From e5b3ca71a59e9d4d4be2ec96d9020c60eee3abe3 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 25 Mar 2021 16:57:28 -0700 Subject: [PATCH 01/68] chore(release): 1.1.7 --- CHANGELOG.md | 2 ++ package-lock.json | 66 ++++++----------------------------------------- package.json | 6 ++--- 3 files changed, 13 insertions(+), 61 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 27451c39..488c2808 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,8 @@ 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. +### [1.1.7](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.1.6...v1.1.7) (2021-03-25) + ### [1.1.6](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.1.5...v1.1.6) (2021-03-25) ### [1.1.5](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.1.4...v1.1.5) (2021-03-25) diff --git a/package-lock.json b/package-lock.json index a685f407..84b680d2 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.1.6", + "version": "1.1.7", "lockfileVersion": 1, "requires": true, "dependencies": { @@ -449,65 +449,15 @@ } }, "@biothings-explorer/call-apis": { - "version": "1.15.1", - "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.15.1.tgz", - "integrity": "sha512-iG0pefAwUd0miXywM+QExYCROZg6Y0vTi9uN51jY9v0L6fOt81JVbZsC6jr6yLc+rIp/umueg9nIlC1iXX0yUQ==", + "version": "1.15.2", + "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.15.2.tgz", + "integrity": "sha512-7kNQ/hXIDsTttBk/nkir9dvv8Hyk/bEUcSxjmE98epPaOUOThT8Xl9IIFks6QiDFuuvZBxje5lrvUt5Rh5sjAQ==", "requires": { "@biothings-explorer/api-response-transform": "^1.8.0", "axios": "^0.21.1", - "biomedical_id_resolver": "^3.4.2", + "biomedical_id_resolver": "^3.4.3", "debug": "^4.3.1", "husky": "^4.3.8" - }, - "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==" - }, - "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" - } - }, - "biomedical_id_resolver": { - "version": "3.4.2", - "resolved": "https://registry.npmjs.org/biomedical_id_resolver/-/biomedical_id_resolver-3.4.2.tgz", - "integrity": "sha512-n121Pi8xss/e0vG8dysBkNZVc+718zH+oPt/VXd4TpE2ZvWEjlhZozNv9EIK80XIH6wLeDR3NvDFKZVqyGUpCA==", - "requires": { - "@commitlint/cli": "^11.0.0", - "@commitlint/config-conventional": "^11.0.0", - "axios": "^0.19.2", - "biolink-model": "^0.1.2", - "debug": "^4.3.1", - "husky": "^4.3.8", - "lodash": "^4.17.21" - }, - "dependencies": { - "axios": { - "version": "0.19.2", - "resolved": "https://registry.npmjs.org/axios/-/axios-0.19.2.tgz", - "integrity": "sha512-fjgm5MvRHLhx+osE2xoekY70AhARk3a6hkN+3Io1jc00jtquGvxYlKlsFUhmUET0V5te6CcZI7lcv2Ym61mjHA==", - "requires": { - "follow-redirects": "1.5.10" - } - } - } - }, - "js-yaml": { - "version": "4.0.0", - "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-4.0.0.tgz", - "integrity": "sha512-pqon0s+4ScYUvX30wxQi3PogGFAlUyH0awepWvwkj4jD4v+ova3RiYw8bmA6x2rDrEaj8i/oWKoRxpVNW+Re8Q==", - "requires": { - "argparse": "^2.0.1" - } - } } }, "@biothings-explorer/json-transformer": { @@ -1527,9 +1477,9 @@ } }, "biomedical_id_resolver": { - "version": "3.4.2", - "resolved": "https://registry.npmjs.org/biomedical_id_resolver/-/biomedical_id_resolver-3.4.2.tgz", - "integrity": "sha512-n121Pi8xss/e0vG8dysBkNZVc+718zH+oPt/VXd4TpE2ZvWEjlhZozNv9EIK80XIH6wLeDR3NvDFKZVqyGUpCA==", + "version": "3.4.3", + "resolved": "https://registry.npmjs.org/biomedical_id_resolver/-/biomedical_id_resolver-3.4.3.tgz", + "integrity": "sha512-/uHFxoViPXTlQOALy3ON8g0yygvoiMMlf54M3qB9rUwl55QUoshOuxm0EB11UqI5QaIesqxWrx1kauvg8a8Naw==", "requires": { "@commitlint/cli": "^11.0.0", "@commitlint/config-conventional": "^11.0.0", diff --git a/package.json b/package.json index e75b45a6..e6b5962c 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.1.6", + "version": "1.1.7", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { @@ -50,10 +50,10 @@ "typescript": "^4.2.3" }, "dependencies": { - "@biothings-explorer/call-apis": "^1.15.1", + "@biothings-explorer/call-apis": "^1.15.2", "@biothings-explorer/smartapi-kg": "^3.1.1", "biolink-model": "^0.3.0", - "biomedical_id_resolver": "^3.4.2", + "biomedical_id_resolver": "^3.4.3", "debug": "^4.3.1", "lodash": "^4.17.21", "ms": "^2.1.3", From 1abf2e165116a469188aa6d718c62a517aa5f17a Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 25 Mar 2021 20:27:18 -0700 Subject: [PATCH 02/68] chore(release): 1.1.8 --- CHANGELOG.md | 2 ++ package-lock.json | 2 +- package.json | 2 +- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 488c2808..e9ec35ab 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,8 @@ 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. +### [1.1.8](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.1.7...v1.1.8) (2021-03-26) + ### [1.1.7](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.1.6...v1.1.7) (2021-03-25) ### [1.1.6](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.1.5...v1.1.6) (2021-03-25) diff --git a/package-lock.json b/package-lock.json index 84b680d2..8aedf298 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.1.7", + "version": "1.1.8", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index e6b5962c..c9c7a5df 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.1.7", + "version": "1.1.8", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { From 2b8d57b70df62aad2cbb7d79d9108bfe1f828234 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 25 Mar 2021 20:54:27 -0700 Subject: [PATCH 03/68] fix: :bug: fix wrong attribute type --- src/graph/knowledge_graph.js | 200 +++++++++++++++++------------------ 1 file changed, 100 insertions(+), 100 deletions(-) diff --git a/src/graph/knowledge_graph.js b/src/graph/knowledge_graph.js index 6d4cb9b7..845281e1 100644 --- a/src/graph/knowledge_graph.js +++ b/src/graph/knowledge_graph.js @@ -3,112 +3,112 @@ const debug = require('debug')('biothings-explorer-trapi:KnowledgeGraph'); const helper = new GraphHelper(); module.exports = class KnowledgeGraph { - constructor() { - this.nodes = {}; - this.edges = {}; - this.kg = { - nodes: this.nodes, - edges: this.edges, - }; - } + constructor() { + this.nodes = {}; + this.edges = {}; + this.kg = { + nodes: this.nodes, + edges: this.edges, + }; + } - getNodes() { - return this.nodes; - } + getNodes() { + return this.nodes; + } - getEdges() { - return this.edges; - } + getEdges() { + return this.edges; + } - _createNode(kgNode) { - const res = { - category: 'biolink:' + kgNode._semanticType, - name: kgNode._label, - attributes: [ - { - name: 'equivalent_identifiers', - value: kgNode._curies, - type: 'biolink:id', - }, - { - name: 'num_soure_nodes', - value: kgNode._sourceNodes.size, - type: 'bts:num_target_nodes', - }, - { - name: 'num_target_nodes', - value: kgNode._targetNodes.size, - type: 'bts:num_target_nodes', - }, - { - name: 'source_qg_nodes', - value: Array.from(kgNode._sourceQGNodes), - type: 'bts:source_qg_nodes', - }, - { - name: 'target_qg_nodes', - value: Array.from(kgNode._targetQGNodes), - type: 'bts:target_qg_nodes', - }, - ], - }; - for (const key in kgNode._nodeAttributes) { - res.attributes.push({ - name: key, - value: kgNode._nodeAttributes[key], - type: 'bts:' + key, - }); + _createNode(kgNode) { + const res = { + category: 'biolink:' + kgNode._semanticType, + name: kgNode._label, + attributes: [ + { + name: 'equivalent_identifiers', + value: kgNode._curies, + type: 'biolink:id', + }, + { + name: 'num_source_nodes', + value: kgNode._sourceNodes.size, + type: 'bts:num_source_nodes', + }, + { + name: 'num_target_nodes', + value: kgNode._targetNodes.size, + type: 'bts:num_target_nodes', + }, + { + name: 'source_qg_nodes', + value: Array.from(kgNode._sourceQGNodes), + type: 'bts:source_qg_nodes', + }, + { + name: 'target_qg_nodes', + value: Array.from(kgNode._targetQGNodes), + type: 'bts:target_qg_nodes', + }, + ], + }; + for (const key in kgNode._nodeAttributes) { + res.attributes.push({ + name: key, + value: kgNode._nodeAttributes[key], + type: 'bts:' + key, + }); + } + return res; } - return res; - } - _createAttributes(kgEdge) { - const attributes = [ - { - name: 'provided_by', - value: Array.from(kgEdge.sources), - type: 'biolink:provided_by', - }, - { - name: 'api', - value: Array.from(kgEdge.apis), - type: 'bts:api', - }, - { - name: 'publications', - value: Array.from(kgEdge.publications), - type: 'biolink:publication', - }, - ]; - for (const key in kgEdge.attributes) { - attributes.push({ - name: key, - value: kgEdge.attributes[key], - type: 'bts:' + key, - }); + _createAttributes(kgEdge) { + const attributes = [ + { + name: 'provided_by', + value: Array.from(kgEdge.sources), + type: 'biolink:provided_by', + }, + { + name: 'api', + value: Array.from(kgEdge.apis), + type: 'bts:api', + }, + { + name: 'publications', + value: Array.from(kgEdge.publications), + type: 'biolink:publication', + }, + ]; + for (const key in kgEdge.attributes) { + attributes.push({ + name: key, + value: kgEdge.attributes[key], + type: 'bts:' + key, + }); + } + return attributes; } - return attributes; - } - _createEdge(kgEdge) { - return { - predicate: kgEdge.predicate, - subject: kgEdge.subject, - object: kgEdge.object, - attributes: this._createAttributes(kgEdge), - }; - } + _createEdge(kgEdge) { + return { + predicate: kgEdge.predicate, + subject: kgEdge.subject, + object: kgEdge.object, + attributes: this._createAttributes(kgEdge), + }; + } - update(bteGraph) { - Object.keys(bteGraph.nodes).map((node) => { - this.nodes[bteGraph.nodes[node]._primaryID] = this._createNode(bteGraph.nodes[node]); - }); - Object.keys(bteGraph.edges).map((edge) => { - this.edges[edge] = this._createEdge(bteGraph.edges[edge]); - }); - this.kg = { - nodes: this.nodes, - edges: this.edges, - }; - } + update(bteGraph) { + Object.keys(bteGraph.nodes).map((node) => { + this.nodes[bteGraph.nodes[node]._primaryID] = this._createNode(bteGraph.nodes[node]); + }); + Object.keys(bteGraph.edges).map((edge) => { + this.edges[edge] = this._createEdge(bteGraph.edges[edge]); + }); + this.kg = { + nodes: this.nodes, + edges: this.edges, + }; + } }; From af3a3dad9a26baad34664d0c299f1f2eb94dcc62 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 25 Mar 2021 20:54:35 -0700 Subject: [PATCH 04/68] chore(release): 1.1.9 --- 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 e9ec35ab..37028834 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. +### [1.1.9](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.1.8...v1.1.9) (2021-03-26) + + +### Bug Fixes + +* :bug: fix wrong attribute type ([2b8d57b](https://github.com/kevinxin90/bte_trapi_query_graph_handler/commit/2b8d57b70df62aad2cbb7d79d9108bfe1f828234)) + ### [1.1.8](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.1.7...v1.1.8) (2021-03-26) ### [1.1.7](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.1.6...v1.1.7) (2021-03-25) diff --git a/package-lock.json b/package-lock.json index 8aedf298..3a6f16e6 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.1.8", + "version": "1.1.9", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index c9c7a5df..d6223ea4 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.1.8", + "version": "1.1.9", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { From 56f9fbfeeb711f0f0cd462d3710c81ebd9b05900 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Fri, 26 Mar 2021 10:34:35 -0700 Subject: [PATCH 05/68] build: :arrow_up: upgrade call-apis package --- package-lock.json | 17 +++++++++-------- package.json | 2 +- 2 files changed, 10 insertions(+), 9 deletions(-) diff --git a/package-lock.json b/package-lock.json index 3a6f16e6..e13277da 100644 --- a/package-lock.json +++ b/package-lock.json @@ -427,15 +427,16 @@ "dev": true }, "@biothings-explorer/api-response-transform": { - "version": "1.8.0", - "resolved": "https://registry.npmjs.org/@biothings-explorer/api-response-transform/-/api-response-transform-1.8.0.tgz", - "integrity": "sha512-WH6A4HIu3pZ0D3/c1sCeHHc77aSJinoGpM2qVdow2BB3c8D3XD8EnnKp9/mnLl4ezO9Ldu0R4P05bo0xXNAqWw==", + "version": "1.9.1", + "resolved": "https://registry.npmjs.org/@biothings-explorer/api-response-transform/-/api-response-transform-1.9.1.tgz", + "integrity": "sha512-5XG1IGTQjadbm6p/OEsljtH0fJtcHFmJs5zkm487WjvgN3t/RQzn7rEA4vXTimR1stgKuUOY+ksJk9P6lXx8gA==", "requires": { "@biothings-explorer/json-transformer": "^1.0.2", "@commitlint/cli": "^11.0.0", "@commitlint/config-conventional": "^11.0.0", "axios": "^0.19.2", - "husky": "^4.3.8" + "husky": "^4.3.8", + "lodash": "^4.17.21" }, "dependencies": { "axios": { @@ -449,11 +450,11 @@ } }, "@biothings-explorer/call-apis": { - "version": "1.15.2", - "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.15.2.tgz", - "integrity": "sha512-7kNQ/hXIDsTttBk/nkir9dvv8Hyk/bEUcSxjmE98epPaOUOThT8Xl9IIFks6QiDFuuvZBxje5lrvUt5Rh5sjAQ==", + "version": "1.15.3", + "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.15.3.tgz", + "integrity": "sha512-HSIdTruqVE1XjS4smPX7roDDjMheZLCPSD9v+OXM2V6yTiZPf70CpTranf0hRI41tLcl7ySVOXnU37mgwlAllg==", "requires": { - "@biothings-explorer/api-response-transform": "^1.8.0", + "@biothings-explorer/api-response-transform": "^1.9.1", "axios": "^0.21.1", "biomedical_id_resolver": "^3.4.3", "debug": "^4.3.1", diff --git a/package.json b/package.json index d6223ea4..710095f7 100644 --- a/package.json +++ b/package.json @@ -50,7 +50,7 @@ "typescript": "^4.2.3" }, "dependencies": { - "@biothings-explorer/call-apis": "^1.15.2", + "@biothings-explorer/call-apis": "^1.15.3", "@biothings-explorer/smartapi-kg": "^3.1.1", "biolink-model": "^0.3.0", "biomedical_id_resolver": "^3.4.3", From afa2c82d20693061d17d4fdc74c7ee10c4c4f912 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Fri, 26 Mar 2021 10:34:42 -0700 Subject: [PATCH 06/68] chore(release): 1.1.10 --- CHANGELOG.md | 2 ++ package-lock.json | 2 +- package.json | 2 +- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 37028834..dde5fc82 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,8 @@ 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. +### [1.1.10](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.1.9...v1.1.10) (2021-03-26) + ### [1.1.9](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.1.8...v1.1.9) (2021-03-26) diff --git a/package-lock.json b/package-lock.json index e13277da..e7d32241 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.1.9", + "version": "1.1.10", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index 710095f7..29776f17 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.1.9", + "version": "1.1.10", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { From 2b80cd330032bc3539e2c494e69f238bf2e71eca Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Fri, 26 Mar 2021 10:38:39 -0700 Subject: [PATCH 07/68] fix: :bug: fix typo in npm release script --- .github/workflows/npm-release.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/npm-release.yml b/.github/workflows/npm-release.yml index abcb9894..00eaa093 100644 --- a/.github/workflows/npm-release.yml +++ b/.github/workflows/npm-release.yml @@ -1,4 +1,4 @@ -name: Publish @biothings-explorer/smartapi-kg Node.js Package to NPM registry +name: Publish @biothings-explorer/query_graph_handler Node.js Package to NPM registry on: push: From a333ae5d42749b96fb05daf21dac94f330688664 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Fri, 26 Mar 2021 10:59:45 -0700 Subject: [PATCH 08/68] build: :arrow_up: upgrade id resolver package --- package-lock.json | 14 +++++++------- package.json | 4 ++-- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/package-lock.json b/package-lock.json index e7d32241..b8bf17ea 100644 --- a/package-lock.json +++ b/package-lock.json @@ -450,13 +450,13 @@ } }, "@biothings-explorer/call-apis": { - "version": "1.15.3", - "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.15.3.tgz", - "integrity": "sha512-HSIdTruqVE1XjS4smPX7roDDjMheZLCPSD9v+OXM2V6yTiZPf70CpTranf0hRI41tLcl7ySVOXnU37mgwlAllg==", + "version": "1.16.0", + "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.16.0.tgz", + "integrity": "sha512-qUnHPOxk5AZZdUJOdGOzwZvPeFnHigJ8EmNl4maV48osAd9qF9j0FNAc9LRZyD272jK1PrHArhnyVrDT6LGdxA==", "requires": { "@biothings-explorer/api-response-transform": "^1.9.1", "axios": "^0.21.1", - "biomedical_id_resolver": "^3.4.3", + "biomedical_id_resolver": "^3.5.0", "debug": "^4.3.1", "husky": "^4.3.8" } @@ -1478,9 +1478,9 @@ } }, "biomedical_id_resolver": { - "version": "3.4.3", - "resolved": "https://registry.npmjs.org/biomedical_id_resolver/-/biomedical_id_resolver-3.4.3.tgz", - "integrity": "sha512-/uHFxoViPXTlQOALy3ON8g0yygvoiMMlf54M3qB9rUwl55QUoshOuxm0EB11UqI5QaIesqxWrx1kauvg8a8Naw==", + "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==", "requires": { "@commitlint/cli": "^11.0.0", "@commitlint/config-conventional": "^11.0.0", diff --git a/package.json b/package.json index 29776f17..9f37c10b 100644 --- a/package.json +++ b/package.json @@ -50,10 +50,10 @@ "typescript": "^4.2.3" }, "dependencies": { - "@biothings-explorer/call-apis": "^1.15.3", + "@biothings-explorer/call-apis": "^1.16.0", "@biothings-explorer/smartapi-kg": "^3.1.1", "biolink-model": "^0.3.0", - "biomedical_id_resolver": "^3.4.3", + "biomedical_id_resolver": "^3.5.0", "debug": "^4.3.1", "lodash": "^4.17.21", "ms": "^2.1.3", From 5943beebc35a149de74f8379e257a4decb1cd3e2 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Fri, 26 Mar 2021 10:59:54 -0700 Subject: [PATCH 09/68] chore(release): 1.2.0 --- 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 dde5fc82..44b66fa3 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. +## [1.2.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.1.10...v1.2.0) (2021-03-26) + + +### Bug Fixes + +* :bug: fix typo in npm release script ([2b80cd3](https://github.com/kevinxin90/bte_trapi_query_graph_handler/commit/2b80cd330032bc3539e2c494e69f238bf2e71eca)) + ### [1.1.10](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.1.9...v1.1.10) (2021-03-26) ### [1.1.9](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.1.8...v1.1.9) (2021-03-26) diff --git a/package-lock.json b/package-lock.json index b8bf17ea..5421e6fb 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.1.10", + "version": "1.2.0", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index 9f37c10b..4bb1c4cd 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.1.10", + "version": "1.2.0", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { From 9e3487693abd220f0f453ccc6d60c500a44e3caf Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Fri, 26 Mar 2021 14:46:16 -0700 Subject: [PATCH 10/68] fix: :bug: fix edge_metadata deepcopy issue --- package-lock.json | 14 +++++++------- package.json | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/package-lock.json b/package-lock.json index 5421e6fb..1fe95064 100644 --- a/package-lock.json +++ b/package-lock.json @@ -427,9 +427,9 @@ "dev": true }, "@biothings-explorer/api-response-transform": { - "version": "1.9.1", - "resolved": "https://registry.npmjs.org/@biothings-explorer/api-response-transform/-/api-response-transform-1.9.1.tgz", - "integrity": "sha512-5XG1IGTQjadbm6p/OEsljtH0fJtcHFmJs5zkm487WjvgN3t/RQzn7rEA4vXTimR1stgKuUOY+ksJk9P6lXx8gA==", + "version": "1.9.2", + "resolved": "https://registry.npmjs.org/@biothings-explorer/api-response-transform/-/api-response-transform-1.9.2.tgz", + "integrity": "sha512-Hv6CUcMEBoeIovbR5OAmOeXwDHmeuYgVGVPU6+9Yr/2W03GNIWqhA5Nm8rb6jSQHm9viqAMQ+cyXSYY8TNafIQ==", "requires": { "@biothings-explorer/json-transformer": "^1.0.2", "@commitlint/cli": "^11.0.0", @@ -450,11 +450,11 @@ } }, "@biothings-explorer/call-apis": { - "version": "1.16.0", - "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.16.0.tgz", - "integrity": "sha512-qUnHPOxk5AZZdUJOdGOzwZvPeFnHigJ8EmNl4maV48osAd9qF9j0FNAc9LRZyD272jK1PrHArhnyVrDT6LGdxA==", + "version": "1.16.1", + "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.16.1.tgz", + "integrity": "sha512-Lx2e++nw0aCuz/3qo4vDuCJNudrJ5t+vwgb5bGG0M1ym4pXENUTlIYjTJd1LU8QNuFVIwHTVEboPtDFE+PesYg==", "requires": { - "@biothings-explorer/api-response-transform": "^1.9.1", + "@biothings-explorer/api-response-transform": "^1.9.2", "axios": "^0.21.1", "biomedical_id_resolver": "^3.5.0", "debug": "^4.3.1", diff --git a/package.json b/package.json index 4bb1c4cd..3736dfce 100644 --- a/package.json +++ b/package.json @@ -50,7 +50,7 @@ "typescript": "^4.2.3" }, "dependencies": { - "@biothings-explorer/call-apis": "^1.16.0", + "@biothings-explorer/call-apis": "^1.16.1", "@biothings-explorer/smartapi-kg": "^3.1.1", "biolink-model": "^0.3.0", "biomedical_id_resolver": "^3.5.0", From 0b6343a6216d8b15141321ca028e71cd5d246578 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Fri, 26 Mar 2021 14:46:28 -0700 Subject: [PATCH 11/68] chore(release): 1.2.1 --- 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 44b66fa3..6c89023c 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. +### [1.2.1](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.2.0...v1.2.1) (2021-03-26) + + +### Bug Fixes + +* :bug: fix edge_metadata deepcopy issue ([9e34876](https://github.com/kevinxin90/bte_trapi_query_graph_handler/commit/9e3487693abd220f0f453ccc6d60c500a44e3caf)) + ## [1.2.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.1.10...v1.2.0) (2021-03-26) diff --git a/package-lock.json b/package-lock.json index 1fe95064..03846228 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.2.0", + "version": "1.2.1", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index 3736dfce..8813f6d5 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.2.0", + "version": "1.2.1", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { From c009b1073bf8617cec7342e0b149f3705c46f4a6 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Sun, 28 Mar 2021 20:50:12 -0700 Subject: [PATCH 12/68] build: :arrow_up: upgrade call-apis --- package-lock.json | 44 ++++++++++++++++++++++---------------------- package.json | 8 ++++---- 2 files changed, 26 insertions(+), 26 deletions(-) diff --git a/package-lock.json b/package-lock.json index 03846228..d2f8feb6 100644 --- a/package-lock.json +++ b/package-lock.json @@ -427,9 +427,9 @@ "dev": true }, "@biothings-explorer/api-response-transform": { - "version": "1.9.2", - "resolved": "https://registry.npmjs.org/@biothings-explorer/api-response-transform/-/api-response-transform-1.9.2.tgz", - "integrity": "sha512-Hv6CUcMEBoeIovbR5OAmOeXwDHmeuYgVGVPU6+9Yr/2W03GNIWqhA5Nm8rb6jSQHm9viqAMQ+cyXSYY8TNafIQ==", + "version": "1.9.3", + "resolved": "https://registry.npmjs.org/@biothings-explorer/api-response-transform/-/api-response-transform-1.9.3.tgz", + "integrity": "sha512-vcN3VJ0W3Itclee+Du7dfYwzNKg7TXt7H06f9ihLxSKyBWgFyLsRrsyMVZVRHqkYfzQUawtCfEHBEI9fPQU/Xg==", "requires": { "@biothings-explorer/json-transformer": "^1.0.2", "@commitlint/cli": "^11.0.0", @@ -450,11 +450,11 @@ } }, "@biothings-explorer/call-apis": { - "version": "1.16.1", - "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.16.1.tgz", - "integrity": "sha512-Lx2e++nw0aCuz/3qo4vDuCJNudrJ5t+vwgb5bGG0M1ym4pXENUTlIYjTJd1LU8QNuFVIwHTVEboPtDFE+PesYg==", + "version": "1.16.2", + "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.16.2.tgz", + "integrity": "sha512-da7ceUs8cXrbKPyOA0KUctT1g21/8KUu1rYd1VdnnMYw3zifAlsIqinHGojyWrjNUVkCe1BOs/efGIx50cav7g==", "requires": { - "@biothings-explorer/api-response-transform": "^1.9.2", + "@biothings-explorer/api-response-transform": "^1.9.3", "axios": "^0.21.1", "biomedical_id_resolver": "^3.5.0", "debug": "^4.3.1", @@ -1020,9 +1020,9 @@ } }, "@types/jest": { - "version": "26.0.21", - "resolved": "https://registry.npmjs.org/@types/jest/-/jest-26.0.21.tgz", - "integrity": "sha512-ab9TyM/69yg7eew9eOwKMUmvIZAKEGZYlq/dhe5/0IMUd/QLJv5ldRMdddSn+u22N13FP3s5jYyktxuBwY0kDA==", + "version": "26.0.22", + "resolved": "https://registry.npmjs.org/@types/jest/-/jest-26.0.22.tgz", + "integrity": "sha512-eeWwWjlqxvBxc4oQdkueW5OF/gtfSceKk4OnOAGlUSwS/liBRtZppbJuz1YkgbrbfGOoeBHun9fOvXnjNwrSOw==", "requires": { "jest-diff": "^26.0.0", "pretty-format": "^26.0.0" @@ -1047,9 +1047,9 @@ "integrity": "sha512-fZQQafSREFyuZcdWFAExYjBiCL7AUCdgsk80iO0q4yihYYdcIiH28CcuPTGFgLOCC8RlW49GSQxdHwZP+I7CNg==" }, "@types/node": { - "version": "14.14.35", - "resolved": "https://registry.npmjs.org/@types/node/-/node-14.14.35.tgz", - "integrity": "sha512-Lt+wj8NVPx0zUmUwumiVXapmaLUcAk3yPuHCFVXras9k5VT9TdhJqKqGVUQCD60OTMCl0qxJ57OiTL0Mic3Iag==" + "version": "14.14.37", + "resolved": "https://registry.npmjs.org/@types/node/-/node-14.14.37.tgz", + "integrity": "sha512-XYmBiy+ohOR4Lh5jE379fV2IU+6Jn4g5qASinhitfyO71b/sCo6MKsMLF5tc7Zf2CE8hViVQyYSobJNke8OvUw==" }, "@types/normalize-package-data": { "version": "2.4.0", @@ -6867,9 +6867,9 @@ } }, "typedoc": { - "version": "0.20.33", - "resolved": "https://registry.npmjs.org/typedoc/-/typedoc-0.20.33.tgz", - "integrity": "sha512-jzNdHmjZRQKwguhpXjIPuIjz+TpdgG2AVY8ta+qpAukv+3rBhTs4AAVd+mkonrHVYlC0EAbuAJ4urkfnn42Hwg==", + "version": "0.20.34", + "resolved": "https://registry.npmjs.org/typedoc/-/typedoc-0.20.34.tgz", + "integrity": "sha512-es+N/KyGPcHl9cAuYh1Z5m7HzwcmfNLghkmb2pzGz7HRDS5GS2uA3hu/c2cv4gCxDsw8pPUPCOvww+Hzf48Kug==", "dev": true, "requires": { "colors": "^1.4.0", @@ -6886,9 +6886,9 @@ } }, "typedoc-default-themes": { - "version": "0.12.9", - "resolved": "https://registry.npmjs.org/typedoc-default-themes/-/typedoc-default-themes-0.12.9.tgz", - "integrity": "sha512-Jd5fYTiqzinZdoIY382W7tQXTwAzWRdg8KbHfaxmb78m1/3jL9riXtk23oBOKwhi8GFVykCOdPzEJKY87/D0LQ==", + "version": "0.12.10", + "resolved": "https://registry.npmjs.org/typedoc-default-themes/-/typedoc-default-themes-0.12.10.tgz", + "integrity": "sha512-fIS001cAYHkyQPidWXmHuhs8usjP5XVJjWB8oZGqkTowZaz3v7g3KDZeeqE82FBrmkAnIBOY3jgy7lnPnqATbA==", "dev": true }, "typescript": { @@ -7034,9 +7034,9 @@ } }, "vscode-textmate": { - "version": "5.3.1", - "resolved": "https://registry.npmjs.org/vscode-textmate/-/vscode-textmate-5.3.1.tgz", - "integrity": "sha512-X4E7iPJzmMsL9AY4MyZrxUt0Dm/kGWreJEGdQgAHXHQrRGDdlwAu9X1LCsQ0VKUCg5wjwSS1LPpy1BOfxIw4Tw==", + "version": "5.4.0", + "resolved": "https://registry.npmjs.org/vscode-textmate/-/vscode-textmate-5.4.0.tgz", + "integrity": "sha512-c0Q4zYZkcLizeYJ3hNyaVUM2AA8KDhNCA3JvXY8CeZSJuBdAy3bAvSbv46RClC4P3dSO9BdwhnKEx2zOo6vP/w==", "dev": true }, "w3c-hr-time": { diff --git a/package.json b/package.json index 8813f6d5..55c37068 100644 --- a/package.json +++ b/package.json @@ -36,8 +36,8 @@ "homepage": "https://github.com/kevinxin90/bte_trapi_query_graph_handler#readme", "devDependencies": { "@types/debug": "^4.1.5", - "@types/jest": "^26.0.21", - "@types/node": "^14.14.35", + "@types/jest": "^26.0.22", + "@types/node": "^14.14.37", "coveralls": "^3.1.0", "jest": "^26.6.3", "prettier": "^2.2.1", @@ -46,11 +46,11 @@ "ts-jest": "^26.5.4", "tslint": "^6.1.3", "tslint-config-prettier": "^1.18.0", - "typedoc": "^0.20.33", + "typedoc": "^0.20.34", "typescript": "^4.2.3" }, "dependencies": { - "@biothings-explorer/call-apis": "^1.16.1", + "@biothings-explorer/call-apis": "^1.16.2", "@biothings-explorer/smartapi-kg": "^3.1.1", "biolink-model": "^0.3.0", "biomedical_id_resolver": "^3.5.0", From 1cc2fca9610323e715fadcc8f065eef8743a2332 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Sun, 28 Mar 2021 20:50:19 -0700 Subject: [PATCH 13/68] chore(release): 1.2.2 --- CHANGELOG.md | 2 ++ package-lock.json | 2 +- package.json | 2 +- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6c89023c..f845fac0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,8 @@ 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. +### [1.2.2](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.2.1...v1.2.2) (2021-03-29) + ### [1.2.1](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.2.0...v1.2.1) (2021-03-26) diff --git a/package-lock.json b/package-lock.json index d2f8feb6..884f567c 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.2.1", + "version": "1.2.2", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index 55c37068..a6aa427b 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.2.1", + "version": "1.2.2", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { From db58226e602e68f1eb638bc3221035a0c873b4e2 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Mon, 29 Mar 2021 11:47:52 -0700 Subject: [PATCH 14/68] feat: :sparkles: upgrade to biolink 1.7.0 --- src/biolink.json | 547 ++++++++++++++++++++++++++++++++--------------- 1 file changed, 376 insertions(+), 171 deletions(-) diff --git a/src/biolink.json b/src/biolink.json index 23584bd0..cda81634 100644 --- a/src/biolink.json +++ b/src/biolink.json @@ -3,7 +3,7 @@ "name": "Biolink-Model", "description": "Entity and association taxonomy and datamodel for life-sciences data", "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "version": "1.4.0", + "version": "1.7.0", "prefixes": { "Aeolus": "http://translator.ncats.nih.gov/Aeolus_", "alliancegenome": "https://www.alliancegenome.org/", @@ -28,6 +28,7 @@ "EDAM-FORMAT": "http://edamontology.org/format_", "EDAM-OPERATION": "http://edamontology.org/operation_", "EDAM-TOPIC": "http://edamontology.org/topic_", + "EFO": "http://www.ebi.ac.uk/efo/EFO_", "ExO": "http://purl.obolibrary.org/obo/ExO_", "fabio": "http://purl.org/spar/fabio/", "foaf": "http://xmlns.com/foaf/0.1/", @@ -49,6 +50,7 @@ "ICD10": "http://translator.ncats.nih.gov/ICD10_", "ICD9": "http://translator.ncats.nih.gov/ICD9_", "interpro": "https://www.ebi.ac.uk/interpro/entry/", + "INO": "http://purl.obolibrary.org/obo/INO_", "isbn": "https://www.isbn-international.org/identifier/", "isni": "https://isni.org/isni/", "issn": "https://portal.issn.org/resource/ISSN/", @@ -69,6 +71,7 @@ "OBOREL": "http://purl.obolibrary.org/obo/RO_", "ORCID": "https://orcid.org/", "ORPHA": "http://www.orpha.net/ORDO/Orphanet_", + "os": "https://github.com/cmungall/owlstar/blob/master/owlstar.ttl", "PathWhiz": "http://smpdb.ca/pathways/#", "PATO-PROPERTY": "http://purl.obolibrary.org/obo/pato#", "pav": "http://purl.org/pav/", @@ -115,6 +118,21 @@ "OIO", "BIOGRID" ], + "enums": { + "logical_interpretation_enum": { + "permissible_values": { + "SomeSome": { + "description": "A modifier on a triple that causes the triple to be interpreted as a some-some statement", + "meaning": "os:SomeSomeInterpretation" + }, + "AllSome": { + "description": "A modifier on a triple that causes the triple to be interpreted as an all-some statement.", + "meaning": "os:AllSomeInterpretation" + }, + "InverseAllSome": null + } + } + }, "subsets": { "model_organism_database": { "description": "Subset that is relevant for a typical Model Organism Database (MOD)" @@ -164,7 +182,7 @@ "symbol type": { "typeof": "string" }, - "frequency": { + "frequency value": { "typeof": "string", "uri": "UO:0000105" }, @@ -405,7 +423,7 @@ "is_a": "type", "domain": "entity", "range": "category type", - "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `bl:Protein`, `bl:GeneProduct`, `bl:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {bl:GenomicEntity, bl:MolecularEntity, bl:NamedThing}", + "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "is_class_field": true, "multivalued": true, "in_subset": [ @@ -953,9 +971,9 @@ "FMA:continuous_with", "FMA:homonym_of", "FMA:related_developmental_entity_of", - "GO:ends_during", - "GO:happens_during", - "GO:inverse_ends_during", + "RO:0002093", + "RO:0002092", + "RO:0002084", "GOREL:0002005", "GOREL:0012006", "HCPCS:mapped_to", @@ -980,12 +998,12 @@ "OBO:envo#has_increased_levels_of", "OBO:has_role", "OBO:nbo#is_about", - "OBOREL:0000053", - "PATO:decreased_in_magnitude_relative_to", - "PATO:has_cross_section", - "PATO:has_relative_magnitude", - "PATO:increased_in_magnitude_relative_to", - "PATO:reciprocal_of", + "RO:0000053", + "PATO-PROPERTY:decreased_in_magnitude_relative_to", + "PATO-PROPERTY:has_cross_section", + "PATO-PROPERTY:has_relative_magnitude", + "PATO-PROPERTY:increased_in_magnitude_relative_to", + "PATO-PROPERTY:reciprocal_of", "RO:0000052", "RO:0002001", "RO:0002002", @@ -1089,7 +1107,6 @@ "translator_minimal" ], "inverse": "superclass of", - "slot_uri": "rdfs:subClassOf", "close_mappings": [ "LOINC:class_of", "LOINC:has_class" @@ -1112,12 +1129,12 @@ "LOINC:has_parent_group", "LOINC:is_presence_guidance_for", "NCIT:gene_product_has_chemical_classification", - "NCIT:gene_is_biomarker_type", - "NCIT:gene_product_is_biomarker_type", - "NCIT:has_inc_parent", - "NCIT:has_nichd_parent", - "NCIT:neoplasm_has_special_category", - "NCIT:role_has_parent", + "NCIT:R36", + "NCIT:R42", + "NCIT:A16", + "NCIT:A11", + "NCIT:A14", + "NCIT:A3", "NDDF:has_dose_form", "OBO:intersection_of", "RXNORM:has_dose_form", @@ -1207,6 +1224,18 @@ "WIKIDATA:Q39893967" ] }, + "opposite of": { + "description": "x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). (This description is from RO. Needs to be rephrased).", + "is_a": "related to", + "symmetric": true, + "exact_mappings": [ + "RO:0002604" + ], + "see_also": [ + "https://doi.org/10.1101/108977", + "https://github.com/biolink/biolink-model/issues/657" + ] + }, "contributor": { "is_a": "related to", "domain": "information content entity", @@ -1293,7 +1322,7 @@ "SEMMEDDB:interacts_with", "DRUGBANK:drug-interaction", "FMA:adheres_to", - "NCIT:has_target", + "NCIT:A7", "PR:non-covalently_bound_to" ] }, @@ -1349,24 +1378,24 @@ "GOREL:0001006", "CTD:inferred", "UPHENO:0000001", - "GO:acts_upstream_of", - "GO:acts_upstream_of_or_within", - "NCIT:allele_plays_altered_role_in_process", - "NCIT:allele_plays_role_in_metabolism_of_chemical_or_drug", - "NCIT:biological_process_has_associated_location", - "NCIT:chemical_or_drug_affects_abnormal_cell", - "NCIT:chemical_or_drug_affects_cell_type_or_tissue", - "NCIT:chemical_or_drug_affects_gene_product", - "NCIT:chemical_or_drug_has_mechanism_of_action", - "NCIT:cytogenetic_abnormality_involves_chromosome", - "NCIT:disease_has_associated_anatomic_site", - "NCIT:disease_has_metastatic_anatomic_site", - "NCIT:disease_has_primary_anatomic_site", - "NCIT:disease_may_have_abnormal_cell", - "NCIT:eo_disease_has_associated_cell_type", - "NCIT:eo_disease_has_associated_eo_anatomy", + "RO:0002263", + "RO:0002264", + "NCIT:R158", + "NCIT:R160", + "NCIT:R30", + "NCIT:R150", + "NCIT:R72", + "NCIT:R146", + "NCIT:R124", + "NCIT:R173", + "NCIT:R100", + "NCIT:R102", + "NCIT:R101", + "NCIT:R113", + "NCIT:R23", + "NCIT:R25", "NCIT:gene_mapped_to_disease", - "NCIT:gene_product_has_abnormality", + "NCIT:R133", "RO:0002343", "RO:0002355", "RO:0002591", @@ -1563,6 +1592,7 @@ "CHEMBL.MECHANISM:releasing_agent" ], "exact_mappings": [ + "RO:0003003", "CTD:increases_expression_of" ] }, @@ -1579,6 +1609,7 @@ "DGIdb:antisense_oligonucleotide" ], "exact_mappings": [ + "RO:0003002", "CTD:decreases_expression_of" ], "narrow_mappings": [ @@ -2252,11 +2283,10 @@ "range": "physical essence or occurrent", "inverse": "regulated by", "close_mappings": [ - "GO:regulated_by", "RO:0002334" ], "exact_mappings": [ - "GO:regulates" + "RO:0002211" ], "narrow_mappings": [ "WIKIDATA_PROPERTY:P128", @@ -2282,17 +2312,16 @@ "inverse": "positively regulated by", "mixin": true, "close_mappings": [ - "GO:positively_regulated_by" + "RO:0002336" ], "exact_mappings": [ - "RO:0002213", - "GO:positively_regulates" + "RO:0002213" ], "narrow_mappings": [ "CHEMBL.MECHANISM:activator", "DGIdb:activator", - "GO:acts_upstream_of_or_within_positive_effect", - "GO:acts_upstream_of_positive_effect", + "RO:0004032", + "RO:0004034", "RO:0002629", "SEMMEDDB:augments" ] @@ -2310,11 +2339,11 @@ "inverse": "negatively regulated by", "mixin": true, "close_mappings": [ - "GO:negatively_regulated_by" + "RO:0002335" ], "exact_mappings": [ "RO:0004035", - "GO:negatively_regulates" + "RO:0002212" ], "broad_mappings": [ "RO:0004033" @@ -2324,8 +2353,6 @@ "CHEMBL.MECHANISM:inhibitor", "CHEMBL.MECHANISM:negative_allosteric_modulator", "CHEMBL.MECHANISM:negative_modulator", - "GO:acts_upstream_of_negative_effect", - "GO:acts_upstream_of_or_within_negative_effect", "RO:0002630" ] }, @@ -2334,53 +2361,53 @@ "mixin": true, "inverse": "negatively regulates" }, - "regulates, process to process": { + "process regulates process": { "is_a": "affects", "mixins": [ "regulates" ], "domain": "occurrent", "range": "occurrent", - "inverse": "regulated by, process to process", + "inverse": "process regulated by process", "exact_mappings": [ "RO:0002211" ] }, - "regulated by, process to process": { + "process regulated by process": { "is_a": "affected by", "domain": "occurrent", "range": "occurrent", - "inverse": "regulates, process to process" + "inverse": "process regulates process" }, - "positively regulates, process to process": { - "is_a": "regulates, process to process", + "process positively regulates process": { + "is_a": "process regulates process", "mixins": [ "positively regulates" ], - "inverse": "positively regulated by, process to process", + "inverse": "process positively regulated by process", "exact_mappings": [ "RO:0002213" ] }, - "positively regulated by, process to process": { - "is_a": "regulated by, process to process", - "inverse": "positively regulates, process to process" + "process positively regulated by process": { + "is_a": "process regulated by process", + "inverse": "process positively regulates process" }, - "negatively regulates, process to process": { - "is_a": "regulates, process to process", + "process negatively regulates process": { + "is_a": "process regulates process", "mixins": [ "negatively regulates" ], - "inverse": "negatively regulated by, process to process", + "inverse": "process negatively regulated by process", "exact_mappings": [ "RO:0002212" ] }, - "negatively regulated by, process to process": { - "is_a": "regulated by, process to process", - "inverse": "negatively regulates, process to process" + "process negatively regulated by process": { + "is_a": "process regulated by process", + "inverse": "process negatively regulates process" }, - "regulates, entity to entity": { + "entity regulates entity": { "aliases": [ "activity directly regulates activity of" ], @@ -2390,7 +2417,7 @@ ], "domain": "molecular entity", "range": "molecular entity", - "inverse": "regulated by, entity to entity", + "inverse": "entity regulated by entity", "local_names": { "translator": "regulates", "ro": "activity directly regulates activity of" @@ -2405,21 +2432,21 @@ "WIKIDATA_PROPERTY:P128" ] }, - "regulated by, entity to entity": { + "entity regulated by entity": { "is_a": "affected by", "domain": "molecular entity", "range": "molecular entity", - "inverse": "regulates, entity to entity" + "inverse": "entity regulates entity" }, - "positively regulates, entity to entity": { + "entity positively regulates entity": { "aliases": [ "activity directly positively regulates activity of" ], - "is_a": "regulates, entity to entity", + "is_a": "entity regulates entity", "mixins": [ "positively regulates" ], - "inverse": "positively regulated by, entity to entity", + "inverse": "entity positively regulated by entity", "local_names": { "translator": "positively regulates", "ro": "activity directly positively regulates activity of" @@ -2440,19 +2467,19 @@ "hetio:UPREGULATES_DuG" ] }, - "positively regulated by, entity to entity": { - "is_a": "regulated by, entity to entity", - "inverse": "positively regulates, entity to entity" + "entity positively regulated by entity": { + "is_a": "entity regulated by entity", + "inverse": "entity positively regulates entity" }, - "negatively regulates, entity to entity": { + "entity negatively regulates entity": { "aliases": [ "activity directly negatively regulates activity of" ], - "is_a": "regulates, entity to entity", + "is_a": "entity regulates entity", "mixins": [ "negatively regulates" ], - "inverse": "negatively regulated by, entity to entity", + "inverse": "entity negatively regulated by entity", "local_names": { "translator": "negatively regulates", "ro": "activity directly negatively regulates activity of" @@ -2470,9 +2497,9 @@ "hetio:DOWNREGULATES_DdG" ] }, - "negatively regulated by, entity to entity": { - "is_a": "regulated by, entity to entity", - "inverse": "negatively regulates, entity to entity" + "entity negatively regulated by entity": { + "is_a": "entity regulated by entity", + "inverse": "entity negatively regulates entity" }, "disrupts": { "is_a": "affects", @@ -2497,6 +2524,19 @@ "description": "describes a relationship where the structure, function, or occurrence of one entity is degraded or interfered with by another.", "inverse": "disrupts" }, + "gene product of": { + "is_a": "related to", + "description": "definition x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x", + "exact_mappings": [ + "RO:0002204" + ], + "domain": "gene product mixin", + "range": "gene", + "inverse": "has gene product", + "in_subset": [ + "translator_minimal" + ] + }, "has gene product": { "is_a": "related to", "description": "holds between a gene and a transcribed and/or translated product generated from it", @@ -2505,6 +2545,7 @@ "in_subset": [ "translator_minimal" ], + "inverse": "gene product of", "close_mappings": [ "PR:has_gene_template" ], @@ -2514,7 +2555,51 @@ "NCIT:gene_encodes_gene_product" ], "narrow_mappings": [ - "NCIT:gene_mutant_encodes_gene_product_sequence_variation" + "NCIT:R178" + ] + }, + "transcribed to": { + "is_a": "related to", + "domain": "gene", + "range": "transcript", + "description": "inverse of transcribed from", + "inverse": "transcribed from", + "exact_mappings": [ + "RO:0002511", + "SIO:010080" + ] + }, + "transcribed from": { + "is_a": "related to", + "domain": "transcript", + "range": "gene", + "inverse": "transcribed to", + "description": "x is transcribed from y if and only if x is synthesized from template y", + "exact_mappings": [ + "RO:0002510", + "SIO:010081" + ] + }, + "translates to": { + "is_a": "related