"OK"},"400":{"description":"Invalid parameter"},"404":{"description":"No values found"},"500":{"description":"Server error"}},"summary":"Retrieves air pollutant exposure levels","x-openapi-router-controller":"swagger_server.controllers.default_controller"}}},"servers":[{"url":"/cmaq_exposures_api/v1"}],"tags":[{"name":"translator"}]},{"_id":"219ac6646d0e2db862b533fb618db5b4","_meta":{"date_created":"2021-03-04T18:22:55.853241+00:00","last_updated":"2021-06-05T07:01:33.739364+00:00","url":"http://bdt-proximity.renci.org:8080/roadway_proximity_api/v1/openapi.json","username":"lstillwe"},"_score":0.5345465,"info":{"contact":{"email":"lisa@renci.org","name":"Lisa Stillwell"},"description":"This API returns the distance in meters from a location of interest to the nearest roadway.\n\nRoadway data are derived from GIS shapefiles provided by the US Federal Highway Administration's Highway Performance Monitoring System (HPMS). See the HPMS Field Manual (https://www.fhwa.dot.gov/policyinformation/hpms/fieldmanual/) for detailed explanation of methods and fields.\n\nResults are limited to major (or primary) roadway types, including interstates, principal arteries, minor arteries, and major collectors, in the United States.\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. For example, Raleigh, North Carolina is at latitude 35.7796 and longitude -78.6382.\n\nIn addition to distance, the API retrieves additional information, including the roadway type, the maximum speed limit, the annual average daily traffic (AADT), and the total number of lanes. See https://www.fhwa.dot.gov/policyinformation/travel_monitoring/pubs/aadt/ for information on how AADT is computed.\n\nThe following roadway types are supported:\n* Off-Network\n* Rural Restricted Access\n* Rural Unrestricted Access\n* Urban Restricted Access\n* Urban Unrestricted Access\n\nIn some cases, roadway type, AADT, and speed are not available in the HPMS data set. In this case, data from the US Census Bureau TIGER (Topologically Integrated Geographic Encoding and Referencing) data set (available at census.gov) was used to obtain roadway type. Roadway segments without roadway type were dropped from the dataset; this amounted to approximately 5% of roadways, many of which had not yet been built. Missing AADT and speeds were populated using a variety of methods. First, a lookup table was built with county averages by roadway type and facility type and populated with values from segments that already had AADT and/or speed. 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[documentation](https://github.com/NCATS-Tangerine/icees-api/tree/master/docs) \n
[source](https://github.com/NCATS-Tangerine/icees-api/tree/master/) \n
[ICEES API example queries](https://github.com/NCATS-Tangerine/icees-api/tree/master/#examples)\n
dictionary for versioning of tables\n
\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
versiontable content
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2.0.0cdw in FHIR format, acs, nearest road, and cmaq from 2010
3.0.0cdw in FHIR format, acs, nearest road, cmaq, and EPR from 2010 to 2016
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[ICEES Overview page](https://researchsoftwareinstitute.github.io/data-translator/apps/icees)\n
[documentation](https://github.com/NCATS-Tangerine/icees-api/tree/master/docs) \n
[source](https://github.com/NCATS-Tangerine/icees-api/tree/master/) \n
[ICEES API example queries](https://github.com/NCATS-Tangerine/icees-api/tree/master/#examples)\n
dictionary for versioning of tables\n
\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
versiontable content
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2.0.0cdw in FHIR format, acs, nearest road, and cmaq from 2010
3.0.0cdw in FHIR format, acs, nearest road, cmaq, and EPR from 2010 to 2016
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The values's format should be a valid UniProtKB accession."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniProt entry by accession","tags":["proteins"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/gene_to_rhea_reaction"},{"$ref":"#/components/x-bte-kgs-operations/protein_to_rhea_reaction"}]}},"/proteins/{accession}/isoforms":{"get":{"description":"","operationId":"getEntriesForIsoforms","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. The values's format should be a valid UniProtKB accession."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniProt isoform entries from parent entry accession","tags":["proteins"]}},"/proteins/{dbtype}:{dbid}":{"get":{"description":"","operationId":"getByCrossReference","parameters":[{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"Cross reference database type, e.g, Ensembl, PDBe, etc. ","in":"path","name":"dbtype","required":true,"schema":{"type":"string"}},{"description":"Cross-reference ID, e.g. ENSP00000351276 for Ensembl","in":"path","name":"dbid","required":true,"schema":{"maxItems":50,"minItems":4,"type":"string"}},{"description":"Reviewed(true) or not Reviewed (false)","in":"query","name":"reviewed","required":false,"schema":{"type":"string"}},{"description":"0 for exclude isoform only and 1 for isoform only","in":"query","name":"isoform","required":false,"schema":{"format":"int32","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniProt entries by UniProt cross reference and its ID","tags":["proteins"]}},"/proteomes":{"get":{"description":"","operationId":"searchProteomes","parameters":[{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"UniProt proteome UPID(s). Comma separated values accepted up to 100.","in":"query","name":"upid","required":false,"schema":{"type":"string"}},{"description":"Search proteome name","in":"query","name":"name","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Organism taxon ID. Comma separated values accepted up to 20.","in":"query","name":"taxid","required":false,"schema":{"type":"string"}},{"description":"Terms the proteome contains","in":"query","name":"keyword","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Proteome cross references such as Genome assembly ID or Biosample ID. Comma separated values accepted up to 20.","in":"query","name":"xref","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Genome accession. Comma separated values accepted up to 20.","in":"query","name":"genome_acc","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Reference Proteome(true) or not reference proteome (false)","in":"query","name":"is_ref_proteome","required":false,"schema":{"type":"string"}},{"description":"Redundant Proteome(true) or non redundant proteome (false)","in":"query","name":"is_redundant","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Proteome"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Proteome"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Search proteomes in UniProt","tags":["proteomes"]}},"/proteomes/genecentric/{upid}":{"get":{"deprecated":true,"description":"","operationId":"getGeneCentricByUpidDeprecated","parameters":[{"description":"UniProt Proteome UPID","in":"path","name":"upid","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Proteome"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Proteome"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid upid parameter. The value format should match the regular expression UP[0-9]{9}."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get gene centric proteins by proteome UPID is deprecated, please use new /genecentric?upid= endpoint","tags":["proteomes"]}},"/proteomes/proteins/{upid}":{"get":{"description":"","operationId":"getProteinsByUpid","parameters":[{"description":"UniProt Proteome UPID","in":"path","name":"upid","required":true,"schema":{"type":"string"}},{"description":"Reviewed(true) or not Reviewed (false)","in":"query","name":"reviewed","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Proteome"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Proteome"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid upid parameter. The value format should match the regular expression UP[0-9]{9}."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get proteins by proteome UPID","tags":["proteomes"]}},"/proteomes/{upid}":{"get":{"description":"","operationId":"getByUpid","parameters":[{"description":"UniProt Proteome UPID","in":"path","name":"upid","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Proteome"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Proteome"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid upid parameter. The value format should match the regular expression UP[0-9]{9}."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get proteome by proteome UPID","tags":["proteomes"]}},"/proteomics":{"get":{"description":"","operationId":"searchProteomics","parameters":[{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"UniProt accession(s). 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Values can be true or false.","in":"query","name":"unique","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"text/x-gff":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Search proteomics peptides in UniProt","tags":["proteomics"]}},"/proteomics/{accession}":{"get":{"description":"","operationId":"getProteomicsByAccession","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. 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Comma separated values accepted up to 100","in":"query","name":"upi","required":false,"schema":{"type":"string"}},{"description":"Search by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc.","in":"query","name":"dbtype","required":false,"schema":{"type":"string"}},{"description":"UniProt accession(s). Comma separated values accepted up to 100.","in":"query","name":"accession","required":false,"schema":{"type":"string"}},{"description":"All UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted up to 100.","in":"query","name":"dbid","required":false,"schema":{"type":"string"}},{"description":"UniProt gene name. Comma separated values accepted up to 20.","in":"query","name":"gene","required":false,"schema":{"type":"string"}},{"description":"UniProt protein name","in":"query","name":"protein","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Organism taxon ID. Comma separated values accepted up to 20.","in":"query","name":"taxid","required":false,"schema":{"type":"string"}},{"description":"Organism name","in":"query","name":"organism","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Sequence CRC64 checksum. eg 4104A3A57D1B08E3","in":"query","name":"sequencechecksum","required":false,"schema":{"type":"string"}},{"description":"Search by InterPro identifier(s). Comma separated values accepted up to 20.","in":"query","name":"ipr","required":false,"schema":{"type":"string"}},{"description":"Search by signature database type, e.g. SMART, SUPFAM, Pfam, PIRSF, PROSITE, etc. Comma separated values accepted up to 20.","in":"query","name":"signaturetype","required":false,"schema":{"type":"string"}},{"description":"Search by signature database id, e.g. SM00044, SSF55073, PF00211, PIRSF039050, PS00452, etc. Comma separated values accepted up to 20.","in":"query","name":"signatureid","required":false,"schema":{"type":"string"}},{"description":"UniProt proteome UPID(s). Comma separated values accepted up to 100.","in":"query","name":"upid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."}},"summary":"Search UniParc entries","tags":["uniparc"]}},"/uniparc/accession/{accession}":{"get":{"description":"","operationId":"getUniParcEntryByUniprotAccession","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. The values's format should be a valid UniProtKB accession."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entry only by UniProt accession","tags":["uniparc"]}},"/uniparc/bestguess":{"get":{"description":"For a given user input (request parameters), Best Guess returns the UniParcEntry with a cross-reference to the longest active UniProtKB sequence (preferably from Swiss-Prot and if not then TrEMBL). It also returns the sequence and related information. If it finds more than one longest active UniProtKB sequence it returns 400 (Bad Request) error response with the list of cross references found.","operationId":"getUniParcBestGuess","parameters":[{"description":"UniParc ID (UPI). Comma separated values accepted up to 100","in":"query","name":"upi","required":false,"schema":{"type":"string"}},{"description":"UniProt accession(s). Comma separated values accepted up to 100.","in":"query","name":"accession","required":false,"schema":{"type":"string"}},{"description":"All UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted up to 100.","in":"query","name":"dbid","required":false,"schema":{"type":"string"}},{"description":"UniProt gene name. Comma separated values accepted up to 20.","in":"query","name":"gene","required":false,"schema":{"type":"string"}},{"description":"Organism taxon ID. Comma separated values accepted up to 20.","in":"query","name":"taxid","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Could not find best guess for the requested filter"}},"summary":"Get UniParc longest sequence for entries.","tags":["uniparc"]}},"/uniparc/dbreference/{dbid}":{"get":{"description":"","operationId":"getUniParcByUniparcAccessions","parameters":[{"description":"All UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq).","in":"path","name":"dbid","required":true,"schema":{"type":"string"}},{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. 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The values's format should be a valid UniProtKB accession."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get natural variants by UniProt accession","tags":["variation"]}}},"servers":[{"url":"https://www.ebi.ac.uk/proteins/api"}],"tags":[{"name":"coordinates"},{"name":"antigen"},{"name":"uniparc"},{"name":"proteomics"},{"name":"features"},{"name":"proteomes"},{"name":"variation"},{"name":"genecentric"},{"name":"proteins"},{"name":"translator"}]},{"_id":"fc8245e92c970298449294fc04211869","_meta":{"date_created":"2021-02-04T00:00:10.655676+00:00","last_updated":"2021-06-05T07:00:56.830742+00:00","slug":"cohdcovid","url":"https://raw.githubusercontent.com/WengLab-InformaticsResearch/cohd_api/cohd_covid/cohd/cohd_oas3.yaml","username":"CaseyTa"},"_score":0.23912436,"components":{"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) for COVID-19 Research API provides access to counts and frequencies (i.e., EHR visit prevalence) of conditions, procedures, drug exposures, and the co-occurrence frequencies between them for a cohort of hospitalized COVID-19 patients and two comparator cohorts of hospitalized influenza patients and hospitalized patients. Count and frequency data were derived from the [Columbia University Medical Center's](http://www.cumc.columbia.edu/) [OHDSI](https://www.ohdsi.org/) database including inpatient. Counts are the number of inpatient visits associated with the concept, e.g., diagnosed with a condition, exposed to a drug, or a procedure was performed. Frequencies are the number of unique visits associated with the concept divided by the total number of visits in the dataset, i.e., prevalence in the electronic health records. To protect patient privacy, all concepts and pairs of concepts where the count <= 10 were excluded, and counts were randomized by the Poisson distribution. \n\nDatasets from three primary cohorts are available: \n1) COVID-19: Hospitalized patients aged 18 or older with a COVID-19 related condition diagnosis and/or a confirmed positive COVID-19 test during their hospitalization period or within the prior 21 days. Date range: March 1, 2020 to September 1, 2020. This cohort is also further stratified by sex (male and female) and age (adult: 18-64, senior: 65+).\n2) General inpatient: All hospitalized patients aged 18 or older. Date range: January 1, 2014 to December 31, 2019.\n3) Influenza: Hospitalized patients aged 18 or older who had at least one occurrence of influenza conditions or pre-coordinated positive measurements or positive influenza testing in the prior 21 days or during their hospitalization period. Date range: January 1, 2014 to December 31, 2019.\n\nBoth hierarchical and non-hierarchical datasets are available for each cohort. In the hierarchical datasets, the counts for each concept include the visits from all descendant concepts. For example, the count for ibuprofen (ID 1177480) includes visits with Ibuprofen 600 MG Oral Tablet (ID 19019073), Ibuprofen 400 MG Oral Tablet (ID 19019072), Ibuprofen 20 MG/ML Oral Suspension (ID 19019050), etc. \n\nClinical concepts (e.g., conditions, procedures, drugs) are coded by their standard concept ID in the [OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki). API methods are provided to map to/from other vocabularies supported in OMOP and other ontologies using the EMBL-EBI Ontology Xref Service (OxO). \n\n\nThe following resources are available through this API: \n\n\n1. Metadata: Metadata on the COHD database, including dataset descriptions, number of concepts, etc. \n\n\n2. OMOP: Access to the common vocabulary for name and concept identifier mapping\n\n\n3. Clinical Frequencies: Access to the counts and frequencies of conditions, procedures, and drug exposures, and the associations between them. Frequency was determined as the number of visits with the code(s) / total number of visits. \n\n\n4. Concept Associations: Inferred associations between concepts using chi-square analysis, ratio between observed to expected frequency, and relative frequency. \n\n\nA [Python notebook](https://github.com/WengLab-InformaticsResearch/cohd_api/blob/master/notebooks/COHD_API_Example.ipynb) demonstrates simple examples of how to use the COHD API.\n\n\nCOHD was developed at the [Columbia University Department of Biomedical Informatics](https://www.dbmi.columbia.edu/) as a collaboration between the [Weng Lab](http://people.dbmi.columbia.edu/~chw7007/), [Tatonetti Lab](http://tatonettilab.org/), and the [NCATS Biomedical Data Translator](https://ncats.nih.gov/translator) program (TReK Team). This work was supported in part by grants: NCATS 1OT2TR003434, NLM R01LM012895, NCATS OT3TR002027, NLM R01LM009886-08A1, and NIGMS R01GM107145.\n\nThe following external resources may be useful: \n[OHDSI](https://www.ohdsi.org/) \n[OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki) \n[Athena](http://athena.ohdsi.org) (OMOP vocabularies, search, concept relationships, concept hierarchy) \n[Atlas](http://www.ohdsi.org/web/atlas/) (OMOP vocabularies, search, concept relationships, concept hierarchy, concept sets) \n[NCATS Biomedical Data Translator](https://sites.google.com/ncats.nih.gov/translator-io/home) \n","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"termsOfService":"http://cohd.io/terms/","title":"Columbia Open Health Data (COHD) for COVID-19 Research","version":"3.0.0","x-accessRestriction":"none","x-implementationLanguage":"Python","x-translator":{"component":"KP","team":["Clinical Data Provider"]},"x-trapi":{"version":"1.0.0"}},"paths":{"/metadata/datasets":{"get":{"description":"Returns a list of datasets, including dataset ID, name, and description.","operationId":"datasets","responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"dataset_description":{"example":"Hospitalized patients with a COVID-19 condition and/or positive lab test (non-hierarchical)","type":"string"},"dataset_id":{"example":1,"type":"integer"},"dataset_name":{"example":"COVID Cohort (non-hierarchical)","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of dataset descriptions."},"default":{"description":"Unexpected error"}},"summary":"Enumerates the datasets available in COHD","tags":["Metadata"]}},"/metadata/domainCounts":{"get":{"description":"Returns a list of domains and the number of concepts in each domain.","operationId":"domainCounts","parameters":[{"description":"The dataset_id of the dataset to query. 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/visitCount":{"get":{"description":"Returns the number of visits in the dataset.","operationId":"visitCount","parameters":[{"description":"The dataset_id of the dataset to query.","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 visit counts."},"default":{"description":"Unexpected error"}},"summary":"The number of visits 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":{"description":"Attempts 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":{"description":"Attempts 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":0.000005585247351056813,"type":"integer"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2008271,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequency of a pair of concepts","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id. Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"q","required":true,"schema":{"type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":19041324,"type":"integer"},"associated_concept_name":{"example":"Acetaminophen 325 MG Oral Tablet [Tylenol]","type":"string"},"associated_domain_id":{"example":"Drug","type":"string"},"concept_count":{"example":277,"type":"integer"},"concept_frequency":{"example":0.0001547113516242737,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptDomainFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id restricted by domain of the associated concept_id. Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptDomainFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id","required":true,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc. See /metadata/domainCounts for a list of valid domain IDs.","example":"Procedure","in":"query","name":"domain","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":2211361,"type":"integer"},"associated_concept_name":{"example":"Radiologic examination, chest, 2 views, frontal and lateral","type":"string"},"associated_domain_id":{"example":"Procedure","type":"string"},"concept_count":{"example":257,"type":"integer"},"concept_frequency":{"example":0.00014354085692216007,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/mostFrequentConcepts":{"get":{"description":"Retrieves the most frequent concepts.","operationId":"mostFrequentConcepts","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The number of concepts to retreieve, e.g., 100. 