to", + "domain": "transcript", + "range": "protein", + "description": "x (amino acid chain/polypeptide) is the ribosomal translation of y (transcript) if and only if a ribosome reads y (transcript) through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces x (amino acid chain/polypeptide)", + "inverse": "translation of", + "close_mappings": [ + "RO:0002513", + "SIO:010082" + ] + }, + "translation of": { + "is_a": "related to", + "domain": "protein", + "range": "transcript", + "description": "inverse of translates to", + "inverse": "translates to", + "close_mappings": [ + "RO:0002512", + "SIO:010083" ] }, "homologous to": { @@ -2799,8 +2884,7 @@ ], "symmetric": true, "exact_mappings": [ - "RO:00002325", - "GO:colocalizes_with" + "RO:00002325" ] }, "genetic association": { @@ -2813,7 +2897,7 @@ }, "gene associated with condition": { "is_a": "genetic association", - "description": "holds between a gene and a disease or phenotypic feature that the gene or its alleles/proday influence, contribute to, or correlate with", + "description": "holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence, contribute to, or correlate with", "domain": "gene", "range": "disease or phenotypic feature", "in_subset": [ @@ -2828,9 +2912,9 @@ "GENO:0000841" ], "narrow_mappings": [ - "NCIT:gene_associated_with_disease", - "NCIT:gene_involved_in_pathogenesis_of_disease", - "NCIT:gene_product_malfunction_associated_with_disease" + "NCIT:R38", + "NCIT:R175", + "NCIT:R48" ] }, "condition associated with gene": { @@ -2875,8 +2959,7 @@ "IDO:0000664" ], "exact_mappings": [ - "RO:0002326", - "GO:contributes_to" + "RO:0002326" ], "narrow_mappings": [ "CTD:marker_mechanism", @@ -2960,7 +3043,8 @@ "domain": "biological entity", "range": "disease or phenotypic feature", "exact_mappings": [ - "RO:0003307" + "RO:0003307", + "CTD:therapeutic" ] }, "exacerbates": { @@ -2969,8 +3053,7 @@ "domain": "biological entity", "range": "disease or phenotypic feature", "exact_mappings": [ - "RO:0003309", - "CTD:therapeutic" + "RO:0003309" ] }, "treats": { @@ -2979,7 +3062,7 @@ ], "is_a": "ameliorates", "description": "holds between a therapeutic procedure or chemical substance and a disease or phenotypic feature that it is used to treat", - "domain": "treatment", + "domain": "chemical or drug or treatement", "range": "disease or phenotypic feature", "in_subset": [ "translator_minimal" @@ -2989,6 +3072,7 @@ "MONDO:disease_responds_to" ], "exact_mappings": [ + "DRUGBANK:treats", "SEMMEDDB:TREATS", "SEMMEDDB:treats", "WIKIDATA_PROPERTY:P2175" @@ -3130,7 +3214,7 @@ ], "symmetric": true, "exact_mappings": [ - "CTD:positivecorrelation" + "CTD:positive_correlation" ] }, "negatively correlated with": { @@ -3143,7 +3227,7 @@ ], "symmetric": true, "exact_mappings": [ - "CTD:negativecorrelation" + "CTD:negative_correlation" ] }, "coexpressed with": { @@ -3178,13 +3262,13 @@ ], "inverse": "has biomarker", "exact_mappings": [ - "NCIT:gene_is_biomarker_of" + "NCIT:R39" ], "broad_mappings": [ "RO:0002607" ], "narrow_mappings": [ - "NCIT:gene_product_is_biomarker_of", + "NCIT:R47", "NCIT:genetic_biomarker_related_to", "NCIT:is_molecular_abnormality_of_disease", "ORPHA:465410", @@ -3204,8 +3288,8 @@ "RO:0002206" ], "narrow_mappings": [ - "NCIT:gene_product_expressed_in_tissue", - "NCIT:gene_product_has_associated_anatomy", + "NCIT:R49", + "NCIT:R46", "RTXKG1:expressed_in" ] }, @@ -3228,6 +3312,7 @@ "description": "holds between a biological entity and a phenotype, where a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature).", "domain": "biological entity", "range": "phenotypic feature", + "inverse": "phenotype of", "notes": [ "check the range" ], @@ -3244,15 +3329,28 @@ ], "broad_mappings": [ "hetio:PRESENTS_DpS", - "NCIT:disease_may_have_finding", + "NCIT:R115", "OMIM:has_phenotype" ], "narrow_mappings": [ - "NCIT:disease_may_have_molecular_abnormality", + "NCIT:R89", "OBO:doid#has_symptom", "RO:0004022" ] }, + "phenotype of": { + "is_a": "related to", + "description": "holds between a phenotype and a biological entity, where a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature).", + "domain": "phenotypic feature", + "range": "biological entity", + "inverse": "has phenotype", + "notes": [ + "check the domain" + ], + "in_subset": [ + "translator_minimal" + ] + }, "occurs in": { "is_a": "related to", "description": "holds between a process and a material entity or site within which the process occurs", @@ -3266,7 +3364,6 @@ ], "exact_mappings": [ "BFO:0000066", - "GO:occurs_in", "PathWhiz:has_location", "SNOMED:occurs_in" ], @@ -3323,18 +3420,18 @@ "HMDB:at_tissue", "HMDB:in_biospecimen", "LOINC:has_imaging_focus", - "NCIT:allele_absent_from_wild-type_chromosomal_location", - "NCIT:allele_in_chromosomal_location", - "NCIT:gene_has_physical_location", - "NCIT:gene_in_chromosomal_location", + "NCIT:R156", + "NCIT:R155", + "NCIT:R145", + "NCIT:R40", "NCIT:is_location_of_anatomic_structure", - "NCIT:procedure_has_completely_excised_anatomy", - "NCIT:procedure_has_excised_anatomy", - "NCIT:procedure_has_imaged_anatomy", - "NCIT:procedure_has_partially_excised_anatomy", - "NCIT:procedure_may_have_completely_excised_anatomy", - "NCIT:procedure_may_have_excised_anatomy", - "NCIT:procedure_may_have_partially_excised_anatomy", + "NCIT:R171", + "NCIT:R167", + "NCIT:R165", + "NCIT:R169", + "NCIT:R170", + "NCIT:R166", + "NCIT:R168", "RO:0002303", "RTXKG1:disease_has_location", "SNOMED:has_finding_site", @@ -3441,7 +3538,6 @@ "BFO:0000051", "BFO:0000055", "WIKIDATA_PROPERTY:P527", - "GO:has_part", "RO:0001019", "RTXKG1:has_part", "RXNORM:consists_of", @@ -3466,7 +3562,7 @@ "NCIT:complex_has_physical_part", "NDDF:has_ingredient", "PathWhiz:has_element_in_bound", - "NCIT:gene_product_has_structural_domain_or_motif", + "NCIT:R50", "PDQ:has_component", "PathWhiz:has_protein_in_complex", "RO:0002104", @@ -3496,7 +3592,6 @@ "SEMMEDDB:part_of", "WIKIDATA_PROPERTY:P361", "FMA:part_of", - "GO:part_of", "RXNORM:constitutes", "RXNORM:part_of" ], @@ -3527,8 +3622,8 @@ "LOINC:multipart_of", "MEDDRA:member_of", "MONDO:part_of_progression_of_disease", - "NCIT:anatomic_structure_is_physical_part_of", - "NCIT:conceptual_part_of", + "NCIT:R82", + "NCIT:R27", "NCIT:is_component_of_chemotherapy_regimen", "NDDF:ingredient_of", "PDQ:component_of", @@ -3605,7 +3700,7 @@ "RO:0002234" ], "narrow_mappings": [ - "NCIT:biological_process_has_result_anatomy", + "NCIT:R31", "OBI:0000299", "PathWhiz:has_right_element", "RO:0002296", @@ -3665,19 +3760,17 @@ "exact_mappings": [ "RO:0000056", "BFO:0000056", - "GO:involved_in", - "RO:participates_in", "RTXKG1:participates_in" ], "narrow_mappings": [ "DRUGBANK:pathway", "HMDB:in_pathway", "LOINC:is_given_pharmaceutical_substance_for", - "NCIT:gene_is_element_in_pathway", - "NCIT:gene_plays_role_in_process", - "NCIT:gene_product_is_element_in_pathway", - "NCIT:gene_product_is_physical_part_of", - "NCIT:gene_product_plays_role_in_biological_process", + "NCIT:R130", + "NCIT:R37", + "NCIT:R131", + "NCIT:R51", + "NCIT:R53", "OBI:0000295", "RO:0002216", "RO:0002505", @@ -3700,7 +3793,7 @@ ], "exact_mappings": [ "RO:0002331", - "GO:is_active_in" + "RO:0002432" ], "narrow_mappings": [ "NCIT:gene_involved_in_molecular_abnormality", @@ -3708,7 +3801,7 @@ "ORPHA:317348", "ORPHA:317349", "ORPHA:327767", - "PATO:towards" + "RO:0002503" ] }, "capable of": { @@ -3723,8 +3816,7 @@ "RTXKG1:capable_of" ], "narrow_mappings": [ - "GO:has_occurrence", - "NCIT:gene_product_has_biochemical_function", + "NCIT:R52", "RO:0002500" ] }, @@ -3738,8 +3830,7 @@ ], "inverse": "enabled by", "exact_mappings": [ - "RO:0002327", - "GO:enables" + "RO:0002327" ] }, "enabled by": { @@ -3782,8 +3873,7 @@ "exact_mappings": [ "RO:0001000", "FMA:derives_from", - "OBO:doid#derives_from", - "RO:derives_from" + "OBO:doid#derives_from" ], "narrow_mappings": [ "CHEBI:has_functional_parent", @@ -3825,8 +3915,8 @@ "food component of": { "is_a": "part of", "description": "holds between a one or more chemical substances present in food, irrespective of nutritional value (i.e. could also be a contaminant or additive)", - "domain": "food component", - "range": "food", + "domain": "chemical substance", + "range": "chemical substance", "in_subset": [ "translator_minimal" ], @@ -3835,8 +3925,8 @@ "has food component": { "is_a": "has part", "description": "holds between food and one or more chemical substances composing it, irrespective of nutritional value (i.e. could also be a contaminant or additive)", - "domain": "food", - "range": "food component", + "domain": "chemical substance", + "range": "chemical substance", "in_subset": [ "translator_minimal" ], @@ -3845,8 +3935,8 @@ "nutrient of": { "is_a": "food component of", "description": "holds between a one or more chemical substances present in food, irrespective of nutritional value (i.e. could also be a contaminant or additive)", - "domain": "food component", - "range": "food", + "domain": "chemical substance", + "range": "chemical substance", "in_subset": [ "translator_minimal" ], @@ -3855,8 +3945,8 @@ "has nutrient": { "is_a": "has food component", "description": "one or more nutrients which are growth factors for a living organism", - "domain": "food", - "range": "nutrient", + "domain": "chemical substance", + "range": "chemical substance", "in_subset": [ "translator_minimal" ], @@ -3952,7 +4042,7 @@ "SEMMEDDB:produces" ], "narrow_mappings": [ - "NCIT:biological_process_has_result_chemical_or_drug", + "NCIT:R29", "SNOMED:has_process_output", "SNOMED:specimen_procedure_of" ] @@ -4043,6 +4133,8 @@ "directly interacts with": { "is_a": "interacts with", "description": "Holds between molecular entities that physically and directly interact\nwith each other", + "domain": "molecular entity", + "range": "molecular entity", "symmetric": true, "related_mappings": [ "GAMMA:kd", @@ -4108,7 +4200,8 @@ "narrow_mappings": [ "NCIT:gene_product_sequence_variation_encoded_by_gene_mutant", "NCIT:gene_product_variant_of_gene_product", - "OMIM:allelic_variant_of" + "OMIM:allelic_variant_of", + "WIKIDATA:P3433" ] }, "is missense variant of": { @@ -4429,6 +4522,15 @@ }, "slot_uri": "rdf:predicate" }, + "logical interpretation": { + "is_a": "association slot", + "required": false, + "domain": "association", + "range": "logical_interpretation_enum", + "exact_mappings": [ + "os:LogicalInterpretation" + ] + }, "relation": { "is_a": "association slot", "description": "The relation which describes an association between a subject and an object in a more granular manner. Usually this is a term from Relation Ontology, but it can be any edge CURIE.", @@ -4470,7 +4572,7 @@ }, "association type": { "is_a": "association slot", - "range": "ontology class", + "range": "category type", "deprecated": "This slot is deprecated in favor of 'category' slot.", "deprecated_element_has_exact_replacement": "category", "description": "connects an association to the category of association (e.g. gene to phenotype)" @@ -4601,6 +4703,10 @@ "multivalued": true, "range": "publication" }, + "associated environmental context": { + "is_a": "association slot", + "description": "An attribute that can be applied to an association where the association holds between two entities located or occurring in a particular environment. For example, two microbial taxa may interact in the context of a human gut; a disease may give rise to a particular phenotype in a particular environmental exposure." + }, "sequence localization attribute": { "is_a": "association slot", "domain": "genomic sequence localization", @@ -4634,6 +4740,32 @@ } }, "classes": { + "ontology class": { + "mixin": true, + "description": "a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type.", + "exact_mappings": [ + "owl:Class", + "schema:Class" + ], + "comments": [ + "This is modeled as a mixin. 'ontology class' should not be the primary type of a node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc", + "Note that formally this is a metaclass. Instances of this class are instances in the graph, but can be the object of 'type' edges. For example, if we had a node in the graph representing a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample, and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity" + ], + "see_also": [ + "https://github.com/biolink/biolink-model/issues/486" + ], + "examples": [ + { + "value": "UBERON:0000955", + "description": "the class 'brain' from the Uberon anatomy ontology" + } + ], + "id_prefixes": [ + "MESH", + "UMLS", + "KEGG.BRITE" + ] + }, "annotation": { "description": "Biolink Model root class for entity annotations.", "abstract": true @@ -4648,6 +4780,9 @@ }, "attribute": { "is_a": "annotation", + "mixins": [ + "ontology class" + ], "description": "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material.", "slots": [ "name", @@ -4699,10 +4834,6 @@ "is_a": "attribute", "description": "describes the severity of a phenotypic feature or disease" }, - "frequency value": { - "is_a": "attribute", - "description": "describes the frequency of occurrence of an event or condition" - }, "relationship quantifier": { "mixin": true }, @@ -4729,6 +4860,9 @@ "has percentage" ] }, + "chemical or drug or treatement": { + "mixin": true + }, "entity": { "description": "Root Biolink Model class for all things and informational relationships, real or imagined.", "abstract": true, @@ -4761,25 +4895,26 @@ "UMLSST:enty" ] }, - "ontology class": { - "is_a": "named thing", - "description": "a concept or class in an ontology, vocabulary or thesaurus", - "id_prefixes": [ - "MESH", - "KEGG.BRITE" - ] - }, "relationship type": { "is_a": "ontology class", "description": "An OWL property used as an edge label" }, "gene ontology class": { + "mixin": true, "description": "an ontology class that describes a functional aspect of a gene, gene prodoct or complex", "is_a": "ontology class", "in_subset": [ "testing" ] }, + "unclassified ontology class": { + "mixin": true, + "description": "this is used for nodes that are taken from an ontology but are not typed using an existing biolink class", + "is_a": "ontology class", + "in_subset": [ + "testing" + ] + }, "taxonomic rank": { "description": "A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)", "is_a": "ontology class", @@ -4796,7 +4931,7 @@ "taxonomic classification" ], "description": "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies.", - "is_a": "ontology class", + "is_a": "named thing", "slot_usage": { "has taxonomic rank": { "range": "taxonomic rank", @@ -5382,7 +5517,8 @@ "is_a": "biological entity", "mixins": [ "thing with taxon", - "physical essence" + "physical essence", + "ontology class" ], "aliases": [ "bioentity" @@ -5413,7 +5549,8 @@ "description": "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system.", "is_a": "biological entity", "mixins": [ - "occurrent" + "occurrent", + "ontology class" ], "id_prefixes": [ "GO", @@ -5434,7 +5571,8 @@ "reaction" ], "mixins": [ - "occurrent" + "occurrent", + "ontology class" ], "slot_usage": { "has input": { @@ -5470,7 +5608,8 @@ "biological process": { "is_a": "biological process or activity", "mixins": [ - "occurrent" + "occurrent", + "ontology class" ], "description": "One or more causally connected executions of molecular functions", "exact_mappings": [ @@ -5478,6 +5617,9 @@ "SIO:000006", "WIKIDATA:Q2996394" ], + "broad_mappings": [ + "WIKIDATA:P682" + ], "id_prefixes": [ "GO", "REACT", @@ -5487,6 +5629,9 @@ }, "pathway": { "is_a": "biological process", + "mixins": [ + "ontology class" + ], "exact_mappings": [ "PW:0000001", "WIKIDATA:Q4915012" @@ -5512,6 +5657,9 @@ "physiology" ], "is_a": "biological process", + "mixins": [ + "ontology class" + ], "close_mappings": [ "UMLSSG:PHYS" ], @@ -5537,6 +5685,9 @@ }, "behavior": { "is_a": "biological process", + "mixins": [ + "ontology class" + ], "exact_mappings": [ "GO:0007610", "UMLSSC:T053", @@ -5566,6 +5717,9 @@ }, "chemical substance": { "is_a": "molecular entity", + "mixins": [ + "ontology class" + ], "description": "May be a chemical entity or a formulation with a chemical entity as active ingredient, or a complex material with multiple chemical entities as part", "slots": [ "is metabolite" @@ -5641,7 +5795,8 @@ "processed material": { "is_a": "chemical substance", "mixins": [ - "mixture" + "mixture", + "ontology class" ], "description": "A chemical substance (often a mixture) processed for consumption for nutritional, medical or technical use.", "exact_mappings": [ @@ -5651,7 +5806,9 @@ "drug": { "is_a": "molecular entity", "mixins": [ - "mixture" + "mixture", + "chemical or drug or treatement", + "ontology class" ], "description": "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease", "comments": [ @@ -5678,25 +5835,26 @@ ] }, "food component": { + "deprecated": "Food component is replaced by a slot/role of chemical substance and will be removed from the Biolink model.", "is_a": "chemical substance", "related_mappings": [ "CHEBI:78295" ] }, "environmental food contaminant": { - "is_a": "food component", + "is_a": "chemical substance", "related_mappings": [ "CHEBI:78299" ] }, "food additive": { - "is_a": "food component", + "is_a": "chemical substance", "related_mappings": [ "CHEBI:64047" ] }, "nutrient": { - "is_a": "food component", + "is_a": "chemical substance", "related_mappings": [ "CHEBI:33284" ] @@ -6023,6 +6181,9 @@ "UMLSSC:T026", "UMLSST:celc" ], + "broad_mappings": [ + "WIKIDATA:P681" + ], "id_prefixes": [ "GO", "MESH", @@ -6132,7 +6293,7 @@ "WIKIDATA:Q7187" ], "id_prefixes": [ - "NCBIGENE", + "NCBIGene", "ENSEMBL", "HGNC", "UniProtKB", @@ -6336,7 +6497,7 @@ "is_a": "RNA product", "id_prefixes": [ "RNACENTRAL", - "NCBIGENE", + "NCBIGene", "ENSEMBL" ], "exact_mappings": [ @@ -6792,7 +6953,8 @@ ], "is_a": "named thing", "mixins": [ - "exposure event" + "exposure event", + "chemical or drug or treatement" ], "description": "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures", "slots": [ @@ -6933,7 +7095,7 @@ "description": "rdf:type of biolink:Association should be fixed at rdf:Statement" }, "category": { - "range": "association", + "range": "category type", "required": false } }, @@ -8532,9 +8694,25 @@ } } }, + "organism taxon to entity association": { + "mixin": true, + "description": "An association between an organism taxon and another entity", + "defining_slots": [ + "subject" + ], + "slot_usage": { + "subject": { + "range": "organism taxon", + "description": "organism taxon that is the subject of the association" + } + } + }, "organism taxon to organism taxon association": { "is_a": "association", "abstract": true, + "mixins": [ + "organism taxon to entity association" + ], "description": "A relationship between two organism taxon nodes", "defining_slots": [ "subject", @@ -8577,6 +8755,9 @@ "defining_slots": [ "predicate" ], + "slots": [ + "associated environmental context" + ], "slot_usage": { "subject": { "range": "organism taxon", @@ -8590,6 +8771,30 @@ }, "predicate": { "subproperty_of": "interacts with" + }, + "associated environmental context": { + "description": "the environment in which the two taxa interact" + } + } + }, + "organism taxon to environment association": { + "is_a": "association", + "abstract": true, + "mixins": [ + "organism taxon to entity association" + ], + "slot_usage": { + "subject": { + "range": "organism taxon", + "role": "interactor taxon", + "description": "the taxon that is the subject of the association" + }, + "object": { + "role": "environmental context", + "description": "the environment in which the organism occurs" + }, + "predicate": { + "description": "predicate describing the relationship between the taxon and the environment" } } } From 06c680a2cb2431ea28964c204ea58e43c1098970 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Mon, 29 Mar 2021 11:48:06 -0700 Subject: [PATCH 15/68] chore(release): 1.3.0 --- 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 f845fac0..579a6704 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. +## [1.3.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.2.2...v1.3.0) (2021-03-29) + + +### Features + +* :sparkles: upgrade to biolink 1.7.0 ([db58226](https://github.com/kevinxin90/bte_trapi_query_graph_handler/commit/db58226e602e68f1eb638bc3221035a0c873b4e2)) + ### [1.2.2](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.2.1...v1.2.2) (2021-03-29) ### [1.2.1](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.2.0...v1.2.1) (2021-03-26) diff --git a/package-lock.json b/package-lock.json index 884f567c..8dc3d373 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.2.2", + "version": "1.3.0", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index a6aa427b..cc0c144b 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.2.2", + "version": "1.3.0", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { From 523956ecea8d2a0216a63ea79b45a43d77ab20b7 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Mon, 29 Mar 2021 12:01:51 -0700 Subject: [PATCH 16/68] test: :white_check_mark: fix broken test --- __test__/integration/biolink.test.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/__test__/integration/biolink.test.js b/__test__/integration/biolink.test.js index f12fb750..b7daf73e 100644 --- a/__test__/integration/biolink.test.js +++ b/__test__/integration/biolink.test.js @@ -18,7 +18,7 @@ describe("Test BioLinkModel class", () => { test("test predicate with no inverse property and symmetric not equal to true", () => { const res = biolink.reverse('has_phenotype'); - expect(res).toBeUndefined(); + expect(res).toBe("phenotype_of"); }) test("test predicate not exist in biolink model", () => { From aaf831ecbdb13c838a4a09d2a92e842dfba2fbeb Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Mon, 29 Mar 2021 12:02:04 -0700 Subject: [PATCH 17/68] chore(release): 1.3.1 --- CHANGELOG.md | 2 ++ package-lock.json | 2 +- package.json | 2 +- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 579a6704..007ef502 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,8 @@ 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. +### [1.3.1](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.3.0...v1.3.1) (2021-03-29) + ## [1.3.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.2.2...v1.3.0) (2021-03-29) diff --git a/package-lock.json b/package-lock.json index 8dc3d373..5993fbf9 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.3.0", + "version": "1.3.1", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index cc0c144b..161564d3 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.3.0", + "version": "1.3.1", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { From 1658ad2f77cbb8c41dba72c871bca595a4495d2f Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Mon, 29 Mar 2021 19:34:37 -0700 Subject: [PATCH 18/68] feat: :sparkles: support trapi quer --- package-lock.json | 20 +- package.json | 4 +- src/index.js | 5 +- src/predicates.json | 16720 ++++++++++++++++++++++++++++++++++++++++++ 4 files changed, 16735 insertions(+), 14 deletions(-) create mode 100644 src/predicates.json diff --git a/package-lock.json b/package-lock.json index 5993fbf9..6783d75c 100644 --- a/package-lock.json +++ b/package-lock.json @@ -427,9 +427,9 @@ "dev": true }, "@biothings-explorer/api-response-transform": { - "version": "1.9.3", - "resolved": "https://registry.npmjs.org/@biothings-explorer/api-response-transform/-/api-response-transform-1.9.3.tgz", - "integrity": "sha512-vcN3VJ0W3Itclee+Du7dfYwzNKg7TXt7H06f9ihLxSKyBWgFyLsRrsyMVZVRHqkYfzQUawtCfEHBEI9fPQU/Xg==", + "version": "1.10.0", + "resolved": "https://registry.npmjs.org/@biothings-explorer/api-response-transform/-/api-response-transform-1.10.0.tgz", + "integrity": "sha512-xeKI66ArD/unJOxvU+shUt1X0kPnGCyk4MIUc35smUFMK+b9MDOrkuKbR9YK7yoEIe7XMzKMhekVfESF+zUB9w==", "requires": { "@biothings-explorer/json-transformer": "^1.0.2", "@commitlint/cli": "^11.0.0", @@ -450,11 +450,11 @@ } }, "@biothings-explorer/call-apis": { - "version": "1.16.2", - "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.16.2.tgz", - "integrity": "sha512-da7ceUs8cXrbKPyOA0KUctT1g21/8KUu1rYd1VdnnMYw3zifAlsIqinHGojyWrjNUVkCe1BOs/efGIx50cav7g==", + "version": "1.17.0", + "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.17.0.tgz", + "integrity": "sha512-OuKnC6RN6TpqYHiTAZdys9n4CqdRQduUuTqUc0GQAJBTZLG/yS3waAX2RZi68VYFECVBpTJpTLmS2gEoF5bZRw==", "requires": { - "@biothings-explorer/api-response-transform": "^1.9.3", + "@biothings-explorer/api-response-transform": "^1.10.0", "axios": "^0.21.1", "biomedical_id_resolver": "^3.5.0", "debug": "^4.3.1", @@ -472,9 +472,9 @@ } }, "@biothings-explorer/smartapi-kg": { - "version": "3.1.1", - "resolved": "https://registry.npmjs.org/@biothings-explorer/smartapi-kg/-/smartapi-kg-3.1.1.tgz", - "integrity": "sha512-Za/vX4iTFIL6FgGgX1zwoiNxphgK2XE/aZQCJFjwGPdmx+UiARVCrUfumkTTV4Ac16jGNFbf6Ad59cs49Ld8mA==", + "version": "3.3.0", + "resolved": "https://registry.npmjs.org/@biothings-explorer/smartapi-kg/-/smartapi-kg-3.3.0.tgz", + "integrity": "sha512-pCoq3w/U6M7mi9ppL+d00IFz01USTg4QJyTuJ/oegbE7uqUd2DcoTeOo9SEIMk9MZPfPlbLvRJ+ZosW4qh6dGA==", "requires": { "@babel/runtime": "^7.13.10", "@commitlint/cli": "^11.0.0", diff --git a/package.json b/package.json index 161564d3..bcd5ef3e 100644 --- a/package.json +++ b/package.json @@ -50,8 +50,8 @@ "typescript": "^4.2.3" }, "dependencies": { - "@biothings-explorer/call-apis": "^1.16.2", - "@biothings-explorer/smartapi-kg": "^3.1.1", + "@biothings-explorer/call-apis": "^1.17.0", + "@biothings-explorer/smartapi-kg": "^3.3.0", "biolink-model": "^0.3.0", "biomedical_id_resolver": "^3.5.0", "debug": "^4.3.1", diff --git a/src/index.js b/src/index.js index e53f77ea..51e0a0bc 100644 --- a/src/index.js +++ b/src/index.js @@ -14,16 +14,17 @@ const Graph = require('./graph/graph'); exports.InvalidQueryGraphError = InvalidQueryGraphError; exports.TRAPIQueryHandler = class TRAPIQueryHandler { - constructor(options = {}, smartAPIPath = undefined) { + constructor(options = {}, smartAPIPath = undefined, predicatesPath = undefined) { this.logs = []; this.options = options; this.resolveOutputIDs = typeof this.options.enableIDResolution === 'undefined' ? true : this.options.enableIDResolution; this.path = smartAPIPath || path.resolve(__dirname, './smartapi_specs.json'); + this.predicatePath = smartAPIPath || path.resolve(__dirname, './predicates.json'); } _loadMetaKG() { - const kg = new meta_kg.default(this.path); + const kg = new meta_kg.default(this.path, this.predicatePath); debug(`Query options are: ${JSON.stringify(this.options)}`); debug(`SmartAPI Specs read from path: ${this.path}`); kg.constructMetaKGSync(this.options); diff --git a/src/predicates.json b/src/predicates.json new file mode 100644 index 00000000..bde4526d --- /dev/null +++ b/src/predicates.json @@ -0,0 +1,16720 @@ +[ + { + "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", + 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"smartapi": { + "id": "fc8245e92c970298449294fc04211869", + "meta": { + "date_created": "2021-02-04T00:00:10.655676+00:00", + "last_updated": "2021-03-29T07:01:01.427095+00:00", + "slug": "cohdcovid", + "url": "https://raw.githubusercontent.com/WengLab-InformaticsResearch/cohd_api/cohd_covid/cohd/cohd_oas3.yaml", + "username": "CaseyTa" + } + }, + "x-translator": { + "component": "KP", + "team": [ + "Clinical Data Provider" + ] + } + }, + "tags": [ + "Metadata", + "OMOP", + "Clinical Frequencies", + "Concept Associations", + "Temporal Clinical Data", + "translator", + "trapi" + ], + "query_operation": { + "path": "/query", + "server": "http://covid.cohd.io/api/", + "method": "post" + }, + "predicates": { + "biolink:ChemicalSubstance": { + "biolink:ChemicalSubstance": [ + "biolink:correlated_with" + ], + "biolink:DiseaseOrPhenotypicFeature": [ + "biolink:correlated_with" + ], + "biolink:Drug": [ + "biolink:correlated_with" + ], + "biolink:PopulationOfIndividualOrganisms": [ + "biolink:correlated_with" + ], + "biolink:Procedure": [ + "biolink:correlated_with" + ] + }, + "biolink:DiseaseOrPhenotypicFeature": { + "biolink:ChemicalSubstance": [ + "biolink:correlated_with" + ], + "biolink:DiseaseOrPhenotypicFeature": [ + "biolink:correlated_with" + ], + "biolink:Drug": [ + "biolink:correlated_with" + ], + "biolink:PopulationOfIndividualOrganisms": [ + "biolink:correlated_with" + ], + "biolink:Procedure": [ + "biolink:correlated_with" + ] + }, + "biolink:Drug": { + "biolink:ChemicalSubstance": [ + "biolink:correlated_with" + ], + "biolink:DiseaseOrPhenotypicFeature": [ + "biolink:correlated_with" + ], + "biolink:Drug": [ + "biolink:correlated_with" + ], + "biolink:PopulationOfIndividualOrganisms": [ + "biolink:correlated_with" + ], + "biolink:Procedure": [ + "biolink:correlated_with" + ] + }, + "biolink:PopulationOfIndividualOrganisms": { + "biolink:ChemicalSubstance": [ + "biolink:correlated_with" + ], + "biolink:DiseaseOrPhenotypicFeature": [ + "biolink:correlated_with" + ], + "biolink:Drug": [ + "biolink:correlated_with" + ], + "biolink:PopulationOfIndividualOrganisms": [ + "biolink:correlated_with" + ], + "biolink:Procedure": [ + "biolink:correlated_with" + ] + }, + "biolink:Procedure": { + "biolink:ChemicalSubstance": [ + "biolink:correlated_with" + ], + "biolink:DiseaseOrPhenotypicFeature": [ + "biolink:correlated_with" + ], + "biolink:Drug": [ + "biolink:correlated_with" + ], + "biolink:PopulationOfIndividualOrganisms": [ + "biolink:correlated_with" + ], + "biolink:Procedure": [ + "biolink:correlated_with" + ] + } + } + } +] \ No newline at end of file From b72ff2b52d4a83d54246ee71a9985c13ebb7e40a Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 30 Mar 2021 18:00:20 -0700 Subject: [PATCH 19/68] refactor: :recycle: add predicates.json as file to be transpiled --- tsconfig.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tsconfig.json b/tsconfig.json index 43f60335..b351fcea 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -14,7 +14,8 @@ "include": [ "./src/**/*", "./src/biolink.json", - "./src/smartapi_specs.json" + "./src/smartapi_specs.json", + "./src/predicates.json" ], "exclude": [ "node_modules", From 2cc704f0543d73b11af24093993b4cbad9e97c34 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 30 Mar 2021 18:00:37 -0700 Subject: [PATCH 20/68] test: :white_check_mark: add a couple query examples for testing --- __test__/data/FDFM_caused_by_ACDY5.json | 21 ++++++++++++++ ...icals_targeting_IL1_Signaling_Pathway.json | 28 +++++++++++++++++++ ...sed_urinary_glycerol_affects_glycerol.json | 22 +++++++++++++++ 3 files changed, 71 insertions(+) create mode 100644 __test__/data/FDFM_caused_by_ACDY5.json create mode 100644 __test__/data/chemicals_targeting_IL1_Signaling_Pathway.json create mode 100644 __test__/data/increased_urinary_glycerol_affects_glycerol.json diff --git a/__test__/data/FDFM_caused_by_ACDY5.json b/__test__/data/FDFM_caused_by_ACDY5.json new file mode 100644 index 00000000..cd546836 --- /dev/null +++ b/__test__/data/FDFM_caused_by_ACDY5.json @@ -0,0 +1,21 @@ +{ + "message": { + "query_graph": { + "nodes": { + "n0": { + "id": "OMIM:606703", + "category": "biolink:Disease" + }, + "n1": { + "category": "biolink:Gene" + } + }, + "edges": { + "e01": { + "subject": "n0", + "object": "n1" + } + } + } + } +} \ No newline at end of file diff --git a/__test__/data/chemicals_targeting_IL1_Signaling_Pathway.json b/__test__/data/chemicals_targeting_IL1_Signaling_Pathway.json new file mode 100644 index 00000000..9b8f375e --- /dev/null +++ b/__test__/data/chemicals_targeting_IL1_Signaling_Pathway.json @@ -0,0 +1,28 @@ +{ + "message": { + "query_graph": { + "nodes": { + "n0": { + "id": "WIKIPATHWAYS:WP195", + "category": "biolink:Pathway" + }, + "n1": { + "category": "biolink:Gene" + }, + "n2": { + "category": "biolink:ChemicalSubstance" + } + }, + "edges": { + "e01": { + "subject": "n0", + "object": "n1" + }, + "e02": { + "subject": "n1", + "object": "n2" + } + } + } + } +} \ No newline at end of file diff --git a/__test__/data/increased_urinary_glycerol_affects_glycerol.json b/__test__/data/increased_urinary_glycerol_affects_glycerol.json new file mode 100644 index 00000000..d11bf5af --- /dev/null +++ b/__test__/data/increased_urinary_glycerol_affects_glycerol.json @@ -0,0 +1,22 @@ +{ + "message": { + "query_graph": { + "nodes": { + "n0": { + "id": "HP:0040301", + "category": "biolink:PhenotypicFeature" + }, + "n1": { + "category": "biolink:ChemicalSubstance" + } + }, + "edges": { + "e01": { + "subject": "n0", + "object": "n1", + "predicate": "biolink:affects" + } + } + } + } +} \ No newline at end of file From defdd656f30a04af85e37ef525d05ec247cc659b Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 30 Mar 2021 18:01:06 -0700 Subject: [PATCH 21/68] feat: :sparkles: restrict to a list of APIs to use in BTE --- src/config.js | 47 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 src/config.js diff --git a/src/config.js b/src/config.js new file mode 100644 index 00000000..7a9a997e --- /dev/null +++ b/src/config.js @@ -0,0 +1,47 @@ +exports.API_LIST = [ + 'QuickGO API', + 'Ontology Lookup Service API', + 'CTD API', + 'OpenTarget API', + 'LitVar API', + 'Human Phenotype Ontology API', + 'UBERON Ontology API', + 'MyDisease.info API', + 'MyVariant.info API', + 'MyGene.info API', + 'SEMMED Disease API', + 'MyChem.info API', + 'SEMMED Anatomy API', + 'SEMMED Gene API', + 'SEMMED Phenotype API', + 'MGIgene2phenotype API', + 'SEMMED Biological Process API', + 'SEMMED Chemical API', + 'DISEASES API', + 'EBIgene2phenotype API', + 'Gene Ontology Biological Process 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 Targeted Association API', + 'Multiomics Wellness KP API', + 'BioLink API', + 'LINCS Data Portal API', + 'Automat IntAct', + 'Automat Cord19 Scibite', + 'Automat Gtopdb', + 'Automat KEGG', + 'Automat Cord19 Scigraph', + 'Automat Uberongraph', + 'Automat Human GOA', + 'Automat HGNC', + 'Automat CTD', + 'Automat HMDB', + 'Automat Hetio', + 'Automat Panther', + 'Automat Pharos', + 'Automat Chembio', + 'Automat Foodb' +] \ No newline at end of file From 07688cb93ebe13be61dd041d2c155a478dac5d5b Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 30 Mar 2021 18:01:33 -0700 Subject: [PATCH 22/68] feat: :sparkles: include TRAPI APIs when constructing meta-kg --- src/index.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/index.js b/src/index.js index 51e0a0bc..be27829f 100644 --- a/src/index.js +++ b/src/index.js @@ -27,7 +27,7 @@ exports.TRAPIQueryHandler = class TRAPIQueryHandler { const kg = new meta_kg.default(this.path, this.predicatePath); debug(`Query options are: ${JSON.stringify(this.options)}`); debug(`SmartAPI Specs read from path: ${this.path}`); - kg.constructMetaKGSync(this.options); + kg.constructMetaKGSync(true, this.options); return kg; } From 94c4f874c20cc3166bff0790fc6d4b0288bc0551 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 30 Mar 2021 18:02:05 -0700 Subject: [PATCH 23/68] refactor: :recycle: update local smartapi specs --- src/smartapi_specs.json | 39441 ++++++++++++++++++-------------------- 1 file changed, 18650 insertions(+), 20791 deletions(-) diff --git a/src/smartapi_specs.json b/src/smartapi_specs.json index 17b47683..f1685366 100644 --- a/src/smartapi_specs.json +++ b/src/smartapi_specs.json @@ -1,17 +1,266 @@ { "took": 90, - "total": 97, - "max_score": 0.747712, + "total": 90, + "max_score": 0.7659169, "hits": [ + { + "_id": "04f42ae00c8e5991b98d0e681dbdc596", + "_meta": { + "date_created": "2021-03-04T18:27:43.614727+00:00", + "last_updated": "2021-03-29T07:00:46.292294+00:00", + "url": "http://bdt-social.renci.org:8080/socio_environmental_exposures_api/v1/openapi.json", + "username": "lstillwe" + }, + "_score": 0.7659169, + "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": "b0c489ea3a4d5aacfd833616d07a037a", "_meta": { "date_created": "2021-01-30T16:08:43.224448+00:00", - "last_updated": "2021-03-05T08:01:15.405933+00:00", + "last_updated": "2021-03-29T07:01:41.169400+00:00", "url": "https://monarch-sandbox.cgrb.oregonstate.edu/openapi.json", "username": "kshefchek" }, - "_score": 0.747712, + "_score": 0.7659169, "info": { "contact": { "email": "shefchek@oregonstate.edu", @@ -753,11 +1002,11 @@ "_id": "55510544e95386a5a8ac3b88f9d00d21", "_meta": { "date_created": "2021-01-30T20:45:51.489336+00:00", - "last_updated": "2021-03-05T08:01:31.854375+00:00", + "last_updated": "2021-03-29T07:02:55.061281+00:00", "url": "https://name-resolution-sri.renci.org/openapi.json", "username": "kshefchek" }, - "_score": 0.747712, + "_score": 0.7659169, "info": { "contact": { "email": "patrick@covar.com", @@ -807,7 +1056,7 @@ "required": false, "schema": { "default": 10, - "maximum": 1000.0, + "maximum": 1000, "title": "Limit", "type": "integer" } @@ -862,41 +1111,125 @@ ] }, { - "_id": "cc7324e732c4ffc7157a468bfbd0778c", + "_id": "34e351cb4eac8bc7dbacf55f1b5ce44b", "_meta": { - "date_created": "2020-05-29T20:56:31.280738+00:00", - "last_updated": "2021-02-17T07:42:22.892704+00:00", - "url": "https://raw.githubusercontent.com/NCATSTranslator/ara-scaffold/master/openapi.yaml", - "username": "MarkDWilliams" + "date_created": "2021-03-04T18:17:41.093656+00:00", + "last_updated": "2021-03-29T07:02:34.551639+00:00", + "url": "http://bdt-cmaq.renci.org:8080/cmaq_exposures_api/v1/openapi.json", + "username": "lstillwe" }, - "_score": 0.747712, + "_score": 0.7659169, "info": { "contact": { - "email": "mark.williams5@nih.gov", - "name": "Mark Williams", - "x-role": "responsible developer" + "email": "lisa@renci.org", + "name": "Lisa Stillwell" }, - "description": "a work in progress ara example", - "termsOfService": "https://opensource.org/licenses/MIT", - "title": "NCATS ARA Scaffold", - "version": "3.0" + "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": { - "/query": { - "post": { + "/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": { - "description": "A query response object" + "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": "POST a ReasonerStdAPI formatted query to the service" + "summary": "Retrieves air pollutant exposure levels", + "x-openapi-router-controller": "swagger_server.controllers.default_controller" } } }, "servers": [ { - "description": "Production server", - "url": "http://transltr.io:7073" + "url": "/cmaq_exposures_api/v1" } ], "tags": [ @@ -913,7 +1246,7 @@ "url": "https://raw.githubusercontent.com/NCATSTranslator/KnowledgeProviderScaffold/master/openapi.yml", "username": "MarkDWilliams" }, - "_score": 0.747712, + "_score": 0.7659169, "info": { "contact": { "email": "mark.williams5@nih.gov", @@ -950,85 +1283,250 @@ ] }, { - "_id": "ec1f4b0cfc37d7c2b9534591767e0c5a", + "_id": "219ac6646d0e2db862b533fb618db5b4", "_meta": { - "date_created": "2021-02-02T00:01:57.640239+00:00", - "last_updated": "2021-02-17T07:42:17.621907+00:00", - "url": "https://stars-app.renci.org/sparql-kp/docs/docs.yaml", - "username": "balhoff" + "date_created": "2021-03-04T18:22:55.853241+00:00", + "last_updated": "2021-03-29T07:04:19.592433+00:00", + "url": "http://bdt-proximity.renci.org:8080/roadway_proximity_api/v1/openapi.json", + "username": "lstillwe" }, - "_score": 0.747712, + "_score": 0.7659169, "info": { "contact": { - "email": "balhoff@renci.org", - "name": "Jim Balhoff" + "email": "lisa@renci.org", + "name": "Lisa Stillwell" }, - "description": "TRAPI interface to integrated ontology knowledgebase", + "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 License", - "url": "https://opensource.org/licenses/MIT" + "name": "MIT", + "url": "http://opensource.org/licenses/MIT" }, - "termsOfService": "https://opensource.org/licenses/MIT", - "title": "Ontology-KP API", - "version": "0.1", + "title": "Roadway Exposures API", + "version": "1.0.0", "x-translator": { "component": "KP", - "team": "SRI" + "team": [ + "Exposures Provider" + ] } }, "paths": { - "/query": { - "post": { - "operationId": "postQuery", + "/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": "limit", - "required": false, + "name": "latitude", + "required": true, "schema": { - "type": "integer" + "format": "double", + "type": "number" } - } - ], - "requestBody": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/TRAPIQueryRequestBody" - } + }, + { + "description": "longitude of the location of interest using decimal format (WGS84 datum)", + "in": "query", + "name": "longitude", + "required": true, + "schema": { + "format": "double", + "type": "number" } }, - "required": true - }, + { + "description": "the maximum search distance between the location of interest and nearest road (meters)", + "in": "query", + "name": "limit_distance", + "schema": { + "default": 500, + "format": "double", + "type": "number" + } + } + ], "responses": { "200": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/TRAPIMessage" + "$ref": "#/components/schemas/RoadwayData" } } }, - "description": "" + "description": "search results matching criteria" }, - "default": { + "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": "528c38e2218202a1095cc70c612af625", + "_meta": { + "date_created": "2021-01-30T18:33:25.822142+00:00", + "last_updated": "2021-03-29T07:03:31.965574+00:00", + "url": "https://edgenormalization-sri.renci.org/apidocs/openapi.yml", + "username": "kshefchek" + }, + "_score": 0.7659169, + "info": { + "contact": { + "email": "bizon@renci.org", + "name": "Chris Bizon", + "x-id": "https://github.com/cbizon", + "x-role": "responsible developer" + }, + "description": "The Biolink Model defines allowed predicates in the Translator ecosystem. Ingesting data from arbitrary sources requires mapping predicates in those sources to Translator predicates.