0 or unspecified will return all matching concepts.","example":100,"in":"query","name":"q","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The domain_id to restrict to, e.g., \"Condition\", \"Drug\", \"Procedure\". See /metadata/domainCounts for a list of valid domain IDs.","example":"Condition","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"(Optional) The vocabulary_id(s) to restrict to, e.g., \"SNOMED\", \"MedDRA\", \"RxNorm\", \"ATC\" etc. Comma separated to include multiple vocabularies, e.g., \"SNOMED,MedDRA\". Default: unrestricted","example":null,"in":"query","name":"vocabulary_id","required":false,"schema":{"type":"string"}},{"description":"(Optional) The concept_class_id(s) to restrict to. concept_class_ids are specific to each vocabulary, e.g.,: [ATC](https://en.wikipedia.org/wiki/Anatomical_Therapeutic_Chemical_Classification_System) {ATC 1st, ATC 2nd, ATC 3rd, ATC 4th, ATC 5th}; [MedDRA](https://en.wikipedia.org/wiki/MedDRA) {PT, HLT, HLGT, SOC}; [RxNorm](https://www.nlm.nih.gov/research/umls/rxnorm/docs/2015/appendix5.html) {Ingredient, Clinical Drug Form, Clinical Drug Comp, Clinical Drug}. Comma separated to include multiple concept_class_ids, e.g., \"PT,HLT\". Default: unrestricted","example":null,"in":"query","name":"concept_class_id","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_class_id":{"example":"Clinical Finding","type":"string"},"concept_count":{"example":233790,"type":"integer"},"concept_frequency":{"example":0.1305774978203572,"type":"integer"},"concept_id":{"example":320128,"type":"integer"},"concept_name":{"example":"Essential hypertension","type":"string"},"dataset_id":{"example":1,"type":"integer"},"domain_id":{"example":"Condition","type":"string"},"vocabulary_id":{"example":"SNOMED","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of most frequent concepts."},"default":{"description":"Unexpected error"}},"summary":"Most frequent concepts [by domain]","tags":["Clinical Frequencies"]}},"/association/chiSquare":{"get":{"description":"Returns the chi-square statistic and p-value between pairs of concepts. Results are returned in descending order of the chi-square statistic. Note that due to large sample sizes, the chi-square can become very large. \n\nThe expected frequencies for the chi-square analysis are calculated based on the single concept frequencies and assuming independence between concepts. P-value is calculated with 1 DOF. \n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"chiSquare","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If this parameter is specified, then the chi-square between concept_id_1 and concept_id_2 is returned. If this parameter is not specified, then a list of chi-squared results between concept_id_1 and other concepts is returned.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"adj_p-value":{"description":"Bonferonni adjusted p-value, adjusted with the total number of pairs of concepts in the dataset.","example":0.0314,"type":"number"},"chi_square":{"example":370026.1780081638,"type":"integer"},"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Instillation of therapeutic substance into bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":4021588,"type":"integer"},"dataset_id":{"example":3,"type":"integer"},"p-value":{"example":0.0314,"type":"number"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of concept pairs and chi-squared values."},"default":{"description":"Unexpected error"}},"summary":"Chi-square analysis on pairs of concepts","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/obsExpRatio":{"get":{"description":"Returns the natural logarithm of the ratio between the observed count and expected count. Expected count is calculated from the single concept frequencies and assuming independence between the concepts. Results are returned in descending order of ln_ratio.\n\nexpected_count = Count_1_and_2 * num_visits / (Count_1 * Count_2)\n\nln_ratio = ln(expected_count)\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Results for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"obsExpRatio","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}},{"description":"The confidence level used for calculating confidence intervals (default 0.99).","example":0.99,"in":"query","name":"confidence","required":false,"schema":{"type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Closed [transurethral] biopsy of bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2003784,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"expected_count":{"example":0.060838982345591645,"type":"integer"},"ln_ratio":{"example":7.561698473261244,"type":"integer"},"observed_count":{"example":117,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concepts and observed-expected frequency ratio."},"default":{"description":"Unexpected error"}},"summary":"Observed Count / Expected Count","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/relativeFrequency":{"get":{"description":"Calculates the relative frequency (i.e., conditional probability) between pairs of concepts. Results are returned in descending order of relative frequency. Note that due to the randomization of the counts, the calculated relative frequencies can exceed the limit of 1.0.\n\nRelative Frequency = Count_1_and_2 / Count_2\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"relativeFrequency","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict concept_id_2 (the base concept) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}},{"description":"The confidence level used for calculating confidence intervals (default 0.99).","example":0.99,"in":"query","name":"confidence","required":false,"schema":{"type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_2_count":{"example":82,"type":"integer"},"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Radical cystectomy","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2003805,"type":"integer"},"concept_pair_count":{"example":29,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"relative_frequency":{"example":0.35365853658536583,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concepts and relative frequency."},"default":{"description":"Unexpected error"}},"summary":"Relative frequency between pairs of concepts","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/predicates":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"additionalProperties":{"description":"Array of predicates","items":{"type":"string"},"type":"array"},"description":"Target map","type":"object"},"description":"Source map","example":{"biolink:ChemicalSubstance":{"biolink:Gene":["biolink:directly_interacts_with","biolink:decreases_activity_of"]}},"type":"object"}}},"description":"Predicates by source and target"}},"summary":"Get supported relationships by source and target","tags":["translator","trapi"]}},"/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.\n \nFor the subject node, the id must be specified (category is ignored).\n \nFor the object node, both the id and category are optional. If id is specified for the object node, then the association between the two identified concepts is returned. If id is not specified and category is specified, the associations between the subject node and all concepts with the specified category are returned. If neither are specified, then the associations between the subject node and all concepts are returned.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.\nAdditional behavior options can be controlled using the optional parameters in query_options.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"id\": \"MONDO:0021113\",\n \"category\": \"biolink:Disease\"\n },\n \"n01\": {\n \"category\": \"biolink:Procedure\"\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicate\": \"biolink:correlated_with\",\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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)."},"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","tags":["translator","trapi"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false}],"x-swagger-router-controller":"swagger_server.controllers.query_controller"}},"/0.9.3/query":{"post":{"description":"This endpoint is temporarily provided to support TRAPI 0.9.3 queries\nQuery 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.\nFor the source node, the curie must be specified (type is ignored).\nFor the target node, both the curie and type are optional. If curie is specified for the target node, then the association between the two identified concepts is returned. If curie is not specified and type is specified, the associations between the source node and all concepts with the specified type are returned. If neither are specified, then the associations between the source node and all concepts are returned.\nCOHD will attempt to map the CURIE to an OMOP concept and the node type to an OMOP domain.","operationId":"query093","requestBody":{"content":{"application/json":{"example":"{\n \"max_results\": 50,\n \"message\": {\n \"query_graph\": {\n \"nodes\": [\n {\n \"id\": \"n00\",\n \"curie\": \"MONDO:0021113\",\n \"type\": \"biolink:Disease\"\n },\n {\n \"id\": \"n01\",\n \"type\": \"biolink:Procedure\"\n }\n ],\n \"edges\": [\n {\n \"id\": \"e00\",\n \"type\": \"biolink:correlated_with\",\n \"source_id\": \"n00\",\n \"target_id\": \"n01\"\n }\n ]\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\n \"dataset_id\": 3,\n \"confidence_interval\": 0.99,\n \"min_cooccurrence\": 50,\n \"threshold\": 0.5,\n \"local_oxo\": true,\n \"ontology_targets\": {\n \"biolink:Disease\": [\"ICD9\", \"SNOMEDCT\", \"DOID\"],\n \"biolink:Drug\": [\"RxNorm\"],\n \"biolink:Procedure\": [\"ICD10PCS\", \"SNOMEDCT\"],\n \"_DEFAULT\": []\n },\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":{"$ref":"#/components/schemas/Message"}}},"description":"successful operation"},"400":{"description":"Invalid status value"}},"summary":"Query COHD following NCATS Translator Reasoner Standard API version 0.9.3","tags":["translator","trapi"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false}],"x-swagger-router-controller":"swagger_server.controllers.query_controller"}},"/translator/biolink_to_omop":{"post":{"description":"Map Biolink CURIEs to OMOP concepts","operationId":"biolink_to_omop","requestBody":{"content":{"application/json":{"example":"{\n \"curies\": [\n \"HP:0002907\",\n \"MONDO:0001187\"\n ]\n}","schema":{"$ref":"#/components/schemas/CurieList"}}},"description":"List of CURIEs","required":true},"responses":{"200":{"content":{"application/json":{"example":"{\n \"MONDO:0001187\": {\n \"distance\": 2,\n \"omop_concept_id\": 197508,\n \"omop_concept_name\": \"Malignant tumor of urinary bladder\"\n }\n}","schema":{"additionalProperties":{"description":"Mapping from OMOP concept to Biolink","properties":{"distance":{"description":"mapping distance","type":"integer"},"omop_concept_id":{"type":"integer"},"omop_concept_name":{"type":"string"}},"type":"object"}}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from Biolink to OMOP","tags":["translator"]}},"/translator/omop_to_biolink":{"post":{"description":"Map OMOP concepts to normalized Biolink nodes using SRI Node Normalizer.","operationId":"omop_to_biolink","requestBody":{"content":{"application/json":{"example":"{\n \"omop_ids\": [\n 78472,\n 197508\n ]\n}","schema":{"$ref":"#/components/schemas/OmopList"}}},"description":"List of OMOP IDs","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"type":"object"},"example":"{\n \"197508\": {\n \"equivalent_identifiers\": [\n {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n {\n \"identifier\": \"DOID:11054\"\n },\n {\n \"identifier\": \"OMIM:109800\"\n },\n {\n \"identifier\": \"UMLS:C0005684\"\n },\n {\n \"identifier\": \"NCIT:C9334\"\n },\n {\n \"identifier\": \"SNOMEDCT:399326009\"\n }\n ],\n \"id\": {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n \"type\": [\n \"biolink:Disease\",\n \"biolink:DiseaseOrPhenotypicFeature\",\n \"biolink:BiologicalEntity\",\n \"biolink:NamedThing\"\n ]\n }\n}","type":"object"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized. Mapping from OMOP concept to Biolink normalized nodes. See [SRI Node Normalizer](https://nodenormalization-sri.renci.org/docs#/) for response format"},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. 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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)","version":"4.0.0","x-accessRestriction":"none","x-implementationLanguage":"Python","x-translator":{"biolink-version":"1.8.2","component":"KP","externalDocs":{"description":"The values for component and team are restricted according to this external JSON schema. 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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":{"description":"Attempts 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. 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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":{"description":"Attempts 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. 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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. 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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":0.000005585247351056813,"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. 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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. \n \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"]}},"/predicates":{"get":{"deprecated":true,"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"additionalProperties":{"description":"Array of predicates","items":{"type":"string"},"type":"array"},"description":"Target map","type":"object"},"description":"Source map","example":{"biolink:ChemicalSubstance":{"biolink:Gene":["biolink:directly_interacts_with","biolink:decreases_activity_of"]}},"type":"object"}}},"description":"Predicates by source and target"}},"summary":"Get supported relationships by source and target","tags":["predicates"]}},"/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 \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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)."},"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","tags":["query"]}},"/1.0.0/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.\nFor the subject node, the id must be specified (category is ignored).\nFor the object node, both the id and category are optional. If id is specified for the object node, then the association between the two identified concepts is returned. If id is not specified and category is specified, the associations between the subject node and all concepts with the specified category are returned. If neither are specified, then the associations between the subject node and all concepts are returned.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.\nAdditional behavior options can be controlled using the optional parameters in query_options.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"id\": \"DOID:9053\",\n \"category\": \"biolink:Disease\"\n },\n \"n01\": {\n \"category\": \"biolink:Procedure\"\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicate\": \"biolink:correlated_with\",\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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. 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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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"version": "2.7.0", + "version": "2.8.0", "license": "ISC", "dependencies": { + "@biothings-explorer/query_graph_handler": "^1.17.1", "@biothings-explorer/smartapi-kg": "^3.8.1", "axios": "^0.21.1", - "biothings-explorer-graphql": "2.1.1", "body-parser": "^1.19.0", - "camelcase": "^6.2.0", "compression": "^1.7.4", "cors": "^2.8.5", "debug": "^4.3.1", @@ -21,18 +20,16 @@ "express": "^4.17.1", "express-rate-limit": "^5.2.6", "express-winston": "^4.1.0", - "graphql-depth-limit": "^1.1.0", "helmet": "^4.4.1", "husky": "^4.3.8", "lodash": "^4.17.21", "node-cron": "^2.0.3", "npm": "^6.14.12", "openapi-validator-middleware": "^3.2.2", - "redis": "^3.0.2", + "redis": "^3.1.1", "snake-case": "^3.0.4", "winston": "^3.3.3", - "winston-daily-rotate-file": "^4.5.1", - "winston-elasticsearch": "^0.7.13" + "winston-daily-rotate-file": "^4.5.1" }, "devDependencies": { "artillery": "^1.6.2", @@ -79,56 +76,6 @@ "z-schema": "^4.2.3" } }, - "node_modules/@apollo/protobufjs": { - "version": "1.0.4", - "resolved": "https://registry.npmjs.org/@apollo/protobufjs/-/protobufjs-1.0.4.tgz", - 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See [standard-version](https://github.com/conventional-changelog/standard-version) for commit guidelines. +### [2.8.1](https://github.com/biothings/BioThings_Explorer_TRAPI/compare/v2.8.0...v2.8.1) (2021-06-05) + + +### Features + +* :sparks: update to consume trapi v1.1 apis ([5b2f465](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/5b2f465483b7e817a0d75721ea16e6655b4bd215)) +* transform graph data from v1.1 to legacy format, uncomment code ([b1d2413](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/b1d24135c7831041a17eda277bfb6264959d957a)) + + +### Bug Fixes + +* add details to meta graph error ([1d36a18](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/1d36a18694e4ca291afda8d25ddc878e33bf1b16)) + ## [2.8.0](https://github.com/biothings/BioThings_Explorer_TRAPI/compare/v2.7.0...v2.8.0) (2021-05-25) diff --git a/package-lock.json b/package-lock.json index 76056389..42a00141 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/single-hop-app", - "version": "2.8.0", + "version": "2.8.1", "lockfileVersion": 2, "requires": true, "packages": { diff --git a/package.json b/package.json index de9cb919..16ddb857 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/single-hop-app", - "version": "2.8.0", + "version": "2.8.1", "description": "App performing single hop query for BioThings Explorer", "main": "src/server.js", "scripts": { From ef19a70ed68eb8436f67ebf4508c281665d1ccc6 Mon Sep 17 00:00:00 2001 From: Anders Riutta Date: Tue, 8 Jun 2021 12:18:17 -0700 Subject: [PATCH 63/75] chore: create CONTRIBUTING.md --- CONTRIBUTING.md | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 CONTRIBUTING.md diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 00000000..46b75eea --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,25 @@ +# How to Contribute + +See the [main README](https://github.com/biothings/BioThings_Explorer_TRAPI#biothings-explorer-trapi-api). This file just has additional details. + +## Set up Dev Environment + +### Small Updates + +If you're just updating one package and your changes won't affect other packages, you don't have to worry about any of this. If your changes will affect multiple packages but primarily affect just one, you may be able to get away with just using [`npm link`](https://docs.npmjs.com/cli/v7/commands/npm-link). + +### Larger Updates + +If your updates will affect multiple packages, you may find it helpful to use [NPM workspaces](https://docs.npmjs.com/cli/v7/using-npm/workspaces). This feature handles linking better when you're simultaneously updating multiple linked packages. Steps to get this working: + +1. Create a new directory and `cd` into it +2. Add a top-level package.json with all the packages and their dependencies hoisted up to the top level ([something like this](https://www.dropbox.com/s/izsofa7r5alwwfd/package.json?dl=0) - notice the `workspaces` key) +3. For each package to be affected by your updates, clone its repo into subdirectory `./packages` ([demo bash script](https://www.dropbox.com/s/upggzaby7b978z8/clone_packages.sh?dl=0) to do this). +4. From the top-level directory, run the following: + +- `npm install` +- `npm run build --workspaces` +- `npm run test --workspaces` + +5. To run an NPM script for a specific package, try `npm run --workspace=package-a` from the top-level directory, e.g., to start the BioThings_Explorer_TRAPI endpoint: `npm run start --workspace='@biothings-explorer/single-hop-app'`. +6. From the directories in `./packages`, you can edit code and run git commands, e.g., `cd './packages/@biothings-explorer/single-hop-app'` and `git pull`. From 06c29d5010737f5de98577d91695dc7002873830 Mon Sep 17 00:00:00 2001 From: Anders Riutta Date: Tue, 8 Jun 2021 13:54:34 -0700 Subject: [PATCH 64/75] chore: add no-op build script --- package.json | 1 + 1 file changed, 1 insertion(+) diff --git a/package.json b/package.json index 16ddb857..9aa70483 100644 --- a/package.json +++ b/package.json @@ -4,6 +4,7 @@ "description": "App performing single hop query for BioThings Explorer", "main": "src/server.js", "scripts": { + "build": "echo 'no build needed'", "start": "nodemon --delay 5 src/server.js", "debug": "DEBUG=* nodemon --delay 5 src/server.js", "test": "jest --forceExit", From dc2b8fcf6891f2e43b5823215f1bbfe1cb05a552 Mon Sep 17 00:00:00 2001 From: Anders Riutta Date: Tue, 8 Jun 2021 16:17:52 -0700 Subject: [PATCH 65/75] chore: clarify CONTRIBUTING.md --- CONTRIBUTING.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 46b75eea..82baaa9f 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -10,7 +10,7 @@ If you're just updating one package and your changes won't affect other packages ### Larger Updates -If your updates will affect multiple packages, you may find it helpful to use [NPM workspaces](https://docs.npmjs.com/cli/v7/using-npm/workspaces). This feature handles linking better when you're simultaneously updating multiple linked packages. Steps to get this working: +If your updates will affect multiple packages, you may find it helpful to use [NPM workspaces](https://docs.npmjs.com/cli/v7/using-npm/workspaces). This feature is better than just `npm link` for handling the case of simultaneously updating multiple linked packages. Note it requires NPM v7+. Steps to get this working: 1. Create a new directory and `cd` into it 2. Add a top-level package.json with all the packages and their dependencies hoisted up to the top level ([something like this](https://www.dropbox.com/s/izsofa7r5alwwfd/package.json?dl=0) - notice the `workspaces` key) @@ -23,3 +23,4 @@ If your updates will affect multiple packages, you may find it helpful to use [N 5. To run an NPM script for a specific package, try `npm run --workspace=package-a` from the top-level directory, e.g., to start the BioThings_Explorer_TRAPI endpoint: `npm run start --workspace='@biothings-explorer/single-hop-app'`. 6. From the directories in `./packages`, you can edit code and run git commands, e.g., `cd './packages/@biothings-explorer/single-hop-app'` and `git pull`. +7. For now, you still need to run the build step for each package affected by your updates: `npm run build --workspaces` from the top-level directory. If it doesn't work immediately, try running it again. (We can automate this in the future.) From 78c43201c1fb563d9cc2096a5f880589dd01abab Mon Sep 17 00:00:00 2001 From: Anders Riutta Date: Tue, 15 Jun 2021 11:52:29 -0700 Subject: [PATCH 66/75] chore: example_foler -> example_folder --- __test__/integration/TRAPIv1.1.test.js | 12 ++++++------ __test__/integration/TRAPIv1.test.js | 12 ++++++------ __test__/integration/routes/v1query_by_api.test.js | 12 ++++++------ __test__/integration/routes/v1query_by_team.test.js | 10 +++++----- 4 files changed, 23 insertions(+), 23 deletions(-) diff --git a/__test__/integration/TRAPIv1.1.test.js b/__test__/integration/TRAPIv1.1.test.js index e00f6312..2d860339 100644 --- a/__test__/integration/TRAPIv1.1.test.js +++ b/__test__/integration/TRAPIv1.1.test.js @@ -5,16 +5,16 @@ var path = require('path'); describe("Testing v1.1 endpoints", () => { - const example_foler = path.resolve(__dirname, '../../examples/v1.1'); + const example_folder = path.resolve(__dirname, '../../examples/v1.1'); const clinical_risk_kp_folder = path.resolve(__dirname, '../../examples/v1.1/multiomics/clinical_risk_kp'); const old_spec_folder = path.resolve(__dirname, "../../examples/v0.9.2"); const invalid_example_folder = path.resolve(__dirname, "../../examples/v1.1/invalid"); const drug2disease_query = JSON.parse(fs.readFileSync(path.join(clinical_risk_kp_folder, 'query_drug_to_disease.json'))); - const gene2chemical_query = JSON.parse(fs.readFileSync(path.join(example_foler, 'query_chemicals_physically_interacts_with_genes.json'))); - const disease2gene_query = JSON.parse(fs.readFileSync(path.join(example_foler, 'query_genes_relate_to_disease.json'))); + const gene2chemical_query = JSON.parse(fs.readFileSync(path.join(example_folder, 'query_chemicals_physically_interacts_with_genes.json'))); + const disease2gene_query = JSON.parse(fs.readFileSync(path.join(example_folder, 'query_genes_relate_to_disease.json'))); const query_using_earlier_trapi_spec = JSON.parse(fs.readFileSync(path.join(old_spec_folder, 'query_genes_relate_to_disease.json'))); - const query_without_category = JSON.parse(fs.readFileSync(path.join(example_foler, 'query_without_input_category.json'))) - const expand_node = JSON.parse(fs.readFileSync(path.join(example_foler, 'query_with_node_to_be_expanded.json'))) + const query_without_category = JSON.parse(fs.readFileSync(path.join(example_folder, 'query_without_input_category.json'))) + const expand_node = JSON.parse(fs.readFileSync(path.join(example_folder, 'query_with_node_to_be_expanded.json'))) test("GET /v1/meta_knowledge_graph", async () => { await request(app) @@ -226,4 +226,4 @@ describe("Testing v1.1 endpoints", () => { // }) // }) -}) \ No newline at end of file +}) diff --git a/__test__/integration/TRAPIv1.test.js b/__test__/integration/TRAPIv1.test.js index 9e056c98..5da49b79 100644 --- a/__test__/integration/TRAPIv1.test.js +++ b/__test__/integration/TRAPIv1.test.js @@ -5,16 +5,16 @@ var path = require('path'); //V1 tests are now skipped. describe.skip("Testing v1 endpoints", () => { - const example_foler = path.resolve(__dirname, '../../examples/v1'); + const example_folder = path.resolve(__dirname, '../../examples/v1'); const clinical_risk_kp_folder = path.resolve(__dirname, '../../examples/v1/multiomics/clinical_risk_kp'); const old_spec_folder = path.resolve(__dirname, "../../examples/v0.9.2"); const invalid_example_folder = path.resolve(__dirname, "../../examples/v1/invalid"); const drug2disease_query = JSON.parse(fs.readFileSync(path.join(clinical_risk_kp_folder, 'query_drug_to_disease.json'))); - const gene2chemical_query = JSON.parse(fs.readFileSync(path.join(example_foler, 'query_chemicals_physically_interacts_with_genes.json'))); - const disease2gene_query = JSON.parse(fs.readFileSync(path.join(example_foler, 'query_genes_relate_to_disease.json'))); + const gene2chemical_query = JSON.parse(fs.readFileSync(path.join(example_folder, 'query_chemicals_physically_interacts_with_genes.json'))); + const disease2gene_query = JSON.parse(fs.readFileSync(path.join(example_folder, 'query_genes_relate_to_disease.json'))); const query_using_earlier_trapi_spec = JSON.parse(fs.readFileSync(path.join(old_spec_folder, 'query_genes_relate_to_disease.json'))); - const query_without_category = JSON.parse(fs.readFileSync(path.join(example_foler, 'query_without_input_category.json'))) - const expand_node = JSON.parse(fs.readFileSync(path.join(example_foler, 'query_with_node_to_be_expanded.json'))) + const query_without_category = JSON.parse(fs.readFileSync(path.join(example_folder, 'query_without_input_category.json'))) + const expand_node = JSON.parse(fs.readFileSync(path.join(example_folder, 'query_with_node_to_be_expanded.json'))) test("GET /v1/predicates", async () => { await request(app) @@ -139,4 +139,4 @@ describe.skip("Testing v1 endpoints", () => { // }) // }) -}) \ No newline at end of file +}) diff --git a/__test__/integration/routes/v1query_by_api.test.js b/__test__/integration/routes/v1query_by_api.test.js index 55db666d..3b12e687 100644 --- a/__test__/integration/routes/v1query_by_api.test.js +++ b/__test__/integration/routes/v1query_by_api.test.js @@ -6,7 +6,7 @@ var path = require('path'); describe("Testing /v1/smartapi/{smartapi_id}/query endpoints", () => { const invalid_example_folder = path.resolve(__dirname, "../../../examples/v1.1/invalid"); - const example_foler = path.resolve(__dirname, '../../../examples/v1.1'); + const example_folder = path.resolve(__dirname, '../../../examples/v1.1'); test("Input query graph that doesn't pass Swagger Validation should return 400 error", async () => { const InvalidInputQueryGraph = { message1: 1 @@ -62,7 +62,7 @@ describe("Testing /v1/smartapi/{smartapi_id}/query endpoints", () => { }) test("Query to Text Mining Targeted Association KP should have id resolution turned off", async () => { - const query = JSON.parse(fs.readFileSync(path.join(example_foler, "textmining/query_chemicals_related_to_gene_or_gene_product.json"))); + const query = JSON.parse(fs.readFileSync(path.join(example_folder, "textmining/query_chemicals_related_to_gene_or_gene_product.json"))); await request(app) .post("/v1/smartapi/978fe380a147a8641caf72320862697b/query/") .send(query) @@ -76,7 +76,7 @@ describe("Testing /v1/smartapi/{smartapi_id}/query endpoints", () => { }) test("Query to Text Mining Targeted Association KP should have id resolution turned off", async () => { - const query = JSON.parse(fs.readFileSync(path.join(example_foler, "textmining/query_chemicals_related_to_gene_or_gene_product.json"))); + const query = JSON.parse(fs.readFileSync(path.join(example_folder, "textmining/query_chemicals_related_to_gene_or_gene_product.json"))); await request(app) .post("/v1/smartapi/978fe380a147a8641caf72320862697b/query/") .send(query) @@ -90,7 +90,7 @@ describe("Testing /v1/smartapi/{smartapi_id}/query endpoints", () => { }) test("Query to non-Text Mining KPs should have id resolution turned on", async () => { - const query = JSON.parse(fs.readFileSync(path.join(example_foler, "serviceprovider/mychem.json"))); + const query = JSON.parse(fs.readFileSync(path.join(example_folder, "serviceprovider/mychem.json"))); await request(app) .post("/v1/smartapi/8f08d1446e0bb9c2b323713ce83e2bd3/query") .send(query) @@ -103,7 +103,7 @@ describe("Testing /v1/smartapi/{smartapi_id}/query endpoints", () => { }) test("Query to Text Mining Co-occurrence KP should be correctly paginated", async () => { - const query = JSON.parse(fs.readFileSync(path.join(example_foler, "textmining/query_chemicals_related_to_disease.json"))); + const query = JSON.parse(fs.readFileSync(path.join(example_folder, "textmining/query_chemicals_related_to_disease.json"))); const apiResponse = await axios.get('https://biothings.ncats.io/text_mining_co_occurrence_kp/query?q=object.id:%22MONDO:0005252%22%20AND%20subject.type:%22ChemicalSubstance%22'); const hits = apiResponse.data.total; await request(app) @@ -117,4 +117,4 @@ describe("Testing /v1/smartapi/{smartapi_id}/query endpoints", () => { expect(Object.keys(response.body.message.knowledge_graph.nodes)).toHaveLength(hits + 1) }) }) -}) \ No newline at end of file +}) diff --git a/__test__/integration/routes/v1query_by_team.test.js b/__test__/integration/routes/v1query_by_team.test.js index f1a7b329..50a45a86 100644 --- a/__test__/integration/routes/v1query_by_team.test.js +++ b/__test__/integration/routes/v1query_by_team.test.js @@ -6,7 +6,7 @@ var path = require('path'); describe("Testing /v1/team/{team_name}/query endpoints", () => { const invalid_example_folder = path.resolve(__dirname, "../../../examples/v1.1/invalid"); - const example_foler = path.resolve(__dirname, '../../../examples/v1.1'); + const example_folder = path.resolve(__dirname, '../../../examples/v1.1'); test("Input query graph that doesn't pass Swagger Validation should return 400 error", async () => { const InvalidInputQueryGraph = { message1: 1 @@ -62,7 +62,7 @@ describe("Testing /v1/team/{team_name}/query endpoints", () => { }) test("Query to Text Mining KPs should have id resolution turned off", async () => { - const query = JSON.parse(fs.readFileSync(path.join(example_foler, "textmining/query_chemicals_related_to_gene_or_gene_product.json"))); + const query = JSON.parse(fs.readFileSync(path.join(example_folder, "textmining/query_chemicals_related_to_gene_or_gene_product.json"))); await request(app) .post("/v1/team/Text Mining Provider/query/") .send(query) @@ -76,7 +76,7 @@ describe("Testing /v1/team/{team_name}/query endpoints", () => { }) test("Query to Service Provider KPs should have id resolution turned on", async () => { - const query = JSON.parse(fs.readFileSync(path.join(example_foler, "textmining/query_chemicals_related_to_gene_or_gene_product.json"))); + const query = JSON.parse(fs.readFileSync(path.join(example_folder, "textmining/query_chemicals_related_to_gene_or_gene_product.json"))); await request(app) .post("/v1/team/Service Provider/query/") .send(query) @@ -93,7 +93,7 @@ describe("Testing /v1/team/{team_name}/query endpoints", () => { }) test("Query to Text Mining Co-occurrence KP should be correctly paginated", async () => { - const query = JSON.parse(fs.readFileSync(path.join(example_foler, "textmining/query_chemicals_related_to_disease.json"))); + const query = JSON.parse(fs.readFileSync(path.join(example_folder, "textmining/query_chemicals_related_to_disease.json"))); const apiResponse = await axios.get('https://biothings.ncats.io/text_mining_co_occurrence_kp/query?q=object.id:%22MONDO:0005252%22%20AND%20subject.type:%22ChemicalSubstance%22'); const hits = apiResponse.data.total; await request(app) @@ -107,4 +107,4 @@ describe("Testing /v1/team/{team_name}/query endpoints", () => { expect(Object.keys(response.body.message.knowledge_graph.nodes)).toHaveLength(hits + 1) }) }) -}) \ No newline at end of file +}) From 7e0fe1d69e22d6697ea760b43295c34849b11ea8 Mon Sep 17 00:00:00 2001 From: Marco Cano Date: Tue, 15 Jun 2021 12:38:41 -0700 Subject: [PATCH 67/75] fix: include check to add apis with meta_knowledge_graph paths conatining 1.1 prefix to the predicates local file --- data/predicates.json | 2 +- data/smartapi_specs.json | 2 +- src/controllers/cron/update_local_smartapi.js | 28 +++++++++++++++++-- 3 files changed, 28 insertions(+), 4 deletions(-) diff --git a/data/predicates.json b/data/predicates.json index bb610ed7..f71c32f1 100644 --- a/data/predicates.json +++ b/data/predicates.json @@ -1 +1 @@ -[{"association":{"api_name":"Ontology-KP API","smartapi":{"id":"ec1f4b0cfc37d7c2b9534591767e0c5a","meta":{"date_created":"2021-03-30T20:24:25.461575+00:00","last_updated":"2021-06-05T07:01:22.273842+00:00","url":"https://stars-app.renci.org/sparql-kp/docs/docs.yaml","username":"balhoff"}},"x-translator":{"component":"KP","team":["Standards Reference Implementation Team"]}},"tags":["translator","trapi"],"query_operation":{"path":"/query","server":"https://stars-app.renci.org/sparql-kp","method":"post"},"predicates_path":"/meta_knowledge_graph","predicates":{"biolink:OntologyClass":{"biolink:Pathway":"biolink:temporally_related_to","biolink:OntologyClass":"biolink:temporally_related_to","biolink:MolecularEntity":"biolink:participates_in","biolink:PhenotypicQuality":"biolink:related_to","biolink:MacromolecularComplexMixin":"biolink:related_to","biolink:ChemicalSubstance":"biolink:related_to","biolink:GrossAnatomicalStructure":"biolink:has_attribute","biolink:PhenotypicFeature":"biolink:related_to","biolink:InformationContentEntity":"biolink:type","biolink:Occurrent":"biolink:temporally_related_to","biolink:PathologicalEntityMixin":"biolink:related_to","biolink:MolecularActivity":"biolink:related_to","biolink:MicroRNA":"biolink:related_to","biolink:NoncodingRNAProduct":"biolink:related_to","biolink:Inheritance":"biolink:related_to","biolink:Onset":"biolink:related_to","biolink:MaterialSample":"biolink:type","biolink:PathologicalProcess":"biolink:related_to","biolink:NamedThing":"biolink:affects","biolink:Metabolite":"biolink:related_to","biolink:Entity":"biolink:affects","biolink:BiologicalProcessOrActivity":"biolink:temporally_related_to","biolink:DiseaseOrPhenotypicFeature":"biolink:related_to","biolink:BiologicalEntity":"biolink:affects","biolink:GeneProductMixin":"biolink:participates_in","biolink:AnatomicalEntity":"biolink:has_attribute","biolink:PhenotypicSex":"biolink:related_to","biolink:GenotypicSex":"biolink:related_to","biolink:CellLine":"biolink:type","biolink:DrugExposure":"biolink:related_to","biolink:EnvironmentalProcess":"biolink:type","biolink:ClinicalAttribute":"biolink:related_to","biolink:BiologicalProcess":"biolink:temporally_related_to","biolink:BiologicalSex":"biolink:related_to","biolink:Drug":"biolink:related_to","biolink:Behavior":"biolink:related_to","biolink:CellularComponent":"biolink:type","biolink:Cell":"biolink:related_to","biolink:Death":"biolink:related_to","biolink:EvidenceType":"biolink:type","biolink:EnvironmentalFeature":"biolink:type","biolink:PhysicalEssence":"biolink:has_attribute","biolink:PhysicalEssenceOrOccurrent":"biolink:affects","biolink:ClinicalModifier":"biolink:related_to","biolink:ClinicalCourse":"biolink:related_to","biolink:Dataset":"biolink:type","biolink:Disease":"biolink:type","biolink:MacromolecularMachineMixin":"biolink:participates_in","biolink:Mixture":"biolink:related_to","biolink:GenomicEntity":"biolink:participates_in","biolink:ChemicalOrDrugOrTreatment":"biolink:related_to","biolink:ExposureEvent":"biolink:related_to","biolink:OrganismalEntity":"biolink:has_attribute","biolink:OrganismAttribute":"biolink:related_to","biolink:PhysicalEntity":"biolink:type","biolink:Protein":"biolink:participates_in","biolink:ThingWithTaxon":"biolink:has_attribute","biolink:PlanetaryEntity":"biolink:type","biolink:LifeStage":"biolink:related_to","biolink:GeneOrGeneProduct":"biolink:participates_in","biolink:RNAProduct":"biolink:related_to","biolink:Transcript":"biolink:related_to","biolink:ProcessedMaterial":"biolink:related_to","biolink:PopulationOfIndividualOrganisms":"biolink:type","biolink:Attribute":"biolink:related_to","biolink:Publication":"biolink:type","biolink:Annotation":"biolink:related_to","biolink:SubjectOfInvestigation":"biolink:type"},"biolink:ChemicalSubstance":{"biolink:PhysicalEssenceOrOccurrent":"biolink:related_to","biolink:NamedThing":"biolink:related_to","biolink:MolecularEntity":"biolink:related_to","biolink:Entity":"biolink:related_to","biolink:Protein":"biolink:related_to","biolink:ThingWithTaxon":"biolink:related_to","biolink:RNAProduct":"biolink:related_to","biolink:Transcript":"biolink:related_to","biolink:OntologyClass":"biolink:related_to","biolink:ChemicalSubstance":"biolink:related_to","biolink:GeneProductMixin":"biolink:related_to","biolink:GenomicEntity":"biolink:related_to","biolink:PhysicalEssence":"biolink:related_to","biolink:BiologicalEntity":"biolink:related_to","biolink:MacromolecularMachineMixin":"biolink:related_to","biolink:GeneOrGeneProduct":"biolink:related_to","biolink:Metabolite":"biolink:related_to","biolink:Mixture":"biolink:related_to","biolink:ProcessedMaterial":"biolink:related_to","biolink:MacromolecularComplexMixin":"biolink:related_to"},"biolink:Occurrent":{"biolink:Pathway":"biolink:temporally_related_to","biolink:Occurrent":"biolink:temporally_related_to","biolink:OntologyClass":"biolink:temporally_related_to","biolink:BiologicalProcess":"biolink:temporally_related_to","biolink:PhysicalEssenceOrOccurrent":"biolink:affects","biolink:ThingWithTaxon":"biolink:participates_in","biolink:DrugExposure":"biolink:related_to","biolink:EnvironmentalProcess":"biolink:related_to","biolink:PathologicalProcess":"biolink:related_to","biolink:LifeStage":"biolink:related_to","biolink:PlanetaryEntity":"biolink:related_to","biolink:Entity":"biolink:affects","biolink:BiologicalEntity":"bi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odingRNAProduct":"biolink:subclass_of","biolink:Transcript":"biolink:superclass_of","biolink:GenomicEntity":"biolink:has_participant","biolink:MolecularEntity":"biolink:has_participant","biolink:DiseaseOrPhenotypicFeature":"biolink:subclass_of","biolink:Gene":"biolink:related_to","biolink:Protein":"biolink:related_to","biolink:PhenotypicFeature":"biolink:caused_by","biolink:RNAProduct":"biolink:related_to"},"biolink:ClinicalModifier":{"biolink:NamedThing":"biolink:superclass_of","biolink:InformationContentEntity":"biolink:superclass_of","biolink:ClinicalModifier":"biolink:superclass_of"},"biolink:ExposureEvent":{"biolink:ExposureEvent":"biolink:subclass_of","biolink:NamedThing":"biolink:related_to","biolink:Disease":"biolink:related_to","biolink:PhenotypicFeature":"biolink:related_to","biolink:BiologicalEntity":"biolink:superclass_of","biolink:DiseaseOrPhenotypicFeature":"biolink:superclass_of","biolink:PathologicalProcess":"biolink:superclass_of","biolink:Phenomenon":"biolink:related_to","biolink:BiologicalProcess":"biolink:related_to","biolink:BiologicalProcessOrActivity":"biolink:subclass_of","biolink:InformationContentEntity":"biolink:superclass_of"},"biolink:FrequencyValue":{"biolink:FrequencyValue":"biolink:subclass_of","biolink:InformationContentEntity":"biolink:related_to","biolink:NamedThing":"biolink:superclass_of","biolink:AdministrativeEntity":"biolink:related_to","biolink:Agent":"biolink:superclass_of"},"biolink:Carbohydrate":{"biolink:ClinicalEntity":"biolink:related_to","biolink:NamedThing":"biolink:superclass_of","biolink:ClinicalIntervention":"biolink:related_to"}}},{"association":{"api_name":"Genetics 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The data are collected by the US Census Bureau and are publicly available.\n\nThe variables are taken from the five-year summary data file of the US Census Bureau ACS, which is constructed from five annual waves of the bureau’s largest household survey. Approximately, two million households have completed the survey annually since calendar year 2005. (Five waves of the survey before 2005 sampled approximately 500,000 households each.) See https://www.census.gov/acs/www/methodology/sample-size-and-data-quality/sample-size/ for more detail. Microdata are available, but small-area data are only available in summary tabulations.\n\nValues are provided at the US Census Block Group level, representing the 2007-2011 and 2012-2016 calendar-year periods for locations within the continental USA. Block groups, the smallest geographic area for which sample survey data are released, generally contain 600 to 3,000 people (e.g., the size of a single city apartment building). Block Groups are aggregates of an average of 39 Blocks each, each of which is delineated by visible and invisible geographic boundaries. Block groups, in turn, are aggregated into Census Tracts, which generally have a population size between 1,200 and 8,000 people, with an optimum size of 4,000 people. Census Tracts aggregate into counties and counties into states. Metropolitan and micropolitan areas are aggregates of counties. See https://www2.census.gov/geo/pdfs/reference/geodiagram.pdf for further detail. Census geography, even Block Groups, may cross municipal lines and may include both urbanized and rural areas. Because population is a large factor in determining Census geography, some Block Groups may cover an extensive rural or wilderness area while others are quite compact. Census Block, Block Group, and Tract boundaries may change somewhat with each decennial Census, but remain stable in between Censuses.\n\nThe US Census Bureau is mandated to preserve the confidentiality of individual-level data. Therefore, data are often summarized, coarsened into categories, or suppressed by complex secret algorithms (especially, but not limited to household income data). In addition, because the variables of interest may only apply to a small subset of Block Group missing data can occur. In some versions of the data, calculated values are suppressed in Block Groups with less than 50 residents.\n\nStandard errors for the socio-demographic variables are provided. Because each of the values in the ACS data files are summary statistics calculated from sample survey data for each Block Group, different samples yield somewhat different values. Therefore, the Census Bureau generates 80 replicate values for selected variables. These provide the basis for the estimated standard errors of the estimates.\n\nThe currently available variables are listed here:\n\n **(2007-2011 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **EstResidentialDensity** - block group population density\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\n **(2012-2016 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **EstTotalPopulation_SE** - standard error of total population in block group\n - 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WGS84 is the World Geodetic System for expressing latitude and longitude. 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These data sets provide 8-hour ozone daily maximums (in ppbV) and daily PM2.5 daily averages (in µg/m3). The US EPA provides estimates at the resolution of US Census tract centroids for the continental US. For a given location, the API returns the estimated exposure for the census tract the location occurs in.\n\nThe API provides exposure estimates for calendar years 2002-2016. Resolution for model estimates is 12 km-squared, provisioned at a resolution of the US Census track centroid. The US census tract definition is from the calendar year 2010 definition of the US Census Bureau, for all years of CMAQ data.\n\nThe data sets sources are derived from air quality monitoring data from the National Air Monitoring Stations and Local Air Monitoring Stations (NAMS/LAMS) and numerical output from the Models-3/Community Multiscale Air Quality (CMAQ - https://www.epa.gov/cmaq).\n\nThe API currently provides the following exposure variables:\n- O3: provides estimated O3 concentration levels. Estimated values are for daily maximums in units of ppbV.\n- PM2.5: provides estimated pm2.5 concentration levels. Estimated values are for daily averages in units of µg/m3.\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. For example, Raleigh, North Carolina is at latitude 35.7796 and longitude -78.6382.