The Biolink Lookup Service can find predicates if they have an exact mapping in the model. The EdgeNormalization service takes this a step further, and attempts to find the best match to a Biolink predicate, even if there is not an explicit mapping. ", + "license": { + "name": "MIT", + "url": "https://opensource.org/licenses/MIT" + }, + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Edge+Normalization&provider_long=the+Translator+Consortium", + "title": "Edge Normalization Service", + "version": "1.0.0", + "x-translator": { + "component": "Utility", + "team": [ + "Standards Reference Implementation Team" + ] + } + }, + "paths": { + "/resolve_predicate": { + "get": { + "description": "Get Biolink model compliant predicate(s) using the passed predicate(s).", + "parameters": [ + { + "in": "query", + "name": "predicate", + "schema": { + "example": [ + "SEMMEDDB:CAUSES", + "RO:0000052" + ], + "items": { + "type": "string" + }, + "type": "array" + } + }, + { + "in": "query", + "name": "version", + "schema": { + "example": "latest", + "type": "string" + } + } + ], + "responses": { + "200": { "content": { - "text/plain": { + "application/json": { "schema": { - "type": "string" + "example": { + "RO:0000052": { + "identifier": "SEMMEDDB:AFFECTS", + "label": "affects" + }, + "SEMMEDDB:CAUSES": { + "identifier": "RO:0002410", + "label": "causes" + } + }, + "type": "object" } } }, - "description": "" + "description": "Results" } }, - "summary": "Submit a TRAPI question graph and retrieve matching solutions" + "summary": "Resolve predicate CURIE(s) into Biolink model compliant counterpart(s), first checking the BioLink model for exact matches of a CURIE. If the CURIE is from the Relation Ontology, the service will check its superproperties until an exact match is found.", + "tags": [ + "redis" + ] + } + } + }, + "servers": [ + { + "description": "Default server", + "url": "https://edgenormalization-sri.renci.org/" + } + ], + "tags": [ + { + "name": "translator" + } + ] + }, + { + "_id": "cc7324e732c4ffc7157a468bfbd0778c", + "_meta": { + "date_created": "2020-05-29T20:56:31.280738+00:00", + "last_updated": "2021-02-17T07:42:22.892704+00:00", + "url": "https://raw.githubusercontent.com/NCATSTranslator/ara-scaffold/master/openapi.yaml", + "username": "MarkDWilliams" + }, + "_score": 0.7659169, + "info": { + "contact": { + "email": "mark.williams5@nih.gov", + "name": "Mark Williams", + "x-role": "responsible developer" + }, + "description": "a work in progress ara example", + "termsOfService": "https://opensource.org/licenses/MIT", + "title": "NCATS ARA Scaffold", + "version": "3.0" + }, + "paths": { + "/query": { + "post": { + "responses": { + "200": { + "description": "A query response object" + } + }, + "summary": "POST a ReasonerStdAPI formatted query to the service" } } }, "servers": [ { - "url": "https://stars-app.renci.org/sparql-kp" + "description": "Production server", + "url": "http://transltr.io:7073" } ], "tags": [ @@ -1041,11 +1539,11 @@ "_id": "230691056df158545fd38bb73379d9c3", "_meta": { "date_created": "2021-02-04T00:04:56.017398+00:00", - "last_updated": "2021-03-05T08:02:37.537367+00:00", + "last_updated": "2021-03-29T07:04:33.251358+00:00", "url": "https://stars-app.renci.org/cam-kp/docs/docs.yaml", "username": "balhoff" }, - "_score": 0.747712, + "_score": 0.7659169, "info": { "contact": { "email": "balhoff@renci.org", @@ -1061,7 +1559,9 @@ "version": "0.1", "x-translator": { "component": "KP", - "team": "Exposures Provider" + "team": [ + "Exposures Provider" + ] } }, "paths": { @@ -1163,372 +1663,278 @@ ] }, { - "_id": "528c38e2218202a1095cc70c612af625", + "_id": "542ba165e1b4227854cf7c0a8addcc79", "_meta": { - "date_created": "2021-01-30T18:33:25.822142+00:00", - "last_updated": "2021-03-05T08:03:42.292851+00:00", - "url": "https://edgenormalization-sri.renci.org/apidocs/openapi.yml", - "username": "kshefchek" + "date_created": "2020-12-07T23:03:47.953540+00:00", + "last_updated": "2021-03-29T07:01:04.538676+00:00", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/opentarget/smartapi.yaml", + "username": "kevinxin90" + }, + "_score": 0.6863549, + "components": { + "x-bte-kgs-operations": { + "gene_related_to_chemical": [ + { + "inputs": [ + { + "id": "ENSEMBL", + "semantic": "Gene" + } + ], + "outputs": [ + { + "id": "CHEMBL.COMPOUND", + "semantic": "ChemicalSubstance" + } + ], + "parameters": { + "datasource": "chembl", + "fields": "drug", + "size": 100, + "target": "{inputs[0]}" + }, + "predicate": "related_to", + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/gene_related_to_chemical" + }, + "source": "CHEMBL", + "supportBatch": false + } + ] + }, + "x-bte-response-mapping": { + "gene_related_to_chemical": { + "CHEMBL.COMPOUND": "data.drug.id", + "moleculeType": "data.drug.molecule_type", + "name": "data.drug.molecule_name" + } + } }, - "_score": 0.747712, "info": { "contact": { - "email": "bizon@renci.org", - "name": "Chris Bizon", - "x-id": "https://github.com/cbizon", + "email": "help@opentarget.org", + "name": "opentarget help desk", "x-role": "responsible developer" }, - "description": "The Biolink Model defines allowed predicates in the Translator ecosystem. Ingesting data from arbitrary sources requires mapping predicates in those sources to Translator predicates.

The Biolink Lookup Service can find predicates if they have an exact mapping in the model. The EdgeNormalization service takes this a step further, and attempts to find the best match to a Biolink predicate, even if there is not an explicit mapping. ", - "license": { - "name": "MIT", - "url": "https://opensource.org/licenses/MIT" - }, - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Edge+Normalization&provider_long=the+Translator+Consortium", - "title": "Edge Normalization Service", - "version": "1.0.0", + "description": "The Opentarget API", + "termsOfService": "http://www.opentarget.org", + "title": "OpenTarget API", + "version": "1.0", "x-translator": { - "component": "Utility", + "component": "KP", "team": [ - "Standards Reference Implementation Team" + "Service Provider" ] } }, "paths": { - "/resolve_predicate": { + "/platform/public/evidence/filter": { "get": { - "description": "Get Biolink model compliant predicate(s) using the passed predicate(s).", "parameters": [ { + "description": "ensembl gene id", + "example": "ENSG00000088832", "in": "query", - "name": "predicate", + "name": "target", + "required": true, "schema": { - "example": [ - "SEMMEDDB:CAUSES", - "RO:0000052" - ], - "items": { - "type": "string" - }, - "type": "array" + "type": "string" } }, { + "description": "size of the output", + "example": 100, "in": "query", - "name": "version", + "name": "size", + "schema": { + "type": "integer" + } + }, + { + "description": "the output field", + "example": "drug", + "in": "query", + "name": "fields", + "schema": { + "type": "string" + } + }, + { + "description": "the data source", + "example": "chembl", + "in": "query", + "name": "datasource", "schema": { - "example": "latest", "type": "string" } } ], "responses": { "200": { - "content": { - "application/json": { - "schema": { - "example": { - "RO:0000052": { - "identifier": "SEMMEDDB:AFFECTS", - "label": "affects" - }, - "SEMMEDDB:CAUSES": { - "identifier": "RO:0002410", - "label": "causes" - } - }, - "type": "object" - } - } - }, - "description": "Results" + "description": "A biosample object" } }, - "summary": "Resolve predicate CURIE(s) into Biolink model compliant counterpart(s), first checking the BioLink model for exact matches of a CURIE. If the CURIE is from the Relation Ontology, the service will check its superproperties until an exact match is found.", - "tags": [ - "redis" + "summary": "retrieve evidence", + "x-bte-kgs-operations": [ + { + "$ref": "#/components/x-bte-kgs-operations/gene_related_to_chemical" + } ] } } }, "servers": [ { - "description": "Default server", - "url": "https://edgenormalization-sri.renci.org/" + "description": "Production server", + "url": "https://platform-api.opentargets.io/v3" } ], "tags": [ { "name": "translator" + }, + { + "name": "opentarget" } ] }, { - "_id": "89590198e93fb9377ab547eb903c5532", + "_id": "d9d71b3d55e767c37346d02b7d6bd0b3", "_meta": { - "date_created": "2019-10-22T04:28:40.627585+00:00", - "last_updated": "2021-02-17T07:42:14.843036+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/broad-pgm/openapi.yml", - "username": "newgene" + "date_created": "2021-01-26T00:01:27.579000+00:00", + "last_updated": "2021-03-29T07:01:11.160124+00:00", + "url": "https://automat.renci.org/intact/openapi.json", + "username": "YaphetKG" }, - "_score": 0.747712, + "_score": 0.6863549, "info": { "contact": { - "email": "translator@broadinstitute.org", - "name": "Broad PGM translator", - "url": "https://translator.ncats.io/broad-pgm-translator/", - "x-id": "https://github.com/broadinstitute/broad-translator", - "x-role": "responsible organization" + "email": "kebedey@renci.org", + "name": "Yaphet Kebede", + "x-id": "https://github.com/yaphetkg", + "x-role": "contributor" }, - "termsOfService": "https://translator.ncats.io/broad-pgm-translator", - "title": "Broad probabilistic graphical models translator", - "version": "0.1.0" + "description": "Molecular (Gene-Gene) interactions from [EBI IntAct (https://www.ebi.ac.uk/intact/)](https://www.ebi.ac.uk/intact/).", + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat IntAct&provider_long=RENCI", + "title": "Automat IntAct", + "version": "1.0.0", + "x-translator": { + "component": "KP", + "team": [ + "Ranking Agent" + ] + } }, "paths": { - "/modelList": { - "get": { + "/query": { + "post": { + "description": "Given a question graph return question graph plus answers.", + "operationId": "reasoner_api_query_post", + "requestBody": { + "content": { + "application/json": { + "schema": { + "allOf": [ + { + "$ref": "#/components/schemas/Query" + } + ], + "example": { + "message": { + "query_graph": { + "edges": {}, + "nodes": { + "n0": { + "category": "biolink:Gene", + "id": "NCBIGene:15" + } + } + } + } + }, + "title": "Request" + } + } + }, + "required": true + }, "responses": { "200": { "content": { "application/json": { "schema": { - "properties": { - "modelID": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" + "$ref": "#/components/schemas/Query" } } }, - "description": "Successful response" + "description": "Successful Response" + }, + "422": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/HTTPValidationError" + } + } + }, + "description": "Validation Error" } }, - "summary": "List available models" + "summary": "Query Reasoner API", + "tags": [ + "translator" + ] } }, - "/{modelID}/modelSignature": { + "/reasonerapi": { "get": { - "parameters": [ - { - "description": "Model identifier", - "in": "path", - "name": "modelID", - "required": true, - "schema": { - "type": "string" - } - } - ], + "description": "Returns a list of question templates that can be used to query this plater instance.", + "operationId": "get_reasoner_api_reasonerapi_get", "responses": { "200": { "content": { "application/json": { "schema": { - "properties": { - "modelID": { - "type": "string" - }, - "variableGroup": { - "items": { - "properties": { - "asInput": { - "type": "boolean" - }, - "asOutput": { - "type": "boolean" - }, - "authorityURL": { - "type": "string" - }, - "groupDistribution": { - "enum": [ - "discrete", - "empirical", - "Gaussian", - "Poisson" - ] - }, - "groupType": { - "enum": [ - "Bollean", - "Number", - "String" - ], - "type": "string" - }, - "groupValue": { - "items": { - "type": "string" - }, - "type": "array" - }, - "modelVariable": { - "items": { - "properties": { - "authorityURI": { - "type": "string" - }, - "groupDistribution": { - "enum": [ - "discrete", - "empirical", - "Gaussian", - "Poisson" - ] - }, - "variableID": { - "type": "string" - }, - "variableType": { - "enum": [ - "Bollean", - "Number", - "String" - ], - "type": "string" - }, - "variableValue": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "type": "array" - }, - "variableGroupID": { - "type": "string" - } - }, - "type": "object" - }, - "type": "array" - } + "items": { + "$ref": "#/components/schemas/Message" }, - "type": "object" + "title": "Response Get Reasoner Api Reasonerapi Get", + "type": "array" } } }, - "description": "Successful response" + "description": "Successful Response" } }, - "summary": "Get model signature" - } - }, - "/evaluateModel": { + "summary": "Get question templates" + }, "post": { + "deprecated": true, + "description": "Handle TRAPI request.", + "operationId": "reasoner_api_reasonerapi_post", "requestBody": { "content": { "application/json": { "schema": { - "properties": { - "modelID": { - "type": "string" - }, - "modelInput": { - "items": { - "properties": { - "modelVariable": { - "items": { - "properties": { - "priorDistribution": { - "properties": { - "GaussianDistribution": { - "properties": { - "distributionMean": { - "type": "number" - }, - "distributionStDev": { - "type": "number" - } - }, - "type": "object" - }, - "PoissonDistribution": { - "properties": { - "lambdaParameter": { - "type": "number" - } - }, - "type": "object" - }, - "discreteDistribution": { - "items": { - "properties": { - "priorProbability": { - "type": "number" - }, - "variableValue": { - "type": "string" - } - }, - "type": "object" - }, - "type": "array" - }, - "empiricalDistribution": { - "properties": { - "distributionMean": { - "type": "number" - }, - "distributionPercentile": { - "items": { - "type": "number" - }, - "type": "array" - }, - "distributionStDev": { - "type": "number" - } - }, - "type": "object" - } - }, - "type": "object" - }, - "variableID": { - "type": "string" - } - }, - "type": "object" - }, - "type": "array" - }, - "variableGroupID": { - "type": "string" - } - }, - "type": "object" - }, - "type": "array" - }, - "modelOutput": { - "items": { - "properties": { - "rawOutput": { - "type": "boolean" - }, - "variableGroupID": { - "type": "string" - }, - "variableID": { - "items": { - "type": "string" - }, - "type": "array" + "allOf": [ + { + "$ref": "#/components/schemas/Query" + } + ], + "example": { + "message": { + "query_graph": { + "edges": {}, + "nodes": { + "n0": { + "category": "biolink:Gene", + "id": "NCBIGene:15" } - }, - "type": "object" - }, - "type": "array" + } + } } }, - "type": "object" + "title": "Request" } } }, @@ -1539,413 +1945,146 @@ "content": { "application/json": { "schema": { - "properties": { - "posteriorProbabilities": { - "items": { - "properties": { - "modelVariable": { - "items": { - "properties": { - "posteriorDistribution": { - "properties": { - "GaussianDistribution": { - "properties": { - "distributionMean": { - "type": "number" - }, - "distributionStDev": { - "type": "number" - } - }, - "type": "object" - }, - "PoissonDistribution": { - "properties": { - "lambdaParameter": { - "type": "number" - } - }, - "type": "object" - }, - "discreteDistribution": { - "items": { - "properties": { - "posteriorProbability": { - "type": "number" - }, - "variableValue": { - "type": "string" - } - }, - "type": "object" - }, - "type": "array" - }, - "empiricalDistribution": { - "properties": { - "distributionMean": { - "type": "number" - }, - "distributionPercentile": { - "items": { - "type": "number" - }, - "type": "array" - }, - "distributionStDev": { - "type": "number" - } - }, - "type": "object" - }, - "rawDistribution": { - "items": { - "type": "number" - }, - "type": "array" - } - }, - "type": "object" - }, - "variableID": { - "type": "string" - } - }, - "type": "object" - }, - "type": "array" - }, - "variableGroupID": { - "type": "string" - } - }, - "type": "object" - }, - "type": "array" - } - }, - "type": "object" + "$ref": "#/components/schemas/Query" + } + } + }, + "description": "Successful Response" + }, + "422": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/HTTPValidationError" } } }, - "description": "Successful response" + "description": "Validation Error" } }, - "summary": "evaluate model" + "summary": "Reasoner Api" } - } - }, - "servers": [ - { - "url": "https://translator.ncats.io/broad-pgm-translator" - } - ], - "tags": [ - { - "name": "translator" - } - ] - }, - { - "_id": "34e351cb4eac8bc7dbacf55f1b5ce44b", - "_meta": { - "date_created": "2021-03-04T18:17:41.093656+00:00", - "last_updated": "2021-03-05T08:05:06.996136+00:00", - "url": "http://bdt-cmaq.renci.org:8080/cmaq_exposures_api/v1/openapi.json", - "username": "lstillwe" - }, - "_score": 0.747712, - "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 \u00b5g/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 \u00b5g/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" + "/cypher": { + "post": { + "description": "Runs cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/).", + "operationId": "cypher_cypher_post", + "requestBody": { + "content": { + "application/json": { + "schema": { + "allOf": [ + { + "$ref": "#/components/schemas/CypherRequest" + } + ], + "example": { + "query": "MATCH (n) RETURN count(n)" + }, + "title": "Request" + } } }, - { - "description": "longitude in decimal degrees format, ie: -80.33", - "in": "query", - "name": "longitude", - "required": true, - "schema": { - "type": "string" - } + "required": true + }, + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/CypherResponse" + } + } + }, + "description": "Successful Response" }, - { - "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" - } + "422": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/HTTPValidationError" + } + } + }, + "description": "Validation Error" } - ], + }, + "summary": "Run cypher query" + } + }, + "/predicates": { + "get": { + "description": "Returns an object where outer keys represent source types with second level keys as targets. And the values of the second level keys is the type of possible edge typesthat connect these concepts.", + "operationId": "predicates_predicates_get", "responses": { "200": { "content": { "application/json": { "schema": { - "properties": { - "values": { + "additionalProperties": { + "additionalProperties": { "items": { - "$ref": "#/components/schemas/inline_response_200_values" + "type": "string" }, "type": "array" - } + }, + "type": "object" }, + "title": "Response Predicates Predicates Get", "type": "object" } } }, - "description": "OK" - }, - "400": { - "description": "Invalid parameter" - }, - "404": { - "description": "No values found" - }, - "500": { - "description": "Server error" + "description": "Successful Response" } }, - "summary": "Retrieves air pollutant exposure levels", - "x-openapi-router-controller": "swagger_server.controllers.default_controller" + "summary": "Get one-hop connection types", + "tags": [ + "translator" + ] } - } - }, - "servers": [ - { - "url": "/cmaq_exposures_api/v1" - } - ], - "tags": [ - { - "name": "translator" - } - ] - }, - { - "_id": "219ac6646d0e2db862b533fb618db5b4", - "_meta": { - "date_created": "2021-03-04T18:22:55.853241+00:00", - "last_updated": "2021-03-05T08:05:13.473502+00:00", - "url": "http://bdt-proximity.renci.org:8080/roadway_proximity_api/v1/openapi.json", - "username": "lstillwe" - }, - "_score": 0.747712, - "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\u00a0https://www.fhwa.dot.gov/policyinformation/travel_monitoring/pubs/aadt/\u00a0for 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\u2019t 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": { + "/graph/schema": { "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": 500.0, - "format": "double", - "type": "number" - } - } - ], + "deprecated": true, + "description": "Get one-hop connection types", + "operationId": "predicates_graph_schema_get", "responses": { "200": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/RoadwayData" + "title": "Response Predicates Graph Schema Get", + "type": "object" } } }, - "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" + "description": "Successful Response" } }, - "summary": "retrieves distance in meters", - "x-openapi-router-controller": "swagger_server.controllers.default_controller" + "summary": "Get one-hop connection types" } - } - }, - "servers": [ - { - "url": "/roadway_proximity_api/v1" - } - ], - "tags": [ - { - "name": "translator" - } - ] - }, - { - "_id": "04f42ae00c8e5991b98d0e681dbdc596", - "_meta": { - "date_created": "2021-03-04T18:27:43.614727+00:00", - "last_updated": "2021-03-05T08:05:14.134499+00:00", - "url": "http://bdt-social.renci.org:8080/socio_environmental_exposures_api/v1/openapi.json", - "username": "lstillwe" - }, - "_score": 0.747712, - "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\u2019s 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\u00a0https://www.census.gov/acs/www/methodology/sample-size-and-data-quality/sample-size/\u00a0for 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\u00a0https://www2.census.gov/geo/pdfs/reference/geodiagram.pdf\u00a0for 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**\u00a0\u2013 the range of years for which this census data is valid\n- **GEOID**\u00a0\u2013 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**\u00a0- estimated population count in block group\n- **MedianHouseholdIncome**\u00a0- estimated median household income\n- **EstResidentialDensity**\u00a0- block group population density\n- **EstPropNonHispWhite**\u00a0\u2013 proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish**\u00a0- proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork**\u00a0- proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto**\u00a0- proportion of the block group households with no automobile\n- **EstPropHouseholdSSI**\u00a0- proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA**\u00a0- proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation**\u00a0- proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout**\u00a0- proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork**\u00a0- proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse**\u00a0- proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild**\u00a0- proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild**\u00a0- 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**\u00a0\u2013 the range of years for which this census data is valid\n- **GEOID**\u00a0\u2013 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**\u00a0- estimated population count in block group\n- **EstTotalPopulation_SE**\u00a0- standard error of total population in block group\n - **EstResidentialDensity**\u00a0- block group population density\n- **EstResidentialDensity_SE**\u00a0- standard error of residential population density in block group\n- **MedianHouseholdIncome**\u00a0- estimated median household income\n- **MedianHouseholdIncome_SE**\u00a0- standard error of median household income\n- **EstPropPersonsNoHealthIns**\u00a0- proportion of the block group population with no health insurance - **EstPropPersonsNoHealthIns_SE**\u00a0- standard error of proportion of the block group population with no health insurance\n- **EstPropNonHispWhite**\u00a0\u2013 proportion of the block group population that is non-Hispanic white\n- **EstPropNonHispWhite_SE**\u00a0- standard error of proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish**\u00a0- proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropPersons5PlusNoEnglish_SE**\u00a0- standard error of proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork**\u00a0- proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto**\u00a0- proportion of the block group households with no automobile\n- **EstPropHouseholdsNoAuto_SE**\u00a0- standard error of proportion of the block group households with no automobile\n- **EstPropHouseholdSSI**\u00a0- proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdSSI_SE**\u00a0- standard error of proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA**\u00a0- proportion of the block group households receiving Public Assistance\n- **EstPropHouseholdPA_SE**\u00a0- standard error of proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation**\u00a0- proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolMaxEducation_SE**\u00a0- standard error of proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout**\u00a0- proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork**\u00a0- proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse**\u00a0- proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdNoSpouse_SE**\u00a0- standard error of proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild**\u00a0- 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**\u00a0- 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**\u00a0- 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**\u00a0- 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": { + "/simple_spec": { "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", + "description": "Returns a list of available predicates when choosing a single source or target curie. Calling this endpoint with no query parameters will return all possible hops for all types.", + "operationId": "simple_spec_simple_spec_get", "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, + "name": "source", + "required": false, "schema": { + "title": "Source", "type": "string" } }, { - "description": "ACS data year range specification", "in": "query", - "name": "years", - "required": true, + "name": "target", + "required": false, "schema": { - "enum": [ - "All (2007-2016)", - "2007-2011", - "2012-2016" - ], + "title": "Target", "type": "string" } } @@ -1955,252 +2094,526 @@ "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" - } + "items": { + "$ref": "#/components/schemas/SimpleSpecElement" }, + "title": "Response Simple Spec Simple Spec Get", + "type": "array" + } + } + }, + "description": "Successful Response" + }, + "422": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/HTTPValidationError" + } + } + }, + "description": "Validation Error" + } + }, + "summary": "Get one-hop connection schema" + } + }, + "/graph/summary": { + "get": { + "description": "Returns a summary of the graph.", + "operationId": "graph_summary_graph_summary_get", + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "title": "Response Graph Summary Graph Summary Get", "type": "object" } } }, - "description": "OK" + "description": "Successful Response" + } + }, + "summary": "Get graph summary" + } + }, + "/overlay": { + "post": { + "description": "Given a ReasonerAPI graph, add support edges for any nodes linked in result bindings.", + "operationId": "overlay_overlay_post", + "requestBody": { + "content": { + "application/json": { + "schema": { + "allOf": [ + { + "$ref": "#/components/schemas/Query" + } + ], + "example": { + "message": { + "knowledge_graph": { + "edges": { + "9f7f9d86cb57e7190aafa57f7564eb05": { + "attributes": [ + { + "type": "WIKIDATA:Q80585", + "value": { + "ctime": 1610437123.7988985, + "predicate": "biolink:part_of", + "provided_by": "panther.get_gene_family_by_gene_family", + "publications": [], + "relation": "BFO:0000050", + "relation_label": "part of", + "source_database": "panther", + "source_id": "PANTHER.FAMILY:PTHR12015:SF170", + "target_id": "PANTHER.FAMILY:PTHR12015" + } + } + ], + "object": "PANTHER.FAMILY:PTHR12015", + "predicate": "biolink:part_of", + "subject": "PANTHER.FAMILY:PTHR12015:SF170" + }, + "dd8ef7a4606c4f8e405e6a5b1b095993": { + "attributes": [ + { + "type": "WIKIDATA:Q80585", + "value": { + "ctime": 1584932086.0009434, + "predicate": "biolink:part_of", + "provided_by": "panther.get_gene_by_gene_family", + "publications": [], + "relation": "BFO:0000050", + "relation_label": "part of", + "source_database": "panther", + "source_id": "NCBIGene:6352", + "target_id": "PANTHER.FAMILY:PTHR12015" + } + } + ], + "object": "PANTHER.FAMILY:PTHR12015", + "predicate": "biolink:part_of", + "subject": "NCBIGene:6352" + } + }, + "nodes": { + "NCBIGene:6352": { + "attributes": [ + { + "type": "WIKIDATA:Q80585", + "value": { + "category": [ + "biolink:BiologicalEntity", + "biolink:GenomicEntity", + "biolink:GeneOrGeneProduct", + "biolink:MacromolecularMachine", + "biolink:NamedThing", + "biolink:MolecularEntity", + "biolink:Gene" + ], + "chromosome": "17", + "equivalent_identifiers": [ + "ENSEMBL:ENSG00000271503", + "NCBIGene:6352", + "NCBIGene:6352", + "HGNC:10632", + "UniProtKB:P13501" + ], + "gene_family": [ + "Chemokine ligands" + ], + "gene_family_id": [ + 483 + ], + "location": "17q12", + "locus_group": "protein-coding gene", + "synonyms": [], + "taxon": 9606 + } + } + ], + "category": [ + "biolink:NamedThing", + "biolink:BiologicalEntity", + "biolink:MolecularEntity", + "biolink:GenomicEntity", + "biolink:GeneOrGeneProduct", + "biolink:MacromolecularMachine", + "biolink:Gene" + ], + "name": "CCL5" + }, + "PANTHER.FAMILY:PTHR12015": { + "attributes": [ + { + "type": "WIKIDATA:Q80585", + "value": { + "category": [ + "biolink:BiologicalEntity", + "biolink:GeneFamily", + "biolink:NamedThing", + "biolink:MolecularEntity", + "biolink:Entity" + ], + "equivalent_identifiers": [ + "PANTHER.FAMILY:PTHR12015" + ], + "synonyms": [] + } + } + ], + "category": [ + "biolink:NamedThing", + "biolink:BiologicalEntity", + "biolink:GeneFamily", + "biolink:MolecularEntity", + "biolink:Entity" + ], + "name": "SMALL INDUCIBLE CYTOKINE A" + }, + "PANTHER.FAMILY:PTHR12015:SF170": { + "attributes": [ + { + "type": "WIKIDATA:Q80585", + "value": { + "category": [ + "biolink:BiologicalEntity", + "biolink:GeneFamily", + "biolink:NamedThing", + "biolink:MolecularEntity", + "biolink:Entity" + ], + "equivalent_identifiers": [ + "PANTHER.FAMILY:PTHR12015:SF170" + ], + "synonyms": [] + } + } + ], + "category": [ + "biolink:NamedThing", + "biolink:BiologicalEntity", + "biolink:GeneFamily", + "biolink:MolecularEntity", + "biolink:Entity" + ], + "name": "C-C MOTIF CHEMOKINE 5" + } + } + }, + "query_graph": { + "edges": { + "e12": { + "object": "n2", + "predicate": "biolink:part_of", + "subject": "n1" + }, + "e23": { + "object": "n2", + "predicate": "biolink:part_of", + "subject": "n3" + } + }, + "nodes": { + "n1": { + "category": "biolink:Gene", + "id": "NCBIGene:6352", + "is_set": false + }, + "n2": { + "category": "biolink:GeneFamily", + "is_set": false + }, + "n3": { + "category": "biolink:GeneFamily", + "is_set": false + } + } + }, + "results": [ + { + "edge_bindings": { + "e12": [ + { + "id": "dd8ef7a4606c4f8e405e6a5b1b095993" + } + ], + "e23": [ + { + "id": "9f7f9d86cb57e7190aafa57f7564eb05" + } + ] + }, + "node_bindings": { + "n1": [ + { + "id": "NCBIGene:6352" + } + ], + "n2": [ + { + "id": "PANTHER.FAMILY:PTHR12015" + } + ], + "n3": [ + { + "id": "PANTHER.FAMILY:PTHR12015:SF170" + } + ] + } + } + ] + } + }, + "title": "Request" + } + } }, - "400": { - "content": {}, - "description": "Invalid parameter" + "required": true + }, + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Message" + } + } + }, + "description": "Successful Response" }, - "404": { - "content": {}, - "description": "No values found" + "422": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/HTTPValidationError" + } + } + }, + "description": "Validation Error" + } + }, + "summary": "Overlay results with available connections between each node.", + "tags": [ + "translator" + ] + } + }, + "/about": { + "get": { + "description": "Returns a JSON describing dataset.", + "operationId": "about_about_get", + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "title": "Response About About Get" + } + } + }, + "description": "Successful Response" + } + }, + "summary": "JSON about dataset" + } + }, + "/{source_type}/{target_type}/{curie}": { + "get": { + "description": "Returns one hop paths from `source_node_type` with `curie` to `target_node_type`.", + "operationId": "one_hop__source_type___target_type___curie__get", + "parameters": [ + { + "in": "path", + "name": "source_type", + "required": true, + "schema": { + "title": "Source Type", + "type": "string" + } }, - "500": { - "content": {}, - "description": "Server error" + { + "in": "path", + "name": "target_type", + "required": true, + "schema": { + "title": "Target Type", + "type": "string" + } + }, + { + "in": "path", + "name": "curie", + "required": true, + "schema": { + "title": "Curie", + "type": "string" + } + } + ], + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "items": {}, + "title": "Response One Hop Source Type Target Type Curie Get", + "type": "array" + } + } + }, + "description": "Successful Response" + }, + "422": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/HTTPValidationError" + } + } + }, + "description": "Validation Error" } }, - "summary": "provides ACS values", - "x-openapi-router-controller": "swagger_server.controllers.default_controller" + "summary": "Get one hop results from source type to target type. Note: Please GET /predicates to determine what target goes with a source" + } + }, + "/{node_type}/{curie}": { + "get": { + "description": "Returns `node` matching `curie`.", + "operationId": "node__node_type___curie__get", + "parameters": [ + { + "in": "path", + "name": "node_type", + "required": true, + "schema": { + "title": "Node Type", + "type": "string" + } + }, + { + "in": "path", + "name": "curie", + "required": true, + "schema": { + "title": "Curie", + "type": "string" + } + } + ], + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "items": {}, + "title": "Response Node Node Type Curie Get", + "type": "array" + } + } + }, + "description": "Successful Response" + }, + "422": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/HTTPValidationError" + } + } + }, + "description": "Validation Error" + } + }, + "summary": "Find `node` by `curie`" } } }, "servers": [ { - "url": "/socio_environmental_exposures_api/v1" + "description": "Default server", + "url": "https://automat.renci.org/intact" } ], "tags": [ { "name": "translator" + }, + { + "name": "automat" } ] }, { - "_id": "71add13e7c8b26b0046cfb8cf5092395", + "_id": "eb28713e2e23160e80e88f3a5dabcca4", "_meta": { - "date_created": "2020-03-12T16:20:50.656877+00:00", - "last_updated": "2021-02-17T07:42:20.416659+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/chembl/smartapi.yaml", + "date_created": "2020-03-12T16:20:11.288144+00:00", + "last_updated": "2021-02-17T07:42:16.930988+00:00", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/RGD/smartapi.yaml", "username": "kevinxin90" }, - "_score": 0.6687226, + "_score": 0.6863549, "components": { "x-bte-kgs-operations": { - "target": { + "hasHomolog": { "inputs": [ { - "id": "chembl", - "semantic": "ChemicalSubstance" + "id": "rgd", + "semantic": "Gene" } ], "outputs": [ { - "id": "chembl", + "id": "symbol", "semantic": "Gene" } ], "parameters": { - "molecule_chembl_id": "{input1}" + "geneid": "{input1}" }, "response-mapping": { - "$ref": "#/components/x-bte-response-mapping/drug-mechanism" + "$ref": "#/components/x-bte-response-mapping/gene-homolog" }, "supportBatch": false } }, "x-bte-response-mapping": { - "drug-mechanism": { + "gene-homolog": { "@context": "http://schema.org", - "@type": "ChemicalSubstance", - "bts:chembl": "chembl", - "bts:target": { - "$input": "bts:chembl", - "$source": "chembl", + "@type": "Gene", + "bts:hasHomolog": { + "$input": "bts:rgd", + "$source": "RGD", "@type": "Gene", - "bts:action": "mechanisms.action_type", - "bts:chembl": "mechanisms.target_chembl_id", - "bts:mechanism": "mechanisms.mechanism_of_action" - } + "bts:symbol": "ensemblGeneSymbol" + }, + "bts:rgd": "rgd" } } }, "info": { "contact": { - "email": "help@chembl.org", - "name": "chembl help desk", + "email": "help@rgd.org", + "name": "rgd help desk", "x-role": "responsible developer" }, - "description": "The ChEMBL API", - "termsOfService": "http://www.ebi.ac.uk/chembl", - "title": "ChEMBL API", - "version": "1.0" - }, + "description": "The RGD API", + "termsOfService": "http://www.rgd.org", + "title": "RGD API", + "version": "1.0" + }, "paths": { - "/data/mechanism.json": { + "/genes/{geneid}": { "get": { "parameters": [ { - "description": "chembl id", - "example": "CHEMBL744", - "in": "query", - "name": "molecule_chembl_id", + "description": "RGD id", + "example": "620465", + "in": "path", + "name": "geneid", "required": true, "schema": { "type": "string" @@ -2209,16 +2622,16 @@ ], "responses": { "200": { - "description": "A drug mechanism object", + "description": "A RGD object", "x-bte-response-mapping": { - "$ref": "#/components/x-bte-response-mapping/drug-mechanism" + "$ref": "#/components/x-bte-response-mapping/gene-homolog" } } }, - "summary": "retrieve drug mechanism", + "summary": "retrieve rgd data", "x-bte-kgs-operations": { - "treats": { - "$ref": "#/components/x-bte-kgs-operations/target" + "associatedWith": { + "$ref": "#/components/x-bte-kgs-operations/hasHomolog" } } } @@ -2227,440 +2640,27 @@ "servers": [ { "description": "Production server", - "url": "http://www.ebi.ac.uk/chembl/api" - } - ], - "tags": [ - { - "name": "publication" - }, - { - "name": "translator" - } - ] - }, - { - "_id": "e9f69b81e755e163fdf6c41a2b5e07c0", - "_meta": { - "date_created": "2021-01-29T00:00:15.735608+00:00", - "last_updated": "2021-03-05T08:01:02.015192+00:00", - "url": "https://openpredict.semanticscience.org/openapi.json", - "username": "vemonet" - }, - "_score": 0.6687226, - "info": { - "contact": { - "email": "vincent.emonet@maastrichtuniversity.nl", - "name": "Institute of Data Science at Maastricht University", - "url": "https://maastrichtuniversity.nl/ids" - }, - "description": "Get predicted targets for a given entity: the **potential drugs treating a given disease**, or the **potential diseases a given drug could treat**. \n\n* Use the `/predict` operation to easily retrieve predictions for a given entity (operation annotated for the [BioThings Explorer](https://x-bte-extension.readthedocs.io/en/latest/x-bte-kgs-operations.html)). \n\n* Predictions are currently produced using the [PREDICT method](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159979/) from the [fair-workflows/openpredict](https://github.com/fair-workflows/openpredict) project. \n\n* You can also install the [OpenPredict Python package](https://pypi.org/project/openpredict/) to train and serve a new model yourself. \n\n* More documentation available at [github.com/MaastrichtU-IDS/translator-openpredict](https://github.com/MaastrichtU-IDS/translator-openpredict) \n\n[![Version](https://img.shields.io/pypi/v/openpredict)](https://pypi.org/project/openpredict) [![Run tests](https://github.com/MaastrichtU-IDS/translator-openpredict/workflows/Run%20tests/badge.svg)](https://github.com/MaastrichtU-IDS/translator-openpredict/actions?query=workflow%3A%22Run+tests%22) \n\nService supported by the [NCATS Translator project](https://ncats.nih.gov/translator/about)", - "license": { - "name": "MIT License", - "url": "https://opensource.org/licenses/MIT" - }, - "termsOfService": "", - "title": "OpenPredict API \ud83d\udd2e\ud83d\udc0d", - "version": "1.0.0", - "x-translator": { - "component": "KP", - "team": [ - "Clinical Data Provider" - ] - } - }, - "paths": { - "/embedding": { - "post": { - "description": "Upload your embedding file: select which types do you have in the embeddings, Drugs, Diseases or Both. \n1. provided embeddings will be added to the model\n2. the model will be retrained\n3. the model evaluation will be stored in a triplestore", - "operationId": "openpredict.openpredict_api.post_embedding", - "parameters": [ - { - "description": "Types of the entities in the embedding", - "in": "query", - "name": "types", - "required": true, - "schema": { - "default": "Both", - "enum": [ - "Drugs", - "Diseases", - "Both" - ], - "type": "string" - } - }, - { - "description": "Name of embedding (eg. TransE_DrugBank_Drug)", - "in": "query", - "name": "emb_name", - "required": true, - "schema": { - "type": "string" - } - }, - { - "description": "Describe how the embeddings was obtained (eg. rdf2vec on drugbank/omim data)", - "in": "query", - "name": "description", - "required": true, - "schema": { - "type": "string" - } - }, - { - "description": "Provide the ID of the run output you want to use as base model to add the embeddings", - "example": "openpredict-baseline-omim-drugbank", - "in": "query", - "name": "model_id", - "required": true, - "schema": { - "type": "string" - } - } - ], - "requestBody": { - "content": { - "multipart/form-data": { - "schema": { - "properties": { - "embedding_file": { - "description": "The embedding file to be uploaded", - "format": "binary", - "type": "string" - } - }, - "type": "object" - } - } - } - }, - "responses": { - "200": { - "description": "OK" - } - }, - "summary": "Upload your embedding for drugs or diseases", - "tags": [ - "openpredict" - ] - } - }, - "/features": { - "get": { - "description": "Return the features trained in the model, for Drugs, Diseases or Both ", - "operationId": "openpredict.openpredict_api.get_features", - "parameters": [ - { - "description": "Type of the entities in the features", - "in": "query", - "name": "type", - "required": true, - "schema": { - "default": "All", - "enum": [ - "All", - "Drugs", - "Diseases", - "Both" - ], - "type": "string" - } - } - ], - "responses": { - "200": { - "content": { - "application/json": {} - }, - "description": "OK" - } - }, - "summary": "Return the features trained in the models", - "tags": [ - "openpredict" - ] - } - }, - "/models": { - "get": { - "description": "Return the models with their training features and scores", - "operationId": "openpredict.openpredict_api.get_models", - "responses": { - "200": { - "content": { - "application/json": {} - }, - "description": "OK" - } - }, - "summary": "Return the models with their training features and scores", - "tags": [ - "openpredict" - ] - } - }, - "/predicates": { - "get": { - "operationId": "openpredict.openpredict_api.get_predicates", - "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" - ] - } - }, - "/predict": { - "get": { - "description": "Return the predicted targets for a given entity: drug (DrugBank ID) or disease (OMIM ID), with confidence scores. Only a drug_id or a disease_id can be provided, the disease_id will be ignored if drug_id is provided This operation is annotated with x-bte-kgs-operations, and follow the BioThings API recommendations.", - "operationId": "openpredict.openpredict_api.get_predict", - "parameters": [ - { - "description": "CURIE of the drug to get prediction of diseases it could treat (e.g. DRUGBANK:DB00394)", - "example": "DRUGBANK:DB00394", - "in": "query", - "name": "drug_id", - "required": false, - "schema": { - "type": "string" - } - }, - { - "description": "CURIE of the disease to get prediction of drugs it could be treated with (e.g. OMIM:246300). Ignored if drug_id provided.", - "in": "query", - "name": "disease_id", - "required": false, - "schema": { - "type": "string" - } - }, - { - "description": "Provide the ID of the run output you want to use as model to use to predict associations", - "example": "openpredict-baseline-omim-drugbank", - "in": "query", - "name": "model_id", - "required": false, - "schema": { - "type": "string" - } - }, - { - "description": "Minimum score of predictions to return (0 to 1)", - "in": "query", - "name": "min_score", - "required": false, - "schema": { - "format": "double", - "maximum": 1, - "minimum": 0, - "type": "number" - } - }, - { - "description": "Maximum score of predictions to return (0 to 1)", - "in": "query", - "name": "max_score", - "required": false, - "schema": { - "format": "double", - "maximum": 1, - "minimum": 0, - "type": "number" - } - }, - { - "description": "Maximum number of results to return, ordered from best score (e.g. 42)", - "in": "query", - "name": "n_results", - "required": false, - "schema": { - "format": "int32", - "minimum": 0, - "type": "integer" - } - } - ], - "responses": { - "200": { - "content": { - "application/json": {} - }, - "description": "Successful Operation" - } - }, - "summary": "Get predicted targets for a given entity", - "tags": [ - "openpredict" - ], - "x-bte-kgs-operations": [ - { - "inputs": [ - { - "id": "biolink:DRUGBANK", - "semantic": "biolink:ChemicalSubstance" - } - ], - "outputs": [ - { - "id": "biolink:OMIM", - "semantic": "biolink:Disease" - } - ], - "parameters": { - "drug_id": "{inputs[0]}" - }, - "predicate": "biolink:treats", - "responseMapping": { - "OMIM": "hits.id" - }, - "supportBatch": false - }, - { - "inputs": [ - { - "id": "biolink:OMIM", - "semantic": "biolink:Disease" - } - ], - "outputs": [ - { - "id": "biolink:DRUGBANK", - "semantic": "biolink:ChemicalSubstance" - } - ], - "parameters": { - "disease_id": "{inputs[0]}" - }, - "predicate": "biolink:treated_by", - "responseMapping": { - "DRUGBANK": "hits.id" - }, - "supportBatch": false - } - ] - } - }, - "/query": { - "post": { - "description": "Send a [ReasonerAPI](https://github.com/NCATSTranslator/ReasonerAPI) query to request the predicted targets given: a source node, and the relation to predict. Use classes and relations from the [BioLink model](https://biolink.github.io/biolink-model)", - "operationId": "openpredict.openpredict_api.post_reasoner_predict", - "requestBody": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Query" - } - } - }, - "description": "Query information to be submitted", - "required": true - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Response" - } - } - }, - "description": "OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized." - }, - "400": { - "content": { - "application/json": { - "schema": { - "type": "string" - } - } - }, - "description": "Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)." - }, - "500": { - "content": { - "application/json": { - "schema": { - "type": "string" - } - } - }, - "description": "Internal server error." - }, - "501": { - "content": { - "application/json": { - "schema": { - "type": "string" - } - } - }, - "description": "Not implemented." - } - }, - "summary": "Query reasoner via one of several inputs", - "tags": [ - "query" - ], - "x-swagger-router-controller": "swagger_server.controllers.query_controller" - } - } - }, - "servers": [ - { - "url": "https://openpredict.semanticscience.org" + "url": "https://rest.rgd.mcw.edu/rgdws" } ], "tags": [ { - "description": "Get relationships supported by this API", "name": "translator" }, { - "description": "Query the models using the Reasoner API", - "name": "reasoner" + "name": "gene" } ] }, { - "_id": "ed85eff6809e354002cbf17231918a89", + "_id": "57539ea28b4e19ecd36074566ca2cd56", "_meta": { - "date_created": "2021-02-03T00:01:02.336283+00:00", - "last_updated": "2021-03-05T08:01:04.507104+00:00", - "url": "https://automat.renci.org/biolink/openapi.json", + "date_created": "2021-01-26T00:07:34.730271+00:00", + "last_updated": "2021-03-29T07:01:26.222141+00:00", + "url": "https://automat.renci.org/gtex/openapi.json", "username": "YaphetKG" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { "email": "kebedey@renci.org", @@ -2668,9 +2668,9 @@ "x-id": "https://github.com/yaphetkg", "x-role": "contributor" }, - "description": "A graph based on the [Monarch API (https://api.monarchinitiative.org/)](https://api.monarchinitiative.org/).", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Biolink&provider_long=RENCI", - "title": "Automat Biolink", + "description": "A graph containing eqtl and sqtl information from [GTEx Portal (https://gtexportal.org/home/)](https://gtexportal.org/home/). Also includes genes that the variants lie within or near.", + "termsOfService": "https://http://robokop.renci.org:7055/tos?service_long=Automat GTEx&provider_long=RENCI", + "title": "Automat GTEx", "version": "1.0.0", "x-translator": { "component": "KP", @@ -3389,7 +3389,7 @@ "servers": [ { "description": "Default server", - "url": "https://automat.renci.org/biolink" + "url": "https://automat.renci.org/gtex" } ], "tags": [ @@ -3397,19 +3397,19 @@ "name": "translator" }, { - "name": "Automat" + "name": "automat" } ] }, { - "_id": "02fdf5136618160a6531a3844bbcde1a", + "_id": "f8f7142da2323703dfa32b8cc4cdff5f", "_meta": { - "date_created": "2021-01-26T00:02:44.437058+00:00", - "last_updated": "2021-03-05T08:00:57.550250+00:00", - "url": "https://automat.renci.org/cord19-scigraph/openapi.json", + "date_created": "2021-01-26T00:02:39.708234+00:00", + "last_updated": "2021-03-29T07:01:28.250099+00:00", + "url": "https://automat.renci.org/viral-proteome/openapi.json", "username": "YaphetKG" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { "email": "kebedey@renci.org", @@ -3417,9 +3417,9 @@ "x-id": "https://github.com/yaphetkg", "x-role": "contributor" }, - "description": "A literature co-occurence graph based on scigraph parsing of the CORD-19 paper set. All triples contain covid-19 as either subject or object.", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat%20Cord19%20Scigraph&provider_long=RENCI", - "title": "Automat Cord19 Scigraph", + "description": "A graph consisting of viral proteins from UniProt, connected by similarity edges from UniRef.", + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Viral Proteome&provider_long=RENCI", + "title": "Automat Viral Proteome", "version": "1.0.0", "x-translator": { "component": "KP", @@ -4138,7 +4138,7 @@ "servers": [ { "description": "Default server", - "url": "https://automat.renci.org/cord19-scigraph" + "url": "https://automat.renci.org/viral-proteome" } ], "tags": [ @@ -4151,14 +4151,14 @@ ] }, { - "_id": "4e03414ea4b39e92ffb97690f8620286", + "_id": "0d3cb44c7d519f06c8a6a8dec43dbf05", "_meta": { - "date_created": "2021-02-04T00:01:09.326724+00:00", - "last_updated": "2021-03-05T08:01:05.676611+00:00", - "url": "https://automat.renci.org/kegg/openapi.json", + "date_created": "2021-01-26T00:02:38.407228+00:00", + "last_updated": "2021-03-29T07:01:44.668320+00:00", + "url": "https://automat.renci.org/covid-phenotypes/openapi.json", "username": "YaphetKG" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { "email": "kebedey@renci.org", @@ -4166,9 +4166,9 @@ "x-id": "https://github.com/yaphetkg", "x-role": "contributor" }, - "description": "A graph based on the [Kyoto Encyclopedia of Genes and Genomes (https://www.genome.jp/kegg/)](https://www.genome.jp/kegg/).", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat KEGG&provider_long=RENCI", - "title": "Automat KEGG", + "description": "A hand-curated graph of phenotypes of covid-19.", + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Covid Phenotypes&provider_long=RENCI", + "title": "Automat Covid Phenotypes", "version": "1.0.0", "x-translator": { "component": "KP", @@ -4887,7 +4887,7 @@ "servers": [ { "description": "Default server", - "url": "https://automat.renci.org/kegg" + "url": "https://automat.renci.org/covid-phenotypes" } ], "tags": [ @@ -4903,11 +4903,11 @@ "_id": "a680e39140826113c3c9f426dc0a7289", "_meta": { "date_created": "2021-01-26T00:00:44.070682+00:00", - "last_updated": "2021-03-05T08:01:10.388367+00:00", + "last_updated": "2021-03-29T07:02:08.222322+00:00", "url": "https://automat.renci.org/cord19-scibite/openapi.json", "username": "YaphetKG" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { "email": "kebedey@renci.org", @@ -4916,7 +4916,7 @@ "x-role": "contributor" }, "description": "A literature co-occurence graph based on the [scibite parsing (https://github.com/SciBiteLabs/CORD19)](https://github.com/SciBiteLabs/CORD19) of the CORD-19 paper set.", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat%20Cord19%20Scibite&provider_long=RENCI", + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Cord19 Scibite&provider_long=RENCI", "title": "Automat Cord19 Scibite", "version": "1.0.0", "x-translator": { @@ -5649,14 +5649,14 @@ ] }, { - "_id": "57539ea28b4e19ecd36074566ca2cd56", + "_id": "523a1ce8b6d4fc9a1d0f9f22321f4c4c", "_meta": { - "date_created": "2021-01-26T00:07:34.730271+00:00", - "last_updated": "2021-03-05T08:01:13.530373+00:00", - "url": "https://automat.renci.org/gtex/openapi.json", + "date_created": "2021-02-03T00:00:48.628394+00:00", + "last_updated": "2021-03-29T07:01:47.129105+00:00", + "url": "https://automat.renci.org/gtopdb/openapi.json", "username": "YaphetKG" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { "email": "kebedey@renci.org", @@ -5664,9 +5664,9 @@ "x-id": "https://github.com/yaphetkg", "x-role": "contributor" }, - "description": "A graph containing eqtl and sqtl information from [GTEx Portal (https://gtexportal.org/home/)](https://gtexportal.org/home/). Also includes genes that the variants lie within or near.", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat%20GTEx&provider_long=RENCI", - "title": "Automat GTEx", + "description": "A graph based on the [IUPHAR Guide to Pharmacology (https://www.guidetopharmacology.org/)](https://www.guidetopharmacology.org/)", + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Gtopdb&provider_long=RENCI", + "title": "Automat Gtopdb", "version": "1.0.0", "x-translator": { "component": "KP", @@ -6385,7 +6385,7 @@ "servers": [ { "description": "Default server", - "url": "https://automat.renci.org/gtex" + "url": "https://automat.renci.org/gtopdb" } ], "tags": [ @@ -6398,14 +6398,120 @@ ] }, { - "_id": "e4594ac1218186891fb2e48c63e182a3", + "_id": "1c056ffc7ed0dd1229e71c4752239465", "_meta": { - "date_created": "2021-02-04T00:00:28.887481+00:00", - "last_updated": "2021-03-05T08:01:30.541815+00:00", - "url": "https://automat.renci.org/uberongraph/openapi.json", + "date_created": "2020-12-07T23:02:21.623909+00:00", + "last_updated": "2021-03-29T07:02:06.907337+00:00", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/ols/smartapi.yaml", + "username": "kevinxin90" + }, + "_score": 0.6863549, + "components": { + "x-bte-kgs-operations": { + "disease_has_subclass_disease": [ + { + "inputs": [ + { + "id": "DOID", + "semantic": "Disease" + } + ], + "outputs": [ + { + "id": "DOID", + "semantic": "Disease" + } + ], + "parameters": { + "id": "{inputs[0]}" + }, + "predicate": "superclass_of", + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/disease_has_subclass_disease" + }, + "source": "DO", + "supportBatch": false + } + ] + }, + "x-bte-response-mapping": { + "disease_has_subclass_disease": { + "DOID": "_embedded.terms.obo_id", + "description": "_embedded.terms.description", + "name": "_embedded.terms.label" + } + } + }, + "info": { + "contact": { + "email": "help@pharmgkb.org", + "name": "pharmgkb help desk", + "x-role": "responsible developer" + }, + "description": "The OLS REST API provides access to key biological data from OLS. The services provide a unified interface to query information about ontology terms from GO (the Gene Ontology) and ECO (the Evidence & Conclusion Ontology), Gene Ontology annotations from the EBI's GOA database, and gene products (proteins from UniProt, RNA from RNAcentral and complexes from ComplexPortal). ", + "termsOfService": "https://www.ebi.ac.uk/OLS/services", + "title": "Ontology Lookup Service API", + "version": "1.0", + "x-translator": { + "component": "KP", + "team": [ + "Service Provider" + ] + } + }, + "paths": { + "/ontologies/doid/children": { + "get": { + "parameters": [ + { + "description": "Put Disease Ontology ID here, e.g. DOID:0050686", + "example": "DOID:0050686", + "in": "query", + "name": "id", + "required": true, + "schema": { + "type": "string" + } + } + ], + "responses": { + "200": { + "description": "A DISEASE Ontology annotation object" + } + }, + "summary": "retrieve the children of specified ontology terms", + "x-bte-kgs-operations": [ + { + "$ref": "#/components/x-bte-kgs-operations/disease_has_subclass_disease" + } + ] + } + } + }, + "servers": [ + { + "description": "Production server", + "url": "https://www.ebi.ac.uk/ols/api" + } + ], + "tags": [ + { + "name": "ontology" + }, + { + "name": "translator" + } + ] + }, + { + "_id": "7b1b6a88cbf2913c4b614fabddcaabb4", + "_meta": { + "date_created": "2021-01-26T00:02:52.903243+00:00", + "last_updated": "2021-03-29T07:02:13.284120+00:00", + "url": "https://automat.renci.org/textminingkp/openapi.json", "username": "YaphetKG" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { "email": "kebedey@renci.org", @@ -6413,9 +6519,9 @@ "x-id": "https://github.com/yaphetkg", "x-role": "contributor" }, - "description": "A graph representation of Uberongraph, an integration of ontologies including GO, CHEBI, Uberon, and HPO.", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Uberongraph&provider_long=RENCI", - "title": "Automat Uberongraph", + "description": " A literature co-occurrence graph created by the Translator Text Mining KP.", + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Textmining KP&provider_long=RENCI", + "title": "Automat Textmining KP", "version": "1.0.0", "x-translator": { "component": "KP", @@ -7134,7 +7240,7 @@ "servers": [ { "description": "Default server", - "url": "https://automat.renci.org/uberongraph" + "url": "https://automat.renci.org/textminingkp" } ], "tags": [ @@ -7147,14 +7253,14 @@ ] }, { - "_id": "b4b45614a935a575292aad3bb726d1f3", + "_id": "4e03414ea4b39e92ffb97690f8620286", "_meta": { - "date_created": "2021-02-04T00:01:49.121558+00:00", - "last_updated": "2021-03-05T08:01:17.366365+00:00", - "url": "https://automat.renci.org/hgnc/openapi.json", + "date_created": "2021-02-04T00:01:09.326724+00:00", + "last_updated": "2021-03-29T07:02:15.917717+00:00", + "url": "https://automat.renci.org/kegg/openapi.json", "username": "YaphetKG" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { "email": "kebedey@renci.org", @@ -7162,9 +7268,9 @@ "x-id": "https://github.com/yaphetkg", "x-role": "contributor" }, - "description": "Gene families from [HGNC (genenames.org)](genenames.org).", - "termsOfService": "http://linkmissing", - "title": "Automat HGNC", + "description": "A graph based on the [Kyoto Encyclopedia of Genes and Genomes (https://www.genome.jp/kegg/)](https://www.genome.jp/kegg/).", + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat KEGG&provider_long=RENCI", + "title": "Automat KEGG", "version": "1.0.0", "x-translator": { "component": "KP", @@ -7883,7 +7989,7 @@ "servers": [ { "description": "Default server", - "url": "https://automat.renci.org/hgnc" + "url": "https://automat.renci.org/kegg" } ], "tags": [ @@ -7896,88 +8002,169 @@ ] }, { - "_id": "cd79363c8f24935bc0fa0659bed8ff58", + "_id": "1f277e1563fcfd124bfae2cc3c4bcdec", "_meta": { - "date_created": "2021-02-25T18:44:45.303276+00:00", - "last_updated": "2021-03-05T08:01:21.198288+00:00", - "slug": "icees", - "url": "https://icees.renci.org:16340/openapi.json", - "username": "patrickkwang" + "date_created": "2021-02-11T00:06:11.157097+00:00", + "last_updated": "2021-03-29T07:02:56.369682+00:00", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/quickgo/smartapi.yaml", + "username": "kevinxin90" + }, + "_score": 0.6863549, + "components": { + "x-bte-kgs-operations": { + "ma_has_subclass_ma": [ + { + "inputs": [ + { + "id": "GO", + "semantic": "MolecularActivity" + } + ], + "outputs": [ + { + "id": "GO", + "semantic": "MolecularActivity" + } + ], + "parameters": { + "goid": "{inputs[0]}" + }, + "predicate": "has_subclass", + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ma_has_subclass_ma" + }, + "source": "Gene Ontology", + "supportBatch": false + } + ] + }, + "x-bte-response-mapping": { + "ma_has_subclass_ma": { + "GO": "results.children.id", + "name": "results.children.name", + "relation": "results.children.relation" + } + } }, - "_score": 0.6687226, "info": { "contact": { - "email": "patrick@covar.com", - "name": "Patrick Wang", - "x-id": "https://github.com/patrickkwang", + "email": "help@pharmgkb.org", + "name": "pharmgkb help desk", "x-role": "responsible developer" }, - "description": "ICEES API \n
[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
", - "termsOfService": "N/A", - "title": "ICEES API", - "version": "4.0.0", + "description": "The QuickGO REST API provides access to key biological data from QuickGO and GOA. The services provide a unified interface to query information about ontology terms from GO (the Gene Ontology) and ECO (the Evidence & Conclusion Ontology), Gene Ontology annotations from the EBI's GOA database, and gene products (proteins from UniProt, RNA from RNAcentral and complexes from ComplexPortal). ", + "termsOfService": "https://www.ebi.ac.uk/QuickGO/services", + "title": "QuickGO API", + "version": "1.0", "x-translator": { "component": "KP", "team": [ - "Exposures Provider" + "Service Provider" ] } }, "paths": { - "/{table}/{year}/cohort": { - "post": { - "description": "Cohort discovery.", - "operationId": "discover_cohort__table___year__cohort_post", + "/ontology/go/terms/{goid}/children": { + "get": { "parameters": [ { + "description": "Put Gene Ontology ID here, e.g. GO:0000082", + "example": "GO:0000082", "in": "path", - "name": "table", + "name": "goid", "required": true, "schema": { - "title": "Table", "type": "string" } - }, - { - "in": "path", - "name": "year", - "required": true, - "schema": { - "title": "Year", - "type": "integer" - } } ], + "responses": { + "200": { + "description": "A gene ontolgoy annotation object" + } + }, + "summary": "retrieve the children of specified ontology terms", + "x-bte-kgs-operations": [ + { + "$ref": "#/components/x-bte-kgs-operations/ma_has_subclass_ma" + } + ] + } + } + }, + "servers": [ + { + "description": "Production server", + "url": "https://www.ebi.ac.uk/QuickGO/services" + } + ], + "tags": [ + { + "name": "ontology" + }, + { + "name": "translator" + } + ] + }, + { + "_id": "02fdf5136618160a6531a3844bbcde1a", + "_meta": { + "date_created": "2021-01-26T00:02:44.437058+00:00", + "last_updated": "2021-03-23T07:02:42.518760+00:00", + "url": "https://automat.renci.org/cord19-scigraph/openapi.json", + "username": "YaphetKG" + }, + "_score": 0.6863549, + "info": { + "contact": { + "email": "kebedey@renci.org", + "name": "Yaphet Kebede", + "x-id": "https://github.com/yaphetkg", + "x-role": "contributor" + }, + "description": "A literature co-occurence graph based on scigraph parsing of the CORD-19 paper set. All triples contain covid-19 as either subject or object.", + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Cord19 Scigraph&provider_long=RENCI", + "title": "Automat Cord19 Scigraph", + "version": "1.0.0", + "x-translator": { + "component": "KP", + "team": [ + "Ranking Agent" + ], + "teams": [ + "Ranker" + ] + } + }, + "paths": { + "/query": { + "post": { + "description": "Given a question graph return question graph plus answers.", + "operationId": "reasoner_api_query_post", "requestBody": { "content": { "application/json": { "schema": { - "anyOf": [ - { - "additionalProperties": { - "anyOf": [ - { - "$ref": "#/components/schemas/Comparison" - }, - { - "$ref": "#/components/schemas/Between" - }, - { - "$ref": "#/components/schemas/In" - } - ] - }, - "type": "object" - }, + "allOf": [ { - "items": { - "$ref": "#/components/schemas/FeatureExplicit" - }, - "type": "array" + "$ref": "#/components/schemas/Query" } ], - "example": {}, - "title": "Req Features" + "example": { + "message": { + "query_graph": { + "edges": {}, + "nodes": { + "n0": { + "category": "biolink:Gene", + "id": "NCBIGene:15" + } + } + } + } + }, + "title": "Request" } } }, @@ -7988,13 +8175,11 @@ "content": { "application/json": { "schema": { - "title": "Response Discover Cohort Table Year Cohort Post", - "type": "object" + "$ref": "#/components/schemas/Query" } - }, - "text/tabular": {} + } }, - "description": "Return the tabular output." + "description": "Successful Response" }, "422": { "content": { @@ -8007,45 +8192,76 @@ "description": "Validation Error" } }, - "summary": "Discover Cohort" + "summary": "Query Reasoner API", + "tags": [ + "translator" + ] } }, - "/{table}/{year}/cohort/dictionary": { + "/reasonerapi": { "get": { - "description": "Get cohort dictionary.", - "operationId": "dictionary__table___year__cohort_dictionary_get", - "parameters": [ - { - "in": "path", - "name": "table", - "required": true, - "schema": { - "title": "Table", - "type": "string" + "description": "Returns a list of question templates that can be used to query this plater instance.", + "operationId": "get_reasoner_api_reasonerapi_get", + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "items": { + "$ref": "#/components/schemas/Message" + }, + "title": "Response Get Reasoner Api Reasonerapi Get", + "type": "array" + } + } + }, + "description": "Successful Response" + } + }, + "summary": "Get question templates" + }, + "post": { + "deprecated": true, + "description": "Handle TRAPI request.", + "operationId": "reasoner_api_reasonerapi_post", + "requestBody": { + "content": { + "application/json": { + "schema": { + "allOf": [ + { + "$ref": "#/components/schemas/Query" + } + ], + "example": { + "message": { + "query_graph": { + "edges": {}, + "nodes": { + "n0": { + "category": "biolink:Gene", + "id": "NCBIGene:15" + } + } + } + } + }, + "title": "Request" + } } }, - { - "in": "path", - "name": "year", - "required": true, - "schema": { - "title": "Year", - "type": "integer" - } - } - ], + "required": true + }, "responses": { "200": { "content": { "application/json": { "schema": { - "title": "Response Dictionary Table Year Cohort Dictionary Get", - "type": "object" + "$ref": "#/components/schemas/Query" } - }, - "text/tabular": {} + } }, - "description": "Return the tabular output." + "description": "Successful Response" }, "422": { "content": { @@ -8058,54 +8274,41 @@ "description": "Validation Error" } }, - "summary": "Dictionary" + "summary": "Reasoner Api" } }, - "/{table}/{year}/cohort/{cohort_id}": { - "get": { - "description": "Get definition of a cohort.", - "operationId": "get_cohort__table___year__cohort__cohort_id__get", - "parameters": [ - { - "in": "path", - "name": "table", - "required": true, - "schema": { - "title": "Table", - "type": "string" - } - }, - { - "in": "path", - "name": "year", - "required": true, - "schema": { - "title": "Year", - "type": "integer" + "/cypher": { + "post": { + "description": "Runs cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/).", + "operationId": "cypher_cypher_post", + "requestBody": { + "content": { + "application/json": { + "schema": { + "allOf": [ + { + "$ref": "#/components/schemas/CypherRequest" + } + ], + "example": { + "query": "MATCH (n) RETURN count(n)" + }, + "title": "Request" + } } }, - { - "in": "path", - "name": "cohort_id", - "required": true, - "schema": { - "title": "Cohort Id", - "type": "string" - } - } - ], + "required": true + }, "responses": { "200": { "content": { "application/json": { "schema": { - "title": "Response Get Cohort Table Year Cohort Cohort Id Get", - "type": "object" + "$ref": "#/components/schemas/CypherResponse" } - }, - "text/tabular": {} + } }, - "description": "Return the tabular output." + "description": "Successful Response" }, "422": { "content": { @@ -8118,176 +8321,100 @@ "description": "Validation Error" } }, - "summary": "Get Cohort" - }, - "put": { - "description": "Cohort discovery.", - "operationId": "edit_cohort__table___year__cohort__cohort_id__put", - "parameters": [ - { - "in": "path", - "name": "table", - "required": true, - "schema": { - "title": "Table", - "type": "string" - } - }, - { - "in": "path", - "name": "year", - "required": true, - "schema": { - "title": "Year", - "type": "integer" - } - }, - { - "in": "path", - "name": "cohort_id", - "required": true, - "schema": { - "title": "Cohort Id", - "type": "string" - } - } - ], - "requestBody": { - "content": { - "application/json": { - "schema": { - "anyOf": [ - { + "summary": "Run cypher query" + } + }, + "/predicates": { + "get": { + "description": "Returns an object where outer keys represent source types with second level keys as targets. And the values of the second level keys is the type of possible edge typesthat connect these concepts.", + "operationId": "predicates_predicates_get", + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "additionalProperties": { "additionalProperties": { - "anyOf": [ - { - "$ref": "#/components/schemas/Comparison" - }, - { - "$ref": "#/components/schemas/Between" - }, - { - "$ref": "#/components/schemas/In" - } - ] + "items": { + "type": "string" + }, + "type": "array" }, "type": "object" }, - { - "items": { - "$ref": "#/components/schemas/FeatureExplicit" - }, - "type": "array" - } - ], - "example": {}, - "title": "Req Features" + "title": "Response Predicates Predicates Get", + "type": "object" + } } - } - }, - "required": true + }, + "description": "Successful Response" + } }, + "summary": "Get one-hop connection types", + "tags": [ + "translator" + ] + } + }, + "/graph/schema": { + "get": { + "deprecated": true, + "description": "Get one-hop connection types", + "operationId": "predicates_graph_schema_get", "responses": { "200": { "content": { "application/json": { "schema": { - "title": "Response Edit Cohort Table Year Cohort Cohort Id Put", + "title": "Response Predicates Graph Schema Get", "type": "object" } - }, - "text/tabular": {} - }, - "description": "Return the tabular output." - }, - "422": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/HTTPValidationError" - } } }, - "description": "Validation Error" + "description": "Successful Response" } }, - "summary": "Edit Cohort" + "summary": "Get one-hop connection types" } }, - "/{table}/{year}/cohort/{cohort_id}/feature_association": { - "post": { - "description": "Hypothesis-driven 2 x 2 feature associations.\n\nUsers select a predefined cohort and two feature variables, and the service\nreturns a 2 x 2 feature table with a correspondingChi Square statistic and\nP value.", - "operationId": "feature_association__table___year__cohort__cohort_id__feature_association_post", + "/simple_spec": { + "get": { + "description": "Returns a list of available predicates when choosing a single source or target curie. Calling this endpoint with no query parameters will return all possible hops for all types.", + "operationId": "simple_spec_simple_spec_get", "parameters": [ { - "in": "path", - "name": "table", - "required": true, + "in": "query", + "name": "source", + "required": false, "schema": { - "title": "Table", + "title": "Source", "type": "string" } }, { - "in": "path", - "name": "year", - "required": true, - "schema": { - "title": "Year", - "type": "integer" - } - }, - { - "in": "path", - "name": "cohort_id", - "required": true, + "in": "query", + "name": "target", + "required": false, "schema": { - "title": "Cohort Id", + "title": "Target", "type": "string" } } ], - "requestBody": { - "content": { - "application/json": { - "schema": { - "allOf": [ - { - "$ref": "#/components/schemas/FeatureAssociation" - } - ], - "example": { - "feature_a": { - "Sex": { - "operator": "=", - "value": "Female" - } - }, - "feature_b": { - "AsthmaDx": { - "operator": "=", - "value": 1 - } - } - }, - "title": "Obj" - } - } - }, - "required": true - }, "responses": { "200": { "content": { "application/json": { "schema": { - "title": "Response Feature Association Table Year Cohort Cohort Id Feature Association Post", - "type": "object" + "items": { + "$ref": "#/components/schemas/SimpleSpecElement" + }, + "title": "Response Simple Spec Simple Spec Get", + "type": "array" } - }, - "text/tabular": {} + } }, - "description": "Return the tabular output." + "description": "Successful Response" }, "422": { "content": { @@ -8300,78 +8427,259 @@ "description": "Validation Error" } }, - "summary": "Feature Association" + "summary": "Get one-hop connection schema" } }, - "/{table}/{year}/cohort/{cohort_id}/feature_association2": { - "post": { - "description": "Hypothesis-driven N x N feature associations.\n\nUsers select a predefined cohort, two feature variables, and bins, which\ncan be combined, and the service returns a N x N feature table with a\ncorresponding Chi Square statistic and P value.", - "operationId": "feature_association2__table___year__cohort__cohort_id__feature_association2_post", - "parameters": [ - { - "in": "path", - "name": "table", - "required": true, - "schema": { - "title": "Table", - "type": "string" - } - }, - { - "in": "path", - "name": "year", - "required": true, - "schema": { - "title": "Year", - "type": "integer" - } - }, - { - "in": "path", - "name": "cohort_id", - "required": true, - "schema": { - "title": "Cohort Id", - "type": "string" - } + "/graph/summary": { + "get": { + "description": "Returns a summary of the graph.", + "operationId": "graph_summary_graph_summary_get", + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "title": "Response Graph Summary Graph Summary Get", + "type": "object" + } + } + }, + "description": "Successful Response" } - ], + }, + "summary": "Get graph summary" + } + }, + "/overlay": { + "post": { + "description": "Given a ReasonerAPI graph, add support edges for any nodes linked in result bindings.", + "operationId": "overlay_overlay_post", "requestBody": { "content": { "application/json": { "schema": { "allOf": [ { - "$ref": "#/components/schemas/FeatureAssociation2" + "$ref": "#/components/schemas/Query" } ], "example": { - "feature_a": { - "Sex": [ - { - "operator": "=", - "value": "Female" + "message": { + "knowledge_graph": { + "edges": { + "9f7f9d86cb57e7190aafa57f7564eb05": { + "attributes": [ + { + "type": "WIKIDATA:Q80585", + "value": { + "ctime": 1610437123.7988985, + "predicate": "biolink:part_of", + "provided_by": "panther.get_gene_family_by_gene_family", + "publications": [], + "relation": "BFO:0000050", + "relation_label": "part of", + "source_database": "panther", + "source_id": "PANTHER.FAMILY:PTHR12015:SF170", + "target_id": "PANTHER.FAMILY:PTHR12015" + } + } + ], + "object": "PANTHER.FAMILY:PTHR12015", + "predicate": "biolink:part_of", + "subject": "PANTHER.FAMILY:PTHR12015:SF170" + }, + "dd8ef7a4606c4f8e405e6a5b1b095993": { + "attributes": [ + { + "type": "WIKIDATA:Q80585", + "value": { + "ctime": 1584932086.0009434, + "predicate": "biolink:part_of", + "provided_by": "panther.get_gene_by_gene_family", + "publications": [], + "relation": "BFO:0000050", + "relation_label": "part of", + "source_database": "panther", + "source_id": "NCBIGene:6352", + "target_id": "PANTHER.FAMILY:PTHR12015" + } + } + ], + "object": "PANTHER.FAMILY:PTHR12015", + "predicate": "biolink:part_of", + "subject": "NCBIGene:6352" + } }, - { - "operator": "=", - "value": "Male" + "nodes": { + "NCBIGene:6352": { + "attributes": [ + { + "type": "WIKIDATA:Q80585", + "value": { + "category": [ + "biolink:BiologicalEntity", + "biolink:GenomicEntity", + "biolink:GeneOrGeneProduct", + "biolink:MacromolecularMachine", + "biolink:NamedThing", + "biolink:MolecularEntity", + "biolink:Gene" + ], + "chromosome": "17", + "equivalent_identifiers": [ + "ENSEMBL:ENSG00000271503", + "NCBIGene:6352", + "NCBIGene:6352", + "HGNC:10632", + "UniProtKB:P13501" + ], + "gene_family": [ + "Chemokine ligands" + ], + "gene_family_id": [ + 483 + ], + "location": "17q12", + "locus_group": "protein-coding gene", + "synonyms": [], + "taxon": 9606 + } + } + ], + "category": [ + "biolink:NamedThing", + "biolink:BiologicalEntity", + "biolink:MolecularEntity", + "biolink:GenomicEntity", + "biolink:GeneOrGeneProduct", + "biolink:MacromolecularMachine", + "biolink:Gene" + ], + "name": "CCL5" + }, + "PANTHER.FAMILY:PTHR12015": { + "attributes": [ + { + "type": "WIKIDATA:Q80585", + "value": { + "category": [ + "biolink:BiologicalEntity", + "biolink:GeneFamily", + "biolink:NamedThing", + "biolink:MolecularEntity", + "biolink:Entity" + ], + "equivalent_identifiers": [ + "PANTHER.FAMILY:PTHR12015" + ], + "synonyms": [] + } + } + ], + "category": [ + "biolink:NamedThing", + "biolink:BiologicalEntity", + "biolink:GeneFamily", + "biolink:MolecularEntity", + "biolink:Entity" + ], + "name": "SMALL INDUCIBLE CYTOKINE A" + }, + "PANTHER.FAMILY:PTHR12015:SF170": { + "attributes": [ + { + "type": "WIKIDATA:Q80585", + "value": { + "category": [ + "biolink:BiologicalEntity", + "biolink:GeneFamily", + "biolink:NamedThing", + "biolink:MolecularEntity", + "biolink:Entity" + ], + "equivalent_identifiers": [ + "PANTHER.FAMILY:PTHR12015:SF170" + ], + "synonyms": [] + } + } + ], + "category": [ + "biolink:NamedThing", + "biolink:BiologicalEntity", + "biolink:GeneFamily", + "biolink:MolecularEntity", + "biolink:Entity" + ], + "name": "C-C MOTIF CHEMOKINE 5" + } } - ] - }, - "feature_b": { - "AsthmaDx": [ - { - "operator": "=", - "value": 1 + }, + "query_graph": { + "edges": { + "e12": { + "object": "n2", + "predicate": "biolink:part_of", + "subject": "n1" + }, + "e23": { + "object": "n2", + "predicate": "biolink:part_of", + "subject": "n3" + } }, + "nodes": { + "n1": { + "category": "biolink:Gene", + "id": "NCBIGene:6352", + "is_set": false + }, + "n2": { + "category": "biolink:GeneFamily", + "is_set": false + }, + "n3": { + "category": "biolink:GeneFamily", + "is_set": false + } + } + }, + "results": [ { - "operator": "=", - "value": 0 + "edge_bindings": { + "e12": [ + { + "id": "dd8ef7a4606c4f8e405e6a5b1b095993" + } + ], + "e23": [ + { + "id": "9f7f9d86cb57e7190aafa57f7564eb05" + } + ] + }, + "node_bindings": { + "n1": [ + { + "id": "NCBIGene:6352" + } + ], + "n2": [ + { + "id": "PANTHER.FAMILY:PTHR12015" + } + ], + "n3": [ + { + "id": "PANTHER.FAMILY:PTHR12015:SF170" + } + ] + } } ] } }, - "title": "Obj" + "title": "Request" } } }, @@ -8382,13 +8690,11 @@ "content": { "application/json": { "schema": { - "title": "Response Feature Association2 Table Year Cohort Cohort Id Feature Association2 Post", - "type": "object" + "$ref": "#/components/schemas/Message" } - }, - "text/tabular": {} + } }, - "description": "Return the tabular output." + "description": "Successful Response" }, "422": { "content": { @@ -8401,174 +8707,76 @@ "description": "Validation Error" } }, - "summary": "Feature Association2" + "summary": "Overlay results with available connections between each node.", + "tags": [ + "translator" + ] } }, - "/{table}/{year}/cohort/{cohort_id}/associations_to_all_features": { - "post": { - "description": "Exploratory 1 X N feature associations.\n\nUsers select a predefined cohort and a feature variable of interest, and\nthe service returns a 1 x N feature table with corrected Chi Square\nstatistics and associated P values.", - "operationId": "associations_to_all_features__table___year__cohort__cohort_id__associations_to_all_features_post", + "/about": { + "get": { + "description": "Returns a JSON describing dataset.", + "operationId": "about_about_get", + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "title": "Response About About Get" + } + } + }, + "description": "Successful Response" + } + }, + "summary": "JSON about dataset" + } + }, + "/{source_type}/{target_type}/{curie}": { + "get": { + "description": "Returns one hop paths from `source_node_type` with `curie` to `target_node_type`.", + "operationId": "one_hop__source_type___target_type___curie__get", "parameters": [ { "in": "path", - "name": "table", + "name": "source_type", "required": true, "schema": { - "title": "Table", + "title": "Source Type", "type": "string" } }, { "in": "path", - "name": "year", + "name": "target_type", "required": true, "schema": { - "title": "Year", - "type": "integer" + "title": "Target Type", + "type": "string" } }, { "in": "path", - "name": "cohort_id", + "name": "curie", "required": true, "schema": { - "title": "Cohort Id", + "title": "Curie", "type": "string" } } ], - "requestBody": { - "content": { - "application/json": { - "schema": { - "allOf": [ - { - "$ref": "#/components/schemas/AllFeaturesAssociation" - } - ], - "example": { - "correction": { - "method": "bonferroni" - }, - "feature": { - "Sex": { - "operator": "=", - "value": "Female" - } - }, - "maximum_p_value": 1 - }, - "title": "Obj" - } - } - }, - "required": true - }, "responses": { "200": { "content": { "application/json": { "schema": { - "title": "Response Associations To All Features Table Year Cohort Cohort Id Associations To All Features Post", - "type": "object" - } - }, - "text/tabular": {} - }, - "description": "Return the tabular output." - }, - "422": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/HTTPValidationError" + "items": {}, + "title": "Response One Hop Source Type Target Type Curie Get", + "type": "array" } } }, - "description": "Validation Error" - } - }, - "summary": "Associations To All Features" - } - }, - "/{table}/{year}/cohort/{cohort_id}/associations_to_all_features2": { - "post": { - "description": "Exploratory 1 X N feature associations.\n\nUsers select a predefined cohort and a feature variable of interest and\nbins, which can be combined, and the service returns a 1 x N feature table\nwith corrected Chi Square statistics and associated P values.", - "operationId": "associations_to_all_features2__table___year__cohort__cohort_id__associations_to_all_features2_post", - "parameters": [ - { - "in": "path", - "name": "table", - "required": true, - "schema": { - "title": "Table", - "type": "string" - } - }, - { - "in": "path", - "name": "year", - "required": true, - "schema": { - "title": "Year", - "type": "integer" - } - }, - { - "in": "path", - "name": "cohort_id", - "required": true, - "schema": { - "title": "Cohort Id", - "type": "string" - } - } - ], - "requestBody": { - "content": { - "application/json": { - "schema": { - "allOf": [ - { - "$ref": "#/components/schemas/AllFeaturesAssociation2" - } - ], - "example": { - "correction": { - "method": "bonferroni" - }, - "feature": { - "Sex": [ - { - "operator": "=", - "value": "Female" - }, - { - "operator": "=", - "value": "Male" - } - ] - }, - "maximum_p_value": 1 - }, - "title": "Obj" - } - } - }, - "required": true - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "title": "Response Associations To All Features2 Table Year Cohort Cohort Id Associations To All Features2 Post", - "type": "object" - } - }, - "text/tabular": {} - }, - "description": "Return the tabular output." + "description": "Successful Response" }, "422": { "content": { @@ -8581,38 +8789,29 @@ "description": "Validation Error" } }, - "summary": "Associations To All Features2" + "summary": "Get one hop results from source type to target type. Note: Please GET /predicates to determine what target goes with a source" } }, - "/{table}/{year}/cohort/{cohort_id}/features": { + "/{node_type}/{curie}": { "get": { - "description": "Feature-rich cohort discovery.