\n","license":{"name":"MIT","url":"http://opensource.org/licenses/MIT"},"title":"CMAQ Exposures API","version":"1.0.0-oas3","x-translator":{"component":"KP","team":["Exposures Provider"]}},"paths":{"/values":{"get":{"description":"Get estimated air pollutant exposure levels based on time and location\n","operationId":"get_values","parameters":[{"description":"start date of range, ie: MM-DD-YYYY","in":"query","name":"start_date","required":true,"schema":{"format":"date","type":"string"}},{"description":"end date of range, ie: MM-DD-YYYY","in":"query","name":"end_date","required":true,"schema":{"format":"date","type":"string"}},{"description":"latitude in decimal degrees format, ie: 35.7","in":"query","name":"latitude","required":true,"schema":{"type":"string"}},{"description":"longitude in decimal degrees format, ie: -80.33","in":"query","name":"longitude","required":true,"schema":{"type":"string"}},{"description":"timezone offset from UTC (utc, eastern, central, mountain, pacific) - default is utc","in":"query","name":"utc_offset","required":false,"schema":{"default":"utc","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"values":{"items":{"$ref":"#/components/schemas/inline_response_200_values"},"type":"array"}},"type":"object"}}},"description":"OK"},"400":{"description":"Invalid parameter"},"404":{"description":"No values found"},"500":{"description":"Server error"}},"summary":"Retrieves air pollutant exposure levels","x-openapi-router-controller":"swagger_server.controllers.default_controller"}}},"servers":[{"url":"/cmaq_exposures_api/v1"}],"tags":[{"name":"translator"}]},{"_id":"219ac6646d0e2db862b533fb618db5b4","_meta":{"date_created":"2021-03-04T18:22:55.853241+00:00","last_updated":"2021-06-05T07:01:33.739364+00:00","url":"http://bdt-proximity.renci.org:8080/roadway_proximity_api/v1/openapi.json","username":"lstillwe"},"_score":0.5345465,"info":{"contact":{"email":"lisa@renci.org","name":"Lisa Stillwell"},"description":"This API returns the distance in meters from a location of interest to the nearest roadway.\n\nRoadway data are derived from GIS shapefiles provided by the US Federal Highway Administration's Highway Performance Monitoring System (HPMS). See the HPMS Field Manual (https://www.fhwa.dot.gov/policyinformation/hpms/fieldmanual/) for detailed explanation of methods and fields.\n\nResults are limited to major (or primary) roadway types, including interstates, principal arteries, minor arteries, and major collectors, in the United States.\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. For example, Raleigh, North Carolina is at latitude 35.7796 and longitude -78.6382.\n\nIn addition to distance, the API retrieves additional information, including the roadway type, the maximum speed limit, the annual average daily traffic (AADT), and the total number of lanes. See https://www.fhwa.dot.gov/policyinformation/travel_monitoring/pubs/aadt/ for information on how AADT is computed.\n\nThe following roadway types are supported:\n* Off-Network\n* Rural Restricted Access\n* Rural Unrestricted Access\n* Urban Restricted Access\n* Urban Unrestricted Access\n\nIn some cases, roadway type, AADT, and speed are not available in the HPMS data set. In this case, data from the US Census Bureau TIGER (Topologically Integrated Geographic Encoding and Referencing) data set (available at census.gov) was used to obtain roadway type. Roadway segments without roadway type were dropped from the dataset; this amounted to approximately 5% of roadways, many of which had not yet been built. Missing AADT and speeds were populated using a variety of methods. First, a lookup table was built with county averages by roadway type and facility type and populated with values from segments that already had AADT and/or speed. Second, in cases in which the lookup table could not be used (e.g., ramps often didn’t match), speeds were assigned based on the function class of the roadway, state averages, or averages for a similar (but different) roadway type.\n\nThe API is currently restricted to calendar year 2016.\n","license":{"name":"MIT","url":"http://opensource.org/licenses/MIT"},"title":"Roadway Exposures API","version":"1.0.0","x-translator":{"component":"KP","team":["Exposures Provider"]}},"paths":{"/distance":{"get":{"description":"Get the distance to the nearest roadway in meters","operationId":"get_distance","parameters":[{"description":"latitude of the location of interest using decimal format (WGS84 datum)","in":"query","name":"latitude","required":true,"schema":{"format":"double","type":"number"}},{"description":"longitude of the location of interest using decimal format (WGS84 datum)","in":"query","name":"longitude","required":true,"schema":{"format":"double","type":"number"}},{"description":"the maximum search distance between the location of interest and nearest road (meters)","in":"query","name":"limit_distance","schema":{"default":500,"format":"double","type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/RoadwayData"}}},"description":"search results matching criteria"},"204":{"content":{},"description":"No content returned - nearest roadway is >500 meters from specified latitude/longitude"},"400":{"content":{},"description":"Bad input parameter"},"404":{"content":{},"description":"No values found"},"500":{"content":{},"description":"Server error"}},"summary":"retrieves distance in meters","x-openapi-router-controller":"swagger_server.controllers.default_controller"}}},"servers":[{"url":"/roadway_proximity_api/v1"}],"tags":[{"name":"translator"}]},{"_id":"1a41e3cd15f2b3bfa21c99900bfa1720","_meta":{"date_created":"2021-04-07T14:48:12.706214+00:00","last_updated":"2021-06-03T07:02:49.245099+00:00","url":"https://trapi.monarchinitiative.org/openapi.json","username":"kshefchek"},"_score":0.5345465,"info":{"contact":{"email":"shefchek@oregonstate.edu","name":"Kent Shefchek","x-id":"https://github.com/kshefchek","x-role":"responsible developer"},"description":"The SRI reference KG aims to aggregate knowledge sources across translator using KGX. 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[documentation](https://github.com/NCATS-Tangerine/icees-api/tree/master/docs) \n
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\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
versiontable content
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2.0.0cdw in FHIR format, acs, nearest road, and cmaq from 2010
3.0.0cdw in FHIR format, acs, nearest road, cmaq, and EPR from 2010 to 2016
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versiontable content
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3.0.0cdw in FHIR format, acs, nearest road, cmaq, and EPR from 2010 to 2016
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The values's format should be a valid UniProtKB accession."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniProt entry by accession","tags":["proteins"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/gene_to_rhea_reaction"},{"$ref":"#/components/x-bte-kgs-operations/protein_to_rhea_reaction"}]}},"/proteins/{accession}/isoforms":{"get":{"description":"","operationId":"getEntriesForIsoforms","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. The values's format should be a valid UniProtKB accession."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniProt isoform entries from parent entry accession","tags":["proteins"]}},"/proteins/{dbtype}:{dbid}":{"get":{"description":"","operationId":"getByCrossReference","parameters":[{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"Cross reference database type, e.g, Ensembl, PDBe, etc. ","in":"path","name":"dbtype","required":true,"schema":{"type":"string"}},{"description":"Cross-reference ID, e.g. ENSP00000351276 for Ensembl","in":"path","name":"dbid","required":true,"schema":{"maxItems":50,"minItems":4,"type":"string"}},{"description":"Reviewed(true) or not Reviewed (false)","in":"query","name":"reviewed","required":false,"schema":{"type":"string"}},{"description":"0 for exclude isoform only and 1 for isoform only","in":"query","name":"isoform","required":false,"schema":{"format":"int32","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniProt entries by UniProt cross reference and its ID","tags":["proteins"]}},"/proteomes":{"get":{"description":"","operationId":"searchProteomes","parameters":[{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"UniProt proteome UPID(s). Comma separated values accepted up to 100.","in":"query","name":"upid","required":false,"schema":{"type":"string"}},{"description":"Search proteome name","in":"query","name":"name","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Organism taxon ID. Comma separated values accepted up to 20.","in":"query","name":"taxid","required":false,"schema":{"type":"string"}},{"description":"Terms the proteome contains","in":"query","name":"keyword","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Proteome cross references such as Genome assembly ID or Biosample ID. Comma separated values accepted up to 20.","in":"query","name":"xref","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Genome accession. Comma separated values accepted up to 20.","in":"query","name":"genome_acc","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Reference Proteome(true) or not reference proteome (false)","in":"query","name":"is_ref_proteome","required":false,"schema":{"type":"string"}},{"description":"Redundant Proteome(true) or non redundant proteome (false)","in":"query","name":"is_redundant","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Proteome"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Proteome"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Search proteomes in UniProt","tags":["proteomes"]}},"/proteomes/genecentric/{upid}":{"get":{"deprecated":true,"description":"","operationId":"getGeneCentricByUpidDeprecated","parameters":[{"description":"UniProt Proteome UPID","in":"path","name":"upid","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Proteome"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Proteome"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid upid parameter. The value format should match the regular expression UP[0-9]{9}."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get gene centric proteins by proteome UPID is deprecated, please use new /genecentric?upid= endpoint","tags":["proteomes"]}},"/proteomes/proteins/{upid}":{"get":{"description":"","operationId":"getProteinsByUpid","parameters":[{"description":"UniProt Proteome UPID","in":"path","name":"upid","required":true,"schema":{"type":"string"}},{"description":"Reviewed(true) or not Reviewed (false)","in":"query","name":"reviewed","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Proteome"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Proteome"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid upid parameter. The value format should match the regular expression UP[0-9]{9}."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get proteins by proteome UPID","tags":["proteomes"]}},"/proteomes/{upid}":{"get":{"description":"","operationId":"getByUpid","parameters":[{"description":"UniProt Proteome UPID","in":"path","name":"upid","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Proteome"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Proteome"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid upid parameter. The value format should match the regular expression UP[0-9]{9}."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get proteome by proteome UPID","tags":["proteomes"]}},"/proteomics":{"get":{"description":"","operationId":"searchProteomics","parameters":[{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"UniProt accession(s). 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Values can be true or false.","in":"query","name":"unique","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"text/x-gff":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Search proteomics peptides in UniProt","tags":["proteomics"]}},"/proteomics/{accession}":{"get":{"description":"","operationId":"getProteomicsByAccession","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. 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Comma separated values accepted up to 100","in":"query","name":"upi","required":false,"schema":{"type":"string"}},{"description":"Search by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc.","in":"query","name":"dbtype","required":false,"schema":{"type":"string"}},{"description":"UniProt accession(s). Comma separated values accepted up to 100.","in":"query","name":"accession","required":false,"schema":{"type":"string"}},{"description":"All UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted up to 100.","in":"query","name":"dbid","required":false,"schema":{"type":"string"}},{"description":"UniProt gene name. Comma separated values accepted up to 20.","in":"query","name":"gene","required":false,"schema":{"type":"string"}},{"description":"UniProt protein name","in":"query","name":"protein","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Organism taxon ID. Comma separated values accepted up to 20.","in":"query","name":"taxid","required":false,"schema":{"type":"string"}},{"description":"Organism name","in":"query","name":"organism","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Sequence CRC64 checksum. eg 4104A3A57D1B08E3","in":"query","name":"sequencechecksum","required":false,"schema":{"type":"string"}},{"description":"Search by InterPro identifier(s). Comma separated values accepted up to 20.","in":"query","name":"ipr","required":false,"schema":{"type":"string"}},{"description":"Search by signature database type, e.g. SMART, SUPFAM, Pfam, PIRSF, PROSITE, etc. Comma separated values accepted up to 20.","in":"query","name":"signaturetype","required":false,"schema":{"type":"string"}},{"description":"Search by signature database id, e.g. SM00044, SSF55073, PF00211, PIRSF039050, PS00452, etc. Comma separated values accepted up to 20.","in":"query","name":"signatureid","required":false,"schema":{"type":"string"}},{"description":"UniProt proteome UPID(s). Comma separated values accepted up to 100.","in":"query","name":"upid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."}},"summary":"Search UniParc entries","tags":["uniparc"]}},"/uniparc/accession/{accession}":{"get":{"description":"","operationId":"getUniParcEntryByUniprotAccession","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. The values's format should be a valid UniProtKB accession."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entry only by UniProt accession","tags":["uniparc"]}},"/uniparc/bestguess":{"get":{"description":"For a given user input (request parameters), Best Guess returns the UniParcEntry with a cross-reference to the longest active UniProtKB sequence (preferably from Swiss-Prot and if not then TrEMBL). It also returns the sequence and related information. If it finds more than one longest active UniProtKB sequence it returns 400 (Bad Request) error response with the list of cross references found.","operationId":"getUniParcBestGuess","parameters":[{"description":"UniParc ID (UPI). Comma separated values accepted up to 100","in":"query","name":"upi","required":false,"schema":{"type":"string"}},{"description":"UniProt accession(s). Comma separated values accepted up to 100.","in":"query","name":"accession","required":false,"schema":{"type":"string"}},{"description":"All UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted up to 100.","in":"query","name":"dbid","required":false,"schema":{"type":"string"}},{"description":"UniProt gene name. Comma separated values accepted up to 20.","in":"query","name":"gene","required":false,"schema":{"type":"string"}},{"description":"Organism taxon ID. Comma separated values accepted up to 20.","in":"query","name":"taxid","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Could not find best guess for the requested filter"}},"summary":"Get UniParc longest sequence for entries.","tags":["uniparc"]}},"/uniparc/dbreference/{dbid}":{"get":{"description":"","operationId":"getUniParcByUniparcAccessions","parameters":[{"description":"All UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq).","in":"path","name":"dbid","required":true,"schema":{"type":"string"}},{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. 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The values's format should be a valid UniProtKB accession."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get natural variants by UniProt accession","tags":["variation"]}}},"servers":[{"url":"https://www.ebi.ac.uk/proteins/api"}],"tags":[{"name":"coordinates"},{"name":"antigen"},{"name":"uniparc"},{"name":"proteomics"},{"name":"features"},{"name":"proteomes"},{"name":"variation"},{"name":"genecentric"},{"name":"proteins"},{"name":"translator"}]},{"_id":"fc8245e92c970298449294fc04211869","_meta":{"date_created":"2021-02-04T00:00:10.655676+00:00","last_updated":"2021-06-05T07:00:56.830742+00:00","slug":"cohdcovid","url":"https://raw.githubusercontent.com/WengLab-InformaticsResearch/cohd_api/cohd_covid/cohd/cohd_oas3.yaml","username":"CaseyTa"},"_score":0.23912436,"components":{"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) for COVID-19 Research API provides access to counts and frequencies (i.e., EHR visit prevalence) of conditions, procedures, drug exposures, and the co-occurrence frequencies between them for a cohort of hospitalized COVID-19 patients and two comparator cohorts of hospitalized influenza patients and hospitalized patients. Count and frequency data were derived from the [Columbia University Medical Center's](http://www.cumc.columbia.edu/) [OHDSI](https://www.ohdsi.org/) database including inpatient. Counts are the number of inpatient visits associated with the concept, e.g., diagnosed with a condition, exposed to a drug, or a procedure was performed. Frequencies are the number of unique visits associated with the concept divided by the total number of visits in the dataset, i.e., prevalence in the electronic health records. To protect patient privacy, all concepts and pairs of concepts where the count <= 10 were excluded, and counts were randomized by the Poisson distribution. \n\nDatasets from three primary cohorts are available: \n1) COVID-19: Hospitalized patients aged 18 or older with a COVID-19 related condition diagnosis and/or a confirmed positive COVID-19 test during their hospitalization period or within the prior 21 days. Date range: March 1, 2020 to September 1, 2020. This cohort is also further stratified by sex (male and female) and age (adult: 18-64, senior: 65+).\n2) General inpatient: All hospitalized patients aged 18 or older. Date range: January 1, 2014 to December 31, 2019.\n3) Influenza: Hospitalized patients aged 18 or older who had at least one occurrence of influenza conditions or pre-coordinated positive measurements or positive influenza testing in the prior 21 days or during their hospitalization period. Date range: January 1, 2014 to December 31, 2019.\n\nBoth hierarchical and non-hierarchical datasets are available for each cohort. In the hierarchical datasets, the counts for each concept include the visits from all descendant concepts. For example, the count for ibuprofen (ID 1177480) includes visits with Ibuprofen 600 MG Oral Tablet (ID 19019073), Ibuprofen 400 MG Oral Tablet (ID 19019072), Ibuprofen 20 MG/ML Oral Suspension (ID 19019050), etc. \n\nClinical concepts (e.g., conditions, procedures, drugs) are coded by their standard concept ID in the [OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki). API methods are provided to map to/from other vocabularies supported in OMOP and other ontologies using the EMBL-EBI Ontology Xref Service (OxO). \n\n\nThe following resources are available through this API: \n\n\n1. Metadata: Metadata on the COHD database, including dataset descriptions, number of concepts, etc. \n\n\n2. OMOP: Access to the common vocabulary for name and concept identifier mapping\n\n\n3. Clinical Frequencies: Access to the counts and frequencies of conditions, procedures, and drug exposures, and the associations between them. Frequency was determined as the number of visits with the code(s) / total number of visits. \n\n\n4. Concept Associations: Inferred associations between concepts using chi-square analysis, ratio between observed to expected frequency, and relative frequency. \n\n\nA [Python notebook](https://github.com/WengLab-InformaticsResearch/cohd_api/blob/master/notebooks/COHD_API_Example.ipynb) demonstrates simple examples of how to use the COHD API.\n\n\nCOHD was developed at the [Columbia University Department of Biomedical Informatics](https://www.dbmi.columbia.edu/) as a collaboration between the [Weng Lab](http://people.dbmi.columbia.edu/~chw7007/), [Tatonetti Lab](http://tatonettilab.org/), and the [NCATS Biomedical Data Translator](https://ncats.nih.gov/translator) program (TReK Team). This work was supported in part by grants: NCATS 1OT2TR003434, NLM R01LM012895, NCATS OT3TR002027, NLM R01LM009886-08A1, and NIGMS R01GM107145.\n\nThe following external resources may be useful: \n[OHDSI](https://www.ohdsi.org/) \n[OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki) \n[Athena](http://athena.ohdsi.org) (OMOP vocabularies, search, concept relationships, concept hierarchy) \n[Atlas](http://www.ohdsi.org/web/atlas/) (OMOP vocabularies, search, concept relationships, concept hierarchy, concept sets) \n[NCATS Biomedical Data Translator](https://sites.google.com/ncats.nih.gov/translator-io/home) \n","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"termsOfService":"http://cohd.io/terms/","title":"Columbia Open Health Data (COHD) for COVID-19 Research","version":"3.0.0","x-accessRestriction":"none","x-implementationLanguage":"Python","x-translator":{"component":"KP","team":["Clinical Data Provider"]},"x-trapi":{"version":"1.0.0"}},"paths":{"/metadata/datasets":{"get":{"description":"Returns a list of datasets, including dataset ID, name, and description.","operationId":"datasets","responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"dataset_description":{"example":"Hospitalized patients with a COVID-19 condition and/or positive lab test (non-hierarchical)","type":"string"},"dataset_id":{"example":1,"type":"integer"},"dataset_name":{"example":"COVID Cohort (non-hierarchical)","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of dataset descriptions."},"default":{"description":"Unexpected error"}},"summary":"Enumerates the datasets available in COHD","tags":["Metadata"]}},"/metadata/domainCounts":{"get":{"description":"Returns a list of domains and the number of concepts in each domain.","operationId":"domainCounts","parameters":[{"description":"The dataset_id of the dataset to query. 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/visitCount":{"get":{"description":"Returns the number of visits in the dataset.","operationId":"visitCount","parameters":[{"description":"The dataset_id of the dataset to query.","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 visit counts."},"default":{"description":"Unexpected error"}},"summary":"The number of visits 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":{"description":"Attempts 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":{"description":"Attempts 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":0.000005585247351056813,"type":"integer"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2008271,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequency of a pair of concepts","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id. Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"q","required":true,"schema":{"type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":19041324,"type":"integer"},"associated_concept_name":{"example":"Acetaminophen 325 MG Oral Tablet [Tylenol]","type":"string"},"associated_domain_id":{"example":"Drug","type":"string"},"concept_count":{"example":277,"type":"integer"},"concept_frequency":{"example":0.0001547113516242737,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptDomainFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id restricted by domain of the associated concept_id. Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptDomainFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id","required":true,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc. See /metadata/domainCounts for a list of valid domain IDs.","example":"Procedure","in":"query","name":"domain","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":2211361,"type":"integer"},"associated_concept_name":{"example":"Radiologic examination, chest, 2 views, frontal and lateral","type":"string"},"associated_domain_id":{"example":"Procedure","type":"string"},"concept_count":{"example":257,"type":"integer"},"concept_frequency":{"example":0.00014354085692216007,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/mostFrequentConcepts":{"get":{"description":"Retrieves the most frequent concepts.","operationId":"mostFrequentConcepts","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The number of concepts to retreieve, e.g., 100. 0 or unspecified will return all matching concepts.","example":100,"in":"query","name":"q","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The domain_id to restrict to, e.g., \"Condition\", \"Drug\", \"Procedure\". See /metadata/domainCounts for a list of valid domain IDs.","example":"Condition","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"(Optional) The vocabulary_id(s) to restrict to, e.g., \"SNOMED\", \"MedDRA\", \"RxNorm\", \"ATC\" etc. Comma separated to include multiple vocabularies, e.g., \"SNOMED,MedDRA\". Default: unrestricted","example":null,"in":"query","name":"vocabulary_id","required":false,"schema":{"type":"string"}},{"description":"(Optional) The concept_class_id(s) to restrict to. concept_class_ids are specific to each vocabulary, e.g.,: [ATC](https://en.wikipedia.org/wiki/Anatomical_Therapeutic_Chemical_Classification_System) {ATC 1st, ATC 2nd, ATC 3rd, ATC 4th, ATC 5th}; [MedDRA](https://en.wikipedia.org/wiki/MedDRA) {PT, HLT, HLGT, SOC}; [RxNorm](https://www.nlm.nih.gov/research/umls/rxnorm/docs/2015/appendix5.html) {Ingredient, Clinical Drug Form, Clinical Drug Comp, Clinical Drug}. Comma separated to include multiple concept_class_ids, e.g., \"PT,HLT\". Default: unrestricted","example":null,"in":"query","name":"concept_class_id","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_class_id":{"example":"Clinical Finding","type":"string"},"concept_count":{"example":233790,"type":"integer"},"concept_frequency":{"example":0.1305774978203572,"type":"integer"},"concept_id":{"example":320128,"type":"integer"},"concept_name":{"example":"Essential hypertension","type":"string"},"dataset_id":{"example":1,"type":"integer"},"domain_id":{"example":"Condition","type":"string"},"vocabulary_id":{"example":"SNOMED","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of most frequent concepts."},"default":{"description":"Unexpected error"}},"summary":"Most frequent concepts [by domain]","tags":["Clinical Frequencies"]}},"/association/chiSquare":{"get":{"description":"Returns the chi-square statistic and p-value between pairs of concepts. Results are returned in descending order of the chi-square statistic. Note that due to large sample sizes, the chi-square can become very large. \n\nThe expected frequencies for the chi-square analysis are calculated based on the single concept frequencies and assuming independence between concepts. P-value is calculated with 1 DOF. \n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"chiSquare","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If this parameter is specified, then the chi-square between concept_id_1 and concept_id_2 is returned. If this parameter is not specified, then a list of chi-squared results between concept_id_1 and other concepts is returned.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"adj_p-value":{"description":"Bonferonni adjusted p-value, adjusted with the total number of pairs of concepts in the dataset.","example":0.0314,"type":"number"},"chi_square":{"example":370026.1780081638,"type":"integer"},"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Instillation of therapeutic substance into bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":4021588,"type":"integer"},"dataset_id":{"example":3,"type":"integer"},"p-value":{"example":0.0314,"type":"number"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of concept pairs and chi-squared values."},"default":{"description":"Unexpected error"}},"summary":"Chi-square analysis on pairs of concepts","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/obsExpRatio":{"get":{"description":"Returns the natural logarithm of the ratio between the observed count and expected count. Expected count is calculated from the single concept frequencies and assuming independence between the concepts. Results are returned in descending order of ln_ratio.\n\nexpected_count = Count_1_and_2 * num_visits / (Count_1 * Count_2)\n\nln_ratio = ln(expected_count)\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Results for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"obsExpRatio","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}},{"description":"The confidence level used for calculating confidence intervals (default 0.99).","example":0.99,"in":"query","name":"confidence","required":false,"schema":{"type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Closed [transurethral] biopsy of bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2003784,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"expected_count":{"example":0.060838982345591645,"type":"integer"},"ln_ratio":{"example":7.561698473261244,"type":"integer"},"observed_count":{"example":117,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concepts and observed-expected frequency ratio."},"default":{"description":"Unexpected error"}},"summary":"Observed Count / Expected Count","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/relativeFrequency":{"get":{"description":"Calculates the relative frequency (i.e., conditional probability) between pairs of concepts. Results are returned in descending order of relative frequency. Note that due to the randomization of the counts, the calculated relative frequencies can exceed the limit of 1.0.\n\nRelative Frequency = Count_1_and_2 / Count_2\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"relativeFrequency","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict concept_id_2 (the base concept) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}},{"description":"The confidence level used for calculating confidence intervals (default 0.99).","example":0.99,"in":"query","name":"confidence","required":false,"schema":{"type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_2_count":{"example":82,"type":"integer"},"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Radical cystectomy","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2003805,"type":"integer"},"concept_pair_count":{"example":29,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"relative_frequency":{"example":0.35365853658536583,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concepts and relative frequency."},"default":{"description":"Unexpected error"}},"summary":"Relative frequency between pairs of concepts","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/predicates":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"additionalProperties":{"description":"Array of predicates","items":{"type":"string"},"type":"array"},"description":"Target map","type":"object"},"description":"Source map","example":{"biolink:ChemicalSubstance":{"biolink:Gene":["biolink:directly_interacts_with","biolink:decreases_activity_of"]}},"type":"object"}}},"description":"Predicates by source and target"}},"summary":"Get supported relationships by source and target","tags":["translator","trapi"]}},"/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.\n \nFor the subject node, the id must be specified (category is ignored).\n \nFor the object node, both the id and category are optional. If id is specified for the object node, then the association between the two identified concepts is returned. If id is not specified and category is specified, the associations between the subject node and all concepts with the specified category are returned. If neither are specified, then the associations between the subject node and all concepts are returned.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.\nAdditional behavior options can be controlled using the optional parameters in query_options.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"id\": \"MONDO:0021113\",\n \"category\": \"biolink:Disease\"\n },\n \"n01\": {\n \"category\": \"biolink:Procedure\"\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicate\": \"biolink:correlated_with\",\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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)."},"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","tags":["translator","trapi"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false}],"x-swagger-router-controller":"swagger_server.controllers.query_controller"}},"/0.9.3/query":{"post":{"description":"This endpoint is temporarily provided to support TRAPI 0.9.3 queries\nQuery 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.\nFor the source node, the curie must be specified (type is ignored).\nFor the target node, both the curie and type are optional. If curie is specified for the target node, then the association between the two identified concepts is returned. If curie is not specified and type is specified, the associations between the source node and all concepts with the specified type are returned. If neither are specified, then the associations between the source node and all concepts are returned.\nCOHD will attempt to map the CURIE to an OMOP concept and the node type to an OMOP domain.","operationId":"query093","requestBody":{"content":{"application/json":{"example":"{\n \"max_results\": 50,\n \"message\": {\n \"query_graph\": {\n \"nodes\": [\n {\n \"id\": \"n00\",\n \"curie\": \"MONDO:0021113\",\n \"type\": \"biolink:Disease\"\n },\n {\n \"id\": \"n01\",\n \"type\": \"biolink:Procedure\"\n }\n ],\n \"edges\": [\n {\n \"id\": \"e00\",\n \"type\": \"biolink:correlated_with\",\n \"source_id\": \"n00\",\n \"target_id\": \"n01\"\n }\n ]\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\n \"dataset_id\": 3,\n \"confidence_interval\": 0.99,\n \"min_cooccurrence\": 50,\n \"threshold\": 0.5,\n \"local_oxo\": true,\n \"ontology_targets\": {\n \"biolink:Disease\": [\"ICD9\", \"SNOMEDCT\", \"DOID\"],\n \"biolink:Drug\": [\"RxNorm\"],\n \"biolink:Procedure\": [\"ICD10PCS\", \"SNOMEDCT\"],\n \"_DEFAULT\": []\n },\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":{"$ref":"#/components/schemas/Message"}}},"description":"successful operation"},"400":{"description":"Invalid status value"}},"summary":"Query COHD following NCATS Translator Reasoner Standard API version 0.9.3","tags":["translator","trapi"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"predicate":"biolink:correlated_with","source":"Columbia Open Health Data KP","supportBatch":false}],"x-swagger-router-controller":"swagger_server.controllers.query_controller"}},"/translator/biolink_to_omop":{"post":{"description":"Map Biolink CURIEs to OMOP concepts","operationId":"biolink_to_omop","requestBody":{"content":{"application/json":{"example":"{\n \"curies\": [\n \"HP:0002907\",\n \"MONDO:0001187\"\n ]\n}","schema":{"$ref":"#/components/schemas/CurieList"}}},"description":"List of CURIEs","required":true},"responses":{"200":{"content":{"application/json":{"example":"{\n \"MONDO:0001187\": {\n \"distance\": 2,\n \"omop_concept_id\": 197508,\n \"omop_concept_name\": \"Malignant tumor of urinary bladder\"\n }\n}","schema":{"additionalProperties":{"description":"Mapping from OMOP concept to Biolink","properties":{"distance":{"description":"mapping distance","type":"integer"},"omop_concept_id":{"type":"integer"},"omop_concept_name":{"type":"string"}},"type":"object"}}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from Biolink to OMOP","tags":["translator"]}},"/translator/omop_to_biolink":{"post":{"description":"Map OMOP concepts to normalized Biolink nodes using SRI Node Normalizer.","operationId":"omop_to_biolink","requestBody":{"content":{"application/json":{"example":"{\n \"omop_ids\": [\n 78472,\n 197508\n ]\n}","schema":{"$ref":"#/components/schemas/OmopList"}}},"description":"List of OMOP IDs","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"type":"object"},"example":"{\n \"197508\": {\n \"equivalent_identifiers\": [\n {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n {\n \"identifier\": \"DOID:11054\"\n },\n {\n \"identifier\": \"OMIM:109800\"\n },\n {\n \"identifier\": \"UMLS:C0005684\"\n },\n {\n \"identifier\": \"NCIT:C9334\"\n },\n {\n \"identifier\": \"SNOMEDCT:399326009\"\n }\n ],\n \"id\": {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n \"type\": [\n \"biolink:Disease\",\n \"biolink:DiseaseOrPhenotypicFeature\",\n \"biolink:BiologicalEntity\",\n \"biolink:NamedThing\"\n ]\n }\n}","type":"object"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized. Mapping from OMOP concept to Biolink normalized nodes. See [SRI Node Normalizer](https://nodenormalization-sri.renci.org/docs#/) for response format"},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. 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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)","version":"4.0.0","x-accessRestriction":"none","x-implementationLanguage":"Python","x-translator":{"biolink-version":"1.8.2","component":"KP","externalDocs":{"description":"The values for component and team are restricted according to this external JSON schema. 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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":{"description":"Attempts 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. 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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":{"description":"Attempts 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. 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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. 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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":0.000005585247351056813,"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. 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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. \n \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"]}},"/predicates":{"get":{"deprecated":true,"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"additionalProperties":{"description":"Array of predicates","items":{"type":"string"},"type":"array"},"description":"Target map","type":"object"},"description":"Source map","example":{"biolink:ChemicalSubstance":{"biolink:Gene":["biolink:directly_interacts_with","biolink:decreases_activity_of"]}},"type":"object"}}},"description":"Predicates by source and target"}},"summary":"Get supported relationships by source and target","tags":["predicates"]}},"/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 \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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)."},"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","tags":["query"]}},"/1.0.0/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.\nFor the subject node, the id must be specified (category is ignored).\nFor the object node, both the id and category are optional. If id is specified for the object node, then the association between the two identified concepts is returned. If id is not specified and category is specified, the associations between the subject node and all concepts with the specified category are returned. If neither are specified, then the associations between the subject node and all concepts are returned.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.\nAdditional behavior options can be controlled using the optional parameters in query_options.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"id\": \"DOID:9053\",\n \"category\": \"biolink:Disease\"\n },\n \"n01\": {\n \"category\": \"biolink:Procedure\"\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicate\": \"biolink:correlated_with\",\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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. 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Census Block, Block Group, and Tract boundaries may change somewhat with each decennial Census, but remain stable in between Censuses.\n\nThe US Census Bureau is mandated to preserve the confidentiality of individual-level data. Therefore, data are often summarized, coarsened into categories, or suppressed by complex secret algorithms (especially, but not limited to household income data). In addition, because the variables of interest may only apply to a small subset of Block Group missing data can occur. In some versions of the data, calculated values are suppressed in Block Groups with less than 50 residents.\n\nStandard errors for the socio-demographic variables are provided. Because each of the values in the ACS data files are summary statistics calculated from sample survey data for each Block Group, different samples yield somewhat different values. Therefore, the Census Bureau generates 80 replicate values for selected variables. These provide the basis for the estimated standard errors of the estimates.\n\nThe currently available variables are listed here:\n\n **(2007-2011 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **EstResidentialDensity** - block group population density\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\n **(2012-2016 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **EstTotalPopulation_SE** - standard error of total population in block group\n - **EstResidentialDensity** - block group population density\n- **EstResidentialDensity_SE** - standard error of residential population density in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **MedianHouseholdIncome_SE** - standard error of median household income\n- **EstPropPersonsNoHealthIns** - proportion of the block group population with no health insurance - **EstPropPersonsNoHealthIns_SE** - standard error of proportion of the block group population with no health insurance\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropNonHispWhite_SE** - standard error of proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropPersons5PlusNoEnglish_SE** - standard error of proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdsNoAuto_SE** - standard error of proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdSSI_SE** - standard error of proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHouseholdPA_SE** - standard error of proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolMaxEducation_SE** - standard error of proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdNoSpouse_SE** - standard error of proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild_SE** - standard error of proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n- **EstPropFemaleHouseholdAnyChild_SE** - standard error of proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\nLocations are expressed using WGS84 decimal format. 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These data sets provide 8-hour ozone daily maximums (in ppbV) and daily PM2.5 daily averages (in µg/m3). The US EPA provides estimates at the resolution of US Census tract centroids for the continental US. For a given location, the API returns the estimated exposure for the census tract the location occurs in.\n\nThe API provides exposure estimates for calendar years 2002-2016. Resolution for model estimates is 12 km-squared, provisioned at a resolution of the US Census track centroid. The US census tract definition is from the calendar year 2010 definition of the US Census Bureau, for all years of CMAQ data.\n\nThe data sets sources are derived from air quality monitoring data from the National Air Monitoring Stations and Local Air Monitoring Stations (NAMS/LAMS) and numerical output from the Models-3/Community Multiscale Air Quality (CMAQ - https://www.epa.gov/cmaq).\n\nThe API currently provides the following exposure variables:\n- O3: provides estimated O3 concentration levels. Estimated values are for daily maximums in units of ppbV.\n- PM2.5: provides estimated pm2.5 concentration levels. Estimated values are for daily averages in units of µg/m3.\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. 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[documentation](https://github.com/NCATS-Tangerine/icees-api/tree/master/docs) \n
[source](https://github.com/NCATS-Tangerine/icees-api/tree/master/) \n
[ICEES API example queries](https://github.com/NCATS-Tangerine/icees-api/tree/master/#examples)\n
dictionary for versioning of tables\n
\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
versiontable content
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2.0.0cdw in FHIR format, acs, nearest road, and cmaq from 2010
3.0.0cdw in FHIR format, acs, nearest road, cmaq, and EPR from 2010 to 2016