\n\nUsers select a predefined cohort as the input parameter, and the service\nreturns a profile of that cohort in terms of all feature variables.", - "operationId": "features__table___year__cohort__cohort_id__features_get", + "description": "Returns `node` matching `curie`.", + "operationId": "node__node_type___curie__get", "parameters": [ { "in": "path", - "name": "table", + "name": "node_type", "required": true, "schema": { - "title": "Table", + "title": "Node Type", "type": "string" } }, { "in": "path", - "name": "year", - "required": true, - "schema": { - "title": "Year", - "type": "integer" - } - }, - { - "in": "path", - "name": "cohort_id", + "name": "curie", "required": true, "schema": { - "title": "Cohort Id", + "title": "Curie", "type": "string" } } @@ -8622,13 +8821,13 @@ "content": { "application/json": { "schema": { - "title": "Response Features Table Year Cohort Cohort Id Features Get", - "type": "object" + "items": {}, + "title": "Response Node Node Type Curie Get", + "type": "array" } - }, - "text/tabular": {} + } }, - "description": "Return the tabular output." + "description": "Successful Response" }, "422": { "content": { @@ -8641,45 +8840,95 @@ "description": "Validation Error" } }, - "summary": "Features" + "summary": "Find `node` by `curie`" } + } + }, + "servers": [ + { + "description": "Default server", + "url": "https://automat.renci.org/cord19-scigraph" + } + ], + "tags": [ + { + "name": "translator" }, - "/{table}/{feature}/identifiers": { - "get": { - "description": "Feature identifiers.", - "operationId": "identifiers__table___feature__identifiers_get", - "parameters": [ - { - "in": "path", - "name": "table", - "required": true, - "schema": { - "title": "Table", - "type": "string" + { + "name": "automat" + } + ] + }, + { + "_id": "e4594ac1218186891fb2e48c63e182a3", + "_meta": { + "date_created": "2021-02-04T00:00:28.887481+00:00", + "last_updated": "2021-03-29T07:02:48.892566+00:00", + "url": "https://automat.renci.org/uberongraph/openapi.json", + "username": "YaphetKG" + }, + "_score": 0.6863549, + "info": { + "contact": { + "email": "kebedey@renci.org", + "name": "Yaphet Kebede", + "x-id": "https://github.com/yaphetkg", + "x-role": "contributor" + }, + "description": "A graph representation of Uberongraph, an integration of ontologies including GO, CHEBI, Uberon, and HPO.", + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Uberongraph&provider_long=RENCI", + "title": "Automat Uberongraph", + "version": "1.0.0", + "x-translator": { + "component": "KP", + "team": [ + "Ranking Agent" + ] + } + }, + "paths": { + "/query": { + "post": { + "description": "Given a question graph return question graph plus answers.", + "operationId": "reasoner_api_query_post", + "requestBody": { + "content": { + "application/json": { + "schema": { + "allOf": [ + { + "$ref": "#/components/schemas/Query" + } + ], + "example": { + "message": { + "query_graph": { + "edges": {}, + "nodes": { + "n0": { + "category": "biolink:Gene", + "id": "NCBIGene:15" + } + } + } + } + }, + "title": "Request" + } } }, - { - "in": "path", - "name": "feature", - "required": true, - "schema": { - "title": "Feature", - "type": "string" - } - } - ], + "required": true + }, "responses": { "200": { "content": { "application/json": { "schema": { - "title": "Response Identifiers Table Feature Identifiers Get", - "type": "object" + "$ref": "#/components/schemas/Query" } - }, - "text/tabular": {} + } }, - "description": "Return the tabular output." + "description": "Successful Response" }, "422": { "content": { @@ -8692,87 +8941,61 @@ "description": "Validation Error" } }, - "summary": "Identifiers" + "summary": "Query Reasoner API", + "tags": [ + "translator" + ] } }, - "/{table}/name/{name}": { + "/reasonerapi": { "get": { - "description": "Return cohort id associated with name.", - "operationId": "get_name__table__name__name__get", - "parameters": [ - { - "in": "path", - "name": "table", - "required": true, - "schema": { - "title": "Table", - "type": "string" - } - }, - { - "in": "path", - "name": "name", - "required": true, - "schema": { - "title": "Name", - "type": "string" - } - } - ], + "description": "Returns a list of question templates that can be used to query this plater instance.", + "operationId": "get_reasoner_api_reasonerapi_get", "responses": { "200": { "content": { "application/json": { "schema": { - "title": "Response Get Name Table Name Name Get", - "type": "object" - } - }, - "text/tabular": {} - }, - "description": "Return the tabular output." - }, - "422": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/HTTPValidationError" + "items": { + "$ref": "#/components/schemas/Message" + }, + "title": "Response Get Reasoner Api Reasonerapi Get", + "type": "array" } } }, - "description": "Validation Error" + "description": "Successful Response" } }, - "summary": "Get Name" + "summary": "Get question templates" }, "post": { - "description": "Associate name with cohort id.", - "operationId": "post_name__table__name__name__post", - "parameters": [ - { - "in": "path", - "name": "table", - "required": true, - "schema": { - "title": "Table", - "type": "string" - } - }, - { - "in": "path", - "name": "name", - "required": true, - "schema": { - "title": "Name", - "type": "string" - } - } - ], + "deprecated": true, + "description": "Handle TRAPI request.", + "operationId": "reasoner_api_reasonerapi_post", "requestBody": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/AddNameById" + "allOf": [ + { + "$ref": "#/components/schemas/Query" + } + ], + "example": { + "message": { + "query_graph": { + "edges": {}, + "nodes": { + "n0": { + "category": "biolink:Gene", + "id": "NCBIGene:15" + } + } + } + } + }, + "title": "Request" } } }, @@ -8783,13 +9006,11 @@ "content": { "application/json": { "schema": { - "title": "Response Post Name Table Name Name Post", - "type": "object" + "$ref": "#/components/schemas/Query" } - }, - "text/tabular": {} + } }, - "description": "Return the tabular output." + "description": "Successful Response" }, "422": { "content": { @@ -8802,73 +9023,26 @@ "description": "Validation Error" } }, - "summary": "Post Name" + "summary": "Reasoner Api" } }, - "/knowledge_graph": { + "/cypher": { "post": { - "description": "Query for knowledge graph associations between concepts.", - "operationId": "knowledge_graph_knowledge_graph_post", - "parameters": [ - { - "in": "query", - "name": "reasoner", - "required": false, - "schema": { - "default": false, - "title": "Reasoner", - "type": "boolean" - } - } - ], + "description": "Runs cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/).", + "operationId": "cypher_cypher_post", "requestBody": { "content": { "application/json": { "schema": { "allOf": [ { - "$ref": "#/components/schemas/Query" + "$ref": "#/components/schemas/CypherRequest" } ], "example": { - "message": { - "query_graph": { - "edges": { - "e00": { - "object": "n01", - "predicate": "biolink:correlated_with", - "subject": "n00" - } - }, - "nodes": { - "n00": { - "category": "biolink:PopulationOfIndividualOrganisms" - }, - "n01": { - "category": "biolink:ChemicalSubstance" - } - } - } - }, - "query_options": { - "cohort_features": { - "AgeStudyStart": { - "operator": "=", - "value": "0-2" - } - }, - "feature": { - "EstResidentialDensity": { - "operator": "<", - "value": 1 - } - }, - "maximum_p_value": 1, - "table": "patient", - "year": 2010 - } + "query": "MATCH (n) RETURN count(n)" }, - "title": "Obj" + "title": "Request" } } }, @@ -8879,13 +9053,11 @@ "content": { "application/json": { "schema": { - "title": "Response Knowledge Graph Knowledge Graph Post", - "type": "object" + "$ref": "#/components/schemas/CypherResponse" } - }, - "text/tabular": {} + } }, - "description": "Return the tabular output." + "description": "Successful Response" }, "422": { "content": { @@ -8898,116 +9070,100 @@ "description": "Validation Error" } }, - "summary": "Knowledge Graph" + "summary": "Run cypher query" } }, - "/knowledge_graph/schema": { + "/predicates": { "get": { - "description": "Query the ICEES clinical reasoner for knowledge graph schema.", - "operationId": "knowledge_graph_schema_knowledge_graph_schema_get", - "parameters": [ - { - "in": "query", - "name": "reasoner", - "required": false, - "schema": { - "default": false, - "title": "Reasoner", - "type": "boolean" - } - } - ], + "description": "Returns an object where outer keys represent source types with second level keys as targets. And the values of the second level keys is the type of possible edge typesthat connect these concepts.", + "operationId": "predicates_predicates_get", "responses": { "200": { "content": { "application/json": { "schema": { - "title": "Response Knowledge Graph Schema Knowledge Graph Schema Get", + "additionalProperties": { + "additionalProperties": { + "items": { + "type": "string" + }, + "type": "array" + }, + "type": "object" + }, + "title": "Response Predicates Predicates Get", "type": "object" } - }, - "text/tabular": {} + } }, - "description": "Return the tabular output." - }, - "422": { + "description": "Successful Response" + } + }, + "summary": "Get one-hop connection types", + "tags": [ + "translator" + ] + } + }, + "/graph/schema": { + "get": { + "deprecated": true, + "description": "Get one-hop connection types", + "operationId": "predicates_graph_schema_get", + "responses": { + "200": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/HTTPValidationError" + "title": "Response Predicates Graph Schema Get", + "type": "object" } } }, - "description": "Validation Error" + "description": "Successful Response" } }, - "summary": "Knowledge Graph Schema" + "summary": "Get one-hop connection types" } }, - "/knowledge_graph_overlay": { - "post": { - "description": "Query for knowledge graph co-occurrence overlay.", - "operationId": "knowledge_graph_overlay_knowledge_graph_overlay_post", + "/simple_spec": { + "get": { + "description": "Returns a list of available predicates when choosing a single source or target curie. Calling this endpoint with no query parameters will return all possible hops for all types.", + "operationId": "simple_spec_simple_spec_get", "parameters": [ { "in": "query", - "name": "reasoner", + "name": "source", "required": false, "schema": { - "default": false, - "title": "Reasoner", - "type": "boolean" - } - } - ], - "requestBody": { - "content": { - "application/json": { - "schema": { - "allOf": [ - { - "$ref": "#/components/schemas/Query" - } - ], - "example": { - "message": { - "knowledge_graph": { - "edges": { - "e00": { - "object": "PUBCHEM:281", - "predicate": "biolink:correlated_with", - "subject": "PUBCHEM:2083" - } - }, - "nodes": { - "PUBCHEM:2083": { - "category": "biolink:Drug" - }, - "PUBCHEM:281": { - "category": "biolink:ChemicalSubstance" - } - } - } - } - }, - "title": "Obj" - } + "title": "Source", + "type": "string" } }, - "required": true - }, + { + "in": "query", + "name": "target", + "required": false, + "schema": { + "title": "Target", + "type": "string" + } + } + ], "responses": { "200": { "content": { "application/json": { "schema": { - "title": "Response Knowledge Graph Overlay Knowledge Graph Overlay Post", - "type": "object" + "items": { + "$ref": "#/components/schemas/SimpleSpecElement" + }, + "title": "Response Simple Spec Simple Spec Get", + "type": "array" } - }, - "text/tabular": {} + } }, - "description": "Return the tabular output." + "description": "Successful Response" }, "422": { "content": { @@ -9020,26 +9176,33 @@ "description": "Validation Error" } }, - "summary": "Knowledge Graph Overlay" + "summary": "Get one-hop connection schema" } }, - "/knowledge_graph_one_hop": { - "post": { - "deprecated": true, - "description": "Query the ICEES clinical reasoner for knowledge graph one hop.", - "operationId": "knowledge_graph_one_hop_knowledge_graph_one_hop_post", - "parameters": [ - { - "in": "query", - "name": "reasoner", - "required": false, - "schema": { - "default": false, - "title": "Reasoner", - "type": "boolean" - } + "/graph/summary": { + "get": { + "description": "Returns a summary of the graph.", + "operationId": "graph_summary_graph_summary_get", + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "title": "Response Graph Summary Graph Summary Get", + "type": "object" + } + } + }, + "description": "Successful Response" } - ], + }, + "summary": "Get graph summary" + } + }, + "/overlay": { + "post": { + "description": "Given a ReasonerAPI graph, add support edges for any nodes linked in result bindings.", + "operationId": "overlay_overlay_post", "requestBody": { "content": { "application/json": { @@ -9052,31 +9215,220 @@ "example": { "message": { "knowledge_graph": { - "edges": {}, - "nodes": {} + "edges": { + "9f7f9d86cb57e7190aafa57f7564eb05": { + "attributes": [ + { + "type": "WIKIDATA:Q80585", + "value": { + "ctime": 1610437123.7988985, + "predicate": "biolink:part_of", + "provided_by": "panther.get_gene_family_by_gene_family", + "publications": [], + "relation": "BFO:0000050", + "relation_label": "part of", + "source_database": "panther", + "source_id": "PANTHER.FAMILY:PTHR12015:SF170", + "target_id": "PANTHER.FAMILY:PTHR12015" + } + } + ], + "object": "PANTHER.FAMILY:PTHR12015", + "predicate": "biolink:part_of", + "subject": "PANTHER.FAMILY:PTHR12015:SF170" + }, + "dd8ef7a4606c4f8e405e6a5b1b095993": { + "attributes": [ + { + "type": "WIKIDATA:Q80585", + "value": { + "ctime": 1584932086.0009434, + "predicate": "biolink:part_of", + "provided_by": "panther.get_gene_by_gene_family", + "publications": [], + "relation": "BFO:0000050", + "relation_label": "part of", + "source_database": "panther", + "source_id": "NCBIGene:6352", + "target_id": "PANTHER.FAMILY:PTHR12015" + } + } + ], + "object": "PANTHER.FAMILY:PTHR12015", + "predicate": "biolink:part_of", + "subject": "NCBIGene:6352" + } + }, + "nodes": { + "NCBIGene:6352": { + "attributes": [ + { + "type": "WIKIDATA:Q80585", + "value": { + "category": [ + "biolink:BiologicalEntity", + "biolink:GenomicEntity", + "biolink:GeneOrGeneProduct", + "biolink:MacromolecularMachine", + "biolink:NamedThing", + "biolink:MolecularEntity", + "biolink:Gene" + ], + "chromosome": "17", + "equivalent_identifiers": [ + "ENSEMBL:ENSG00000271503", + "NCBIGene:6352", + "NCBIGene:6352", + "HGNC:10632", + "UniProtKB:P13501" + ], + "gene_family": [ + "Chemokine ligands" + ], + "gene_family_id": [ + 483 + ], + "location": "17q12", + "locus_group": "protein-coding gene", + "synonyms": [], + "taxon": 9606 + } + } + ], + "category": [ + "biolink:NamedThing", + "biolink:BiologicalEntity", + "biolink:MolecularEntity", + "biolink:GenomicEntity", + "biolink:GeneOrGeneProduct", + "biolink:MacromolecularMachine", + "biolink:Gene" + ], + "name": "CCL5" + }, + "PANTHER.FAMILY:PTHR12015": { + "attributes": [ + { + "type": "WIKIDATA:Q80585", + "value": { + "category": [ + "biolink:BiologicalEntity", + "biolink:GeneFamily", + "biolink:NamedThing", + "biolink:MolecularEntity", + "biolink:Entity" + ], + "equivalent_identifiers": [ + "PANTHER.FAMILY:PTHR12015" + ], + "synonyms": [] + } + } + ], + "category": [ + "biolink:NamedThing", + "biolink:BiologicalEntity", + "biolink:GeneFamily", + "biolink:MolecularEntity", + "biolink:Entity" + ], + "name": "SMALL INDUCIBLE CYTOKINE A" + }, + "PANTHER.FAMILY:PTHR12015:SF170": { + "attributes": [ + { + "type": "WIKIDATA:Q80585", + "value": { + "category": [ + "biolink:BiologicalEntity", + "biolink:GeneFamily", + "biolink:NamedThing", + "biolink:MolecularEntity", + "biolink:Entity" + ], + "equivalent_identifiers": [ + "PANTHER.FAMILY:PTHR12015:SF170" + ], + "synonyms": [] + } + } + ], + "category": [ + "biolink:NamedThing", + "biolink:BiologicalEntity", + "biolink:GeneFamily", + "biolink:MolecularEntity", + "biolink:Entity" + ], + "name": "C-C MOTIF CHEMOKINE 5" + } + } }, "query_graph": { "edges": { - "e00": { - "object": "n01", - "predicate": "biolink:correlated_with", - "subject": "n00" + "e12": { + "object": "n2", + "predicate": "biolink:part_of", + "subject": "n1" + }, + "e23": { + "object": "n2", + "predicate": "biolink:part_of", + "subject": "n3" } }, "nodes": { - "n00": { - "category": "biolink:Drug", - "id": "PUBCHEM:2083" + "n1": { + "category": "biolink:Gene", + "id": "NCBIGene:6352", + "is_set": false }, - "n01": { - "category": "biolink:ChemicalSubstance" + "n2": { + "category": "biolink:GeneFamily", + "is_set": false + }, + "n3": { + "category": "biolink:GeneFamily", + "is_set": false } } }, - "results": [] + "results": [ + { + "edge_bindings": { + "e12": [ + { + "id": "dd8ef7a4606c4f8e405e6a5b1b095993" + } + ], + "e23": [ + { + "id": "9f7f9d86cb57e7190aafa57f7564eb05" + } + ] + }, + "node_bindings": { + "n1": [ + { + "id": "NCBIGene:6352" + } + ], + "n2": [ + { + "id": "PANTHER.FAMILY:PTHR12015" + } + ], + "n3": [ + { + "id": "PANTHER.FAMILY:PTHR12015:SF170" + } + ] + } + } + ] } }, - "title": "Obj" + "title": "Request" } } }, @@ -9087,13 +9439,11 @@ "content": { "application/json": { "schema": { - "title": "Response Knowledge Graph One Hop Knowledge Graph One Hop Post", - "type": "object" + "$ref": "#/components/schemas/Message" } - }, - "text/tabular": {} + } }, - "description": "Return the tabular output." + "description": "Successful Response" }, "422": { "content": { @@ -9106,79 +9456,76 @@ "description": "Validation Error" } }, - "summary": "Knowledge Graph One Hop" + "summary": "Overlay results with available connections between each node.", + "tags": [ + "translator" + ] } }, - "/query": { - "post": { - "description": "Query the ICEES clinical reasoner for knowledge graph one hop.", - "operationId": "knowledge_graph_one_hop_query_post", + "/about": { + "get": { + "description": "Returns a JSON describing dataset.", + "operationId": "about_about_get", + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "title": "Response About About Get" + } + } + }, + "description": "Successful Response" + } + }, + "summary": "JSON about dataset" + } + }, + "/{source_type}/{target_type}/{curie}": { + "get": { + "description": "Returns one hop paths from `source_node_type` with `curie` to `target_node_type`.", + "operationId": "one_hop__source_type___target_type___curie__get", "parameters": [ { - "in": "query", - "name": "reasoner", - "required": false, + "in": "path", + "name": "source_type", + "required": true, "schema": { - "default": false, - "title": "Reasoner", - "type": "boolean" + "title": "Source Type", + "type": "string" } - } - ], - "requestBody": { - "content": { - "application/json": { - "schema": { - "allOf": [ - { - "$ref": "#/components/schemas/Query" - } - ], - "example": { - "message": { - "knowledge_graph": { - "edges": {}, - "nodes": {} - }, - "query_graph": { - "edges": { - "e00": { - "object": "n01", - "predicate": "biolink:correlated_with", - "subject": "n00" - } - }, - "nodes": { - "n00": { - "category": "biolink:Drug", - "id": "PUBCHEM:2083" - }, - "n01": { - "category": "biolink:ChemicalSubstance" - } - } - }, - "results": [] - } - }, - "title": "Obj" - } + }, + { + "in": "path", + "name": "target_type", + "required": true, + "schema": { + "title": "Target Type", + "type": "string" } }, - "required": true - }, + { + "in": "path", + "name": "curie", + "required": true, + "schema": { + "title": "Curie", + "type": "string" + } + } + ], "responses": { "200": { "content": { "application/json": { "schema": { - "title": "Response Knowledge Graph One Hop Query Post", - "type": "object" + "items": {}, + "title": "Response One Hop Source Type Target Type Curie Get", + "type": "array" } - }, - "text/tabular": {} + } }, - "description": "Return the tabular output." + "description": "Successful Response" }, "422": { "content": { @@ -9191,41 +9538,29 @@ "description": "Validation Error" } }, - "summary": "Knowledge Graph One Hop", - "tags": [ - "reasoner" - ] + "summary": "Get one hop results from source type to target type. Note: Please GET /predicates to determine what target goes with a source" } }, - "/bins": { + "/{node_type}/{curie}": { "get": { - "description": "Return bin values.", - "operationId": "handle_bins_bins_get", + "description": "Returns `node` matching `curie`.", + "operationId": "node__node_type___curie__get", "parameters": [ { - "in": "query", - "name": "year", - "required": false, - "schema": { - "title": "Year", - "type": "string" - } - }, - { - "in": "query", - "name": "table", - "required": false, + "in": "path", + "name": "node_type", + "required": true, "schema": { - "title": "Table", + "title": "Node Type", "type": "string" } }, { - "in": "query", - "name": "feature", - "required": false, + "in": "path", + "name": "curie", + "required": true, "schema": { - "title": "Feature", + "title": "Curie", "type": "string" } } @@ -9235,13 +9570,13 @@ "content": { "application/json": { "schema": { - "title": "Response Handle Bins Bins Get", - "type": "object" + "items": {}, + "title": "Response Node Node Type Curie Get", + "type": "array" } - }, - "text/tabular": {} + } }, - "description": "Return the tabular output." + "description": "Successful Response" }, "422": { "content": { @@ -9254,13 +9589,14 @@ "description": "Validation Error" } }, - "summary": "Handle Bins" + "summary": "Find `node` by `curie`" } } }, "servers": [ { - "url": "https://icees.renci.org:16340" + "description": "Default server", + "url": "https://automat.renci.org/uberongraph" } ], "tags": [ @@ -9268,19 +9604,19 @@ "name": "translator" }, { - "name": "reasoner" + "name": "automat" } ] }, { - "_id": "7c481f0761132876e6b953547623f594", + "_id": "ed85eff6809e354002cbf17231918a89", "_meta": { - "date_created": "2021-01-26T00:03:04.513280+00:00", - "last_updated": "2021-03-05T08:01:45.835325+00:00", - "url": "https://automat.renci.org/pharos/openapi.json", + "date_created": "2021-02-03T00:01:02.336283+00:00", + "last_updated": "2021-03-29T07:02:22.560964+00:00", + "url": "https://automat.renci.org/biolink/openapi.json", "username": "YaphetKG" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { "email": "kebedey@renci.org", @@ -9288,9 +9624,9 @@ "x-id": "https://github.com/yaphetkg", "x-role": "contributor" }, - "description": "A graph based on [Pharos (pharos.nih.gov)](pharos.nih.gov).", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat%20Panther&provider_long=RENCI", - "title": "Automat Pharos", + "description": "A graph based on the [Monarch API (https://api.monarchinitiative.org/)](https://api.monarchinitiative.org/).", + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Biolink&provider_long=RENCI", + "title": "Automat Biolink", "version": "1.0.0", "x-translator": { "component": "KP", @@ -10009,7 +10345,7 @@ "servers": [ { "description": "Default server", - "url": "https://automat.renci.org/pharos" + "url": "https://automat.renci.org/biolink" } ], "tags": [ @@ -10017,19 +10353,19 @@ "name": "translator" }, { - "name": "automat" + "name": "Automat" } ] }, { - "_id": "523a1ce8b6d4fc9a1d0f9f22321f4c4c", + "_id": "49015a5444165956a9e45655dc1ea389", "_meta": { - "date_created": "2021-02-03T00:00:48.628394+00:00", - "last_updated": "2021-03-05T08:01:53.593235+00:00", - "url": "https://automat.renci.org/gtopdb/openapi.json", + "date_created": "2021-01-26T00:04:34.149152+00:00", + "last_updated": "2021-03-29T07:02:40.542987+00:00", + "url": "https://automat.renci.org/human-goa/openapi.json", "username": "YaphetKG" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { "email": "kebedey@renci.org", @@ -10037,9 +10373,9 @@ "x-id": "https://github.com/yaphetkg", "x-role": "contributor" }, - "description": "A graph based on the [IUPHAR Guide to Pharmacology (https://www.guidetopharmacology.org/)](https://www.guidetopharmacology.org/)", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Gtopdb&provider_long=RENCI", - "title": "Automat Gtopdb", + "description": " Human Gene Ontology Annotations from the GO consortium.", + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Human GOA&provider_long=RENCI", + "title": "Automat Human GOA", "version": "1.0.0", "x-translator": { "component": "KP", @@ -10758,7 +11094,7 @@ "servers": [ { "description": "Default server", - "url": "https://automat.renci.org/gtopdb" + "url": "https://automat.renci.org/human-goa" } ], "tags": [ @@ -10771,14 +11107,14 @@ ] }, { - "_id": "1c0aff2a70b1ed677867c0db8011746f", + "_id": "b4b45614a935a575292aad3bb726d1f3", "_meta": { - "date_created": "2021-02-03T16:03:16.375825+00:00", - "last_updated": "2021-03-05T08:01:43.934872+00:00", - "url": "https://automat.renci.org/ontological-hierarchy/openapi.json", + "date_created": "2021-02-04T00:01:49.121558+00:00", + "last_updated": "2021-03-29T07:02:23.101235+00:00", + "url": "https://automat.renci.org/hgnc/openapi.json", "username": "YaphetKG" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { "email": "kebedey@renci.org", @@ -10786,9 +11122,9 @@ "x-id": "https://github.com/yaphetkg", "x-role": "contributor" }, - "description": "A graph for ontological hierarchy extracted from Uberongraph.", + "description": "Gene families from [HGNC (genenames.org)](genenames.org).", "termsOfService": "http://linkmissing", - "title": "Automat Ontological Hierarchy", + "title": "Automat HGNC", "version": "1.0.0", "x-translator": { "component": "KP", @@ -11507,7 +11843,7 @@ "servers": [ { "description": "Default server", - "url": "https://automat.renci.org/ontological-hierarchy" + "url": "https://automat.renci.org/hgnc" } ], "tags": [ @@ -11515,19 +11851,19 @@ "name": "translator" }, { - "name": "Automat" + "name": "automat" } ] }, { - "_id": "786e41a17dbb75399f22e09858f828b7", + "_id": "3e74f67bd571c74f1832829a5b5a40eb", "_meta": { - "date_created": "2021-01-26T00:02:48.347118+00:00", - "last_updated": "2021-03-05T08:01:56.897130+00:00", - "url": "https://automat.renci.org/chembio/openapi.json", + "date_created": "2021-02-01T00:07:19.265482+00:00", + "last_updated": "2021-03-29T07:02:56.123973+00:00", + "url": "https://automat.renci.org/ctd/openapi.json", "username": "YaphetKG" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { "email": "kebedey@renci.org", @@ -11535,9 +11871,9 @@ "x-id": "https://github.com/yaphetkg", "x-role": "contributor" }, - "description": "A graph based on [chem2bio2rdf (http://cheminfov.informatics.indiana.edu:8080/c2b2r/)](http://cheminfov.informatics.indiana.edu:8080/c2b2r/).", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat%20Chembio&provider_long=RENCI", - "title": "Automat Chembio", + "description": "A graph based on the [Comparative Toxicogenomics Database (ctdbase.org)](ctdbase.org).", + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat CTD&provider_long=RENCI", + "title": "Automat CTD", "version": "1.0.0", "x-translator": { "component": "KP", @@ -12256,7 +12592,7 @@ "servers": [ { "description": "Default server", - "url": "https://automat.renci.org/chembio" + "url": "https://automat.renci.org/ctd" } ], "tags": [ @@ -12269,14 +12605,14 @@ ] }, { - "_id": "a49ee52f6fb81a71cca84e9806732b76", + "_id": "3f3c925151f42aac9a5aca7a7eabe814", "_meta": { - "date_created": "2021-01-26T00:02:43.141214+00:00", - "last_updated": "2021-03-05T08:01:57.486090+00:00", - "url": "https://automat.renci.org/foodb/openapi.json", + "date_created": "2021-02-03T00:04:18.945970+00:00", + "last_updated": "2021-03-29T07:02:49.455455+00:00", + "url": "https://automat.renci.org/mychem/openapi.json", "username": "YaphetKG" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { "email": "kebedey@renci.org", @@ -12284,9 +12620,9 @@ "x-id": "https://github.com/yaphetkg", "x-role": "contributor" }, - "description": "A graph of the food/chemical relationships in [foodb.ca](foodb.ca).", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat%20Foodb&provider_long=RENCI", - "title": "Automat Foodb", + "description": "A graph integrating DrugBank, DrugCentral, and Aeolus data as provided by [mychem.info](mychem.info).", + "termsOfService": "http://http://robokop.renci.org:7055/tos?service_long=Automat Mychem&provider_long=RENCI", + "title": "Automat MyChem", "version": "1.0.0", "x-translator": { "component": "KP", @@ -13005,7 +13341,7 @@ "servers": [ { "description": "Default server", - "url": "https://automat.renci.org/foodb" + "url": "https://automat.renci.org/mychem" } ], "tags": [ @@ -13018,14 +13354,14 @@ ] }, { - "_id": "0d3cb44c7d519f06c8a6a8dec43dbf05", + "_id": "51742c9f6ca40d46bdeb6facd76257ff", "_meta": { - "date_created": "2021-01-26T00:02:38.407228+00:00", - "last_updated": "2021-03-05T08:02:09.236344+00:00", - "url": "https://automat.renci.org/covid-phenotypes/openapi.json", + "date_created": "2021-02-03T00:02:35.479989+00:00", + "last_updated": "2021-03-29T07:03:21.190649+00:00", + "url": "https://automat.renci.org/hmdb/openapi.json", "username": "YaphetKG" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { "email": "kebedey@renci.org", @@ -13033,9 +13369,9 @@ "x-id": "https://github.com/yaphetkg", "x-role": "contributor" }, - "description": "A hand-curated graph of phenotypes of covid-19.", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat%20Covid%20Phenotypes&provider_long=RENCI", - "title": "Automat Covid Phenotypes", + "description": "A graph based on the [Human Metabolome DataBase (hmdb.org)](hmdb.org).", + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat HMDB&provider_long=RENCI", + "title": "Automat HMDB", "version": "1.0.0", "x-translator": { "component": "KP", @@ -13754,7 +14090,7 @@ "servers": [ { "description": "Default server", - "url": "https://automat.renci.org/covid-phenotypes" + "url": "https://automat.renci.org/hmdb" } ], "tags": [ @@ -13767,60 +14103,88 @@ ] }, { - "_id": "d9d71b3d55e767c37346d02b7d6bd0b3", + "_id": "cd79363c8f24935bc0fa0659bed8ff58", "_meta": { - "date_created": "2021-01-26T00:01:27.579000+00:00", - "last_updated": "2021-03-05T08:02:10.428414+00:00", - "url": "https://automat.renci.org/intact/openapi.json", - "username": "YaphetKG" + "date_created": "2021-02-25T18:44:45.303276+00:00", + "last_updated": "2021-03-29T07:03:19.540529+00:00", + "slug": "icees", + "url": "https://icees.renci.org:16340/openapi.json", + "username": "patrickkwang" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { - "email": "kebedey@renci.org", - "name": "Yaphet Kebede", - "x-id": "https://github.com/yaphetkg", - "x-role": "contributor" + "email": "patrick@covar.com", + "name": "Patrick Wang", + "x-id": "https://github.com/patrickkwang", + "x-role": "responsible developer" }, - "description": "Molecular (Gene-Gene) interactions from [EBI IntAct (https://www.ebi.ac.uk/intact/)](https://www.ebi.ac.uk/intact/).", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat%20IntAct&provider_long=RENCI", - "title": "Automat IntAct", - "version": "1.0.0", + "description": "ICEES API \n
[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
", + "termsOfService": "N/A", + "title": "ICEES API", + "version": "4.0.0", "x-translator": { "component": "KP", "team": [ - "Ranking Agent" + "Exposures Provider" ] } }, "paths": { - "/query": { + "/{table}/{year}/cohort": { "post": { - "description": "Given a question graph return question graph plus answers.", - "operationId": "reasoner_api_query_post", + "description": "Cohort discovery.", + "operationId": "discover_cohort__table___year__cohort_post", + "parameters": [ + { + "in": "path", + "name": "table", + "required": true, + "schema": { + "title": "Table", + "type": "string" + } + }, + { + "in": "path", + "name": "year", + "required": true, + "schema": { + "title": "Year", + "type": "integer" + } + } + ], "requestBody": { "content": { "application/json": { "schema": { - "allOf": [ + "anyOf": [ { - "$ref": "#/components/schemas/Query" - } - ], - "example": { - "message": { - "query_graph": { - "edges": {}, - "nodes": { - "n0": { - "category": "biolink:Gene", - "id": "NCBIGene:15" + "additionalProperties": { + "anyOf": [ + { + "$ref": "#/components/schemas/Comparison" + }, + { + "$ref": "#/components/schemas/Between" + }, + { + "$ref": "#/components/schemas/In" } - } - } + ] + }, + "type": "object" + }, + { + "items": { + "$ref": "#/components/schemas/FeatureExplicit" + }, + "type": "array" } - }, - "title": "Request" + ], + "example": {}, + "title": "Req Features" } } }, @@ -13831,11 +14195,13 @@ "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Query" + "title": "Response Discover Cohort Table Year Cohort Post", + "type": "object" } - } + }, + "text/tabular": {} }, - "description": "Successful Response" + "description": "Return the tabular output." }, "422": { "content": { @@ -13848,76 +14214,105 @@ "description": "Validation Error" } }, - "summary": "Query Reasoner API", - "tags": [ - "translator" - ] + "summary": "Discover Cohort" } }, - "/reasonerapi": { + "/{table}/{year}/cohort/dictionary": { "get": { - "description": "Returns a list of question templates that can be used to query this plater instance.", - "operationId": "get_reasoner_api_reasonerapi_get", + "description": "Get cohort dictionary.", + "operationId": "dictionary__table___year__cohort_dictionary_get", + "parameters": [ + { + "in": "path", + "name": "table", + "required": true, + "schema": { + "title": "Table", + "type": "string" + } + }, + { + "in": "path", + "name": "year", + "required": true, + "schema": { + "title": "Year", + "type": "integer" + } + } + ], "responses": { "200": { "content": { "application/json": { "schema": { - "items": { - "$ref": "#/components/schemas/Message" - }, - "title": "Response Get Reasoner Api Reasonerapi Get", - "type": "array" + "title": "Response Dictionary Table Year Cohort Dictionary Get", + "type": "object" + } + }, + "text/tabular": {} + }, + "description": "Return the tabular output." + }, + "422": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/HTTPValidationError" } } }, - "description": "Successful Response" + "description": "Validation Error" } }, - "summary": "Get question templates" - }, - "post": { - "deprecated": true, - "description": "Handle TRAPI request.", - "operationId": "reasoner_api_reasonerapi_post", - "requestBody": { - "content": { - "application/json": { - "schema": { - "allOf": [ - { - "$ref": "#/components/schemas/Query" - } - ], - "example": { - "message": { - "query_graph": { - "edges": {}, - "nodes": { - "n0": { - "category": "biolink:Gene", - "id": "NCBIGene:15" - } - } - } - } - }, - "title": "Request" - } + "summary": "Dictionary" + } + }, + "/{table}/{year}/cohort/{cohort_id}": { + "get": { + "description": "Get definition of a cohort.", + "operationId": "get_cohort__table___year__cohort__cohort_id__get", + "parameters": [ + { + "in": "path", + "name": "table", + "required": true, + "schema": { + "title": "Table", + "type": "string" } }, - "required": true - }, + { + "in": "path", + "name": "year", + "required": true, + "schema": { + "title": "Year", + "type": "integer" + } + }, + { + "in": "path", + "name": "cohort_id", + "required": true, + "schema": { + "title": "Cohort Id", + "type": "string" + } + } + ], "responses": { "200": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Query" + "title": "Response Get Cohort Table Year Cohort Cohort Id Get", + "type": "object" } - } + }, + "text/tabular": {} }, - "description": "Successful Response" + "description": "Return the tabular output." }, "422": { "content": { @@ -13930,26 +14325,70 @@ "description": "Validation Error" } }, - "summary": "Reasoner Api" - } - }, - "/cypher": { - "post": { - "description": "Runs cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/).", - "operationId": "cypher_cypher_post", + "summary": "Get Cohort" + }, + "put": { + "description": "Cohort discovery.", + "operationId": "edit_cohort__table___year__cohort__cohort_id__put", + "parameters": [ + { + "in": "path", + "name": "table", + "required": true, + "schema": { + "title": "Table", + "type": "string" + } + }, + { + "in": "path", + "name": "year", + "required": true, + "schema": { + "title": "Year", + "type": "integer" + } + }, + { + "in": "path", + "name": "cohort_id", + "required": true, + "schema": { + "title": "Cohort Id", + "type": "string" + } + } + ], "requestBody": { "content": { "application/json": { "schema": { - "allOf": [ + "anyOf": [ { - "$ref": "#/components/schemas/CypherRequest" + "additionalProperties": { + "anyOf": [ + { + "$ref": "#/components/schemas/Comparison" + }, + { + "$ref": "#/components/schemas/Between" + }, + { + "$ref": "#/components/schemas/In" + } + ] + }, + "type": "object" + }, + { + "items": { + "$ref": "#/components/schemas/FeatureExplicit" + }, + "type": "array" } ], - "example": { - "query": "MATCH (n) RETURN count(n)" - }, - "title": "Request" + "example": {}, + "title": "Req Features" } } }, @@ -13960,11 +14399,13 @@ "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/CypherResponse" + "title": "Response Edit Cohort Table Year Cohort Cohort Id Put", + "type": "object" } - } + }, + "text/tabular": {} }, - "description": "Successful Response" + "description": "Return the tabular output." }, "422": { "content": { @@ -13977,100 +14418,83 @@ "description": "Validation Error" } }, - "summary": "Run cypher query" - } - }, - "/predicates": { - "get": { - "description": "Returns an object where outer keys represent source types with second level keys as targets. And the values of the second level keys is the type of possible edge typesthat connect these concepts.", - "operationId": "predicates_predicates_get", - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "additionalProperties": { - "additionalProperties": { - "items": { - "type": "string" - }, - "type": "array" - }, - "type": "object" - }, - "title": "Response Predicates Predicates Get", - "type": "object" - } - } - }, - "description": "Successful Response" - } - }, - "summary": "Get one-hop connection types", - "tags": [ - "translator" - ] - } - }, - "/graph/schema": { - "get": { - "deprecated": true, - "description": "Get one-hop connection types", - "operationId": "predicates_graph_schema_get", - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "title": "Response Predicates Graph Schema Get", - "type": "object" - } - } - }, - "description": "Successful Response" - } - }, - "summary": "Get one-hop connection types" + "summary": "Edit Cohort" } }, - "/simple_spec": { - "get": { - "description": "Returns a list of available predicates when choosing a single source or target curie. Calling this endpoint with no query parameters will return all possible hops for all types.", - "operationId": "simple_spec_simple_spec_get", + "/{table}/{year}/cohort/{cohort_id}/feature_association": { + "post": { + "description": "Hypothesis-driven 2 x 2 feature associations.\n\nUsers select a predefined cohort and two feature variables, and the service\nreturns a 2 x 2 feature table with a correspondingChi Square statistic and\nP value.", + "operationId": "feature_association__table___year__cohort__cohort_id__feature_association_post", "parameters": [ { - "in": "query", - "name": "source", - "required": false, + "in": "path", + "name": "table", + "required": true, "schema": { - "title": "Source", + "title": "Table", "type": "string" } }, { - "in": "query", - "name": "target", - "required": false, + "in": "path", + "name": "year", + "required": true, "schema": { - "title": "Target", + "title": "Year", + "type": "integer" + } + }, + { + "in": "path", + "name": "cohort_id", + "required": true, + "schema": { + "title": "Cohort Id", "type": "string" } } ], + "requestBody": { + "content": { + "application/json": { + "schema": { + "allOf": [ + { + "$ref": "#/components/schemas/FeatureAssociation" + } + ], + "example": { + "feature_a": { + "Sex": { + "operator": "=", + "value": "Female" + } + }, + "feature_b": { + "AsthmaDx": { + "operator": "=", + "value": 1 + } + } + }, + "title": "Obj" + } + } + }, + "required": true + }, "responses": { "200": { "content": { "application/json": { "schema": { - "items": { - "$ref": "#/components/schemas/SimpleSpecElement" - }, - "title": "Response Simple Spec Simple Spec Get", - "type": "array" + "title": "Response Feature Association Table Year Cohort Cohort Id Feature Association Post", + "type": "object" } - } + }, + "text/tabular": {} }, - "description": "Successful Response" + "description": "Return the tabular output." }, "422": { "content": { @@ -14083,259 +14507,78 @@ "description": "Validation Error" } }, - "summary": "Get one-hop connection schema" + "summary": "Feature Association" } }, - "/graph/summary": { - "get": { - "description": "Returns a summary of the graph.", - "operationId": "graph_summary_graph_summary_get", - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "title": "Response Graph Summary Graph Summary Get", - "type": "object" - } - } - }, - "description": "Successful Response" - } - }, - "summary": "Get graph summary" - } - }, - "/overlay": { + "/{table}/{year}/cohort/{cohort_id}/feature_association2": { "post": { - "description": "Given a ReasonerAPI graph, add support edges for any nodes linked in result bindings.", - "operationId": "overlay_overlay_post", + "description": "Hypothesis-driven N x N feature associations.\n\nUsers select a predefined cohort, two feature variables, and bins, which\ncan be combined, and the service returns a N x N feature table with a\ncorresponding Chi Square statistic and P value.", + "operationId": "feature_association2__table___year__cohort__cohort_id__feature_association2_post", + "parameters": [ + { + "in": "path", + "name": "table", + "required": true, + "schema": { + "title": "Table", + "type": "string" + } + }, + { + "in": "path", + "name": "year", + "required": true, + "schema": { + "title": "Year", + "type": "integer" + } + }, + { + "in": "path", + "name": "cohort_id", + "required": true, + "schema": { + "title": "Cohort Id", + "type": "string" + } + } + ], "requestBody": { "content": { "application/json": { "schema": { "allOf": [ { - "$ref": "#/components/schemas/Query" + "$ref": "#/components/schemas/FeatureAssociation2" } ], "example": { - "message": { - "knowledge_graph": { - "edges": { - "9f7f9d86cb57e7190aafa57f7564eb05": { - "attributes": [ - { - "type": "WIKIDATA:Q80585", - "value": { - "ctime": 1610437123.7988985, - "predicate": "biolink:part_of", - "provided_by": "panther.get_gene_family_by_gene_family", - "publications": [], - "relation": "BFO:0000050", - "relation_label": "part of", - "source_database": "panther", - "source_id": "PANTHER.FAMILY:PTHR12015:SF170", - "target_id": "PANTHER.FAMILY:PTHR12015" - } - } - ], - "object": "PANTHER.FAMILY:PTHR12015", - "predicate": "biolink:part_of", - "subject": "PANTHER.FAMILY:PTHR12015:SF170" - }, - "dd8ef7a4606c4f8e405e6a5b1b095993": { - "attributes": [ - { - "type": "WIKIDATA:Q80585", - "value": { - "ctime": 1584932086.0009434, - "predicate": "biolink:part_of", - "provided_by": "panther.get_gene_by_gene_family", - "publications": [], - "relation": "BFO:0000050", - "relation_label": "part of", - "source_database": "panther", - "source_id": "NCBIGene:6352", - "target_id": "PANTHER.FAMILY:PTHR12015" - } - } - ], - "object": "PANTHER.FAMILY:PTHR12015", - "predicate": "biolink:part_of", - "subject": "NCBIGene:6352" - } + "feature_a": { + "Sex": [ + { + "operator": "=", + "value": "Female" }, - "nodes": { - "NCBIGene:6352": { - "attributes": [ - { - "type": "WIKIDATA:Q80585", - "value": { - "category": [ - "biolink:BiologicalEntity", - "biolink:GenomicEntity", - "biolink:GeneOrGeneProduct", - "biolink:MacromolecularMachine", - "biolink:NamedThing", - "biolink:MolecularEntity", - "biolink:Gene" - ], - "chromosome": "17", - "equivalent_identifiers": [ - "ENSEMBL:ENSG00000271503", - "NCBIGene:6352", - "NCBIGene:6352", - "HGNC:10632", - "UniProtKB:P13501" - ], - "gene_family": [ - "Chemokine ligands" - ], - "gene_family_id": [ - 483 - ], - "location": "17q12", - "locus_group": "protein-coding gene", - "synonyms": [], - "taxon": 9606 - } - } - ], - "category": [ - "biolink:NamedThing", - "biolink:BiologicalEntity", - "biolink:MolecularEntity", - "biolink:GenomicEntity", - "biolink:GeneOrGeneProduct", - "biolink:MacromolecularMachine", - "biolink:Gene" - ], - "name": "CCL5" - }, - "PANTHER.FAMILY:PTHR12015": { - "attributes": [ - { - "type": "WIKIDATA:Q80585", - "value": { - "category": [ - "biolink:BiologicalEntity", - "biolink:GeneFamily", - "biolink:NamedThing", - "biolink:MolecularEntity", - "biolink:Entity" - ], - "equivalent_identifiers": [ - "PANTHER.FAMILY:PTHR12015" - ], - "synonyms": [] - } - } - ], - "category": [ - "biolink:NamedThing", - "biolink:BiologicalEntity", - "biolink:GeneFamily", - "biolink:MolecularEntity", - "biolink:Entity" - ], - "name": "SMALL INDUCIBLE CYTOKINE A" - }, - "PANTHER.FAMILY:PTHR12015:SF170": { - "attributes": [ - { - "type": "WIKIDATA:Q80585", - "value": { - "category": [ - "biolink:BiologicalEntity", - "biolink:GeneFamily", - "biolink:NamedThing", - "biolink:MolecularEntity", - "biolink:Entity" - ], - "equivalent_identifiers": [ - "PANTHER.FAMILY:PTHR12015:SF170" - ], - "synonyms": [] - } - } - ], - "category": [ - "biolink:NamedThing", - "biolink:BiologicalEntity", - "biolink:GeneFamily", - "biolink:MolecularEntity", - "biolink:Entity" - ], - "name": "C-C MOTIF CHEMOKINE 5" - } + { + "operator": "=", + "value": "Male" } - }, - "query_graph": { - "edges": { - "e12": { - "object": "n2", - "predicate": "biolink:part_of", - "subject": "n1" - }, - "e23": { - "object": "n2", - "predicate": "biolink:part_of", - "subject": "n3" - } + ] + }, + "feature_b": { + "AsthmaDx": [ + { + "operator": "=", + "value": 1 }, - "nodes": { - "n1": { - "category": "biolink:Gene", - "id": "NCBIGene:6352", - "is_set": false - }, - "n2": { - "category": "biolink:GeneFamily", - "is_set": false - }, - "n3": { - "category": "biolink:GeneFamily", - "is_set": false - } - } - }, - "results": [ { - "edge_bindings": { - "e12": [ - { - "id": "dd8ef7a4606c4f8e405e6a5b1b095993" - } - ], - "e23": [ - { - "id": "9f7f9d86cb57e7190aafa57f7564eb05" - } - ] - }, - "node_bindings": { - "n1": [ - { - "id": "NCBIGene:6352" - } - ], - "n2": [ - { - "id": "PANTHER.FAMILY:PTHR12015" - } - ], - "n3": [ - { - "id": "PANTHER.FAMILY:PTHR12015:SF170" - } - ] - } + "operator": "=", + "value": 0 } ] } }, - "title": "Request" + "title": "Obj" } } }, @@ -14346,11 +14589,13 @@ "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Message" + "title": "Response Feature Association2 Table Year Cohort Cohort Id Feature Association2 Post", + "type": "object" } - } + }, + "text/tabular": {} }, - "description": "Successful Response" + "description": "Return the tabular output." }, "422": { "content": { @@ -14363,76 +14608,81 @@ "description": "Validation Error" } }, - "summary": "Overlay results with available connections between each node.", - "tags": [ - "translator" - ] - } - }, - "/about": { - "get": { - "description": "Returns a JSON describing dataset.", - "operationId": "about_about_get", - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "title": "Response About About Get" - } - } - }, - "description": "Successful Response" - } - }, - "summary": "JSON about dataset" + "summary": "Feature Association2" } }, - "/{source_type}/{target_type}/{curie}": { - "get": { - "description": "Returns one hop paths from `source_node_type` with `curie` to `target_node_type`.", - "operationId": "one_hop__source_type___target_type___curie__get", + "/{table}/{year}/cohort/{cohort_id}/associations_to_all_features": { + "post": { + "description": "Exploratory 1 X N feature associations.\n\nUsers select a predefined cohort and a feature variable of interest, and\nthe service returns a 1 x N feature table with corrected Chi Square\nstatistics and associated P values.", + "operationId": "associations_to_all_features__table___year__cohort__cohort_id__associations_to_all_features_post", "parameters": [ { "in": "path", - "name": "source_type", + "name": "table", "required": true, "schema": { - "title": "Source Type", + "title": "Table", "type": "string" } }, { "in": "path", - "name": "target_type", + "name": "year", "required": true, "schema": { - "title": "Target Type", - "type": "string" + "title": "Year", + "type": "integer" } }, { "in": "path", - "name": "curie", + "name": "cohort_id", "required": true, "schema": { - "title": "Curie", + "title": "Cohort Id", "type": "string" } } ], + "requestBody": { + "content": { + "application/json": { + "schema": { + "allOf": [ + { + "$ref": "#/components/schemas/AllFeaturesAssociation" + } + ], + "example": { + "correction": { + "method": "bonferroni" + }, + "feature": { + "Sex": { + "operator": "=", + "value": "Female" + } + }, + "maximum_p_value": 1 + }, + "title": "Obj" + } + } + }, + "required": true + }, "responses": { "200": { "content": { "application/json": { "schema": { - "items": {}, - "title": "Response One Hop Source Type Target Type Curie Get", - "type": "array" + "title": "Response Associations To All Features Table Year Cohort Cohort Id Associations To All Features Post", + "type": "object" } - } + }, + "text/tabular": {} }, - "description": "Successful Response" + "description": "Return the tabular output." }, "422": { "content": { @@ -14445,131 +14695,70 @@ "description": "Validation Error" } }, - "summary": "Get one hop results from source type to target type. Note: Please GET /predicates to determine what target goes with a source" + "summary": "Associations To All Features" } }, - "/{node_type}/{curie}": { - "get": { - "description": "Returns `node` matching `curie`.", - "operationId": "node__node_type___curie__get", + "/{table}/{year}/cohort/{cohort_id}/associations_to_all_features2": { + "post": { + "description": "Exploratory 1 X N feature associations.\n\nUsers select a predefined cohort and a feature variable of interest and\nbins, which can be combined, and the service returns a 1 x N feature table\nwith corrected Chi Square statistics and associated P values.", + "operationId": "associations_to_all_features2__table___year__cohort__cohort_id__associations_to_all_features2_post", "parameters": [ { "in": "path", - "name": "node_type", + "name": "table", "required": true, "schema": { - "title": "Node Type", + "title": "Table", "type": "string" } }, { "in": "path", - "name": "curie", + "name": "year", "required": true, "schema": { - "title": "Curie", + "title": "Year", + "type": "integer" + } + }, + { + "in": "path", + "name": "cohort_id", + "required": true, + "schema": { + "title": "Cohort Id", "type": "string" } } ], - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "items": {}, - "title": "Response Node Node Type Curie Get", - "type": "array" - } - } - }, - "description": "Successful Response" - }, - "422": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/HTTPValidationError" - } - } - }, - "description": "Validation Error" - } - }, - "summary": "Find `node` by `curie`" - } - } - }, - "servers": [ - { - "description": "Default server", - "url": "https://automat.renci.org/intact" - } - ], - "tags": [ - { - "name": "translator" - }, - { - "name": "automat" - } - ] - }, - { - "_id": "3e74f67bd571c74f1832829a5b5a40eb", - "_meta": { - "date_created": "2021-02-01T00:07:19.265482+00:00", - "last_updated": "2021-03-05T08:02:28.441615+00:00", - "url": "https://automat.renci.org/ctd/openapi.json", - "username": "YaphetKG" - }, - "_score": 0.6687226, - "info": { - "contact": { - "email": "kebedey@renci.org", - "name": "Yaphet Kebede", - "x-id": "https://github.com/yaphetkg", - "x-role": "contributor" - }, - "description": "A graph based on the [Comparative Toxicogenomics Database (ctdbase.org)](ctdbase.org).", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat CTD&provider_long=RENCI", - "title": "Automat CTD", - "version": "1.0.0", - "x-translator": { - "component": "KP", - "team": [ - "Ranking Agent" - ] - } - }, - "paths": { - "/query": { - "post": { - "description": "Given a question graph return question graph plus answers.", - "operationId": "reasoner_api_query_post", "requestBody": { "content": { "application/json": { "schema": { "allOf": [ { - "$ref": "#/components/schemas/Query" + "$ref": "#/components/schemas/AllFeaturesAssociation2" } ], "example": { - "message": { - "query_graph": { - "edges": {}, - "nodes": { - "n0": { - "category": "biolink:Gene", - "id": "NCBIGene:15" - } + "correction": { + "method": "bonferroni" + }, + "feature": { + "Sex": [ + { + "operator": "=", + "value": "Female" + }, + { + "operator": "=", + "value": "Male" } - } - } + ] + }, + "maximum_p_value": 1 }, - "title": "Request" + "title": "Obj" } } }, @@ -14580,11 +14769,13 @@ "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Query" + "title": "Response Associations To All Features2 Table Year Cohort Cohort Id Associations To All Features2 Post", + "type": "object" } - } + }, + "text/tabular": {} }, - "description": "Successful Response" + "description": "Return the tabular output." }, "422": { "content": { @@ -14597,61 +14788,198 @@ "description": "Validation Error" } }, - "summary": "Query Reasoner API", - "tags": [ - "translator" - ] + "summary": "Associations To All Features2" } }, - "/reasonerapi": { + "/{table}/{year}/cohort/{cohort_id}/features": { "get": { - "description": "Returns a list of question templates that can be used to query this plater instance.", - "operationId": "get_reasoner_api_reasonerapi_get", - "responses": { + "description": "Feature-rich cohort discovery.\n\nUsers select a predefined cohort as the input parameter, and the service\nreturns a profile of that cohort in terms of all feature variables.", + "operationId": "features__table___year__cohort__cohort_id__features_get", + "parameters": [ + { + "in": "path", + "name": "table", + "required": true, + "schema": { + "title": "Table", + "type": "string" + } + }, + { + "in": "path", + "name": "year", + "required": true, + "schema": { + "title": "Year", + "type": "integer" + } + }, + { + "in": "path", + "name": "cohort_id", + "required": true, + "schema": { + "title": "Cohort Id", + "type": "string" + } + } + ], + "responses": { "200": { "content": { "application/json": { "schema": { - "items": { - "$ref": "#/components/schemas/Message" - }, - "title": "Response Get Reasoner Api Reasonerapi Get", - "type": "array" + "title": "Response Features Table Year Cohort Cohort Id Features Get", + "type": "object" + } + }, + "text/tabular": {} + }, + "description": "Return the tabular output." + }, + "422": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/HTTPValidationError" } } }, - "description": "Successful Response" + "description": "Validation Error" } }, - "summary": "Get question templates" + "summary": "Features" + } + }, + "/{table}/{feature}/identifiers": { + "get": { + "description": "Feature identifiers.", + "operationId": "identifiers__table___feature__identifiers_get", + "parameters": [ + { + "in": "path", + "name": "table", + "required": true, + "schema": { + "title": "Table", + "type": "string" + } + }, + { + "in": "path", + "name": "feature", + "required": true, + "schema": { + "title": "Feature", + "type": "string" + } + } + ], + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "title": "Response Identifiers Table Feature Identifiers Get", + "type": "object" + } + }, + "text/tabular": {} + }, + "description": "Return the tabular output." + }, + "422": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/HTTPValidationError" + } + } + }, + "description": "Validation Error" + } + }, + "summary": "Identifiers" + } + }, + "/{table}/name/{name}": { + "get": { + "description": "Return cohort id associated with name.", + "operationId": "get_name__table__name__name__get", + "parameters": [ + { + "in": "path", + "name": "table", + "required": true, + "schema": { + "title": "Table", + "type": "string" + } + }, + { + "in": "path", + "name": "name", + "required": true, + "schema": { + "title": "Name", + "type": "string" + } + } + ], + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "title": "Response Get Name Table Name Name Get", + "type": "object" + } + }, + "text/tabular": {} + }, + "description": "Return the tabular output." + }, + "422": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/HTTPValidationError" + } + } + }, + "description": "Validation Error" + } + }, + "summary": "Get Name" }, "post": { - "deprecated": true, - "description": "Handle TRAPI request.", - "operationId": "reasoner_api_reasonerapi_post", + "description": "Associate name with cohort id.", + "operationId": "post_name__table__name__name__post", + "parameters": [ + { + "in": "path", + "name": "table", + "required": true, + "schema": { + "title": "Table", + "type": "string" + } + }, + { + "in": "path", + "name": "name", + "required": true, + "schema": { + "title": "Name", + "type": "string" + } + } + ], "requestBody": { "content": { "application/json": { "schema": { - "allOf": [ - { - "$ref": "#/components/schemas/Query" - } - ], - "example": { - "message": { - "query_graph": { - "edges": {}, - "nodes": { - "n0": { - "category": "biolink:Gene", - "id": "NCBIGene:15" - } - } - } - } - }, - "title": "Request" + "$ref": "#/components/schemas/AddNameById" } } }, @@ -14662,11 +14990,13 @@ "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Query" + "title": "Response Post Name Table Name Name Post", + "type": "object" } - } + }, + "text/tabular": {} }, - "description": "Successful Response" + "description": "Return the tabular output." }, "422": { "content": { @@ -14679,26 +15009,73 @@ "description": "Validation Error" } }, - "summary": "Reasoner Api" + "summary": "Post Name" } }, - "/cypher": { + "/knowledge_graph": { "post": { - "description": "Runs cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/).", - "operationId": "cypher_cypher_post", + "description": "Query for knowledge graph associations between concepts.", + "operationId": "knowledge_graph_knowledge_graph_post", + "parameters": [ + { + "in": "query", + "name": "reasoner", + "required": false, + "schema": { + "default": false, + "title": "Reasoner", + "type": "boolean" + } + } + ], "requestBody": { "content": { "application/json": { "schema": { "allOf": [ { - "$ref": "#/components/schemas/CypherRequest" + "$ref": "#/components/schemas/Query" } ], "example": { - "query": "MATCH (n) RETURN count(n)" + "message": { + "query_graph": { + "edges": { + "e00": { + "object": "n01", + "predicate": "biolink:correlated_with", + "subject": "n00" + } + }, + "nodes": { + "n00": { + "category": "biolink:PopulationOfIndividualOrganisms" + }, + "n01": { + "category": "biolink:ChemicalSubstance" + } + } + } + }, + "query_options": { + "cohort_features": { + "AgeStudyStart": { + "operator": "=", + "value": "0-2" + } + }, + "feature": { + "EstResidentialDensity": { + "operator": "<", + "value": 1 + } + }, + "maximum_p_value": 1, + "table": "patient", + "year": 2010 + } }, - "title": "Request" + "title": "Obj" } } }, @@ -14709,11 +15086,13 @@ "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/CypherResponse" + "title": "Response Knowledge Graph Knowledge Graph Post", + "type": "object" } - } + }, + "text/tabular": {} }, - "description": "Successful Response" + "description": "Return the tabular output." }, "422": { "content": { @@ -14726,100 +15105,137 @@ "description": "Validation Error" } }, - "summary": "Run cypher query" + "summary": "Knowledge Graph" } }, - "/predicates": { + "/knowledge_graph/schema": { "get": { - "description": "Returns an object where outer keys represent source types with second level keys as targets. And the values of the second level keys is the type of possible edge typesthat connect these concepts.", - "operationId": "predicates_predicates_get", + "description": "Query the ICEES clinical reasoner for knowledge graph schema.", + "operationId": "knowledge_graph_schema_knowledge_graph_schema_get", + "parameters": [ + { + "in": "query", + "name": "reasoner", + "required": false, + "schema": { + "default": false, + "title": "Reasoner", + "type": "boolean" + } + } + ], "responses": { "200": { "content": { "application/json": { "schema": { - "additionalProperties": { - "additionalProperties": { - "items": { - "type": "string" - }, - "type": "array" - }, - "type": "object" - }, - "title": "Response Predicates Predicates Get", + "title": "Response Knowledge Graph Schema Knowledge Graph Schema Get", "type": "object" } + }, + "text/tabular": {} + }, + "description": "Return the tabular output." + }, + "422": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/HTTPValidationError" + } } }, - "description": "Successful Response" + "description": "Validation Error" } }, - "summary": "Get one-hop connection types", - "tags": [ - "translator" - ] + "summary": "Knowledge Graph Schema" } }, - "/graph/schema": { + "/predicates": { "get": { - "deprecated": true, - "description": "Get one-hop connection types", - "operationId": "predicates_graph_schema_get", + "description": "Get meta-knowledge graph.", + "operationId": "predicates_predicates_get", "responses": { "200": { "content": { "application/json": { - "schema": { - "title": "Response Predicates Graph Schema Get", - "type": "object" - } - } + "schema": {} + }, + "text/tabular": {} }, - "description": "Successful Response" + "description": "Return the tabular output." } }, - "summary": "Get one-hop connection types" + "summary": "Predicates", + "tags": [ + "reasoner" + ] } }, - "/simple_spec": { - "get": { - "description": "Returns a list of available predicates when choosing a single source or target curie. Calling this endpoint with no query parameters will return all possible hops for all types.", - "operationId": "simple_spec_simple_spec_get", + "/knowledge_graph_overlay": { + "post": { + "description": "Query for knowledge graph co-occurrence overlay.", + "operationId": "knowledge_graph_overlay_knowledge_graph_overlay_post", "parameters": [ { "in": "query", - "name": "source", - "required": false, - "schema": { - "title": "Source", - "type": "string" - } - }, - { - "in": "query", - "name": "target", + "name": "reasoner", "required": false, "schema": { - "title": "Target", - "type": "string" + "default": false, + "title": "Reasoner", + "type": "boolean" } } ], + "requestBody": { + "content": { + "application/json": { + "schema": { + "allOf": [ + { + "$ref": "#/components/schemas/Query" + } + ], + "example": { + "message": { + "knowledge_graph": { + "edges": { + "e00": { + "object": "PUBCHEM:281", + "predicate": "biolink:correlated_with", + "subject": "PUBCHEM:2083" + } + }, + "nodes": { + "PUBCHEM:2083": { + "category": "biolink:Drug" + }, + "PUBCHEM:281": { + "category": "biolink:ChemicalSubstance" + } + } + } + } + }, + "title": "Obj" + } + } + }, + "required": true + }, "responses": { "200": { "content": { "application/json": { "schema": { - "items": { - "$ref": "#/components/schemas/SimpleSpecElement" - }, - "title": "Response Simple Spec Simple Spec Get", - "type": "array" + "title": "Response Knowledge Graph Overlay Knowledge Graph Overlay Post", + "type": "object" } - } + }, + "text/tabular": {} }, - "description": "Successful Response" + "description": "Return the tabular output." }, "422": { "content": { @@ -14832,33 +15248,26 @@ "description": "Validation Error" } }, - "summary": "Get one-hop connection schema" - } - }, - "/graph/summary": { - "get": { - "description": "Returns a summary of the graph.", - "operationId": "graph_summary_graph_summary_get", - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "title": "Response Graph Summary Graph Summary Get", - "type": "object" - } - } - }, - "description": "Successful Response" - } - }, - "summary": "Get graph summary" + "summary": "Knowledge Graph Overlay" } }, - "/overlay": { + "/knowledge_graph_one_hop": { "post": { - "description": "Given a ReasonerAPI graph, add support edges for any nodes linked in result bindings.", - "operationId": "overlay_overlay_post", + "deprecated": true, + "description": "Query the ICEES clinical reasoner for knowledge graph one hop.", + "operationId": "knowledge_graph_one_hop_knowledge_graph_one_hop_post", + "parameters": [ + { + "in": "query", + "name": "reasoner", + "required": false, + "schema": { + "default": true, + "title": "Reasoner", + "type": "boolean" + } + } + ], "requestBody": { "content": { "application/json": { @@ -14871,220 +15280,31 @@ "example": { "message": { "knowledge_graph": { + "edges": {}, + "nodes": {} + }, + "query_graph": { "edges": { - "9f7f9d86cb57e7190aafa57f7564eb05": { - "attributes": [ - { - "type": "WIKIDATA:Q80585", - "value": { - "ctime": 1610437123.7988985, - "predicate": "biolink:part_of", - "provided_by": "panther.get_gene_family_by_gene_family", - "publications": [], - "relation": "BFO:0000050", - "relation_label": "part of", - "source_database": "panther", - "source_id": "PANTHER.FAMILY:PTHR12015:SF170", - "target_id": "PANTHER.FAMILY:PTHR12015" - } - } - ], - "object": "PANTHER.FAMILY:PTHR12015", - "predicate": "biolink:part_of", - "subject": "PANTHER.FAMILY:PTHR12015:SF170" - }, - "dd8ef7a4606c4f8e405e6a5b1b095993": { - "attributes": [ - { - "type": "WIKIDATA:Q80585", - "value": { - "ctime": 1584932086.0009434, - "predicate": "biolink:part_of", - "provided_by": "panther.get_gene_by_gene_family", - "publications": [], - "relation": "BFO:0000050", - "relation_label": "part of", - "source_database": "panther", - "source_id": "NCBIGene:6352", - "target_id": "PANTHER.FAMILY:PTHR12015" - } - } - ], - "object": "PANTHER.FAMILY:PTHR12015", - "predicate": "biolink:part_of", - "subject": "NCBIGene:6352" + "e00": { + "object": "n01", + "predicate": "biolink:correlated_with", + "subject": "n00" } }, "nodes": { - "NCBIGene:6352": { - "attributes": [ - { - "type": "WIKIDATA:Q80585", - "value": { - "category": [ - "biolink:BiologicalEntity", - "biolink:GenomicEntity", - "biolink:GeneOrGeneProduct", - "biolink:MacromolecularMachine", - "biolink:NamedThing", - "biolink:MolecularEntity", - "biolink:Gene" - ], - "chromosome": "17", - "equivalent_identifiers": [ - "ENSEMBL:ENSG00000271503", - "NCBIGene:6352", - "NCBIGene:6352", - "HGNC:10632", - "UniProtKB:P13501" - ], - "gene_family": [ - "Chemokine ligands" - ], - "gene_family_id": [ - 483 - ], - "location": "17q12", - "locus_group": "protein-coding gene", - "synonyms": [], - "taxon": 9606 - } - } - ], - "category": [ - "biolink:NamedThing", - "biolink:BiologicalEntity", - "biolink:MolecularEntity", - "biolink:GenomicEntity", - "biolink:GeneOrGeneProduct", - "biolink:MacromolecularMachine", - "biolink:Gene" - ], - "name": "CCL5" - }, - "PANTHER.FAMILY:PTHR12015": { - "attributes": [ - { - "type": "WIKIDATA:Q80585", - "value": { - "category": [ - "biolink:BiologicalEntity", - "biolink:GeneFamily", - "biolink:NamedThing", - "biolink:MolecularEntity", - "biolink:Entity" - ], - "equivalent_identifiers": [ - "PANTHER.FAMILY:PTHR12015" - ], - "synonyms": [] - } - } - ], - "category": [ - "biolink:NamedThing", - "biolink:BiologicalEntity", - "biolink:GeneFamily", - "biolink:MolecularEntity", - "biolink:Entity" - ], - "name": "SMALL INDUCIBLE CYTOKINE A" - }, - "PANTHER.FAMILY:PTHR12015:SF170": { - "attributes": [ - { - "type": "WIKIDATA:Q80585", - "value": { - "category": [ - "biolink:BiologicalEntity", - "biolink:GeneFamily", - "biolink:NamedThing", - "biolink:MolecularEntity", - "biolink:Entity" - ], - "equivalent_identifiers": [ - "PANTHER.FAMILY:PTHR12015:SF170" - ], - "synonyms": [] - } - } - ], - "category": [ - "biolink:NamedThing", - "biolink:BiologicalEntity", - "biolink:GeneFamily", - "biolink:MolecularEntity", - "biolink:Entity" - ], - "name": "C-C MOTIF CHEMOKINE 5" - } - } - }, - "query_graph": { - "edges": { - "e12": { - "object": "n2", - "predicate": "biolink:part_of", - "subject": "n1" - }, - "e23": { - "object": "n2", - "predicate": "biolink:part_of", - "subject": "n3" - } - }, - "nodes": { - "n1": { - "category": "biolink:Gene", - "id": "NCBIGene:6352", - "is_set": false - }, - "n2": { - "category": "biolink:GeneFamily", - "is_set": false + "n00": { + "category": "biolink:Drug", + "id": "PUBCHEM:2083" }, - "n3": { - "category": "biolink:GeneFamily", - "is_set": false + "n01": { + "category": "biolink:ChemicalSubstance" } } }, - "results": [ - { - "edge_bindings": { - "e12": [ - { - "id": "dd8ef7a4606c4f8e405e6a5b1b095993" - } - ], - "e23": [ - { - "id": "9f7f9d86cb57e7190aafa57f7564eb05" - } - ] - }, - "node_bindings": { - "n1": [ - { - "id": "NCBIGene:6352" - } - ], - "n2": [ - { - "id": "PANTHER.FAMILY:PTHR12015" - } - ], - "n3": [ - { - "id": "PANTHER.FAMILY:PTHR12015:SF170" - } - ] - } - } - ] + "results": [] } }, - "title": "Request" + "title": "Obj" } } }, @@ -15095,11 +15315,13 @@ "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Message" + "title": "Response Knowledge Graph One Hop Knowledge Graph One Hop Post", + "type": "object" } - } + }, + "text/tabular": {} }, - "description": "Successful Response" + "description": "Return the tabular output." }, "422": { "content": { @@ -15112,76 +15334,79 @@ "description": "Validation Error" } }, - "summary": "Overlay results with available connections between each node.", - "tags": [ - "translator" - ] - } - }, - "/about": { - "get": { - "description": "Returns a JSON describing dataset.", - "operationId": "about_about_get", - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "title": "Response About About Get" - } - } - }, - "description": "Successful Response" - } - }, - "summary": "JSON about dataset" + "summary": "Knowledge Graph One Hop" } }, - "/{source_type}/{target_type}/{curie}": { - "get": { - "description": "Returns one hop paths from `source_node_type` with `curie` to `target_node_type`.", - "operationId": "one_hop__source_type___target_type___curie__get", + "/query": { + "post": { + "description": "Query the ICEES clinical reasoner for knowledge graph one hop.", + "operationId": "knowledge_graph_one_hop_query_post", "parameters": [ { - "in": "path", - "name": "source_type", - "required": true, - "schema": { - "title": "Source Type", - "type": "string" - } - }, - { - "in": "path", - "name": "target_type", - "required": true, - "schema": { - "title": "Target Type", - "type": "string" - } - }, - { - "in": "path", - "name": "curie", - "required": true, + "in": "query", + "name": "reasoner", + "required": false, "schema": { - "title": "Curie", - "type": "string" + "default": true, + "title": "Reasoner", + "type": "boolean" } } ], + "requestBody": { + "content": { + "application/json": { + "schema": { + "allOf": [ + { + "$ref": "#/components/schemas/Query" + } + ], + "example": { + "message": { + "knowledge_graph": { + "edges": {}, + "nodes": {} + }, + "query_graph": { + "edges": { + "e00": { + "object": "n01", + "predicate": "biolink:correlated_with", + "subject": "n00" + } + }, + "nodes": { + "n00": { + "category": "biolink:Drug", + "id": "PUBCHEM:2083" + }, + "n01": { + "category": "biolink:ChemicalSubstance" + } + } + }, + "results": [] + } + }, + "title": "Obj" + } + } + }, + "required": true + }, "responses": { "200": { "content": { "application/json": { "schema": { - "items": {}, - "title": "Response One Hop Source Type Target Type Curie Get", - "type": "array" + "title": "Response Knowledge Graph One Hop Query Post", + "type": "object" } - } + }, + "text/tabular": {} }, - "description": "Successful Response" + "description": "Return the tabular output." }, "422": { "content": { @@ -15194,29 +15419,41 @@ "description": "Validation Error" } }, - "summary": "Get one hop results from source type to target type. Note: Please GET /predicates to determine what target goes with a source" + "summary": "Knowledge Graph One Hop", + "tags": [ + "reasoner" + ] } }, - "/{node_type}/{curie}": { + "/bins": { "get": { - "description": "Returns `node` matching `curie`.", - "operationId": "node__node_type___curie__get", + "description": "Return bin values.", + "operationId": "handle_bins_bins_get", "parameters": [ { - "in": "path", - "name": "node_type", - "required": true, + "in": "query", + "name": "year", + "required": false, "schema": { - "title": "Node Type", + "title": "Year", "type": "string" } }, { - "in": "path", - "name": "curie", - "required": true, + "in": "query", + "name": "table", + "required": false, "schema": { - "title": "Curie", + "title": "Table", + "type": "string" + } + }, + { + "in": "query", + "name": "feature", + "required": false, + "schema": { + "title": "Feature", "type": "string" } } @@ -15226,13 +15463,13 @@ "content": { "application/json": { "schema": { - "items": {}, - "title": "Response Node Node Type Curie Get", - "type": "array" + "title": "Response Handle Bins Bins Get", + "type": "object" } - } + }, + "text/tabular": {} }, - "description": "Successful Response" + "description": "Return the tabular output." }, "422": { "content": { @@ -15245,14 +15482,13 @@ "description": "Validation Error" } }, - "summary": "Find `node` by `curie`" + "summary": "Handle Bins" } } }, "servers": [ { - "description": "Default server", - "url": "https://automat.renci.org/ctd" + "url": "https://icees.renci.org:16340" } ], "tags": [ @@ -15260,19 +15496,19 @@ "name": "translator" }, { - "name": "automat" + "name": "reasoner" } ] }, { - "_id": "49015a5444165956a9e45655dc1ea389", + "_id": "132da307d445fac70a403a5e623107d5", "_meta": { - "date_created": "2021-01-26T00:04:34.149152+00:00", - "last_updated": "2021-03-05T08:02:10.994708+00:00", - "url": "https://automat.renci.org/human-goa/openapi.json", + "date_created": "2021-02-04T00:00:37.939131+00:00", + "last_updated": "2021-03-29T07:03:26.875445+00:00", + "url": "https://automat.renci.org/hetio/openapi.json", "username": "YaphetKG" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { "email": "kebedey@renci.org", @@ -15280,9 +15516,9 @@ "x-id": "https://github.com/yaphetkg", "x-role": "contributor" }, - "description": " Human Gene Ontology Annotations from the GO consortium.", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat%20Human%20GOA&provider_long=RENCI", - "title": "Automat Human GOA", + "description": "A graph based on [hetionet (het.io)](het.io).", + "termsOfService": "http://linkmissing", + "title": "Automat Hetio", "version": "1.0.0", "x-translator": { "component": "KP", @@ -16001,7 +16237,7 @@ "servers": [ { "description": "Default server", - "url": "https://automat.renci.org/human-goa" + "url": "https://automat.renci.org/hetio" } ], "tags": [ @@ -16014,14 +16250,14 @@ ] }, { - "_id": "7b1b6a88cbf2913c4b614fabddcaabb4", + "_id": "a3cfb0c18f630ce73ccf86b1db5117db", "_meta": { - "date_created": "2021-01-26T00:02:52.903243+00:00", - "last_updated": "2021-03-05T08:02:27.845868+00:00", - "url": "https://automat.renci.org/textminingkp/openapi.json", + "date_created": "2021-02-03T00:00:38.618714+00:00", + "last_updated": "2021-03-29T07:04:10.254897+00:00", + "url": "https://automat.renci.org/panther/openapi.json", "username": "YaphetKG" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { "email": "kebedey@renci.org", @@ -16029,9 +16265,9 @@ "x-id": "https://github.com/yaphetkg", "x-role": "contributor" }, - "description": " A literature co-occurrence graph created by the Translator Text Mining KP.", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat%20Textmining%20KP&provider_long=RENCI", - "title": "Automat Textmining KP", + "description": " A graph of gene families and pathways from [Panther (pantherdb.org)](pantherdb.org)", + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Panther&provider_long=RENCI", + "title": "Automat Panther", "version": "1.0.0", "x-translator": { "component": "KP", @@ -16750,7 +16986,7 @@ "servers": [ { "description": "Default server", - "url": "https://automat.renci.org/textminingkp" + "url": "https://automat.renci.org/panther" } ], "tags": [ @@ -16763,14 +16999,14 @@ ] }, { - "_id": "f8f7142da2323703dfa32b8cc4cdff5f", + "_id": "7c481f0761132876e6b953547623f594", "_meta": { - "date_created": "2021-01-26T00:02:39.708234+00:00", - "last_updated": "2021-03-05T08:02:21.678041+00:00", - "url": "https://automat.renci.org/viral-proteome/openapi.json", + "date_created": "2021-01-26T00:03:04.513280+00:00", + "last_updated": "2021-03-29T07:04:04.240631+00:00", + "url": "https://automat.renci.org/pharos/openapi.json", "username": "YaphetKG" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { "email": "kebedey@renci.org", @@ -16778,9 +17014,9 @@ "x-id": "https://github.com/yaphetkg", "x-role": "contributor" }, - "description": "A graph consisting of viral proteins from UniProt, connected by similarity edges from UniRef.", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat%20Viral%20Proteome&provider_long=RENCI", - "title": "Automat Viral Proteome", + "description": "A graph based on [Pharos (pharos.nih.gov)](pharos.nih.gov).", + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Pharos&provider_long=RENCI", + "title": "Automat Pharos", "version": "1.0.0", "x-translator": { "component": "KP", @@ -17499,7 +17735,7 @@ "servers": [ { "description": "Default server", - "url": "https://automat.renci.org/viral-proteome" + "url": "https://automat.renci.org/pharos" } ], "tags": [ @@ -17512,223 +17748,172 @@ ] }, { - "_id": "a3cfb0c18f630ce73ccf86b1db5117db", + "_id": "e9f69b81e755e163fdf6c41a2b5e07c0", "_meta": { - "date_created": "2021-02-03T00:00:38.618714+00:00", - "last_updated": "2021-03-05T08:02:08.084187+00:00", - "url": "https://automat.renci.org/panther/openapi.json", - "username": "YaphetKG" + "date_created": "2021-01-29T00:00:15.735608+00:00", + "last_updated": "2021-03-29T07:04:11.343019+00:00", + "url": "https://openpredict.semanticscience.org/openapi.json", + "username": "vemonet" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { - "email": "kebedey@renci.org", - "name": "Yaphet Kebede", - "x-id": "https://github.com/yaphetkg", - "x-role": "contributor" + "email": "vincent.emonet@maastrichtuniversity.nl", + "name": "Institute of Data Science at Maastricht University", + "url": "https://maastrichtuniversity.nl/ids" }, - "description": " A graph of gene families and pathways from [Panther (pantherdb.org)](pantherdb.org)", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Panther&provider_long=RENCI", - "title": "Automat Panther", + "description": "Get predicted targets for a given entity: the **potential drugs treating a given disease**, or the **potential diseases a given drug could treat**. \n\n* Use the `/predict` operation to easily retrieve predictions for a given entity (operation annotated for the [BioThings Explorer](https://x-bte-extension.readthedocs.io/en/latest/x-bte-kgs-operations.html)). \n\n* Predictions are currently produced using the [PREDICT method](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159979/) from the [fair-workflows/openpredict](https://github.com/fair-workflows/openpredict) project. \n\n* You can also install the [OpenPredict Python package](https://pypi.org/project/openpredict/) to train and serve a new model yourself. \n\n* More documentation available at [github.com/MaastrichtU-IDS/translator-openpredict](https://github.com/MaastrichtU-IDS/translator-openpredict) \n\n[![Version](https://img.shields.io/pypi/v/openpredict)](https://pypi.org/project/openpredict) [![Run tests](https://github.com/MaastrichtU-IDS/translator-openpredict/workflows/Run%20tests/badge.svg)](https://github.com/MaastrichtU-IDS/translator-openpredict/actions?query=workflow%3A%22Run+tests%22) \n\nService supported by the [NCATS Translator project](https://ncats.nih.gov/translator/about)", + "license": { + "name": "MIT License", + "url": "https://opensource.org/licenses/MIT" + }, + "termsOfService": "", + "title": "OpenPredict API", "version": "1.0.0", "x-translator": { "component": "KP", "team": [ - "Ranking Agent" + "Clinical Data Provider" ] + }, + "x-trapi": { + "version": "1.0.0" } }, "paths": { - "/query": { + "/embedding": { "post": { - "description": "Given a question graph return question graph plus answers.", - "operationId": "reasoner_api_query_post", + "description": "Upload your embedding file: select which types do you have in the embeddings, Drugs, Diseases or Both. \n1. provided embeddings will be added to the model\n2. the model will be retrained\n3. the model evaluation will be stored in a triplestore", + "operationId": "openpredict.openpredict_api.post_embedding", + "parameters": [ + { + "description": "Types of the entities in the embedding", + "in": "query", + "name": "types", + "required": true, + "schema": { + "default": "Both", + "enum": [ + "Drugs", + "Diseases", + "Both" + ], + "type": "string" + } + }, + { + "description": "Name of embedding (eg. TransE_DrugBank_Drug)", + "in": "query", + "name": "emb_name", + "required": true, + "schema": { + "type": "string" + } + }, + { + "description": "Describe how the embeddings was obtained (eg. rdf2vec on drugbank/omim data)", + "in": "query", + "name": "description", + "required": true, + "schema": { + "type": "string" + } + }, + { + "description": "Provide the ID of the run output you want to use as base model to add the embeddings", + "example": "openpredict-baseline-omim-drugbank", + "in": "query", + "name": "model_id", + "required": true, + "schema": { + "type": "string" + } + } + ], "requestBody": { "content": { - "application/json": { + "multipart/form-data": { "schema": { - "allOf": [ - { - "$ref": "#/components/schemas/Query" - } - ], - "example": { - "message": { - "query_graph": { - "edges": {}, - "nodes": { - "n0": { - "category": "biolink:Gene", - "id": "NCBIGene:15" - } - } - } + "properties": { + "embedding_file": { + "description": "The embedding file to be uploaded", + "format": "binary", + "type": "string" } }, - "title": "Request" + "type": "object" } } - }, - "required": true + } }, "responses": { "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Query" - } - } - }, - "description": "Successful Response" - }, - "422": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/HTTPValidationError" - } - } - }, - "description": "Validation Error" + "description": "OK" } }, - "summary": "Query Reasoner API", + "summary": "Upload your embedding for drugs or diseases", "tags": [ - "translator" + "openpredict" ] } }, - "/reasonerapi": { + "/features": { "get": { - "description": "Returns a list of question templates that can be used to query this plater instance.", - "operationId": "get_reasoner_api_reasonerapi_get", - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "items": { - "$ref": "#/components/schemas/Message" - }, - "title": "Response Get Reasoner Api Reasonerapi Get", - "type": "array" - } - } - }, - "description": "Successful Response" - } - }, - "summary": "Get question templates" - }, - "post": { - "deprecated": true, - "description": "Handle TRAPI request.", - "operationId": "reasoner_api_reasonerapi_post", - "requestBody": { - "content": { - "application/json": { - "schema": { - "allOf": [ - { - "$ref": "#/components/schemas/Query" - } - ], - "example": { - "message": { - "query_graph": { - "edges": {}, - "nodes": { - "n0": { - "category": "biolink:Gene", - "id": "NCBIGene:15" - } - } - } - } - }, - "title": "Request" - } + "description": "Return the features trained in the model, for Drugs, Diseases or Both ", + "operationId": "openpredict.openpredict_api.get_features", + "parameters": [ + { + "description": "Type of the entities in the features", + "in": "query", + "name": "type", + "required": true, + "schema": { + "default": "All", + "enum": [ + "All", + "Drugs", + "Diseases", + "Both" + ], + "type": "string" } - }, - "required": true - }, + } + ], "responses": { "200": { "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Query" - } - } - }, - "description": "Successful Response" - }, - "422": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/HTTPValidationError" - } - } + "application/json": {} }, - "description": "Validation Error" + "description": "OK" } }, - "summary": "Reasoner Api" + "summary": "Return the features trained in the models", + "tags": [ + "openpredict" + ] } }, - "/cypher": { - "post": { - "description": "Runs cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/).", - "operationId": "cypher_cypher_post", - "requestBody": { - "content": { - "application/json": { - "schema": { - "allOf": [ - { - "$ref": "#/components/schemas/CypherRequest" - } - ], - "example": { - "query": "MATCH (n) RETURN count(n)" - }, - "title": "Request" - } - } - }, - "required": true - }, + "/models": { + "get": { + "description": "Return the models with their training features and scores", + "operationId": "openpredict.openpredict_api.get_models", "responses": { "200": { "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/CypherResponse" - } - } - }, - "description": "Successful