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The values's format should be a valid UniProtKB accession."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniProt isoform entries from parent entry accession","tags":["proteins"]}},"/proteins/{dbtype}:{dbid}":{"get":{"description":"","operationId":"getByCrossReference","parameters":[{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. 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When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"UniProt proteome UPID(s). Comma separated values accepted up to 100.","in":"query","name":"upid","required":false,"schema":{"type":"string"}},{"description":"Search proteome name","in":"query","name":"name","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Organism taxon ID. Comma separated values accepted up to 20.","in":"query","name":"taxid","required":false,"schema":{"type":"string"}},{"description":"Terms the proteome contains","in":"query","name":"keyword","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Proteome cross references such as Genome assembly ID or Biosample ID. Comma separated values accepted up to 20.","in":"query","name":"xref","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Genome accession. Comma separated values accepted up to 20.","in":"query","name":"genome_acc","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Reference Proteome(true) or not reference proteome (false)","in":"query","name":"is_ref_proteome","required":false,"schema":{"type":"string"}},{"description":"Redundant Proteome(true) or non redundant proteome (false)","in":"query","name":"is_redundant","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Proteome"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Proteome"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Search proteomes in UniProt","tags":["proteomes"]}},"/proteomes/genecentric/{upid}":{"get":{"deprecated":true,"description":"","operationId":"getGeneCentricByUpidDeprecated","parameters":[{"description":"UniProt Proteome UPID","in":"path","name":"upid","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Proteome"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Proteome"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid upid parameter. The value format should match the regular expression UP[0-9]{9}."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get gene centric proteins by proteome UPID is deprecated, please use new /genecentric?upid= endpoint","tags":["proteomes"]}},"/proteomes/proteins/{upid}":{"get":{"description":"","operationId":"getProteinsByUpid","parameters":[{"description":"UniProt Proteome UPID","in":"path","name":"upid","required":true,"schema":{"type":"string"}},{"description":"Reviewed(true) or not Reviewed (false)","in":"query","name":"reviewed","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Proteome"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Proteome"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid upid parameter. The value format should match the regular expression UP[0-9]{9}."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get proteins by proteome UPID","tags":["proteomes"]}},"/proteomes/{upid}":{"get":{"description":"","operationId":"getByUpid","parameters":[{"description":"UniProt Proteome UPID","in":"path","name":"upid","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Proteome"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Proteome"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid upid parameter. The value format should match the regular expression UP[0-9]{9}."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get proteome by proteome UPID","tags":["proteomes"]}},"/proteomics":{"get":{"description":"","operationId":"searchProteomics","parameters":[{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"UniProt accession(s). Comma separated values accepted up to 100.","in":"query","name":"accession","required":false,"schema":{"type":"string"}},{"description":"Organism taxon ID. Comma separated values accepted up to 20.","in":"query","name":"taxid","required":false,"schema":{"type":"string"}},{"description":"UniProt proteome UPID(s). Comma separated values accepted up to 100.","in":"query","name":"upid","required":false,"schema":{"type":"string"}},{"description":"Proteomics data source(s): Proteomics data source(s): MaxQB, PeptideAtlas, EPD or ProteomicsDB. Comma separated values accepted up to 2.","in":"query","name":"datasource","required":false,"schema":{"maxItems":2147483647,"minItems":3,"type":"string"}},{"description":"Peptide sequence. Comma separated values accepted up to 20.","in":"query","name":"peptide","required":false,"schema":{"maxItems":2147483647,"minItems":4,"type":"string"}},{"description":"Peptide uniqueness (unique peptides map to one gene group only). Values can be true or false.","in":"query","name":"unique","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}},"text/x-gff":{"schema":{"items":{"$ref":"#/components/schemas/ProteinFeatureInfo"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Search proteomics peptides in UniProt","tags":["proteomics"]}},"/proteomics/{accession}":{"get":{"description":"","operationId":"getProteomicsByAccession","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ProteinFeatureInfo"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. The values's format should be a valid UniProtKB accession."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-gff":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get proteomics peptides mapped to UniProt by accession","tags":["proteomics"]}},"/uniparc":{"get":{"description":"","operationId":"searchUniParc","parameters":[{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"UniParc ID (UPI). Comma separated values accepted up to 100","in":"query","name":"upi","required":false,"schema":{"type":"string"}},{"description":"Search by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc.","in":"query","name":"dbtype","required":false,"schema":{"type":"string"}},{"description":"UniProt accession(s). Comma separated values accepted up to 100.","in":"query","name":"accession","required":false,"schema":{"type":"string"}},{"description":"All UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted up to 100.","in":"query","name":"dbid","required":false,"schema":{"type":"string"}},{"description":"UniProt gene name. Comma separated values accepted up to 20.","in":"query","name":"gene","required":false,"schema":{"type":"string"}},{"description":"UniProt protein name","in":"query","name":"protein","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Organism taxon ID. Comma separated values accepted up to 20.","in":"query","name":"taxid","required":false,"schema":{"type":"string"}},{"description":"Organism name","in":"query","name":"organism","required":false,"schema":{"maxItems":50,"minItems":3,"type":"string"}},{"description":"Sequence CRC64 checksum. eg 4104A3A57D1B08E3","in":"query","name":"sequencechecksum","required":false,"schema":{"type":"string"}},{"description":"Search by InterPro identifier(s). Comma separated values accepted up to 20.","in":"query","name":"ipr","required":false,"schema":{"type":"string"}},{"description":"Search by signature database type, e.g. SMART, SUPFAM, Pfam, PIRSF, PROSITE, etc. Comma separated values accepted up to 20.","in":"query","name":"signaturetype","required":false,"schema":{"type":"string"}},{"description":"Search by signature database id, e.g. SM00044, SSF55073, PF00211, PIRSF039050, PS00452, etc. Comma separated values accepted up to 20.","in":"query","name":"signatureid","required":false,"schema":{"type":"string"}},{"description":"UniProt proteome UPID(s). Comma separated values accepted up to 100.","in":"query","name":"upid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."}},"summary":"Search UniParc entries","tags":["uniparc"]}},"/uniparc/accession/{accession}":{"get":{"description":"","operationId":"getUniParcEntryByUniprotAccession","parameters":[{"description":"UniProt accession","in":"path","name":"accession","required":true,"schema":{"type":"string"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid accession parameter. The values's format should be a valid UniProtKB accession."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entry only by UniProt accession","tags":["uniparc"]}},"/uniparc/bestguess":{"get":{"description":"For a given user input (request parameters), Best Guess returns the UniParcEntry with a cross-reference to the longest active UniProtKB sequence (preferably from Swiss-Prot and if not then TrEMBL). It also returns the sequence and related information. If it finds more than one longest active UniProtKB sequence it returns 400 (Bad Request) error response with the list of cross references found.","operationId":"getUniParcBestGuess","parameters":[{"description":"UniParc ID (UPI). Comma separated values accepted up to 100","in":"query","name":"upi","required":false,"schema":{"type":"string"}},{"description":"UniProt accession(s). Comma separated values accepted up to 100.","in":"query","name":"accession","required":false,"schema":{"type":"string"}},{"description":"All UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted up to 100.","in":"query","name":"dbid","required":false,"schema":{"type":"string"}},{"description":"UniProt gene name. Comma separated values accepted up to 20.","in":"query","name":"gene","required":false,"schema":{"type":"string"}},{"description":"Organism taxon ID. Comma separated values accepted up to 20.","in":"query","name":"taxid","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Could not find best guess for the requested filter"}},"summary":"Get UniParc longest sequence for entries.","tags":["uniparc"]}},"/uniparc/dbreference/{dbid}":{"get":{"description":"","operationId":"getUniParcByUniparcAccessions","parameters":[{"description":"All UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq).","in":"path","name":"dbid","required":true,"schema":{"type":"string"}},{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entries by all UniParc cross reference accessions","tags":["uniparc"]}},"/uniparc/proteome/{upid}":{"get":{"description":"","operationId":"getByProteomeId","parameters":[{"description":"UniProt Proteome UPID","in":"path","name":"upid","required":true,"schema":{"type":"string"}},{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"application/xml":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}},"text/x-fasta":{"schema":{"items":{"$ref":"#/components/schemas/Entry"},"type":"array"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entries by Proteome UPID","tags":["uniparc"]}},"/uniparc/sequence":{"post":{"description":"","operationId":"getBySequence","parameters":[{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/UniparcSequenceParam"}},"application/xml":{"schema":{"$ref":"#/components/schemas/UniparcSequenceParam"}},"text/plain":{"schema":{"$ref":"#/components/schemas/UniparcSequenceParam"}}},"description":"Post uniparc Sequence in text, json or xml content type. Look the expected model in Data Type column","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid request Parameter."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entries by sequence","tags":["uniparc"]}},"/uniparc/upi/{upi}":{"get":{"description":"","operationId":"getUniParcEntryByUpId","parameters":[{"description":"UniParc ID (UPI)","in":"path","name":"upi","required":true,"schema":{"type":"string"}},{"description":"Response filter by Cross reference database type, e.g EMBL, RefSeq, Ensembl, etc. Comma separated values accepted.","in":"query","name":"rfDdtype","required":false,"schema":{"type":"string"}},{"description":"Response filter by all UniParc cross reference accessions, eg. AAC02967 (EMBL) or XP_006524055 (RefSeq). Comma separated values accepted.","in":"query","name":"rfDbid","required":false,"schema":{"type":"string"}},{"description":"Response filter by Active(true) or not Active(false) Cross reference.","in":"query","name":"rfActive","required":false,"schema":{"type":"string"}},{"description":"Response filter by organism taxon ID. Comma separated values accepted.","in":"query","name":"rfTaxId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Entry"}},"application/xml":{"schema":{"$ref":"#/components/schemas/Entry"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/Entry"}}},"description":"successful operation"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Invalid upid parameter. The value format should match the regular expression UPI[\\w]{10}."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"application/xml":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}},"text/x-fasta":{"schema":{"$ref":"#/components/schemas/ErrorMessage"}}},"description":"Resources not found"}},"summary":"Get UniParc entry by UniParc UPI","tags":["uniparc"]}},"/variation":{"get":{"description":"Among the available response content types, PEFF format (PSI Extended FASTA Format from the Human Proteome Organisation - Proteomics Standards Initiative, HUPO-PSI) is provided with only variants reported in the output.","operationId":"searchVariation","parameters":[{"description":"Off set, page starting point, with default value 0","in":"query","name":"offset","required":false,"schema":{"default":0,"format":"int32","minimum":0,"type":"integer"}},{"description":"Page size with default value 100. When page size is -1, it returns all records and offset will be ignored","in":"query","name":"size","required":false,"schema":{"default":100,"format":"int32","type":"integer"}},{"description":"Filter by the sourceType for variants: uniprot, large scale study and mixed. Comma separated values accepted up to 2.","in":"query","name":"sourcetype","required":false,"schema":{"type":"string"}},{"description":"Filter by consequenceType for variants: missense, stop gained or stop lost. Comma separated values accepted up to 2.","in":"query","name":"consequencetype","required":false,"schema":{"type":"string"}},{"description":"Search by specific wildType amino acid. Options: Any single letter amino acid and * for stop codon. Comma separated values accepted up to 20.","in":"query","name":"wildtype","required":false,"schema":{"type":"string"}},{"description":"Filter by the alternativeSequence amino acid. Any single letter amino acid and * for stopcodon and - for deletions. 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Syntax is \"disease=disease name\" Do Not use quotes. Example; disease=breast carcinoma","in":"query","name":"disease","required":false,"schema":{"type":"string"}},{"description":"Parameter used to search by the DO identifier. Syntax is \"doid=DOID:#\" Do Not use quotes. Example; doid=DOID:3459","in":"query","name":"doid","required":false,"schema":{"type":"string"}},{"description":"limit the number of records returned, default is 10","in":"query","name":"limit","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"A query response object with 'documents' property, each document corresponds to a disease that matched the query criteria.","x-responseValueType":[{"path":"lincs.cell","valueType":"http://identifiers.org/"}]}},"summary":"Query for LINCS cell line identifiers by disease, the diseases are captured from the Disease Ontology (DO) vocabulary.","tags":["diseases","query","LINCS","SchuererLab","cells"]}}},"servers":[{"description":"Production server","url":"http://lincsportal.ccs.miami.edu/dcic/api/"}],"tags":[{"name":"small molecule"},{"name":"query"},{"name":"cells"},{"name":"gene"},{"name":"diseases"},{"name":"LINCS"},{"name":"SchuererLab"},{"name":"signature"},{"name":"translator"}]},{"_id":"fc8245e92c970298449294fc04211869","_meta":{"date_created":"2021-02-04T00:00:10.655676+00:00","last_updated":"2021-06-15T07:01:14.311819+00:00","slug":"cohdcovid","url":"https://raw.githubusercontent.com/WengLab-InformaticsResearch/cohd_api/cohd_covid/cohd/cohd_oas3.yaml","username":"CaseyTa"},"_score":0.24307013,"components":{"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) for COVID-19 Research API provides access to counts and frequencies (i.e., EHR visit prevalence) of conditions, procedures, drug exposures, and the co-occurrence frequencies between them for a cohort of hospitalized COVID-19 patients and two comparator cohorts of hospitalized influenza patients and hospitalized patients. Count and frequency data were derived from the [Columbia University Medical Center's](http://www.cumc.columbia.edu/) [OHDSI](https://www.ohdsi.org/) database including inpatient. Counts are the number of inpatient visits associated with the concept, e.g., diagnosed with a condition, exposed to a drug, or a procedure was performed. Frequencies are the number of unique visits associated with the concept divided by the total number of visits in the dataset, i.e., prevalence in the electronic health records. To protect patient privacy, all concepts and pairs of concepts where the count <= 10 were excluded, and counts were randomized by the Poisson distribution. \n\nDatasets from three primary cohorts are available: \n1) COVID-19: Hospitalized patients aged 18 or older with a COVID-19 related condition diagnosis and/or a confirmed positive COVID-19 test during their hospitalization period or within the prior 21 days. Date range: March 1, 2020 to September 1, 2020. This cohort is also further stratified by sex (male and female) and age (adult: 18-64, senior: 65+).\n2) General inpatient: All hospitalized patients aged 18 or older. Date range: January 1, 2014 to December 31, 2019.\n3) Influenza: Hospitalized patients aged 18 or older who had at least one occurrence of influenza conditions or pre-coordinated positive measurements or positive influenza testing in the prior 21 days or during their hospitalization period. Date range: January 1, 2014 to December 31, 2019.\n\nBoth hierarchical and non-hierarchical datasets are available for each cohort. In the hierarchical datasets, the counts for each concept include the visits from all descendant concepts. For example, the count for ibuprofen (ID 1177480) includes visits with Ibuprofen 600 MG Oral Tablet (ID 19019073), Ibuprofen 400 MG Oral Tablet (ID 19019072), Ibuprofen 20 MG/ML Oral Suspension (ID 19019050), etc. \n\nClinical concepts (e.g., conditions, procedures, drugs) are coded by their standard concept ID in the [OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki). API methods are provided to map to/from other vocabularies supported in OMOP and other ontologies using the EMBL-EBI Ontology Xref Service (OxO). \n\n\nThe following resources are available through this API: \n\n\n1. Metadata: Metadata on the COHD database, including dataset descriptions, number of concepts, etc. \n\n\n2. OMOP: Access to the common vocabulary for name and concept identifier mapping\n\n\n3. Clinical Frequencies: Access to the counts and frequencies of conditions, procedures, and drug exposures, and the associations between them. Frequency was determined as the number of visits with the code(s) / total number of visits. \n\n\n4. Concept Associations: Inferred associations between concepts using chi-square analysis, ratio between observed to expected frequency, and relative frequency. \n\n\nA [Python notebook](https://github.com/WengLab-InformaticsResearch/cohd_api/blob/master/notebooks/COHD_API_Example.ipynb) demonstrates simple examples of how to use the COHD API.\n\n\nCOHD was developed at the [Columbia University Department of Biomedical Informatics](https://www.dbmi.columbia.edu/) as a collaboration between the [Weng Lab](http://people.dbmi.columbia.edu/~chw7007/), [Tatonetti Lab](http://tatonettilab.org/), and the [NCATS Biomedical Data Translator](https://ncats.nih.gov/translator) program (TReK Team). This work was supported in part by grants: NCATS 1OT2TR003434, NLM R01LM012895, NCATS OT3TR002027, NLM R01LM009886-08A1, and NIGMS R01GM107145.\n\nThe following external resources may be useful: \n[OHDSI](https://www.ohdsi.org/) \n[OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki) \n[Athena](http://athena.ohdsi.org) (OMOP vocabularies, search, concept relationships, concept hierarchy) \n[Atlas](http://www.ohdsi.org/web/atlas/) (OMOP vocabularies, search, concept relationships, concept hierarchy, concept sets) \n[NCATS Biomedical Data Translator](https://sites.google.com/ncats.nih.gov/translator-io/home) \n","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"termsOfService":"http://cohd.io/terms/","title":"Columbia Open Health Data (COHD) for COVID-19 Research","version":"3.0.0","x-accessRestriction":"none","x-implementationLanguage":"Python","x-translator":{"component":"KP","team":["Clinical Data Provider"]},"x-trapi":{"version":"1.0.0"}},"paths":{"/metadata/datasets":{"get":{"description":"Returns a list of datasets, including dataset ID, name, and description.","operationId":"datasets","responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"dataset_description":{"example":"Hospitalized patients with a COVID-19 condition and/or positive lab test (non-hierarchical)","type":"string"},"dataset_id":{"example":1,"type":"integer"},"dataset_name":{"example":"COVID Cohort (non-hierarchical)","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of dataset descriptions."},"default":{"description":"Unexpected error"}},"summary":"Enumerates the datasets available in COHD","tags":["Metadata"]}},"/metadata/domainCounts":{"get":{"description":"Returns a list of domains and the number of concepts in each domain.","operationId":"domainCounts","parameters":[{"description":"The dataset_id of the dataset to query. 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. 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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. 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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":{"description":"Attempts 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":{"description":"Attempts 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":0.000005585247351056813,"type":"integer"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2008271,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequency of a pair of concepts","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id. Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"q","required":true,"schema":{"type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":19041324,"type":"integer"},"associated_concept_name":{"example":"Acetaminophen 325 MG Oral Tablet [Tylenol]","type":"string"},"associated_domain_id":{"example":"Drug","type":"string"},"concept_count":{"example":277,"type":"integer"},"concept_frequency":{"example":0.0001547113516242737,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/associatedConceptDomainFreq":{"get":{"description":"Retrieves observed clinical frequencies of all pairs of concepts given a concept id restricted by domain of the associated concept_id. Results are returned in descending order of paired concept count. Note that the largest paired concept counts are often dominated by associated concepts with high prevalence.","operationId":"associatedConceptDomainFreq","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id","required":true,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc. See /metadata/domainCounts for a list of valid domain IDs.","example":"Procedure","in":"query","name":"domain","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"associated_concept_id":{"example":2211361,"type":"integer"},"associated_concept_name":{"example":"Radiologic examination, chest, 2 views, frontal and lateral","type":"string"},"associated_domain_id":{"example":"Procedure","type":"string"},"concept_count":{"example":257,"type":"integer"},"concept_frequency":{"example":0.00014354085692216007,"type":"integer"},"concept_id":{"example":192855,"type":"integer"},"dataset_id":{"example":1,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of associated concept frequencies."},"default":{"description":"Unexpected error"}},"summary":"Clinical frequencies of all pairs of concepts given a concept id","tags":["Clinical Frequencies"]}},"/frequencies/mostFrequentConcepts":{"get":{"description":"Retrieves the most frequent concepts.","operationId":"mostFrequentConcepts","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The number of concepts to retreieve, e.g., 100. 0 or unspecified will return all matching concepts.","example":100,"in":"query","name":"q","required":false,"schema":{"type":"integer"}},{"description":"(Optional) The domain_id to restrict to, e.g., \"Condition\", \"Drug\", \"Procedure\". See /metadata/domainCounts for a list of valid domain IDs.","example":"Condition","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"(Optional) The vocabulary_id(s) to restrict to, e.g., \"SNOMED\", \"MedDRA\", \"RxNorm\", \"ATC\" etc. Comma separated to include multiple vocabularies, e.g., \"SNOMED,MedDRA\". Default: unrestricted","example":null,"in":"query","name":"vocabulary_id","required":false,"schema":{"type":"string"}},{"description":"(Optional) The concept_class_id(s) to restrict to. concept_class_ids are specific to each vocabulary, e.g.,: [ATC](https://en.wikipedia.org/wiki/Anatomical_Therapeutic_Chemical_Classification_System) {ATC 1st, ATC 2nd, ATC 3rd, ATC 4th, ATC 5th}; [MedDRA](https://en.wikipedia.org/wiki/MedDRA) {PT, HLT, HLGT, SOC}; [RxNorm](https://www.nlm.nih.gov/research/umls/rxnorm/docs/2015/appendix5.html) {Ingredient, Clinical Drug Form, Clinical Drug Comp, Clinical Drug}. Comma separated to include multiple concept_class_ids, e.g., \"PT,HLT\". Default: unrestricted","example":null,"in":"query","name":"concept_class_id","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_class_id":{"example":"Clinical Finding","type":"string"},"concept_count":{"example":233790,"type":"integer"},"concept_frequency":{"example":0.1305774978203572,"type":"integer"},"concept_id":{"example":320128,"type":"integer"},"concept_name":{"example":"Essential hypertension","type":"string"},"dataset_id":{"example":1,"type":"integer"},"domain_id":{"example":"Condition","type":"string"},"vocabulary_id":{"example":"SNOMED","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of most frequent concepts."},"default":{"description":"Unexpected error"}},"summary":"Most frequent concepts [by domain]","tags":["Clinical Frequencies"]}},"/association/chiSquare":{"get":{"description":"Returns the chi-square statistic and p-value between pairs of concepts. Results are returned in descending order of the chi-square statistic. Note that due to large sample sizes, the chi-square can become very large. \n\nThe expected frequencies for the chi-square analysis are calculated based on the single concept frequencies and assuming independence between concepts. P-value is calculated with 1 DOF. \n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"chiSquare","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If this parameter is specified, then the chi-square between concept_id_1 and concept_id_2 is returned. If this parameter is not specified, then a list of chi-squared results between concept_id_1 and other concepts is returned.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"adj_p-value":{"description":"Bonferonni adjusted p-value, adjusted with the total number of pairs of concepts in the dataset.","example":0.0314,"type":"number"},"chi_square":{"example":370026.1780081638,"type":"integer"},"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Instillation of therapeutic substance into bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":4021588,"type":"integer"},"dataset_id":{"example":3,"type":"integer"},"p-value":{"example":0.0314,"type":"number"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of concept pairs and chi-squared values."},"default":{"description":"Unexpected error"}},"summary":"Chi-square analysis on pairs of concepts","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/chi_square"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/obsExpRatio":{"get":{"description":"Returns the natural logarithm of the ratio between the observed count and expected count. Expected count is calculated from the single concept frequencies and assuming independence between the concepts. Results are returned in descending order of ln_ratio.\n\nexpected_count = Count_1_and_2 * num_visits / (Count_1 * Count_2)\n\nln_ratio = ln(expected_count)\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Results for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"obsExpRatio","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}},{"description":"The confidence level used for calculating confidence intervals (default 0.99).","example":0.99,"in":"query","name":"confidence","required":false,"schema":{"type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Closed [transurethral] biopsy of bladder","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2003784,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"expected_count":{"example":0.060838982345591645,"type":"integer"},"ln_ratio":{"example":7.561698473261244,"type":"integer"},"observed_count":{"example":117,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concepts and observed-expected frequency ratio."},"default":{"description":"Unexpected error"}},"summary":"Observed Count / Expected Count","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","confidence":0.99,"dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/obs_exp_ratio"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/association/relativeFrequency":{"get":{"description":"Calculates the relative frequency (i.e., conditional probability) between pairs of concepts. Results are returned in descending order of relative frequency. Note that due to the randomization of the counts, the calculated relative frequencies can exceed the limit of 1.0.\n\nRelative Frequency = Count_1_and_2 / Count_2\n\nThis method has overloaded behavior based on the specified parameters:\n\n1) concept_id_1 and concept_id_2: Result for the pair (concept_id_1, concept_id_2)\n2) concept_id_1: Results for all pairs of concepts that include concept_id_1\n3) concept_id_1 and domain: Results for all pairs of concepts including concept_id_1 and where concept_id_2 belongs to the specified domain\n","operationId":"relativeFrequency","parameters":[{"description":"The dataset_id of the dataset to query. Default dataset is the 5-year dataset.","example":1,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"192855\"","example":192855,"in":"query","name":"concept_id_1","required":true,"schema":{"type":"integer"}},{"description":"An OMOP concept id, e.g., \"2008271\". If concept_id_2 is unspecified, then this method will return all pairs of concepts with concept_id_1.","example":2008271,"in":"query","name":"concept_id_2","required":false,"schema":{"type":"integer"}},{"description":"An OMOP domain id, e.g., \"Condition\", \"Drug\", \"Procedure\", etc., to restrict concept_id_2 (the base concept) to. If this parameter is not specified, then the domain is unrestricted. See /metadata/domainCounts for a list of valid domain IDs.","example":"Drug","in":"query","name":"domain","required":false,"schema":{"type":"string"}},{"description":"An OMOP concept_class_id, e.g., \"Ingredient\", to restrict the associated concept (concept_id_2) to. If this parameter is not specified, then the concept_class_id is unrestricted. Example useful usage would be to have domain=\"Drug\" and concept_class=\"Ingredient\"","example":"Ingredient","in":"query","name":"concept_class","required":false,"schema":{"type":"string"}},{"description":"The confidence level used for calculating confidence intervals (default 0.99).","example":0.99,"in":"query","name":"confidence","required":false,"schema":{"type":"number"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_2_count":{"example":82,"type":"integer"},"concept_2_domain":{"example":"Procedure","type":"string"},"concept_2_name":{"example":"Radical cystectomy","type":"string"},"concept_id_1":{"example":192855,"type":"integer"},"concept_id_2":{"example":2003805,"type":"integer"},"concept_pair_count":{"example":29,"type":"integer"},"dataset_id":{"example":1,"type":"integer"},"relative_frequency":{"example":0.35365853658536583,"type":"integer"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of paired concepts and relative frequency."},"default":{"description":"Unexpected error"}},"summary":"Relative frequency between pairs of concepts","tags":["Concept Associations"],"x-bte-kgs-operations":[{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Disease"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Condition"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false},{"inputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"outputs":[{"id":"biolink:OMOP","semantic":"biolink:Drug"}],"parameters":{"concept_id_1":"{inputs[0]}","dataset_id":3,"domain":"Drug"},"predicate":"biolink:correlated_with","response_mapping":{"$ref":"#/components/x-bte-kgs-response-mappings/relative_frequency"},"source":"Columbia Open Health Data KP","supportBatch":false}]}},"/predicates":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"additionalProperties":{"description":"Array of predicates","items":{"type":"string"},"type":"array"},"description":"Target map","type":"object"},"description":"Source map","example":{"biolink:ChemicalSubstance":{"biolink:Gene":["biolink:directly_interacts_with","biolink:decreases_activity_of"]}},"type":"object"}}},"description":"Predicates by source and target"}},"summary":"Get supported relationships by source and target","tags":["translator","trapi"]}},"/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.\n \nFor the subject node, the id must be specified (category is ignored).\n \nFor the object node, both the id and category are optional. If id is specified for the object node, then the association between the two identified concepts is returned. If id is not specified and category is specified, the associations between the subject node and all concepts with the specified category are returned. If neither are specified, then the associations between the subject node and all concepts are returned.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.\nAdditional behavior options can be controlled using the optional parameters in query_options.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"id\": \"MONDO:0021113\",\n \"category\": \"biolink:Disease\"\n },\n \"n01\": {\n \"category\": \"biolink:Procedure\"\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicate\": \"biolink:correlated_with\",\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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. 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Only single hop queries are supported. See the example query_graph.\nFor the source node, the curie must be specified (type is ignored).\nFor the target node, both the curie and type are optional. If curie is specified for the target node, then the association between the two identified concepts is returned. If curie is not specified and type is specified, the associations between the source node and all concepts with the specified type are returned. 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Count and frequency data were derived from the [Columbia University Medical Center's](http://www.cumc.columbia.edu/) [OHDSI](https://www.ohdsi.org/) database including inpatient 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)","version":"4.0.0","x-accessRestriction":"none","x-implementationLanguage":"Python","x-translator":{"biolink-version":"1.8.2","component":"KP","externalDocs":{"description":"The values for component and team are restricted according to this external JSON schema. 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See schema and examples at url","url":"https://github.com/NCATSTranslator/translator_extensions/blob/\\ production/x-trapi/"},"version":"1.1.0"}},"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. 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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. 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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. 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The hierarchical definitions were derived from the OMOP concept_ancestor table. See the documentation on OMOP's concept_ancestor table on [ohdsi.org](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:concept_ancestor) and [GitHub](https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT_ANCESTOR).","operationId":"conceptDescendants","parameters":[{"description":"An OMOP concept ID, e.g., 313217","example":313217,"in":"query","name":"concept_id","required":true,"schema":{"type":"integer"}},{"description":"The vocabulary_id to restrict ancestors to. For conditions, SNOMED and MedDRA are used. For drugs, RxNorm and ATC are used. For procedures, SNOMED, MedDRA, and ICD10PCS are used. Default: unrestricted","example":null,"in":"query","name":"vocabulary_id","required":false,"schema":{"type":"string"}},{"description":"The concept_class_id to restrict ancestors to. Only certain hierarchical concept_class_ids are used in each vocabuarly: [ATC](https://en.wikipedia.org/wiki/Anatomical_Therapeutic_Chemical_Classification_System) {ATC 1st, ATC 2nd, ATC 3rd, ATC 4th, ATC 5th}; [MedDRA](https://en.wikipedia.org/wiki/MedDRA) {PT, HLT, HLGT, SOC}; [RxNorm](https://www.nlm.nih.gov/research/umls/rxnorm/docs/2015/appendix5.html) {Ingredient, Clinical Drug Form, Clinical Drug Comp, Clinical Drug}. Default: unrestricted","example":null,"in":"query","name":"concept_class_id","required":false,"schema":{"type":"string"}},{"description":"The dataset_id to retrieve counts from. Default: 3 (5-year hierarchical data set)","example":3,"in":"query","name":"dataset_id","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_class_id":{"example":"Clinical Finding","type":"string"},"concept_code":{"example":"49436004","type":"string"},"concept_count":{"example":53272,"type":"integer"},"concept_name":{"example":"Atrial fibrillation","type":"string"},"descendant_concept_id":{"example":313217,"type":"integer"},"domain_id":{"example":"Condition","type":"string"},"max_levels_of_separation":{"example":0,"type":"integer"},"min_levels_of_separation":{"example":0,"type":"integer"},"standard_concept":{"example":"S","type":"string"},"vocabulary_id":{"example":"SNOMED","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of concepts."},"default":{"description":"Unexpected error"}},"summary":"Retrieve the concept's hierarchical descendants","tags":["OMOP"]}},"/omop/mapToStandardConceptID":{"get":{"description":"Uses the OMOP concept_relationship table to map from a non-standard concept code (e.g., ICD9CM 715.3) to a standard OMOP concept ID (e.g., 72990). This method may return multiple results if vocabulary_id is not specified and the concept_code is not unique across vocabularies. If both concept_code and vocabulary_id are specified, then 1 result will be returned at most. ","operationId":"mapToStandardConceptID","parameters":[{"description":"The concept code to map from, e.g., 715.3","example":"715.3","in":"query","name":"concept_code","required":true,"schema":{"type":"string"}},{"description":"The vocabulary (e.g., \"ICD9CM\") that the concept code belongs to. If this parameter is not specified, the method will return mappings from any source vocabulary with matching concept code. See /omop/vocabularies for the list of supported vocabularies.","example":"ICD9CM","in":"query","name":"vocabulary_id","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"source_concept_code":{"example":"715.3","type":"string"},"source_concept_id":{"example":44834979,"type":"integer"},"source_concept_name":{"example":"Osteoarthrosis, localized, not specified whether primary or secondary","type":"string"},"source_vocabulary_id":{"example":"ICD9CM","type":"string"},"standard_concept_id":{"example":72990,"type":"integer"},"standard_concept_name":{"example":"Localized osteoarthrosis uncertain if primary OR secondary","type":"string"},"standard_domain_id":{"example":"Condition","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of concepts."},"default":{"description":"Unexpected error"}},"summary":"Map from a non-standard concept code to a standard OMOP concept ID","tags":["OMOP"]}},"/omop/mapFromStandardConceptID":{"get":{"description":"Uses the OMOP concept_relationship table to map from a standard concept ID (e.g., 72990) to concept code(s) (e.g., ICD9CM 715.3, 715.31, 715.32, etc.). An OMOP standard concept ID may map to many concepts in the external vocabulary.","operationId":"mapFromStandardConceptID","parameters":[{"description":"The standard OMOP concept id to map from, e.g., 72990","example":72990,"in":"query","name":"concept_id","required":true,"schema":{"type":"integer"}},{"description":"The vocabulary (e.g., \"ICD9CM\") to map to. If this parameter is not specified, the method will return mappings to any matching vocabularies. See /omop/vocabularies for the list of supported vocabularies.","example":"ICD9CM","in":"query","name":"vocabulary_id","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"concept_class_id":{"example":"4-dig nonbill code","type":"string"},"concept_code":{"example":"715.3","type":"string"},"concept_id":{"example":44834979,"type":"integer"},"concept_name":{"example":"Osteoarthrosis, localized, not specified whether primary or secondary","type":"string"},"domain_id":{"example":"Condition","type":"string"},"standard_concept":{"example":null,"type":"string"},"vocabulary_id":{"example":"ICD9CM","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of concepts."},"default":{"description":"Unexpected error"}},"summary":"Map from a standard concept ID to concept code(s) in an external vocabulary","tags":["OMOP"]}},"/omop/vocabularies":{"get":{"description":"List of vocabulary_ids. Useful if you need to use /omop/mapToStandardConceptID to map a concept code from a source vocabulary to the OMOP standard vocabulary.","operationId":"vocabularies","responses":{"200":{"content":{"application/json":{"schema":{"properties":{"results":{"items":{"properties":{"vocabulary_id":{"example":"SNOMED","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"An array of vocabularies."},"default":{"description":"Unexpected error"}},"summary":"List of vocabularies","tags":["OMOP"]}},"/omop/xrefToOMOP":{"get":{"description":"Attempts 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":{"description":"Attempts 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":0.000005585247351056813,"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. \n \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"]}},"/predicates":{"get":{"deprecated":true,"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"additionalProperties":{"description":"Array of predicates","items":{"type":"string"},"type":"array"},"description":"Target map","type":"object"},"description":"Source map","example":{"biolink:ChemicalSubstance":{"biolink:Gene":["biolink:directly_interacts_with","biolink:decreases_activity_of"]}},"type":"object"}}},"description":"Predicates by source and target"}},"summary":"Get supported relationships by source and target","tags":["predicates"]}},"/meta_knowledge_graph":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns meta knowledge graph representation of this TRAPI web service."}},"summary":"Meta knowledge graph representation of this TRAPI web service.","tags":["meta_knowledge_graph"]}},"/query":{"post":{"description":"Query the COHD API following the [NCATS Translator Reasoner Standard API](https://github.com/NCATSTranslator/ReasonerAPI). Only single hop queries are supported. See the example query_graph.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"ids\": [\"DOID:9053\"],\n \"categories\": [\"biolink:Disease\"]\n },\n \"n01\": {\n \"categories\": [\"biolink:Procedure\"]\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicates\": [\"biolink:correlated_with\"],\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\n \"dataset_id\": 3,\n \"confidence_interval\": 0.99,\n \"min_cooccurrence\": 50,\n \"threshold\": 0.5,\n \"local_oxo\": true,\n \"max_results\": 50,\n \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\n \"biolink_only\": true\n }\n}","schema":{"$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)."},"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","tags":["query"]}},"/1.0.0/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.\nFor the subject node, the id must be specified (category is ignored).\nFor the object node, both the id and category are optional. If id is specified for the object node, then the association between the two identified concepts is returned. If id is not specified and category is specified, the associations between the subject node and all concepts with the specified category are returned. If neither are specified, then the associations between the subject node and all concepts are returned.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.\nAdditional behavior options can be controlled using the optional parameters in query_options.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"id\": \"DOID:9053\",\n \"category\": \"biolink:Disease\"\n },\n \"n01\": {\n \"category\": \"biolink:Procedure\"\n }\n },\n \"edges\": {\n \"e00\": {\n \"predicate\": \"biolink:correlated_with\",\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\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 \"ontology_targets\": {\n \"biolink:Disease\": [\n \"ICD9\",\n \"SNOMEDCT\",\n \"DOID\"\n ],\n \"biolink:Drug\": [\n \"RxNorm\"\n ],\n \"biolink:Procedure\": [\n \"ICD10PCS\",\n \"SNOMEDCT\"\n ],\n \"_DEFAULT\": []\n },\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":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Query COHD following NCATS TRAPI 1.0","tags":["translator"]}},"/translator/biolink_to_omop":{"post":{"description":"Map Biolink CURIEs to OMOP concepts","operationId":"biolink_to_omop","requestBody":{"content":{"application/json":{"example":"{\n \"curies\": [\n \"HP:0002907\",\n \"MONDO:0001187\"\n ]\n}","schema":{"$ref":"#/components/schemas/CurieList"}}},"description":"List of CURIEs","required":true},"responses":{"200":{"content":{"application/json":{"example":"{\n \"MONDO:0001187\": {\n \"distance\": 2,\n \"omop_concept_id\": 197508,\n \"omop_concept_name\": \"Malignant tumor of urinary bladder\"\n }\n}","schema":{"additionalProperties":{"description":"Mapping from OMOP concept to Biolink","properties":{"distance":{"description":"mapping distance","type":"integer"},"omop_concept_id":{"type":"integer"},"omop_concept_name":{"type":"string"}},"type":"object"}}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from Biolink to OMOP","tags":["translator"]}},"/translator/omop_to_biolink":{"post":{"description":"Map OMOP concepts to normalized Biolink nodes using SRI Node Normalizer.","operationId":"omop_to_biolink","requestBody":{"content":{"application/json":{"example":"{\n \"omop_ids\": [\n 78472,\n 197508\n ]\n}","schema":{"$ref":"#/components/schemas/OmopList"}}},"description":"List of OMOP IDs","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"additionalProperties":{"type":"object"},"example":"{\n \"197508\": {\n \"equivalent_identifiers\": [\n {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n {\n \"identifier\": \"DOID:11054\"\n },\n {\n \"identifier\": \"OMIM:109800\"\n },\n {\n \"identifier\": \"UMLS:C0005684\"\n },\n {\n \"identifier\": \"NCIT:C9334\"\n },\n {\n \"identifier\": \"SNOMEDCT:399326009\"\n }\n ],\n \"id\": {\n \"identifier\": \"MONDO:0001187\",\n \"label\": \"urinary bladder cancer\"\n },\n \"type\": [\n \"biolink:Disease\",\n \"biolink:DiseaseOrPhenotypicFeature\",\n \"biolink:BiologicalEntity\",\n \"biolink:NamedThing\"\n ]\n }\n}","type":"object"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized. Mapping from OMOP concept to Biolink normalized nodes. See [SRI Node Normalizer](https://nodenormalization-sri.renci.org/docs#/) for response format"},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."