Response" - }, - "422": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/HTTPValidationError" - } - } + "application/json": {} }, - "description": "Validation Error" + "description": "OK" } }, - "summary": "Run cypher query" + "summary": "Return the models with their training features and scores", + "tags": [ + "openpredict" + ] } }, "/predicates": { "get": { - "description": "Returns an object where outer keys represent source types with second level keys as targets. And the values of the second level keys is the type of possible edge typesthat connect these concepts.", - "operationId": "predicates_predicates_get", + "operationId": "openpredict.openpredict_api.get_predicates", "responses": { "200": { "content": { @@ -17736,585 +17921,475 @@ "schema": { "additionalProperties": { "additionalProperties": { + "description": "Array of predicates", "items": { "type": "string" }, "type": "array" }, + "description": "Target map", "type": "object" }, - "title": "Response Predicates Predicates Get", + "description": "Source map", + "example": { + "biolink:ChemicalSubstance": { + "biolink:Gene": [ + "biolink:directly_interacts_with", + "biolink:decreases_activity_of" + ] + } + }, "type": "object" } } }, - "description": "Successful Response" + "description": "Predicates by source and target" } }, - "summary": "Get one-hop connection types", + "summary": "Get supported relationships by source and target", "tags": [ "translator" ] } }, - "/graph/schema": { - "get": { - "deprecated": true, - "description": "Get one-hop connection types", - "operationId": "predicates_graph_schema_get", - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "title": "Response Predicates Graph Schema Get", - "type": "object" - } - } - }, - "description": "Successful Response" - } - }, - "summary": "Get one-hop connection types" - } - }, - "/simple_spec": { + "/predict": { "get": { - "description": "Returns a list of available predicates when choosing a single source or target curie. Calling this endpoint with no query parameters will return all possible hops for all types.", - "operationId": "simple_spec_simple_spec_get", + "description": "Return the predicted targets for a given entity: drug (DrugBank ID) or disease (OMIM ID), with confidence scores. Only a drug_id or a disease_id can be provided, the disease_id will be ignored if drug_id is provided This operation is annotated with x-bte-kgs-operations, and follow the BioThings API recommendations.", + "operationId": "openpredict.openpredict_api.get_predict", "parameters": [ { + "description": "CURIE of the drug to get prediction of diseases it could treat (e.g. DRUGBANK:DB00394)", + "example": "DRUGBANK:DB00394", "in": "query", - "name": "source", + "name": "drug_id", "required": false, "schema": { - "title": "Source", "type": "string" } }, { + "description": "CURIE of the disease to get prediction of drugs it could be treated with (e.g. OMIM:246300). Ignored if drug_id provided.", "in": "query", - "name": "target", + "name": "disease_id", + "required": false, + "schema": { + "type": "string" + } + }, + { + "description": "Provide the ID of the run output you want to use as model to use to predict associations", + "example": "openpredict-baseline-omim-drugbank", + "in": "query", + "name": "model_id", "required": false, "schema": { - "title": "Target", "type": "string" } + }, + { + "description": "Minimum score of predictions to return (0 to 1)", + "in": "query", + "name": "min_score", + "required": false, + "schema": { + "format": "double", + "maximum": 1, + "minimum": 0, + "type": "number" + } + }, + { + "description": "Maximum score of predictions to return (0 to 1)", + "in": "query", + "name": "max_score", + "required": false, + "schema": { + "format": "double", + "maximum": 1, + "minimum": 0, + "type": "number" + } + }, + { + "description": "Maximum number of results to return, ordered from best score (e.g. 42)", + "in": "query", + "name": "n_results", + "required": false, + "schema": { + "format": "int32", + "minimum": 0, + "type": "integer" + } + } + ], + "responses": { + "200": { + "content": { + "application/json": {} + }, + "description": "Successful Operation" } + }, + "summary": "Get predicted targets for a given entity", + "tags": [ + "biothings" ], + "x-bte-kgs-operations": [ + { + "inputs": [ + { + "id": "biolink:DRUGBANK", + "semantic": "biolink:ChemicalSubstance" + } + ], + "outputs": [ + { + "id": "biolink:OMIM", + "semantic": "biolink:Disease" + } + ], + "parameters": { + "drug_id": "{inputs[0]}" + }, + "predicate": "biolink:treats", + "responseMapping": { + "OMIM": "hits.id" + }, + "supportBatch": false + }, + { + "inputs": [ + { + "id": "biolink:OMIM", + "semantic": "biolink:Disease" + } + ], + "outputs": [ + { + "id": "biolink:DRUGBANK", + "semantic": "biolink:ChemicalSubstance" + } + ], + "parameters": { + "disease_id": "{inputs[0]}" + }, + "predicate": "biolink:treated_by", + "responseMapping": { + "DRUGBANK": "hits.id" + }, + "supportBatch": false + } + ] + } + }, + "/query": { + "post": { + "description": "Send a [ReasonerAPI](https://github.com/NCATSTranslator/ReasonerAPI) query to request the predicted targets given: a source node, and the relation to predict. Use classes and relations from the [BioLink model](https://biolink.github.io/biolink-model)", + "operationId": "openpredict.openpredict_api.post_reasoner_predict", + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Query" + } + } + }, + "description": "Query information to be submitted", + "required": true + }, "responses": { "200": { "content": { "application/json": { "schema": { - "items": { - "$ref": "#/components/schemas/SimpleSpecElement" - }, - "title": "Response Simple Spec Simple Spec Get", - "type": "array" + "$ref": "#/components/schemas/Response" } } }, - "description": "Successful Response" + "description": "OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized." }, - "422": { + "400": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/HTTPValidationError" + "type": "string" } } }, - "description": "Validation Error" - } - }, - "summary": "Get one-hop connection schema" - } - }, - "/graph/summary": { - "get": { - "description": "Returns a summary of the graph.", - "operationId": "graph_summary_graph_summary_get", - "responses": { - "200": { + "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": { - "title": "Response Graph Summary Graph Summary Get", - "type": "object" + "type": "string" } } }, - "description": "Successful Response" - } - }, - "summary": "Get graph summary" - } - }, - "/overlay": { - "post": { - "description": "Given a ReasonerAPI graph, add support edges for any nodes linked in result bindings.", - "operationId": "overlay_overlay_post", - "requestBody": { - "content": { - "application/json": { - "schema": { - "allOf": [ - { - "$ref": "#/components/schemas/Query" - } - ], - "example": { - "message": { - "knowledge_graph": { - "edges": { - "9f7f9d86cb57e7190aafa57f7564eb05": { - "attributes": [ - { - "type": "WIKIDATA:Q80585", - "value": { - "ctime": 1610437123.7988985, - "predicate": "biolink:part_of", - "provided_by": "panther.get_gene_family_by_gene_family", - "publications": [], - "relation": "BFO:0000050", - "relation_label": "part of", - "source_database": "panther", - "source_id": "PANTHER.FAMILY:PTHR12015:SF170", - "target_id": "PANTHER.FAMILY:PTHR12015" - } - } - ], - "object": "PANTHER.FAMILY:PTHR12015", - "predicate": "biolink:part_of", - "subject": "PANTHER.FAMILY:PTHR12015:SF170" - }, - "dd8ef7a4606c4f8e405e6a5b1b095993": { - "attributes": [ - { - "type": "WIKIDATA:Q80585", - "value": { - "ctime": 1584932086.0009434, - "predicate": "biolink:part_of", - "provided_by": "panther.get_gene_by_gene_family", - "publications": [], - "relation": "BFO:0000050", - "relation_label": "part of", - "source_database": "panther", - "source_id": "NCBIGene:6352", - "target_id": "PANTHER.FAMILY:PTHR12015" - } - } - ], - "object": "PANTHER.FAMILY:PTHR12015", - "predicate": "biolink:part_of", - "subject": "NCBIGene:6352" - } - }, - "nodes": { - "NCBIGene:6352": { - "attributes": [ - { - "type": "WIKIDATA:Q80585", - "value": { - "category": [ - "biolink:BiologicalEntity", - "biolink:GenomicEntity", - "biolink:GeneOrGeneProduct", - "biolink:MacromolecularMachine", - "biolink:NamedThing", - "biolink:MolecularEntity", - "biolink:Gene" - ], - "chromosome": "17", - "equivalent_identifiers": [ - "ENSEMBL:ENSG00000271503", - "NCBIGene:6352", - "NCBIGene:6352", - "HGNC:10632", - "UniProtKB:P13501" - ], - "gene_family": [ - "Chemokine ligands" - ], - "gene_family_id": [ - 483 - ], - "location": "17q12", - "locus_group": "protein-coding gene", - "synonyms": [], - "taxon": 9606 - } - } - ], - "category": [ - "biolink:NamedThing", - "biolink:BiologicalEntity", - "biolink:MolecularEntity", - "biolink:GenomicEntity", - "biolink:GeneOrGeneProduct", - "biolink:MacromolecularMachine", - "biolink:Gene" - ], - "name": "CCL5" - }, - "PANTHER.FAMILY:PTHR12015": { - "attributes": [ - { - "type": "WIKIDATA:Q80585", - "value": { - "category": [ - "biolink:BiologicalEntity", - "biolink:GeneFamily", - "biolink:NamedThing", - "biolink:MolecularEntity", - "biolink:Entity" - ], - "equivalent_identifiers": [ - "PANTHER.FAMILY:PTHR12015" - ], - "synonyms": [] - } - } - ], - "category": [ - "biolink:NamedThing", - "biolink:BiologicalEntity", - "biolink:GeneFamily", - "biolink:MolecularEntity", - "biolink:Entity" - ], - "name": "SMALL INDUCIBLE CYTOKINE A" - }, - "PANTHER.FAMILY:PTHR12015:SF170": { - "attributes": [ - { - "type": "WIKIDATA:Q80585", - "value": { - "category": [ - "biolink:BiologicalEntity", - "biolink:GeneFamily", - "biolink:NamedThing", - "biolink:MolecularEntity", - "biolink:Entity" - ], - "equivalent_identifiers": [ - "PANTHER.FAMILY:PTHR12015:SF170" - ], - "synonyms": [] - } - } - ], - "category": [ - "biolink:NamedThing", - "biolink:BiologicalEntity", - "biolink:GeneFamily", - "biolink:MolecularEntity", - "biolink:Entity" - ], - "name": "C-C MOTIF CHEMOKINE 5" - } - } - }, - "query_graph": { - "edges": { - "e12": { - "object": "n2", - "predicate": "biolink:part_of", - "subject": "n1" - }, - "e23": { - "object": "n2", - "predicate": "biolink:part_of", - "subject": "n3" - } - }, - "nodes": { - "n1": { - "category": "biolink:Gene", - "id": "NCBIGene:6352", - "is_set": false - }, - "n2": { - "category": "biolink:GeneFamily", - "is_set": false - }, - "n3": { - "category": "biolink:GeneFamily", - "is_set": false - } - } - }, - "results": [ - { - "edge_bindings": { - "e12": [ - { - "id": "dd8ef7a4606c4f8e405e6a5b1b095993" - } - ], - "e23": [ - { - "id": "9f7f9d86cb57e7190aafa57f7564eb05" - } - ] - }, - "node_bindings": { - "n1": [ - { - "id": "NCBIGene:6352" - } - ], - "n2": [ - { - "id": "PANTHER.FAMILY:PTHR12015" - } - ], - "n3": [ - { - "id": "PANTHER.FAMILY:PTHR12015:SF170" - } - ] - } - } - ] - } - }, - "title": "Request" - } - } + "description": "Internal server error." }, - "required": true - }, - "responses": { - "200": { + "501": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Message" + "type": "string" } } }, - "description": "Successful Response" - }, - "422": { + "description": "Not implemented." + } + }, + "summary": "Query reasoner via one of several inputs", + "tags": [ + "trapi" + ], + "x-swagger-router-controller": "swagger_server.controllers.query_controller" + } + } + }, + "servers": [ + { + "url": "https://openpredict.semanticscience.org" + } + ], + "tags": [ + { + "description": "Get relationships supported by this API", + "name": "translator" + }, + { + "description": "Query the models using the Reasoner API", + "name": "trapi" + } + ] + }, + { + "_id": "89054eff6ee6d91641d278d9ffdb3993", + "_meta": { + "date_created": "2021-01-20T00:00:12.144499+00:00", + "last_updated": "2021-03-29T07:04:12.761521+00:00", + "url": "https://api.collaboratory.semanticscience.org/openapi.json", + "username": "vemonet" + }, + "_score": 0.6863549, + "info": { + "contact": { + "email": "vincent.emonet@maastrichtuniversity.nl" + }, + "description": "Translator Reasoner API for the Knowledge Collaboratory, hosted on the [Nanopublications network](http://nanopub.org/wordpress/), for annotated drug indications or any other BioLink-compliant claims. \n\n This Open API supports [Translator Reasoner API](https://github.com/NCATSTranslator/ReasonerAPI) version `1.0.0` queries and the [`KGX`](https://github.com/biolink/kgx) format \n\nSee the API GitHub repository: [github.com/MaastrichtU-IDS/knowledge-collaboratory-api](https://github.com/MaastrichtU-IDS/knowledge-collaboratory-api) \n\nThis service is supported by the [NCATS Translator project](https://ncats.nih.gov/translator/about)", + "license": { + "name": "MIT license", + "url": "https://opensource.org/licenses/MIT" + }, + "termsOfService": "https://github.com/MaastrichtU-IDS/knowledge-collaboratory-api/blob/master/LICENSE", + "title": "Translator Knowledge Collaboratory API", + "version": "1.0.0", + "x-translator": { + "component": "KP", + "team": [ + "Clinical Data Provider" + ] + }, + "x-trapi": { + "version": "1.0.0" + } + }, + "paths": { + "/kgx": { + "get": { + "operationId": "api.get_kgx", + "responses": { + "200": { "content": { - "application/json": { + "application/zip": { "schema": { - "$ref": "#/components/schemas/HTTPValidationError" + "format": "binary", + "type": "string" } } }, - "description": "Validation Error" + "description": "Zip file with nodes and edges files in KGX TSV format" } }, - "summary": "Overlay results with available connections between each node.", + "summary": "Get the Knowledge Collaboratory drug indications in KGX TSV format (TSV files in a .zip)", "tags": [ "translator" ] } }, - "/about": { + "/predicates": { "get": { - "description": "Returns a JSON describing dataset.", - "operationId": "about_about_get", + "operationId": "api.get_predicates", "responses": { "200": { "content": { "application/json": { "schema": { - "title": "Response About About Get" + "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": "Successful Response" + "description": "Predicates by source and target" } }, - "summary": "JSON about dataset" + "summary": "Get supported relationships by source and target", + "tags": [ + "translator" + ] } }, - "/{source_type}/{target_type}/{curie}": { - "get": { - "description": "Returns one hop paths from `source_node_type` with `curie` to `target_node_type`.", - "operationId": "one_hop__source_type___target_type___curie__get", - "parameters": [ - { - "in": "path", - "name": "source_type", - "required": true, - "schema": { - "title": "Source Type", - "type": "string" - } - }, - { - "in": "path", - "name": "target_type", - "required": true, - "schema": { - "title": "Target Type", - "type": "string" + "/query": { + "post": { + "description": "Send a [ReasonerAPI](https://github.com/NCATSTranslator/ReasonerAPI) query to request the predicted targets given: a source node, and the relation to predict. Use classes and relations from the [BioLink model](https://biolink.github.io/biolink-model)", + "operationId": "api.post_reasoner_query", + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Query" + } } }, - { - "in": "path", - "name": "curie", - "required": true, - "schema": { - "title": "Curie", - "type": "string" - } - } - ], + "description": "Query information to be submitted", + "required": true + }, "responses": { "200": { "content": { "application/json": { "schema": { - "items": {}, - "title": "Response One Hop Source Type Target Type Curie Get", - "type": "array" + "$ref": "#/components/schemas/Response" } } }, - "description": "Successful Response" + "description": "OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized." }, - "422": { + "400": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/HTTPValidationError" + "type": "string" } } }, - "description": "Validation Error" - } - }, - "summary": "Get one hop results from source type to target type. Note: Please GET /predicates to determine what target goes with a source" - } - }, - "/{node_type}/{curie}": { - "get": { - "description": "Returns `node` matching `curie`.", - "operationId": "node__node_type___curie__get", - "parameters": [ - { - "in": "path", - "name": "node_type", - "required": true, - "schema": { - "title": "Node Type", - "type": "string" - } + "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)." }, - { - "in": "path", - "name": "curie", - "required": true, - "schema": { - "title": "Curie", - "type": "string" - } - } - ], - "responses": { - "200": { + "500": { "content": { "application/json": { "schema": { - "items": {}, - "title": "Response Node Node Type Curie Get", - "type": "array" + "type": "string" } } }, - "description": "Successful Response" + "description": "Internal server error." }, - "422": { + "501": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/HTTPValidationError" + "type": "string" } } }, - "description": "Validation Error" + "description": "Not implemented." } }, - "summary": "Find `node` by `curie`" + "summary": "Query reasoner via one of several inputs", + "tags": [ + "trapi" + ], + "x-swagger-router-controller": "swagger_server.controllers.query_controller" } } }, "servers": [ { - "description": "Default server", - "url": "https://automat.renci.org/panther" + "url": "https://api.collaboratory.semanticscience.org" } ], "tags": [ { - "name": "translator" + "description": "Query reasoner using a predefined question type", + "name": "trapi" }, { - "name": "automat" + "name": "translator" } ] }, { - "_id": "1f277e1563fcfd124bfae2cc3c4bcdec", + "_id": "dca415f2d792976af9d642b7e73f7a41", "_meta": { - "date_created": "2021-02-11T00:06:11.157097+00:00", - "last_updated": "2021-03-05T08:02:08.299160+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/quickgo/smartapi.yaml", + "date_created": "2020-12-07T23:08:24.199007+00:00", + "last_updated": "2021-03-29T07:03:32.230606+00:00", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/litvar/smartapi.yaml", "username": "kevinxin90" }, - "_score": 0.6687226, + "_score": 0.6863549, "components": { "x-bte-kgs-operations": { - "ma_has_subclass_ma": [ + "variant_located_in_gene": [ { "inputs": [ { - "id": "GO", - "semantic": "MolecularActivity" + "id": "DBSNP", + "semantic": "SequenceVariant" } ], "outputs": [ { - "id": "GO", - "semantic": "MolecularActivity" + "id": "SYMBOL", + "semantic": "Gene" } ], "parameters": { - "goid": "{inputs[0]}" + "variantid": "{inputs[0]}%23%23" }, - "predicate": "has_subclass", + "predicate": "located_in", "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ma_has_subclass_ma" + "$ref": "#/components/x-bte-response-mapping/variant_located_in_gene" }, - "source": "Gene Ontology", + "source": "dbsnp", "supportBatch": false } ] }, "x-bte-response-mapping": { - "ma_has_subclass_ma": { - "GO": "results.children.id", - "name": "results.children.name", - "relation": "results.children.relation" + "variant_located_in_gene": { + "SYMBOL": "gene.name" } } }, "info": { "contact": { - "email": "help@pharmgkb.org", - "name": "pharmgkb help desk", - "x-role": "responsible developer" + "email": "luzh@ncbi.nlm.nih.gov", + "name": "Zhiyong Lu" }, - "description": "The QuickGO REST API provides access to key biological data from QuickGO and GOA. The services provide a unified interface to query information about ontology terms from GO (the Gene Ontology) and ECO (the Evidence & Conclusion Ontology), Gene Ontology annotations from the EBI's GOA database, and gene products (proteins from UniProt, RNA from RNAcentral and complexes from ComplexPortal). ", - "termsOfService": "https://www.ebi.ac.uk/QuickGO/services", - "title": "QuickGO API", - "version": "1.0", + "description": "LitVar allows the search and retrieval of variant relevant information from the biomedical literature and shows key biological relations between a variant and its close related entities (e.g. genes, diseases, and drugs). The LitVar results are automatically extracted (with regular updates) from over 27 million PubMed articles as well as applicable full-text articles in PubMed Central.", + "termsOfService": "https://www.ncbi.nlm.nih.gov/home/about/policies/", + "title": "LitVar API", + "version": "1.0.0", "x-translator": { "component": "KP", "team": [ @@ -18323,14 +18398,14 @@ } }, "paths": { - "/ontology/go/terms/{goid}/children": { + "/entity/litvar/{variantid}": { "get": { "parameters": [ { - "description": "Put Gene Ontology ID here, e.g. GO:0000082", - "example": "GO:0000082", + "description": "rsid", + "example": "rs121913527", "in": "path", - "name": "goid", + "name": "variantid", "required": true, "schema": { "type": "string" @@ -18339,13 +18414,13 @@ ], "responses": { "200": { - "description": "A gene ontolgoy annotation object" + "description": "publications mentioned the submitted variant" } }, - "summary": "retrieve the children of specified ontology terms", + "summary": "Retrieve PMIDs of publications mentioning submitted variants", "x-bte-kgs-operations": [ { - "$ref": "#/components/x-bte-kgs-operations/ma_has_subclass_ma" + "$ref": "#/components/x-bte-kgs-operations/variant_located_in_gene" } ] } @@ -18354,12 +18429,12 @@ "servers": [ { "description": "Production server", - "url": "https://www.ebi.ac.uk/QuickGO/services" + "url": "https://www.ncbi.nlm.nih.gov/research/bionlp/litvar/api/v1" } ], "tags": [ { - "name": "ontology" + "name": "variant" }, { "name": "translator" @@ -18367,14 +18442,14 @@ ] }, { - "_id": "9d7ab69df070c2c1b9ce89e750569b5b", + "_id": "786e41a17dbb75399f22e09858f828b7", "_meta": { - "date_created": "2021-01-26T00:00:59.341300+00:00", - "last_updated": "2021-03-05T08:03:39.876297+00:00", - "url": "https://automat.renci.org/chemical-normalization/openapi.json", + "date_created": "2021-01-26T00:02:48.347118+00:00", + "last_updated": "2021-03-29T07:03:51.419861+00:00", + "url": "https://automat.renci.org/chembio/openapi.json", "username": "YaphetKG" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { "email": "kebedey@renci.org", @@ -18382,9 +18457,9 @@ "x-id": "https://github.com/yaphetkg", "x-role": "contributor" }, - "description": "A graph linking together similar compounds. Two compounds are linked by an edge in the graph if they are equivalent when charge, salts, and stereochemistry are ignored.", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat%20Chemical%20normalization&provider_long=RENCI", - "title": "Automat Chemical normalization", + "description": "A graph based on [chem2bio2rdf (http://cheminfov.informatics.indiana.edu:8080/c2b2r/)](http://cheminfov.informatics.indiana.edu:8080/c2b2r/).", + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Chembio&provider_long=RENCI", + "title": "Automat Chembio", "version": "1.0.0", "x-translator": { "component": "KP", @@ -19103,7 +19178,7 @@ "servers": [ { "description": "Default server", - "url": "https://automat.renci.org/chemical-normalization" + "url": "https://automat.renci.org/chembio" } ], "tags": [ @@ -19116,14 +19191,14 @@ ] }, { - "_id": "3f3c925151f42aac9a5aca7a7eabe814", + "_id": "9d7ab69df070c2c1b9ce89e750569b5b", "_meta": { - "date_created": "2021-02-03T00:04:18.945970+00:00", - "last_updated": "2021-03-05T08:03:37.560390+00:00", - "url": "https://automat.renci.org/mychem/openapi.json", + "date_created": "2021-01-26T00:00:59.341300+00:00", + "last_updated": "2021-03-29T07:03:51.982362+00:00", + "url": "https://automat.renci.org/chemical-normalization/openapi.json", "username": "YaphetKG" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { "email": "kebedey@renci.org", @@ -19131,9 +19206,9 @@ "x-id": "https://github.com/yaphetkg", "x-role": "contributor" }, - "description": "A graph integrating DrugBank, DrugCentral, and Aeolus data as provided by [mychem.info](mychem.info).", - "termsOfService": "http://http://robokop.renci.org:7055/tos?service_long=Automat Mychem&provider_long=RENCI", - "title": "Automat MyChem", + "description": "A graph linking together similar compounds. Two compounds are linked by an edge in the graph if they are equivalent when charge, salts, and stereochemistry are ignored.", + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Chemical Normalization&provider_long=RENCI", + "title": "Automat Chemical normalization", "version": "1.0.0", "x-translator": { "component": "KP", @@ -19852,7 +19927,7 @@ "servers": [ { "description": "Default server", - "url": "https://automat.renci.org/mychem" + "url": "https://automat.renci.org/chemical-normalization" } ], "tags": [ @@ -19865,14 +19940,14 @@ ] }, { - "_id": "132da307d445fac70a403a5e623107d5", + "_id": "1c0aff2a70b1ed677867c0db8011746f", "_meta": { - "date_created": "2021-02-04T00:00:37.939131+00:00", - "last_updated": "2021-03-05T08:02:37.087131+00:00", - "url": "https://automat.renci.org/hetio/openapi.json", + "date_created": "2021-02-03T16:03:16.375825+00:00", + "last_updated": "2021-03-29T07:04:13.339365+00:00", + "url": "https://automat.renci.org/ontological-hierarchy/openapi.json", "username": "YaphetKG" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { "email": "kebedey@renci.org", @@ -19880,9 +19955,9 @@ "x-id": "https://github.com/yaphetkg", "x-role": "contributor" }, - "description": "A graph based on [hetionet (het.io)](het.io).", + "description": "A graph for ontological hierarchy extracted from Uberongraph.", "termsOfService": "http://linkmissing", - "title": "Automat Hetio", + "title": "Automat Ontological Hierarchy", "version": "1.0.0", "x-translator": { "component": "KP", @@ -20601,7 +20676,7 @@ "servers": [ { "description": "Default server", - "url": "https://automat.renci.org/hetio" + "url": "https://automat.renci.org/ontological-hierarchy" } ], "tags": [ @@ -20609,58 +20684,42 @@ "name": "translator" }, { - "name": "automat" + "name": "Automat" } ] }, { - "_id": "b9ba5e7ead2b07d7c132b1ce9ff30cce", + "_id": "a49ee52f6fb81a71cca84e9806732b76", "_meta": { - "date_created": "2021-02-23T19:08:10.676980+00:00", - "last_updated": "2021-03-05T08:03:40.467697+00:00", - "slug": "strider", - "url": "https://strider.renci.org/openapi.json", - "username": "patrickkwang" + "date_created": "2021-01-26T00:02:43.141214+00:00", + "last_updated": "2021-03-29T07:04:13.892270+00:00", + "url": "https://automat.renci.org/foodb/openapi.json", + "username": "YaphetKG" }, - "_score": 0.6687226, + "_score": 0.6863549, "info": { "contact": { - "email": "patrick@covar.com", - "name": "Patrick Wang", - "x-id": "https://github.com/patrickkwang", - "x-role": "responsible developer" + "email": "kebedey@renci.org", + "name": "Yaphet Kebede", + "x-id": "https://github.com/yaphetkg", + "x-role": "contributor" }, - "description": "Translator Autonomous Relay Agent", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Strider&provider_long=the%20Renaissance%20Computing%20Institute&provider_short=RENCI", - "title": "Strider", + "description": "A graph of the food/chemical relationships in [foodb.ca](foodb.ca).", + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Foodb&provider_long=RENCI", + "title": "Automat Foodb", "version": "1.0.0", "x-translator": { - "component": "ARA", + "component": "KP", "team": [ "Ranking Agent" ] } }, "paths": { - "/aquery": { + "/query": { "post": { - "description": "Start query processing.", - "operationId": "async_query_aquery_post", - "parameters": [ - { - "in": "query", - "name": "log_level", - "required": false, - "schema": { - "allOf": [ - { - "$ref": "#/components/schemas/LogLevelEnum" - } - ], - "default": "ERROR" - } - } - ], + "description": "Given a question graph return question graph plus answers.", + "operationId": "reasoner_api_query_post", "requestBody": { "content": { "application/json": { @@ -20673,26 +20732,17 @@ "example": { "message": { "query_graph": { - "edges": { - "e01": { - "object": "n1", - "predicate": "biolink:has_phenotype", - "subject": "n0" - } - }, + "edges": {}, "nodes": { "n0": { - "category": "biolink:Disease", - "id": "MONDO:0005148" - }, - "n1": { - "category": "biolink:PhenotypicFeature" + "category": "biolink:Gene", + "id": "NCBIGene:15" } } } } }, - "title": "Query" + "title": "Request" } } }, @@ -20702,7 +20752,9 @@ "200": { "content": { "application/json": { - "schema": {} + "schema": { + "$ref": "#/components/schemas/Query" + } } }, "description": "Successful Response" @@ -20718,68 +20770,38 @@ "description": "Validation Error" } }, - "summary": "Async Query" + "summary": "Query Reasoner API", + "tags": [ + "translator" + ] } }, - "/query_result": { - "post": { - "description": "Get results for a running or finished query ", - "operationId": "get_results_query_result_post", - "parameters": [ - { - "in": "query", - "name": "qid", - "required": true, - "schema": { - "title": "Qid", - "type": "string" - } - } - ], + "/reasonerapi": { + "get": { + "description": "Returns a list of question templates that can be used to query this plater instance.", + "operationId": "get_reasoner_api_reasonerapi_get", "responses": { "200": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Response" + "items": { + "$ref": "#/components/schemas/Message" + }, + "title": "Response Get Reasoner Api Reasonerapi Get", + "type": "array" } } }, "description": "Successful Response" - }, - "422": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/HTTPValidationError" - } - } - }, - "description": "Validation Error" } }, - "summary": "Get Results" - } - }, - "/query": { + "summary": "Get question templates" + }, "post": { - "description": "Handle synchronous query.", - "operationId": "sync_query_query_post", - "parameters": [ - { - "in": "query", - "name": "log_level", - "required": false, - "schema": { - "allOf": [ - { - "$ref": "#/components/schemas/LogLevelEnum" - } - ], - "default": "ERROR" - } - } - ], + "deprecated": true, + "description": "Handle TRAPI request.", + "operationId": "reasoner_api_reasonerapi_post", "requestBody": { "content": { "application/json": { @@ -20792,26 +20814,17 @@ "example": { "message": { "query_graph": { - "edges": { - "e01": { - "object": "n1", - "predicate": "biolink:has_phenotype", - "subject": "n0" - } - }, + "edges": {}, "nodes": { "n0": { - "category": "biolink:Disease", - "id": "MONDO:0005148" - }, - "n1": { - "category": "biolink:PhenotypicFeature" + "category": "biolink:Gene", + "id": "NCBIGene:15" } } } } }, - "title": "Query" + "title": "Request" } } }, @@ -20822,7 +20835,7 @@ "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Response" + "$ref": "#/components/schemas/Query" } } }, @@ -20839,22 +20852,26 @@ "description": "Validation Error" } }, - "summary": "Sync Query", - "tags": [ - "reasoner" - ] + "summary": "Reasoner Api" } }, - "/ars": { + "/cypher": { "post": { - "description": "Handle ARS message.", - "operationId": "handle_ars_ars_post", + "description": "Runs cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/).", + "operationId": "cypher_cypher_post", "requestBody": { "content": { "application/json": { "schema": { - "title": "Data", - "type": "object" + "allOf": [ + { + "$ref": "#/components/schemas/CypherRequest" + } + ], + "example": { + "query": "MATCH (n) RETURN count(n)" + }, + "title": "Request" } } }, @@ -20864,7 +20881,9 @@ "200": { "content": { "application/json": { - "schema": {} + "schema": { + "$ref": "#/components/schemas/CypherResponse" + } } }, "description": "Successful Response" @@ -20880,72 +20899,96 @@ "description": "Validation Error" } }, - "summary": "Handle Ars" + "summary": "Run cypher query" } }, - "/plan": { - "post": { - "description": "Generate plans for traversing knowledge providers.", - "operationId": "generate_traversal_plan_plan_post", - "requestBody": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Query" - } - } - }, - "required": true - }, + "/predicates": { + "get": { + "description": "Returns an object where outer keys represent source types with second level keys as targets. And the values of the second level keys is the type of possible edge typesthat connect these concepts.", + "operationId": "predicates_predicates_get", "responses": { "200": { "content": { "application/json": { "schema": { - "items": { + "additionalProperties": { + "additionalProperties": { + "items": { + "type": "string" + }, + "type": "array" + }, "type": "object" }, - "title": "Response Generate Traversal Plan Plan Post", - "type": "array" + "title": "Response Predicates Predicates Get", + "type": "object" } } }, "description": "Successful Response" - }, - "422": { + } + }, + "summary": "Get one-hop connection types", + "tags": [ + "translator" + ] + } + }, + "/graph/schema": { + "get": { + "deprecated": true, + "description": "Get one-hop connection types", + "operationId": "predicates_graph_schema_get", + "responses": { + "200": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/HTTPValidationError" + "title": "Response Predicates Graph Schema Get", + "type": "object" } } }, - "description": "Validation Error" + "description": "Successful Response" } }, - "summary": "Generate Traversal Plan" + "summary": "Get one-hop connection types" } }, - "/score": { - "post": { - "description": "Score results.", - "operationId": "score_results_score_post", - "requestBody": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Query" - } + "/simple_spec": { + "get": { + "description": "Returns a list of available predicates when choosing a single source or target curie. Calling this endpoint with no query parameters will return all possible hops for all types.", + "operationId": "simple_spec_simple_spec_get", + "parameters": [ + { + "in": "query", + "name": "source", + "required": false, + "schema": { + "title": "Source", + "type": "string" } }, - "required": true - }, + { + "in": "query", + "name": "target", + "required": false, + "schema": { + "title": "Target", + "type": "string" + } + } + ], "responses": { "200": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Message" + "items": { + "$ref": "#/components/schemas/SimpleSpecElement" + }, + "title": "Response Simple Spec Simple Spec Get", + "type": "array" } } }, @@ -20962,487 +21005,256 @@ "description": "Validation Error" } }, - "summary": "Score Results" - } - } - }, - "servers": [ - { - "url": "https://strider.renci.org" - } - ], - "tags": [ - { - "name": "translator" - }, - { - "name": "reasoner" - } - ] - }, - { - "_id": "1c056ffc7ed0dd1229e71c4752239465", - "_meta": { - "date_created": "2020-12-07T23:02:21.623909+00:00", - "last_updated": "2021-03-05T08:03:40.688463+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/ols/smartapi.yaml", - "username": "kevinxin90" - }, - "_score": 0.6687226, - "components": { - "x-bte-kgs-operations": { - "disease_has_subclass_disease": [ - { - "inputs": [ - { - "id": "DOID", - "semantic": "Disease" - } - ], - "outputs": [ - { - "id": "DOID", - "semantic": "Disease" - } - ], - "parameters": { - "id": "{inputs[0]}" - }, - "predicate": "has_subclass", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/disease_has_subclass_disease" - }, - "source": "disease ontology", - "supportBatch": false - } - ] - }, - "x-bte-response-mapping": { - "disease_has_subclass_disease": { - "DOID": "_embedded.terms.obo_id", - "description": "_embedded.terms.description", - "name": "_embedded.terms.label" + "summary": "Get one-hop connection schema" } - } - }, - "info": { - "contact": { - "email": "help@pharmgkb.org", - "name": "pharmgkb help desk", - "x-role": "responsible developer" }, - "description": "The OLS REST API provides access to key biological data from OLS. The services provide a unified interface to query information about ontology terms from GO (the Gene Ontology) and ECO (the Evidence & Conclusion Ontology), Gene Ontology annotations from the EBI's GOA database, and gene products (proteins from UniProt, RNA from RNAcentral and complexes from ComplexPortal). ", - "termsOfService": "https://www.ebi.ac.uk/OLS/services", - "title": "Ontology Lookup Service API", - "version": "1.0", - "x-translator": { - "component": "KP", - "team": [ - "Service Provider" - ] - } - }, - "paths": { - "/ontologies/doid/children": { + "/graph/summary": { "get": { - "parameters": [ - { - "description": "Put Disease Ontology ID here, e.g. DOID:0050686", - "example": "DOID:0050686", - "in": "query", - "name": "id", - "required": true, - "schema": { - "type": "string" - } - } - ], + "description": "Returns a summary of the graph.", + "operationId": "graph_summary_graph_summary_get", "responses": { "200": { - "description": "A DISEASE ontolgoy annotation object", - "x-bte-response-mapping": { - "$ref": "#/components/x-bte-response-mapping/hasChildren" - } + "content": { + "application/json": { + "schema": { + "title": "Response Graph Summary Graph Summary Get", + "type": "object" + } + } + }, + "description": "Successful Response" } }, - "summary": "retrieve the children of specified ontology terms", - "x-bte-kgs-operations": [ - { - "$ref": "#/components/x-bte-kgs-operations/disease_has_subclass_disease" - } - ] - } - } - }, - "servers": [ - { - "description": "Production server", - "url": "https://www.ebi.ac.uk/ols/api" - } - ], - "tags": [ - { - "name": "ontology" - }, - { - "name": "translator" - } - ] - }, - { - "_id": "0212611d1c670f9107baf00b77f0889a", - "_meta": { - "date_created": "2020-12-07T23:03:01.381530+00:00", - "last_updated": "2021-03-05T08:03:48.689244+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/CTD/smartapi.yaml", - "username": "kevinxin90" - }, - "_score": 0.6687226, - "components": { - "x-bte-kgs-operations": { - "chemical2gene": [ - { - "inputs": [ - { - "id": "MESH", - "semantic": "ChemicalSubstance" - } - ], - "outputs": [ - { - "id": "NCBIGENE", - "semantic": "Gene" - } - ], - "parameters": { - "format": "json", - "inputTerms": "{inputs[0]}", - "inputType": "chem", - "report": "genes_curated" - }, - "predicate": "related_to", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/drug-gene" - }, - "source": "CTD", - "supportBatch": false - } - ], - "gene2disease": [ - { - "inputs": [ - { - "id": "NCBIGENE", - "semantic": "Gene" - } - ], - "outputs": [ - { - "id": "MESH", - "semantic": "Disease" - } - ], - "parameters": { - "format": "json", - "inputTerms": "{inputs[0]}", - "inputType": "gene", - "report": "diseases_curated" - }, - "predicate": "related_to", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/gene-disease" - }, - "source": "CTD", - "supportBatch": false - } - ] - }, - "x-bte-response-mapping": { - "drug-gene": { - "NCBIGENE": "data.GeneId", - "inTaxon": "data.OrganismId", - "pubmed": "data.PubMedIds" - }, - "gene-disease": { - "MESH": "data.DiseaseID", - "name": "data.DiseaseName", - "pubmed": "data.PubMedIDs" + "summary": "Get graph summary" } - } - }, - "info": { - "contact": { - "email": "help@ctd.org", - "name": "CTD help desk", - "x-role": "responsible developer" }, - "description": "The CTD API", - "termsOfService": "http://ctdbase.org/help/linking.jsp#batchqueries", - "title": "CTD API", - "version": "1.0", - "x-translator": { - "component": "KP", - "team": [ - "Service Provider" - ] - } - }, - "paths": { - "/batchQuery.go": { - "get": { - "parameters": [ - { - "description": "The Input type of query", - "example": "chem", - "in": "query", - "name": "inputType", - "required": true, - "schema": { - "type": "string" - } - }, - { - "description": "The Input value of query, usually a mesh ID", - "example": "D003634", - "in": "query", - "name": "inputTerms", - "required": true, - "schema": { - "type": "string" - } - }, - { - "description": "The Output of query", - "example": "genes_curated", - "in": "query", - "name": "report", - "required": true, - "schema": { - "type": "string" - } - }, - { - "description": "The output format", - "example": "json", - "in": "query", - "name": "format", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "response object" - } - }, - "summary": "retrieve relationship data", - "x-bte-kgs-operations": [ - { - "$ref": "#/components/x-bte-kgs-operations/gene2disease" - }, - { - "$ref": "#/components/x-bte-kgs-operations/chemical2gene" - } - ] - } - } - }, - "servers": [ - { - "description": "Production server", - "url": "http://ctdbase.org/tools" - } - ], - "tags": [ - { - "name": "translator" - }, - { - "name": "ctd" - } - ] - }, - { - "_id": "ddd4fdce05c3e1b7b4499c80b8e3fb00", - "_meta": { - "date_created": "2021-02-03T00:02:04.073044+00:00", - "last_updated": "2021-03-05T08:04:47.840947+00:00", - "url": "https://aragorn.renci.org/openapi.json", - "username": "PhillipsOwen" - }, - "_score": 0.6687226, - "info": { - "contact": { - "email": "patrick@covar.com", - "name": "Patrick Wang", - "x-id": "https://github.com/patrickkwang", - "x-role": "responsible developer" - }, - "description": "ARAGORN: Performs a query operation which compiles data from numerous ARAGORN ranking agent services.", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=ARAGORN&provider_long=RENCI", - "title": "ARAGORN", - "version": "0.0.2", - "x-translator": { - "component": "ARA", - "team": [ - "Ranking Agent" - ] - } - }, - "paths": { - "/query": { + "/overlay": { "post": { - "description": "Performs a query operation which compiles data from numerous ARAGORN ranking agent services.