}},"summary":"Map from OMOP to Biolink","tags":["translator"]}}},"servers":[{"url":"https://cohd.io/api/"}],"tags":[{"description":"COHD metadata","name":"Metadata"},{"description":"OMOP Common Data Model concepts","name":"OMOP"},{"description":"Clinical frequency data","name":"Clinical Frequencies"},{"description":"Estimated association between concepts","name":"Concept Associations"},{"description":"Concept-age distributions, concept-pair delta distributions, and temporal analyses","name":"Temporal Clinical Data"},{"description":"Get supported relationships by source and target","name":"predicates"},{"description":"Query reasoner using a predefined question type","name":"query"},{"description":"Required for SmartAPI validation of x-translator","name":"translator"},{"description":"Required for SmartAPI validation of x-trapi","name":"trapi"}]}]} \ No newline at end of file diff --git a/src/controllers/cron/update_local_smartapi.js b/src/controllers/cron/update_local_smartapi.js index 753b5826..ff31b14c 100644 --- a/src/controllers/cron/update_local_smartapi.js +++ b/src/controllers/cron/update_local_smartapi.js @@ -6,6 +6,7 @@ const cron = require('node-cron'); const getTRAPIWithPredicatesEndpoint = (specs) => { const trapi = []; + let special_cases = [] specs.map((spec) => { try { if ( @@ -16,7 +17,9 @@ const getTRAPIWithPredicatesEndpoint = (specs) => { "/query" in spec.paths && "x-trapi" in spec.info && spec.servers.length && - "/predicates" in spec.paths || "/meta_knowledge_graph" in spec.paths + "/predicates" in spec.paths || + "/meta_knowledge_graph" in spec.paths || + "/1.1/meta_knowledge_graph" in spec.paths ) { let api = { association: { @@ -46,10 +49,25 @@ const getTRAPIWithPredicatesEndpoint = (specs) => { //1.1 api['predicates_path'] = "/meta_knowledge_graph"; trapi.push(api); + } + if ( + "/1.1/meta_knowledge_graph" in spec.paths && + Object.prototype.hasOwnProperty.call(spec.info["x-trapi"], "version") && + spec.info["x-trapi"].version.includes("1.1") + ) { + //1.1 + api['predicates_path'] = "/1.1/meta_knowledge_graph"; + trapi.push(api); + special_cases.push({name: spec.info['title'], id: spec['_id']}) }else if("/predicates" in spec.paths ){ //1.0 api['predicates_path'] = "/predicates"; trapi.push(api); + }else{ + debug( + `[error]: Unable to parse spec, ${spec ? spec.info.title : spec + }. Endpoint required not found.` + ); } } } catch (err) { @@ -59,6 +77,12 @@ const getTRAPIWithPredicatesEndpoint = (specs) => { ); } }); + if (special_cases.length) { + debug( + `Found some APIs with unexpected endpoint "/1.1/meta_knowledge_graph":` + ); + debug(`${JSON.stringify(special_cases)}`); + } return trapi; } @@ -71,7 +95,7 @@ const constructQueryUrl = (serverUrl, path) => { const getPredicatesFromGraphData = (predicate_endpoint, data) => { //if /predicates just return normal response - if (predicate_endpoint !== '/meta_knowledge_graph') { + if (!['/meta_knowledge_graph', '/1.1/meta_knowledge_graph'].includes(predicate_endpoint)) { return data } // transform graph data to legacy format > object.subject : predicates From 5d129ccf17c365200a128fcfaf5e797a3cc9f00f Mon Sep 17 00:00:00 2001 From: Marco Cano Date: Tue, 15 Jun 2021 18:18:10 -0700 Subject: [PATCH 68/75] update test, upgrade dependency --- __test__/integration/TRAPIv1.1.test.js | 2 +- package.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/__test__/integration/TRAPIv1.1.test.js b/__test__/integration/TRAPIv1.1.test.js index 2d860339..bdc1db90 100644 --- a/__test__/integration/TRAPIv1.1.test.js +++ b/__test__/integration/TRAPIv1.1.test.js @@ -202,7 +202,7 @@ describe("Testing v1.1 endpoints", () => { expect(response.body.message.knowledge_graph).toHaveProperty("edges"); expect(response.body.message.knowledge_graph.nodes).toHaveProperty("MONDO:0016575"); expect(response.body.message.knowledge_graph.nodes).toHaveProperty("UMLS:C0008780"); - expect(response.body.message.knowledge_graph.nodes["UMLS:C0008780"]).toHaveProperty("category", "biolink:PhenotypicFeature"); + expect(response.body.message.knowledge_graph.nodes["UMLS:C0008780"]).toHaveProperty("categories", ["biolink:PhenotypicFeature"]); }) }) diff --git a/package.json b/package.json index 9aa70483..5da6a07c 100644 --- a/package.json +++ b/package.json @@ -43,7 +43,7 @@ "supertest": "^6.1.3" }, "dependencies": { - "@biothings-explorer/query_graph_handler": "^1.17.1", + "@biothings-explorer/query_graph_handler": "^1.17.3", "@biothings-explorer/smartapi-kg": "^3.8.1", "axios": "^0.21.1", "body-parser": "^1.19.0", From 25602ffe5de4144991dfcd64b411efcf9e6f17d2 Mon Sep 17 00:00:00 2001 From: Marco Cano Date: Tue, 15 Jun 2021 18:25:01 -0700 Subject: [PATCH 69/75] fix: update pkg lock --- package-lock.json | 25 ++++++++++++------------- 1 file changed, 12 insertions(+), 13 deletions(-) diff --git a/package-lock.json b/package-lock.json index 42a00141..a1fe8e72 100644 --- a/package-lock.json +++ b/package-lock.json @@ -5,11 +5,10 @@ "requires": true, "packages": { "": { - "name": "@biothings-explorer/single-hop-app", - "version": "2.8.0", + "version": "2.8.1", "license": "ISC", "dependencies": { - "@biothings-explorer/query_graph_handler": "^1.17.1", + "@biothings-explorer/query_graph_handler": "^1.17.3", "@biothings-explorer/smartapi-kg": "^3.8.1", "axios": "^0.21.1", "body-parser": "^1.19.0", @@ -507,18 +506,18 @@ } }, "node_modules/@biothings-explorer/query_graph_handler": { - "version": "1.17.1", - "resolved": "https://registry.npmjs.org/@biothings-explorer/query_graph_handler/-/query_graph_handler-1.17.1.tgz", - "integrity": "sha512-XKkEU850AbrOlxjd2bQMcDCxP6zXx1Ah9BMn/3XXG1XUrjjdhuhSFV2CpQKj1TJ7RNYNgKi6BNCs5Ua01glE1w==", + "version": "1.17.3", + "resolved": "https://registry.npmjs.org/@biothings-explorer/query_graph_handler/-/query_graph_handler-1.17.3.tgz", + "integrity": "sha512-z9O/jnfSH8Oa3roJqwuTZ/+vzoAz/Lh8j7IXOncvsiP4D1ZTkb3dDGGAuIgD7yOb98B5PdfMYH7vNZLeKpG4Sw==", "dependencies": { "@biothings-explorer/call-apis": "^1.23.1", "@biothings-explorer/smartapi-kg": "^3.8.1", - "biolink-model": "^0.3.0", + "biolink-model": "^0.3.1", "biomedical_id_resolver": "^3.9.0", "debug": "^4.3.1", "lodash": "^4.17.21", "ms": "^2.1.3", - "redis": "^3.0.2" + "redis": "^3.1.1" } }, "node_modules/@biothings-explorer/query_graph_handler/node_modules/ms": { @@ -18647,18 +18646,18 @@ } }, "@biothings-explorer/query_graph_handler": { - "version": "1.17.1", - "resolved": "https://registry.npmjs.org/@biothings-explorer/query_graph_handler/-/query_graph_handler-1.17.1.tgz", - "integrity": "sha512-XKkEU850AbrOlxjd2bQMcDCxP6zXx1Ah9BMn/3XXG1XUrjjdhuhSFV2CpQKj1TJ7RNYNgKi6BNCs5Ua01glE1w==", + "version": "1.17.3", + "resolved": "https://registry.npmjs.org/@biothings-explorer/query_graph_handler/-/query_graph_handler-1.17.3.tgz", + "integrity": "sha512-z9O/jnfSH8Oa3roJqwuTZ/+vzoAz/Lh8j7IXOncvsiP4D1ZTkb3dDGGAuIgD7yOb98B5PdfMYH7vNZLeKpG4Sw==", "requires": { "@biothings-explorer/call-apis": "^1.23.1", "@biothings-explorer/smartapi-kg": "^3.8.1", - "biolink-model": "^0.3.0", + "biolink-model": "^0.3.1", "biomedical_id_resolver": "^3.9.0", "debug": "^4.3.1", "lodash": "^4.17.21", "ms": "^2.1.3", - "redis": "^3.0.2" + "redis": "^3.1.1" }, "dependencies": { "ms": { From cb10ee492abb8177679eac92752c67ced65f783e Mon Sep 17 00:00:00 2001 From: Marco Cano Date: Wed, 16 Jun 2021 17:21:58 -0700 Subject: [PATCH 70/75] build: upgrade handler and dep call executor --- package-lock.json | 147 +++++++++++++++------------------------------- package.json | 2 +- 2 files changed, 49 insertions(+), 100 deletions(-) diff --git a/package-lock.json b/package-lock.json index a1fe8e72..f1aad41f 100644 --- a/package-lock.json +++ b/package-lock.json @@ -8,7 +8,7 @@ "version": "2.8.1", "license": "ISC", "dependencies": { - "@biothings-explorer/query_graph_handler": "^1.17.3", + "@biothings-explorer/query_graph_handler": "^1.17.5", "@biothings-explorer/smartapi-kg": "^3.8.1", "axios": "^0.21.1", "body-parser": "^1.19.0", @@ -455,10 +455,19 @@ "version": "0.19.2", "resolved": "https://registry.npmjs.org/axios/-/axios-0.19.2.tgz", "integrity": "sha512-fjgm5MvRHLhx+osE2xoekY70AhARk3a6hkN+3Io1jc00jtquGvxYlKlsFUhmUET0V5te6CcZI7lcv2Ym61mjHA==", + "deprecated": "Critical security vulnerability fixed in v0.21.1. For more information, see https://github.com/axios/axios/pull/3410", "dependencies": { "follow-redirects": "1.5.10" } }, + "node_modules/@biothings-explorer/api-response-transform/node_modules/debug": { + "version": "3.1.0", + "resolved": "https://registry.npmjs.org/debug/-/debug-3.1.0.tgz", + "integrity": "sha512-OX8XqP7/1a9cqkxYw2yXss15f26NKWBpDXQd0/uK/KPqdQhxbPa994hnzjcE2VqQpDslf55723cKPUOGSmMY3g==", + "dependencies": { + "ms": "2.0.0" + } + }, "node_modules/@biothings-explorer/api-response-transform/node_modules/follow-redirects": { "version": "1.5.10", "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.5.10.tgz", @@ -470,23 +479,15 @@ "node": ">=4.0" } }, - "node_modules/@biothings-explorer/api-response-transform/node_modules/follow-redirects/node_modules/debug": { - "version": "3.1.0", - "resolved": "https://registry.npmjs.org/debug/-/debug-3.1.0.tgz", - "integrity": "sha512-OX8XqP7/1a9cqkxYw2yXss15f26NKWBpDXQd0/uK/KPqdQhxbPa994hnzjcE2VqQpDslf55723cKPUOGSmMY3g==", - "dependencies": { - "ms": "2.0.0" - } - }, "node_modules/@biothings-explorer/api-response-transform/node_modules/ms": { "version": "2.0.0", "resolved": "https://registry.npmjs.org/ms/-/ms-2.0.0.tgz", "integrity": "sha1-VgiurfwAvmwpAd9fmGF4jeDVl8g=" }, "node_modules/@biothings-explorer/call-apis": { - "version": "1.23.1", - "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.23.1.tgz", - "integrity": "sha512-0dIc/duAHG+2STf+XIv3BLirswua6xAUfJzu5zEuO5yj3IjLBQoLbXEdl9hYhthpgVH0fP2k+YvUQFHtC8P7kQ==", + "version": "1.23.2", + "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.23.2.tgz", + "integrity": "sha512-mYT60yqdKJjBT0Lh5g76/XpcibQ0o5I1H5cORJ6EzokuoMYLY+LQXJnSm0mnJjtX5H1AisB4tSvwdnd6VwePQw==", "dependencies": { "@biothings-explorer/api-response-transform": "^1.11.0", "axios": "^0.21.1", @@ -506,11 +507,11 @@ } }, "node_modules/@biothings-explorer/query_graph_handler": { - "version": "1.17.3", - "resolved": "https://registry.npmjs.org/@biothings-explorer/query_graph_handler/-/query_graph_handler-1.17.3.tgz", - "integrity": "sha512-z9O/jnfSH8Oa3roJqwuTZ/+vzoAz/Lh8j7IXOncvsiP4D1ZTkb3dDGGAuIgD7yOb98B5PdfMYH7vNZLeKpG4Sw==", + "version": "1.17.5", + "resolved": "https://registry.npmjs.org/@biothings-explorer/query_graph_handler/-/query_graph_handler-1.17.5.tgz", + "integrity": "sha512-si0IzHUD7YlC4QurHV7N8RXDRjyc5WE9QVlhZk8/baLukxrc6zpAkC5yqNcjNGHR2OWvMZ1r8HHMtiANfvC1Ag==", "dependencies": { - "@biothings-explorer/call-apis": "^1.23.1", + "@biothings-explorer/call-apis": "^1.23.2", "@biothings-explorer/smartapi-kg": "^3.8.1", "biolink-model": "^0.3.1", "biomedical_id_resolver": "^3.9.0", @@ -5039,11 +5040,6 @@ "tslib": "^2.0.3" } }, - "node_modules/dot-case/node_modules/tslib": { - "version": "2.0.3", - "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.0.3.tgz", - "integrity": "sha512-uZtkfKblCEQtZKBF6EBXVZeQNl82yqtDQdv+eck8u7tdPxjLu2/lp5/uPW+um2tpuxINHWy3GhiccY7QgEaVHQ==" - }, "node_modules/dot-prop": { "version": "5.3.0", "resolved": "https://registry.npmjs.org/dot-prop/-/dot-prop-5.3.0.tgz", @@ -9166,9 +9162,9 @@ } }, "node_modules/jsonata": { - 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}, "node_modules/snapdragon": { "version": "0.8.2", "resolved": "https://registry.npmjs.org/snapdragon/-/snapdragon-0.8.2.tgz", @@ -17389,6 +17365,11 @@ "integrity": "sha1-NEiaLKwMCcHMEO2RugEVlNQzO+I=", "dev": true }, + "node_modules/tslib": { + "version": "2.3.0", + "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.3.0.tgz", + "integrity": "sha512-N82ooyxVNm6h1riLCoyS9e3fuJ3AMG2zIZs2Gd1ATcSFjSA23Q0fzjjZeh0jbJvWVDZ0cJT8yaNNaaXHzueNjg==" + }, "node_modules/tunnel-agent": { "version": "0.6.0", "resolved": "https://registry.npmjs.org/tunnel-agent/-/tunnel-agent-0.6.0.tgz", @@ -18598,22 +18579,20 @@ "follow-redirects": "1.5.10" } }, + "debug": { + "version": "3.1.0", + "resolved": "https://registry.npmjs.org/debug/-/debug-3.1.0.tgz", + "integrity": "sha512-OX8XqP7/1a9cqkxYw2yXss15f26NKWBpDXQd0/uK/KPqdQhxbPa994hnzjcE2VqQpDslf55723cKPUOGSmMY3g==", + "requires": { + "ms": "2.0.0" + } + }, "follow-redirects": { "version": "1.5.10", "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.5.10.tgz", "integrity": "sha512-0V5l4Cizzvqt5D44aTXbFZz+FtyXV1vrDN6qrelxtfYQKW0KO0W2T/hkE8xvGa/540LkZlkaUjO4ailYTFtHVQ==", "requires": { "debug": "=3.1.0" - 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"resolved": "https://registry.npmjs.org/@biothings-explorer/query_graph_handler/-/query_graph_handler-1.17.3.tgz", - "integrity": "sha512-z9O/jnfSH8Oa3roJqwuTZ/+vzoAz/Lh8j7IXOncvsiP4D1ZTkb3dDGGAuIgD7yOb98B5PdfMYH7vNZLeKpG4Sw==", + "version": "1.17.5", + "resolved": "https://registry.npmjs.org/@biothings-explorer/query_graph_handler/-/query_graph_handler-1.17.5.tgz", + "integrity": "sha512-si0IzHUD7YlC4QurHV7N8RXDRjyc5WE9QVlhZk8/baLukxrc6zpAkC5yqNcjNGHR2OWvMZ1r8HHMtiANfvC1Ag==", "requires": { - "@biothings-explorer/call-apis": "^1.23.1", + "@biothings-explorer/call-apis": "^1.23.2", "@biothings-explorer/smartapi-kg": "^3.8.1", "biolink-model": "^0.3.1", "biomedical_id_resolver": "^3.9.0", @@ -22360,13 +22339,6 @@ "requires": { "no-case": "^3.0.4", "tslib": "^2.0.3" - }, - "dependencies": { - "tslib": { - "version": "2.0.3", - "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.0.3.tgz", - "integrity": "sha512-uZtkfKblCEQtZKBF6EBXVZeQNl82yqtDQdv+eck8u7tdPxjLu2/lp5/uPW+um2tpuxINHWy3GhiccY7QgEaVHQ==" - } } }, "dot-prop": { @@ -25657,9 +25629,9 @@ } }, "jsonata": { - "version": "1.8.3", - "resolved": "https://registry.npmjs.org/jsonata/-/jsonata-1.8.3.tgz", - "integrity": "sha512-r6ztI6ohbpRo77AxBm6vMs3aHZi2L2PaakW7TCPwSkeGcuAZ/SxXGLWH2Npwqq5+YBM/fg/g0EXg/pI9HvXQ8Q==" + "version": "1.8.4", + "resolved": "https://registry.npmjs.org/jsonata/-/jsonata-1.8.4.tgz", + "integrity": "sha512-OqzmM5IICtm/687zckG5BROZzInGCEuKojpYs48H8RnkII8Np+o912ryvhnYwsRrSI24TQRG/qqrSwBuaneDbg==" }, "jsonfile": { "version": "6.1.0", @@ -25917,13 +25889,6 @@ "integrity": "sha512-7fm3l3NAF9WfN6W3JOmf5drwpVqX78JtoGJ3A6W0a6ZnldM41w2fV5D490psKFTpMds8TJse/eHLFFsNHHjHgg==", "requires": { "tslib": "^2.0.3" - }, - "dependencies": { - "tslib": { - "version": "2.0.3", - "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.0.3.tgz", - "integrity": "sha512-uZtkfKblCEQtZKBF6EBXVZeQNl82yqtDQdv+eck8u7tdPxjLu2/lp5/uPW+um2tpuxINHWy3GhiccY7QgEaVHQ==" - } } }, "lowercase-keys": { @@ -26267,13 +26232,6 @@ "requires": { "lower-case": "^2.0.2", "tslib": "^2.0.3" - }, - "dependencies": { - "tslib": { - "version": "2.0.3", - "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.0.3.tgz", - "integrity": "sha512-uZtkfKblCEQtZKBF6EBXVZeQNl82yqtDQdv+eck8u7tdPxjLu2/lp5/uPW+um2tpuxINHWy3GhiccY7QgEaVHQ==" - } } }, "node-cron": { @@ -29874,13 +29832,6 @@ "requires": { "no-case": "^3.0.4", "tslib": "^2.0.3" - }, - "dependencies": { - "tslib": { - "version": "2.2.0", - "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.2.0.tgz", - "integrity": "sha512-gS9GVHRU+RGn5KQM2rllAlR3dU6m7AcpJKdtH8gFvQiC4Otgk98XnmMU+nZenHt/+VhnBPWwgrJsyrdcw6i23w==" - } } }, "pascalcase": { @@ -30850,13 +30801,6 @@ "requires": { "dot-case": "^3.0.4", "tslib": "^2.0.3" - }, - "dependencies": { - "tslib": { - "version": "2.0.3", - "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.0.3.tgz", - "integrity": "sha512-uZtkfKblCEQtZKBF6EBXVZeQNl82yqtDQdv+eck8u7tdPxjLu2/lp5/uPW+um2tpuxINHWy3GhiccY7QgEaVHQ==" - } } }, "snapdragon": { @@ -31849,6 +31793,11 @@ "integrity": "sha1-NEiaLKwMCcHMEO2RugEVlNQzO+I=", "dev": true }, + "tslib": { + "version": "2.3.0", + "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.3.0.tgz", + "integrity": "sha512-N82ooyxVNm6h1riLCoyS9e3fuJ3AMG2zIZs2Gd1ATcSFjSA23Q0fzjjZeh0jbJvWVDZ0cJT8yaNNaaXHzueNjg==" + }, "tunnel-agent": { "version": "0.6.0", "resolved": "https://registry.npmjs.org/tunnel-agent/-/tunnel-agent-0.6.0.tgz", diff --git a/package.json b/package.json index 5da6a07c..b0c160e0 100644 --- a/package.json +++ b/package.json @@ -43,7 +43,7 @@ "supertest": "^6.1.3" }, "dependencies": { - "@biothings-explorer/query_graph_handler": "^1.17.3", + "@biothings-explorer/query_graph_handler": "^1.17.5", "@biothings-explorer/smartapi-kg": "^3.8.1", "axios": "^0.21.1", "body-parser": "^1.19.0", From d148778034130aaf1b4f95f496e284933f311727 Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Fri, 25 Jun 2021 15:33:34 -0700 Subject: [PATCH 71/75] chore: ignore built folder --- .gitignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitignore b/.gitignore index 2bd26476..3906687f 100644 --- a/.gitignore +++ b/.gitignore @@ -115,3 +115,5 @@ processed*.txt report*.json .DS_Store + +built From 554b13696cff3b8e275f200be85b45c0883ef593 Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Fri, 25 Jun 2021 15:34:17 -0700 Subject: [PATCH 72/75] chore: add bte prefix to debugger name --- src/controllers/association.js | 2 +- src/controllers/cron/update_local_smartapi.js | 2 +- src/controllers/meta_knowledge_graph.js | 2 +- src/routes/performance.js | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/controllers/association.js b/src/controllers/association.js index 7b6e6c29..bc322282 100644 --- a/src/controllers/association.js +++ b/src/controllers/association.js @@ -3,7 +3,7 @@ const fs = require("fs"); var path = require('path'); const util = require('util'); const readFile = util.promisify(fs.readFile); -const debug = require("debug")("biothings-explorer-trapi:metakg"); +const debug = require("debug")("bte:biothings-explorer-trapi:metakg"); module.exports = async (sub = undefined, obj = undefined, pred = undefined, api = undefined, source = undefined) => { const smartapi_specs = path.resolve(__dirname, '../../data/smartapi_specs.json'); diff --git a/src/controllers/cron/update_local_smartapi.js b/src/controllers/cron/update_local_smartapi.js index ff31b14c..384ce320 100644 --- a/src/controllers/cron/update_local_smartapi.js +++ b/src/controllers/cron/update_local_smartapi.js @@ -1,4 +1,4 @@ -const debug = require("debug")("biothings-explorer-trapi:cron"); +const debug = require("debug")("bte:biothings-explorer-trapi:cron"); const axios = require("axios"); const fs = require("fs"); var path = require('path'); diff --git a/src/controllers/meta_knowledge_graph.js b/src/controllers/meta_knowledge_graph.js index e4337d9c..1ffbe821 100644 --- a/src/controllers/meta_knowledge_graph.js +++ b/src/controllers/meta_knowledge_graph.js @@ -6,7 +6,7 @@ const util = require('util'); const PredicatesLoadingError = require("../utils/errors/predicates_error"); const ids = require("./ids"); const readFile = util.promisify(fs.readFile); -const debug = require("debug")("biothings-explorer-trapi:metakg"); +const debug = require("debug")("bte:biothings-explorer-trapi:metakg"); module.exports = class MetaKnowledgeGraphHandler { constructor(smartapiID = undefined, team = undefined) { diff --git a/src/routes/performance.js b/src/routes/performance.js index 86cbaf29..9777785c 100644 --- a/src/routes/performance.js +++ b/src/routes/performance.js @@ -1,6 +1,6 @@ var path = require('path'); const fs = require('fs'); -const debug = require("debug")("biothings-explorer-trapi:performance"); +const debug = require("debug")("bte:biothings-explorer-trapi:performance"); class RoutePerformance { setRoutes(app) { From b162a803b0091f52f85c01318d0af9509c44ce2e Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Fri, 25 Jun 2021 15:39:30 -0700 Subject: [PATCH 73/75] build: :hammer: new debug and debug-all scripts --- package.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/package.json b/package.json index b0c160e0..ff0044d9 100644 --- a/package.json +++ b/package.json @@ -6,7 +6,8 @@ "scripts": { "build": "echo 'no build needed'", "start": "nodemon --delay 5 src/server.js", - "debug": "DEBUG=* nodemon --delay 5 src/server.js", + "debug": "DEBUG=biomedical-id-resolver,bte* nodemon --delay 5 src/server.js", + "debug-all": "DEBUG=* nodemon --delay 5 src/server.js", "test": "jest --forceExit", "test-cov": "jest --coverage", "coveralls": "jest --coverage --forceExit && cat ./coverage/lcov.info | ./node_modules/coveralls/bin/coveralls.js && rm -rf ./coverage", From 4d0635c40db7237f4844bbdb275a7d042bb05407 Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Fri, 25 Jun 2021 15:50:17 -0700 Subject: [PATCH 74/75] build: :hammer: remove localhost CORS errors --- package.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/package.json b/package.json index ff0044d9..ab7c0fab 100644 --- a/package.json +++ b/package.json @@ -8,10 +8,10 @@ "start": "nodemon --delay 5 src/server.js", "debug": "DEBUG=biomedical-id-resolver,bte* nodemon --delay 5 src/server.js", "debug-all": "DEBUG=* nodemon --delay 5 src/server.js", - "test": "jest --forceExit", - "test-cov": "jest --coverage", - "coveralls": "jest --coverage --forceExit && cat ./coverage/lcov.info | ./node_modules/coveralls/bin/coveralls.js && rm -rf ./coverage", - "test-coveralls": "jest --coverage --forceExit && cat ./coverage/lcov.info | ./node_modules/coveralls/bin/coveralls.js --verbose", + "test": "jest --forceExit --env node", + "test-cov": "jest --coverage --env node", + "coveralls": "jest --coverage --forceExit --env node && cat ./coverage/lcov.info | ./node_modules/coveralls/bin/coveralls.js && rm -rf ./coverage", + "test-coveralls": "jest --coverage --forceExit --env node && cat ./coverage/lcov.info | ./node_modules/coveralls/bin/coveralls.js --verbose", "release": "standard-version", "release:minor": "standard-version --release-as minor", "release:patch": "standard-version --release-as patch", From 701f3d93ff8ee6d1113cf0f34e1cda387521c8ce Mon Sep 17 00:00:00 2001 From: Chunlei Wu Date: Fri, 25 Jun 2021 15:53:14 -0700 Subject: [PATCH 75/75] build: :hammer: updated package-lock.json --- package-lock.json | 1 + 1 file changed, 1 insertion(+) diff --git a/package-lock.json b/package-lock.json index f1aad41f..703d24d4 100644 --- a/package-lock.json +++ b/package-lock.json @@ -5,6 +5,7 @@ "requires": true, "packages": { "": { + "name": "@biothings-explorer/single-hop-app", "version": "2.8.1", "license": "ISC", "dependencies": {