\nThe services are called in the following order, each passing their output to the next service as an input:\n\nStrider -> (optional) Answer Coalesce -> ARAGORN-Ranker:omnicorp overlay -> ARAGORN-Ranker:weight correctness -> ARAGORN-Ranker:score", - "operationId": "query_handler_query_post", - "parameters": [ - { - "in": "query", - "name": "answer_coalesce_type", - "required": false, - "schema": { - "allOf": [ - { - "$ref": "#/components/schemas/MethodName" - } - ], - "default": "graph" - } - } - ], + "description": "Given a ReasonerAPI graph, add support edges for any nodes linked in result bindings.", + "operationId": "overlay_overlay_post", "requestBody": { "content": { "application/json": { "schema": { "allOf": [ { - "$ref": "#/components/schemas/Response" + "$ref": "#/components/schemas/Query" } ], - "default": { + "example": { "message": { - "query_graph": { + "knowledge_graph": { "edges": { - "e01": { - "object": "n1", - "predicate": "biolink:correlated_with", - "subject": "n0" + "9f7f9d86cb57e7190aafa57f7564eb05": { + "attributes": [ + { + "type": "WIKIDATA:Q80585", + "value": { + "ctime": 1610437123.7988985, + "predicate": "biolink:part_of", + "provided_by": "panther.get_gene_family_by_gene_family", + "publications": [], + "relation": "BFO:0000050", + "relation_label": "part of", + "source_database": "panther", + "source_id": "PANTHER.FAMILY:PTHR12015:SF170", + "target_id": "PANTHER.FAMILY:PTHR12015" + } + } + ], + "object": "PANTHER.FAMILY:PTHR12015", + "predicate": "biolink:part_of", + "subject": "PANTHER.FAMILY:PTHR12015:SF170" + }, + "dd8ef7a4606c4f8e405e6a5b1b095993": { + "attributes": [ + { + "type": "WIKIDATA:Q80585", + "value": { + "ctime": 1584932086.0009434, + "predicate": "biolink:part_of", + "provided_by": "panther.get_gene_by_gene_family", + "publications": [], + "relation": "BFO:0000050", + "relation_label": "part of", + "source_database": "panther", + "source_id": "NCBIGene:6352", + "target_id": "PANTHER.FAMILY:PTHR12015" + } + } + ], + "object": "PANTHER.FAMILY:PTHR12015", + "predicate": "biolink:part_of", + "subject": "NCBIGene:6352" } }, "nodes": { - "n0": { - "category": "biolink:Disease", - "id": "MONDO:0004979" + "NCBIGene:6352": { + "attributes": [ + { + "type": "WIKIDATA:Q80585", + "value": { + "category": [ + "biolink:BiologicalEntity", + "biolink:GenomicEntity", + "biolink:GeneOrGeneProduct", + "biolink:MacromolecularMachine", + "biolink:NamedThing", + "biolink:MolecularEntity", + "biolink:Gene" + ], + "chromosome": "17", + "equivalent_identifiers": [ + "ENSEMBL:ENSG00000271503", + "NCBIGene:6352", + "NCBIGene:6352", + "HGNC:10632", + "UniProtKB:P13501" + ], + "gene_family": [ + "Chemokine ligands" + ], + "gene_family_id": [ + 483 + ], + "location": "17q12", + "locus_group": "protein-coding gene", + "synonyms": [], + "taxon": 9606 + } + } + ], + "category": [ + "biolink:NamedThing", + "biolink:BiologicalEntity", + "biolink:MolecularEntity", + "biolink:GenomicEntity", + "biolink:GeneOrGeneProduct", + "biolink:MacromolecularMachine", + "biolink:Gene" + ], + "name": "CCL5" }, - "n1": { - "category": "biolink:ChemicalSubstance" + "PANTHER.FAMILY:PTHR12015": { + "attributes": [ + { + "type": "WIKIDATA:Q80585", + "value": { + "category": [ + "biolink:BiologicalEntity", + "biolink:GeneFamily", + "biolink:NamedThing", + "biolink:MolecularEntity", + "biolink:Entity" + ], + "equivalent_identifiers": [ + "PANTHER.FAMILY:PTHR12015" + ], + "synonyms": [] + } + } + ], + "category": [ + "biolink:NamedThing", + "biolink:BiologicalEntity", + "biolink:GeneFamily", + "biolink:MolecularEntity", + "biolink:Entity" + ], + "name": "SMALL INDUCIBLE CYTOKINE A" + }, + "PANTHER.FAMILY:PTHR12015:SF170": { + "attributes": [ + { + "type": "WIKIDATA:Q80585", + "value": { + "category": [ + "biolink:BiologicalEntity", + "biolink:GeneFamily", + "biolink:NamedThing", + "biolink:MolecularEntity", + "biolink:Entity" + ], + "equivalent_identifiers": [ + "PANTHER.FAMILY:PTHR12015:SF170" + ], + "synonyms": [] + } + } + ], + "category": [ + "biolink:NamedThing", + "biolink:BiologicalEntity", + "biolink:GeneFamily", + "biolink:MolecularEntity", + "biolink:Entity" + ], + "name": "C-C MOTIF CHEMOKINE 5" } } - } - } - }, - "title": "Response" - } - } - } - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Response" - } - } - }, - "description": "Successful Response" - }, - "422": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/HTTPValidationError" - } - } - }, - "description": "Validation Error" - } - }, - "summary": "Query Handler", - "tags": [ - "ARAGORN" - ] - } - } - }, - "servers": [ - { - "description": "Default server", - "url": "https://aragorn.renci.org" - } - ], - "tags": [ - { - "name": "translator" - }, - { - "name": "ARA" - } - ] - }, - { - "_id": "51742c9f6ca40d46bdeb6facd76257ff", - "_meta": { - "date_created": "2021-02-03T00:02:35.479989+00:00", - "last_updated": "2021-03-05T08:04:48.411287+00:00", - "url": "https://automat.renci.org/hmdb/openapi.json", - "username": "YaphetKG" - }, - "_score": 0.6687226, - "info": { - "contact": { - "email": "kebedey@renci.org", - "name": "Yaphet Kebede", - "x-id": "https://github.com/yaphetkg", - "x-role": "contributor" - }, - "description": "A graph based on the [Human Metabolome DataBase (hmdb.org)](hmdb.org).", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat HMDB&provider_long=RENCI", - "title": "Automat HMDB", - "version": "1.0.0", - "x-translator": { - "component": "KP", - "team": [ - "Ranking Agent" - ] - } - }, - "paths": { - "/query": { - "post": { - "description": "Given a question graph return question graph plus answers.", - "operationId": "reasoner_api_query_post", - "requestBody": { - "content": { - "application/json": { - "schema": { - "allOf": [ - { - "$ref": "#/components/schemas/Query" - } - ], - "example": { - "message": { + }, "query_graph": { - "edges": {}, + "edges": { + "e12": { + "object": "n2", + "predicate": "biolink:part_of", + "subject": "n1" + }, + "e23": { + "object": "n2", + "predicate": "biolink:part_of", + "subject": "n3" + } + }, "nodes": { - "n0": { + "n1": { "category": "biolink:Gene", - "id": "NCBIGene:15" + "id": "NCBIGene:6352", + "is_set": false + }, + "n2": { + "category": "biolink:GeneFamily", + "is_set": false + }, + "n3": { + "category": "biolink:GeneFamily", + "is_set": false } } - } + }, + "results": [ + { + "edge_bindings": { + "e12": [ + { + "id": "dd8ef7a4606c4f8e405e6a5b1b095993" + } + ], + "e23": [ + { + "id": "9f7f9d86cb57e7190aafa57f7564eb05" + } + ] + }, + "node_bindings": { + "n1": [ + { + "id": "NCBIGene:6352" + } + ], + "n2": [ + { + "id": "PANTHER.FAMILY:PTHR12015" + } + ], + "n3": [ + { + "id": "PANTHER.FAMILY:PTHR12015:SF170" + } + ] + } + } + ] } }, "title": "Request" @@ -21456,7 +21268,7 @@ "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Query" + "$ref": "#/components/schemas/Message" } } }, @@ -21473,72 +21285,72 @@ "description": "Validation Error" } }, - "summary": "Query Reasoner API", + "summary": "Overlay results with available connections between each node.", "tags": [ "translator" ] } }, - "/reasonerapi": { + "/about": { "get": { - "description": "Returns a list of question templates that can be used to query this plater instance.", - "operationId": "get_reasoner_api_reasonerapi_get", + "description": "Returns a JSON describing dataset.", + "operationId": "about_about_get", "responses": { "200": { "content": { "application/json": { "schema": { - "items": { - "$ref": "#/components/schemas/Message" - }, - "title": "Response Get Reasoner Api Reasonerapi Get", - "type": "array" + "title": "Response About About Get" } } }, "description": "Successful Response" } }, - "summary": "Get question templates" - }, - "post": { - "deprecated": true, - "description": "Handle TRAPI request.", - "operationId": "reasoner_api_reasonerapi_post", - "requestBody": { - "content": { - "application/json": { - "schema": { - "allOf": [ - { - "$ref": "#/components/schemas/Query" - } - ], - "example": { - "message": { - "query_graph": { - "edges": {}, - "nodes": { - "n0": { - "category": "biolink:Gene", - "id": "NCBIGene:15" - } - } - } - } - }, - "title": "Request" - } + "summary": "JSON about dataset" + } + }, + "/{source_type}/{target_type}/{curie}": { + "get": { + "description": "Returns one hop paths from `source_node_type` with `curie` to `target_node_type`.", + "operationId": "one_hop__source_type___target_type___curie__get", + "parameters": [ + { + "in": "path", + "name": "source_type", + "required": true, + "schema": { + "title": "Source Type", + "type": "string" } }, - "required": true - }, + { + "in": "path", + "name": "target_type", + "required": true, + "schema": { + "title": "Target Type", + "type": "string" + } + }, + { + "in": "path", + "name": "curie", + "required": true, + "schema": { + "title": "Curie", + "type": "string" + } + } + ], "responses": { "200": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Query" + "items": {}, + "title": "Response One Hop Source Type Target Type Curie Get", + "type": "array" } } }, @@ -21555,522 +21367,7 @@ "description": "Validation Error" } }, - "summary": "Reasoner Api" - } - }, - "/cypher": { - "post": { - "description": "Runs cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/).", - "operationId": "cypher_cypher_post", - "requestBody": { - "content": { - "application/json": { - "schema": { - "allOf": [ - { - "$ref": "#/components/schemas/CypherRequest" - } - ], - "example": { - "query": "MATCH (n) RETURN count(n)" - }, - "title": "Request" - } - } - }, - "required": true - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/CypherResponse" - } - } - }, - "description": "Successful Response" - }, - "422": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/HTTPValidationError" - } - } - }, - "description": "Validation Error" - } - }, - "summary": "Run cypher query" - } - }, - "/predicates": { - "get": { - "description": "Returns an object where outer keys represent source types with second level keys as targets. And the values of the second level keys is the type of possible edge typesthat connect these concepts.", - "operationId": "predicates_predicates_get", - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "additionalProperties": { - "additionalProperties": { - "items": { - "type": "string" - }, - "type": "array" - }, - "type": "object" - }, - "title": "Response Predicates Predicates Get", - "type": "object" - } - } - }, - "description": "Successful Response" - } - }, - "summary": "Get one-hop connection types", - "tags": [ - "translator" - ] - } - }, - "/graph/schema": { - "get": { - "deprecated": true, - "description": "Get one-hop connection types", - "operationId": "predicates_graph_schema_get", - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "title": "Response Predicates Graph Schema Get", - "type": "object" - } - } - }, - "description": "Successful Response" - } - }, - "summary": "Get one-hop connection types" - } - }, - "/simple_spec": { - "get": { - "description": "Returns a list of available predicates when choosing a single source or target curie. Calling this endpoint with no query parameters will return all possible hops for all types.", - "operationId": "simple_spec_simple_spec_get", - "parameters": [ - { - "in": "query", - "name": "source", - "required": false, - "schema": { - "title": "Source", - "type": "string" - } - }, - { - "in": "query", - "name": "target", - "required": false, - "schema": { - "title": "Target", - "type": "string" - } - } - ], - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "items": { - "$ref": "#/components/schemas/SimpleSpecElement" - }, - "title": "Response Simple Spec Simple Spec Get", - "type": "array" - } - } - }, - "description": "Successful Response" - }, - "422": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/HTTPValidationError" - } - } - }, - "description": "Validation Error" - } - }, - "summary": "Get one-hop connection schema" - } - }, - "/graph/summary": { - "get": { - "description": "Returns a summary of the graph.", - "operationId": "graph_summary_graph_summary_get", - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "title": "Response Graph Summary Graph Summary Get", - "type": "object" - } - } - }, - "description": "Successful Response" - } - }, - "summary": "Get graph summary" - } - }, - "/overlay": { - "post": { - "description": "Given a ReasonerAPI graph, add support edges for any nodes linked in result bindings.", - "operationId": "overlay_overlay_post", - "requestBody": { - "content": { - "application/json": { - "schema": { - "allOf": [ - { - "$ref": "#/components/schemas/Query" - } - ], - "example": { - "message": { - "knowledge_graph": { - "edges": { - "9f7f9d86cb57e7190aafa57f7564eb05": { - "attributes": [ - { - "type": "WIKIDATA:Q80585", - "value": { - "ctime": 1610437123.7988985, - "predicate": "biolink:part_of", - "provided_by": "panther.get_gene_family_by_gene_family", - "publications": [], - "relation": "BFO:0000050", - "relation_label": "part of", - "source_database": "panther", - "source_id": "PANTHER.FAMILY:PTHR12015:SF170", - "target_id": "PANTHER.FAMILY:PTHR12015" - } - } - ], - "object": "PANTHER.FAMILY:PTHR12015", - "predicate": "biolink:part_of", - "subject": "PANTHER.FAMILY:PTHR12015:SF170" - }, - "dd8ef7a4606c4f8e405e6a5b1b095993": { - "attributes": [ - { - "type": "WIKIDATA:Q80585", - "value": { - "ctime": 1584932086.0009434, - "predicate": "biolink:part_of", - "provided_by": "panther.get_gene_by_gene_family", - "publications": [], - "relation": "BFO:0000050", - "relation_label": "part of", - "source_database": "panther", - "source_id": "NCBIGene:6352", - "target_id": "PANTHER.FAMILY:PTHR12015" - } - } - ], - "object": "PANTHER.FAMILY:PTHR12015", - "predicate": "biolink:part_of", - "subject": "NCBIGene:6352" - } - }, - "nodes": { - "NCBIGene:6352": { - "attributes": [ - { - "type": "WIKIDATA:Q80585", - "value": { - "category": [ - "biolink:BiologicalEntity", - "biolink:GenomicEntity", - "biolink:GeneOrGeneProduct", - "biolink:MacromolecularMachine", - "biolink:NamedThing", - "biolink:MolecularEntity", - "biolink:Gene" - ], - "chromosome": "17", - "equivalent_identifiers": [ - "ENSEMBL:ENSG00000271503", - "NCBIGene:6352", - "NCBIGene:6352", - "HGNC:10632", - "UniProtKB:P13501" - ], - "gene_family": [ - "Chemokine ligands" - ], - "gene_family_id": [ - 483 - ], - "location": "17q12", - "locus_group": "protein-coding gene", - "synonyms": [], - "taxon": 9606 - } - } - ], - "category": [ - "biolink:NamedThing", - "biolink:BiologicalEntity", - "biolink:MolecularEntity", - "biolink:GenomicEntity", - "biolink:GeneOrGeneProduct", - "biolink:MacromolecularMachine", - "biolink:Gene" - ], - "name": "CCL5" - }, - "PANTHER.FAMILY:PTHR12015": { - "attributes": [ - { - "type": "WIKIDATA:Q80585", - "value": { - "category": [ - "biolink:BiologicalEntity", - "biolink:GeneFamily", - "biolink:NamedThing", - "biolink:MolecularEntity", - "biolink:Entity" - ], - "equivalent_identifiers": [ - "PANTHER.FAMILY:PTHR12015" - ], - "synonyms": [] - } - } - ], - "category": [ - "biolink:NamedThing", - "biolink:BiologicalEntity", - "biolink:GeneFamily", - "biolink:MolecularEntity", - "biolink:Entity" - ], - "name": "SMALL INDUCIBLE CYTOKINE A" - }, - "PANTHER.FAMILY:PTHR12015:SF170": { - "attributes": [ - { - "type": "WIKIDATA:Q80585", - "value": { - "category": [ - "biolink:BiologicalEntity", - "biolink:GeneFamily", - "biolink:NamedThing", - "biolink:MolecularEntity", - "biolink:Entity" - ], - "equivalent_identifiers": [ - "PANTHER.FAMILY:PTHR12015:SF170" - ], - "synonyms": [] - } - } - ], - "category": [ - "biolink:NamedThing", - "biolink:BiologicalEntity", - "biolink:GeneFamily", - "biolink:MolecularEntity", - "biolink:Entity" - ], - "name": "C-C MOTIF CHEMOKINE 5" - } - } - }, - "query_graph": { - "edges": { - "e12": { - "object": "n2", - "predicate": "biolink:part_of", - "subject": "n1" - }, - "e23": { - "object": "n2", - "predicate": "biolink:part_of", - "subject": "n3" - } - }, - "nodes": { - "n1": { - "category": "biolink:Gene", - "id": "NCBIGene:6352", - "is_set": false - }, - "n2": { - "category": "biolink:GeneFamily", - "is_set": false - }, - "n3": { - "category": "biolink:GeneFamily", - "is_set": false - } - } - }, - "results": [ - { - "edge_bindings": { - "e12": [ - { - "id": "dd8ef7a4606c4f8e405e6a5b1b095993" - } - ], - "e23": [ - { - "id": "9f7f9d86cb57e7190aafa57f7564eb05" - } - ] - }, - "node_bindings": { - "n1": [ - { - "id": "NCBIGene:6352" - } - ], - "n2": [ - { - "id": "PANTHER.FAMILY:PTHR12015" - } - ], - "n3": [ - { - "id": "PANTHER.FAMILY:PTHR12015:SF170" - } - ] - } - } - ] - } - }, - "title": "Request" - } - } - }, - "required": true - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Message" - } - } - }, - "description": "Successful Response" - }, - "422": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/HTTPValidationError" - } - } - }, - "description": "Validation Error" - } - }, - "summary": "Overlay results with available connections between each node.", - "tags": [ - "translator" - ] - } - }, - "/about": { - "get": { - "description": "Returns a JSON describing dataset.", - "operationId": "about_about_get", - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "title": "Response About About Get" - } - } - }, - "description": "Successful Response" - } - }, - "summary": "JSON about dataset" - } - }, - "/{source_type}/{target_type}/{curie}": { - "get": { - "description": "Returns one hop paths from `source_node_type` with `curie` to `target_node_type`.", - "operationId": "one_hop__source_type___target_type___curie__get", - "parameters": [ - { - "in": "path", - "name": "source_type", - "required": true, - "schema": { - "title": "Source Type", - "type": "string" - } - }, - { - "in": "path", - "name": "target_type", - "required": true, - "schema": { - "title": "Target Type", - "type": "string" - } - }, - { - "in": "path", - "name": "curie", - "required": true, - "schema": { - "title": "Curie", - "type": "string" - } - } - ], - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "items": {}, - "title": "Response One Hop Source Type Target Type Curie Get", - "type": "array" - } - } - }, - "description": "Successful Response" - }, - "422": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/HTTPValidationError" - } - } - }, - "description": "Validation Error" - } - }, - "summary": "Get one hop results from source type to target type. Note: Please GET /predicates to determine what target goes with a source" + "summary": "Get one hop results from source type to target type. Note: Please GET /predicates to determine what target goes with a source" } }, "/{node_type}/{curie}": { @@ -22128,7 +21425,7 @@ "servers": [ { "description": "Default server", - "url": "https://automat.renci.org/hmdb" + "url": "https://automat.renci.org/foodb" } ], "tags": [ @@ -22140,142 +21437,6 @@ } ] }, - { - "_id": "542ba165e1b4227854cf7c0a8addcc79", - "_meta": { - "date_created": "2020-12-07T23:03:47.953540+00:00", - "last_updated": "2021-03-05T08:05:01.535385+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/opentarget/smartapi.yaml", - "username": "kevinxin90" - }, - "_score": 0.6687226, - "components": { - "x-bte-kgs-operations": { - "gene_related_to_chemical": [ - { - "inputs": [ - { - "id": "ENSEMBL", - "semantic": "Gene" - } - ], - "outputs": [ - { - "id": "CHEMBL.COMPOUND", - "semantic": "ChemicalSubstance" - } - ], - "parameters": { - "datasource": "chembl", - "fields": "drug", - "size": 100, - "target": "{inputs[0]}" - }, - "predicate": "related_to", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/gene_related_to_chemical" - }, - "source": "CHEMBL", - "supportBatch": false - } - ] - }, - "x-bte-response-mapping": { - "gene_related_to_chemical": { - "CHEMBL.COMPOUND": "data.drug.id", - "moleculeType": "data.drug.molecule_type", - "name": "data.drug.molecule_name" - } - } - }, - "info": { - "contact": { - "email": "help@opentarget.org", - "name": "opentarget help desk", - "x-role": "responsible developer" - }, - "description": "The Opentarget API", - "termsOfService": "http://www.opentarget.org", - "title": "OpenTarget API", - "version": "1.0", - "x-translator": { - "component": "KP", - "team": [ - "Service Provider" - ] - } - }, - "paths": { - "/platform/public/evidence/filter": { - "get": { - "parameters": [ - { - "description": "ensembl gene id", - "example": "ENSG00000088832", - "in": "query", - "name": "target", - "required": true, - "schema": { - "type": "string" - } - }, - { - "description": "size of the output", - "example": 100, - "in": "query", - "name": "size", - "schema": { - "type": "integer" - } - }, - { - "description": "the output field", - "example": "drug", - "in": "query", - "name": "fields", - "schema": { - "type": "string" - } - }, - { - "description": "the data source", - "example": "chembl", - "in": "query", - "name": "datasource", - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "A biosample object" - } - }, - "summary": "retrieve evidence", - "x-bte-kgs-operations": [ - { - "$ref": "#/components/x-bte-kgs-operations/gene_related_to_chemical" - } - ] - } - } - }, - "servers": [ - { - "description": "Production server", - "url": "https://platform-api.opentargets.io/v3" - } - ], - "tags": [ - { - "name": "translator" - }, - { - "name": "opentarget" - } - ] - }, { "_id": "4f7b6f661ac61ed64190d5b26d87aff5", "_meta": { @@ -22284,7 +21445,7 @@ "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/robokop_extend/smartapi.yaml", "username": "kevinxin90" }, - "_score": 0.6687226, + "_score": 0.6863549, "components": { "x-bte-kgs-operations": { "associatedWith": { @@ -22543,175 +21704,74 @@ ] }, { - "_id": "dca415f2d792976af9d642b7e73f7a41", - "_meta": { - "date_created": "2020-12-07T23:08:24.199007+00:00", - "last_updated": "2021-03-05T08:04:48.869827+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/litvar/smartapi.yaml", - "username": "kevinxin90" - }, - "_score": 0.6687226, - "components": { - "x-bte-kgs-operations": { - "variant_located_in_gene": [ - { - "inputs": [ - { - "id": "DBSNP", - "semantic": "SequenceVariant" - } - ], - "outputs": [ - { - "id": "SYMBOL", - "semantic": "Gene" - } - ], - "parameters": { - "variantid": "{inputs[0]}%23%23" - }, - "predicate": "located_in", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/variant_located_in_gene" - }, - "source": "dbsnp", - "supportBatch": false - } - ] - }, - "x-bte-response-mapping": { - "variant_located_in_gene": { - "SYMBOL": "gene.name" - } - } - }, - "info": { - "contact": { - "email": "luzh@ncbi.nlm.nih.gov", - "name": "Zhiyong Lu" - }, - "description": "LitVar allows the search and retrieval of variant relevant information from the biomedical literature and shows key biological relations between a variant and its close related entities (e.g. genes, diseases, and drugs). The LitVar results are automatically extracted (with regular updates) from over 27 million PubMed articles as well as applicable full-text articles in PubMed Central.", - "termsOfService": "https://www.ncbi.nlm.nih.gov/home/about/policies/", - "title": "LitVar API", - "version": "1.0.0", - "x-translator": { - "component": "KP", - "team": [ - "Service Provider" - ] - } - }, - "paths": { - "/entity/litvar/{variantid}": { - "get": { - "parameters": [ - { - "description": "rsid", - "example": "rs121913527", - "in": "path", - "name": "variantid", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "publications mentioned the submitted variant" - } - }, - "summary": "Retrieve PMIDs of publications mentioning submitted variants", - "x-bte-kgs-operations": [ - { - "$ref": "#/components/x-bte-kgs-operations/variant_located_in_gene" - } - ] - } - } - }, - "servers": [ - { - "description": "Production server", - "url": "https://www.ncbi.nlm.nih.gov/research/bionlp/litvar/api/v1" - } - ], - "tags": [ - { - "name": "variant" - }, - { - "name": "translator" - } - ] - }, - { - "_id": "eb28713e2e23160e80e88f3a5dabcca4", + "_id": "71add13e7c8b26b0046cfb8cf5092395", "_meta": { - "date_created": "2020-03-12T16:20:11.288144+00:00", - "last_updated": "2021-02-17T07:42:16.930988+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/RGD/smartapi.yaml", + "date_created": "2020-03-12T16:20:50.656877+00:00", + "last_updated": "2021-02-17T07:42:20.416659+00:00", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/chembl/smartapi.yaml", "username": "kevinxin90" }, - "_score": 0.6687226, + "_score": 0.6863549, "components": { "x-bte-kgs-operations": { - "hasHomolog": { + "target": { "inputs": [ { - "id": "rgd", - "semantic": "Gene" + "id": "chembl", + "semantic": "ChemicalSubstance" } ], "outputs": [ { - "id": "symbol", + "id": "chembl", "semantic": "Gene" } ], "parameters": { - "geneid": "{input1}" + "molecule_chembl_id": "{input1}" }, "response-mapping": { - "$ref": "#/components/x-bte-response-mapping/gene-homolog" + "$ref": "#/components/x-bte-response-mapping/drug-mechanism" }, "supportBatch": false } }, "x-bte-response-mapping": { - "gene-homolog": { + "drug-mechanism": { "@context": "http://schema.org", - "@type": "Gene", - "bts:hasHomolog": { - "$input": "bts:rgd", - "$source": "RGD", + "@type": "ChemicalSubstance", + "bts:chembl": "chembl", + "bts:target": { + "$input": "bts:chembl", + "$source": "chembl", "@type": "Gene", - "bts:symbol": "ensemblGeneSymbol" - }, - "bts:rgd": "rgd" + "bts:action": "mechanisms.action_type", + "bts:chembl": "mechanisms.target_chembl_id", + "bts:mechanism": "mechanisms.mechanism_of_action" + } } } }, "info": { "contact": { - "email": "help@rgd.org", - "name": "rgd help desk", + "email": "help@chembl.org", + "name": "chembl help desk", "x-role": "responsible developer" }, - "description": "The RGD API", - "termsOfService": "http://www.rgd.org", - "title": "RGD API", + "description": "The ChEMBL API", + "termsOfService": "http://www.ebi.ac.uk/chembl", + "title": "ChEMBL API", "version": "1.0" }, "paths": { - "/genes/{geneid}": { + "/data/mechanism.json": { "get": { "parameters": [ { - "description": "RGD id", - "example": "620465", - "in": "path", - "name": "geneid", + "description": "chembl id", + "example": "CHEMBL744", + "in": "query", + "name": "molecule_chembl_id", "required": true, "schema": { "type": "string" @@ -22720,16 +21780,16 @@ ], "responses": { "200": { - "description": "A RGD object", + "description": "A drug mechanism object", "x-bte-response-mapping": { - "$ref": "#/components/x-bte-response-mapping/gene-homolog" + "$ref": "#/components/x-bte-response-mapping/drug-mechanism" } } }, - "summary": "retrieve rgd data", + "summary": "retrieve drug mechanism", "x-bte-kgs-operations": { - "associatedWith": { - "$ref": "#/components/x-bte-kgs-operations/hasHomolog" + "treats": { + "$ref": "#/components/x-bte-kgs-operations/target" } } } @@ -22738,122 +21798,100 @@ "servers": [ { "description": "Production server", - "url": "https://rest.rgd.mcw.edu/rgdws" + "url": "http://www.ebi.ac.uk/chembl/api" } ], "tags": [ { - "name": "translator" + "name": "publication" }, { - "name": "gene" + "name": "translator" } ] }, { - "_id": "99592dd5fc3a69d3ed27692f3f278e47", + "_id": "ddd4fdce05c3e1b7b4499c80b8e3fb00", "_meta": { - "date_created": "2021-02-05T18:12:55.364895+00:00", - "last_updated": "2021-03-05T08:01:13.891663+00:00", - "url": "https://raw.githubusercontent.com/broadinstitute/genetics-kp-dev/master/transaltorRegistry.yaml", - "username": "marcdubybroad" + "date_created": "2021-02-03T00:02:04.073044+00:00", + "last_updated": "2021-03-29T07:04:51.179716+00:00", + "url": "https://aragorn.renci.org/openapi.json", + "username": "PhillipsOwen" }, - "_score": 0.62646353, + "_score": 0.6863549, "info": { "contact": { - "email": "mduby@broadinstitute.org", - "name": "Marc Duby", - "url": "https://github.com/broadinstitute/genetics-kp-dev" + "email": "patrick@covar.com", + "name": "Patrick Wang", + "x-id": "https://github.com/patrickkwang", + "x-role": "responsible developer" }, - "description": "A Translator API for Genetic Disease Asociation", - "termsOfService": "http://www.apache.org/licenses/LICENSE-2.0.html", - "title": "Genetics Provider", - "version": "1.0.0", - "x-reasoner_standard_version": "1.0.0", + "description": "ARAGORN: Performs a query operation which compiles data from numerous ARAGORN ranking agent services.", + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=ARAGORN&provider_long=RENCI", + "title": "ARAGORN", + "version": "0.0.2", "x-translator": { - "component": "KP", + "component": "ARA", "team": [ - "Genetics Provider" + "Ranking Agent" ] } }, "paths": { - "/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:Gene": { - "biolink:Disease": [ - "biolink:gene_associated_with_condition" - ] - } - }, - "type": "object" - } - } - }, - "description": "Predicates by source and target" - } - }, - "summary": "Get Genetics Provider supported relationships by source and target", - "tags": [ - "predicates", - "1.0.0" - ] - } - }, "/query": { "post": { - "description": "", - "operationId": "query", + "description": "Performs a query operation which compiles data from numerous ARAGORN ranking agent services.\nThe services are called in the following order, each passing their output to the next service as an input:\n\nStrider -> (optional) Answer Coalesce -> ARAGORN-Ranker:omnicorp overlay -> ARAGORN-Ranker:weight correctness -> ARAGORN-Ranker:score", + "operationId": "query_handler_query_post", + "parameters": [ + { + "in": "query", + "name": "answer_coalesce_type", + "required": false, + "schema": { + "allOf": [ + { + "$ref": "#/components/schemas/MethodName" + } + ], + "default": "graph" + } + } + ], "requestBody": { "content": { "application/json": { - "example": { - "message": { - "query_graph": { - "edges": { - "e00": { - "object": "n01", - "predicate": "biolink:gene_associated_with_condition", - "subject": "n00" - } - }, - "nodes": { - "n00": { - "category": "biolink:Gene", - "id": "NCBIGene:1803" + "schema": { + "allOf": [ + { + "$ref": "#/components/schemas/Response" + } + ], + "default": { + "message": { + "query_graph": { + "edges": { + "e01": { + "object": "n1", + "predicate": "biolink:correlated_with", + "subject": "n0" + } }, - "n01": { - "category": "biolink:Disease" + "nodes": { + "n0": { + "category": "biolink:Disease", + "id": "MONDO:0004979" + }, + "n1": { + "category": "biolink:ChemicalSubstance" + } } } } - } - }, - "schema": { - "$ref": "#/components/schemas/Query" + }, + "title": "Response" } } - }, - "description": "Query information to be submitted", - "required": true + } }, "responses": { "200": { @@ -22864,196 +21902,366 @@ } } }, - "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." + "description": "Successful Response" }, - "501": { + "422": { "content": { "application/json": { "schema": { - "type": "string" + "$ref": "#/components/schemas/HTTPValidationError" } } }, - "description": "Not implemented." + "description": "Validation Error" } }, - "summary": "Query Genetics Provider TRAPI API as KP", + "summary": "Query Handler", "tags": [ - "query", - "1.0.0" - ], - "x-swagger-router-controller": "swagger_server.controllers.query_controller" + "ARAGORN" + ] } } }, "servers": [ { - "url": "https://translator.broadinstitute.org/genetics_provider/trapi/v1.0" + "description": "Default server", + "url": "https://aragorn.renci.org" } ], "tags": [ - { - "name": "1.0.0" - }, { "name": "translator" }, { - "name": "x-translator" - }, - { - "name": "reasoner" - }, - { - "name": "metadata" - }, - { - "name": "query" + "name": "ARA" } ] }, { - "_id": "08f5b7b0c0a70245f8f42af19327611a", + "_id": "b9ba5e7ead2b07d7c132b1ce9ff30cce", "_meta": { - "date_created": "2020-12-11T17:16:15.751363+00:00", - "last_updated": "2021-03-05T08:00:47.280986+00:00", - "slug": "genetics_kp", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/genetics_provider/smartapi.yaml", - "username": "kevinxin90" + "date_created": "2021-02-23T19:08:10.676980+00:00", + "last_updated": "2021-03-29T07:04:51.721425+00:00", + "slug": "strider", + "url": "https://strider.renci.org/openapi.json", + "username": "patrickkwang" }, - "_score": 0.6048277, + "_score": 0.6863549, "info": { "contact": { - "email": "mvon@broadinstitute.org", - "name": "Marcin von Grotthuss" + "email": "patrick@covar.com", + "name": "Patrick Wang", + "x-id": "https://github.com/patrickkwang", + "x-role": "responsible developer" }, - "description": "A ReasonerStdAPI for Genetics Provider", - "termsOfService": "https://translator.broadinstitute.org", - "title": "Genetics Provider API", + "description": "Translator Autonomous Relay Agent", + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Strider&provider_long=the%20Renaissance%20Computing%20Institute&provider_short=RENCI", + "title": "Strider", "version": "1.0.0", - "x-reasoner_standard_version": "0.9.1", "x-translator": { - "component": "KP", + "component": "ARA", "team": [ - "Genetics Provider" + "Ranking Agent" ] } }, "paths": { - "/predicates": { - "get": { + "/aquery": { + "post": { + "description": "Start query processing.", + "operationId": "async_query_aquery_post", + "parameters": [ + { + "in": "query", + "name": "log_level", + "required": false, + "schema": { + "allOf": [ + { + "$ref": "#/components/schemas/LogLevelEnum" + } + ], + "default": "ERROR" + } + } + ], + "requestBody": { + "content": { + "application/json": { + "schema": { + "allOf": [ + { + "$ref": "#/components/schemas/Query" + } + ], + "example": { + "message": { + "query_graph": { + "edges": { + "e01": { + "object": "n1", + "predicate": "biolink:has_phenotype", + "subject": "n0" + } + }, + "nodes": { + "n0": { + "category": "biolink:Disease", + "id": "MONDO:0005148" + }, + "n1": { + "category": "biolink:PhenotypicFeature" + } + } + } + } + }, + "title": "Query" + } + } + }, + "required": true + }, + "responses": { + "200": { + "content": { + "application/json": { + "schema": {} + } + }, + "description": "Successful Response" + }, + "422": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/HTTPValidationError" + } + } + }, + "description": "Validation Error" + } + }, + "summary": "Async Query" + } + }, + "/query_result": { + "post": { + "description": "Get results for a running or finished query ", + "operationId": "get_results_query_result_post", + "parameters": [ + { + "in": "query", + "name": "qid", + "required": true, + "schema": { + "title": "Qid", + "type": "string" + } + } + ], "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": { - "disease": { - "gene": [ - "associated" - ] - } - }, - "type": "object" + "$ref": "#/components/schemas/Response" } } }, - "description": "Predicates by source and target" + "description": "Successful Response" + }, + "422": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/HTTPValidationError" + } + } + }, + "description": "Validation Error" } }, - "summary": "Get supported relationships by source and target" + "summary": "Get Results" } }, "/query": { "post": { + "description": "Handle synchronous query.", + "operationId": "sync_query_query_post", + "parameters": [ + { + "in": "query", + "name": "log_level", + "required": false, + "schema": { + "allOf": [ + { + "$ref": "#/components/schemas/LogLevelEnum" + } + ], + "default": "ERROR" + } + } + ], "requestBody": { "content": { "application/json": { - "example": { - "message": { - "query_graph": { - "edges": [ - { - "id": "e00", - "source_id": "n00", - "target_id": "n03", - "type": "associated" - }, - { - "id": "e00", - "source_id": "n01", - "target_id": "n03", - "type": "associated" - }, - { - "id": "e00", - "source_id": "n02", - "target_id": "n03", - "type": "associated" - } - ], - "nodes": [ - { - "curie": "NCBIGENE:5468", - "id": "n00", - "type": "gene" - }, - { - "curie": "NCBIGENE:5469", - "id": "n01", - "type": "gene" - }, - { - "curie": "NCBIGENE:5470", - "id": "n02", - "type": "gene" + "schema": { + "allOf": [ + { + "$ref": "#/components/schemas/Query" + } + ], + "example": { + "message": { + "query_graph": { + "edges": { + "e01": { + "object": "n1", + "predicate": "biolink:has_phenotype", + "subject": "n0" + } }, - { - "id": "n03", - "type": "disease" + "nodes": { + "n0": { + "category": "biolink:Disease", + "id": "MONDO:0005148" + }, + "n1": { + "category": "biolink:PhenotypicFeature" + } } - ] + } } + }, + "title": "Query" + } + } + }, + "required": true + }, + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Response" } - }, + } + }, + "description": "Successful Response" + }, + "422": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/HTTPValidationError" + } + } + }, + "description": "Validation Error" + } + }, + "summary": "Sync Query", + "tags": [ + "reasoner" + ] + } + }, + "/ars": { + "post": { + "description": "Handle ARS message.", + "operationId": "handle_ars_ars_post", + "requestBody": { + "content": { + "application/json": { + "schema": { + "title": "Data", + "type": "object" + } + } + }, + "required": true + }, + "responses": { + "200": { + "content": { + "application/json": { + "schema": {} + } + }, + "description": "Successful Response" + }, + "422": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/HTTPValidationError" + } + } + }, + "description": "Validation Error" + } + }, + "summary": "Handle Ars" + } + }, + "/plan": { + "post": { + "description": "Generate plans for traversing knowledge providers.", + "operationId": "generate_traversal_plan_plan_post", + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Query" + } + } + }, + "required": true + }, + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "items": { + "type": "object" + }, + "title": "Response Generate Traversal Plan Plan Post", + "type": "array" + } + } + }, + "description": "Successful Response" + }, + "422": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/HTTPValidationError" + } + } + }, + "description": "Validation Error" + } + }, + "summary": "Generate Traversal Plan" + } + }, + "/score": { + "post": { + "description": "Score results.", + "operationId": "score_results_score_post", + "requestBody": { + "content": { + "application/json": { "schema": { "$ref": "#/components/schemas/Query" } } }, - "description": "A message with question graph.", "required": true }, "responses": { @@ -23065,25 +22273,29 @@ } } }, - "description": "A message with knowledge graph and answers." + "description": "Successful Response" + }, + "422": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/HTTPValidationError" + } + } + }, + "description": "Validation Error" } }, - "summary": "Get answers to a question", - "tags": [ - "0.9.2" - ] + "summary": "Score Results" } } }, "servers": [ { - "url": "https://translator.broadinstitute.org/genetics_data_provider/" + "url": "https://strider.renci.org" } ], "tags": [ - { - "name": "0.9.2" - }, { "name": "translator" }, @@ -23093,39 +22305,34 @@ ] }, { - "_id": "20051e07e2e70ecba18e6bf8f2ca680b", + "_id": "99592dd5fc3a69d3ed27692f3f278e47", "_meta": { - "date_created": "2021-01-23T22:44:15.777639+00:00", - "last_updated": "2021-03-05T08:01:02.491021+00:00", - "url": "https://raw.githubusercontent.com/NCATSTranslator/Explanatory-Agent/master/Agent/smart-api.yaml", - "username": "tziomics" + "date_created": "2021-02-05T18:12:55.364895+00:00", + "last_updated": "2021-03-09T08:01:08.262488+00:00", + "url": "https://raw.githubusercontent.com/broadinstitute/genetics-kp-dev/master/transaltorRegistry.yaml", + "username": "marcdubybroad" }, - "_score": 0.6048277, + "_score": 0.64482534, "info": { "contact": { - "email": "rw37@drexel.edu", - "name": "Rosina Weber", - "x-id": "RosinaWeber", - "x-role": "responsible developer" - }, - "description": "A Translator Reasoner API for the Explanatory Agent", - "license": { - "name": "To Be Determined", - "url": "TBD" + "email": "mduby@broadinstitute.org", + "name": "Marc Duby", + "url": "https://github.com/broadinstitute/genetics-kp-dev" }, - "termsOfService": "TBD", - "title": "Explanatory Agent API", - "version": "1.0", + "description": "A Translator API for Genetic Disease Asociation", + "termsOfService": "http://www.apache.org/licenses/LICENSE-2.0.html", + "title": "Genetics Provider", + "version": "1.0.0", "x-reasoner_standard_version": "1.0.0", "x-translator": { - "component": "ARA", + "component": "KP", "team": [ - "Explanatory Agent" + "Genetics Provider" ] } }, "paths": { - "/predicates/": { + "/predicates": { "get": { "responses": { "200": { @@ -23145,9 +22352,9 @@ }, "description": "Source map", "example": { - "biolink:Disease": { - "biolink:Gene": [ - "biolink:condition_associated_with_gene" + "biolink:Gene": { + "biolink:Disease": [ + "biolink:gene_associated_with_condition" ] } }, @@ -23158,27 +22365,48 @@ "description": "Predicates by source and target" } }, - "summary": "Get supported relationships by source and target", + "summary": "Get Genetics Provider supported relationships by source and target", "tags": [ - "Predicates" - ], - "x-accessRestriction": "none" + "predicates", + "1.0.0" + ] } }, - "/query/": { + "/query": { "post": { - "externalDocs": { - "url": "https://github.com/NCATSTranslator/Explanatory-Agent/tree/master/Agent" - }, + "description": "", + "operationId": "query", "requestBody": { "content": { "application/json": { + "example": { + "message": { + "query_graph": { + "edges": { + "e00": { + "object": "n01", + "predicate": "biolink:gene_associated_with_condition", + "subject": "n00" + } + }, + "nodes": { + "n00": { + "category": "biolink:Gene", + "id": "NCBIGene:1803" + }, + "n01": { + "category": "biolink:Disease" + } + } + } + } + }, "schema": { "$ref": "#/components/schemas/Query" } } }, - "description": "A message with question graph.", + "description": "Query information to be submitted", "required": true }, "responses": { @@ -23190,50 +22418,83 @@ } } }, - "description": "A message with knowledge graph and answers." + "description": "OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized." }, "400": { - "description": "The request provided does not conform to the TRAPI standard." + "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": { - "description": "An internal server error has occurred." + "content": { + "application/json": { + "schema": { + "type": "string" + } + } + }, + "description": "Internal server error." + }, + "501": { + "content": { + "application/json": { + "schema": { + "type": "string" + } + } + }, + "description": "Not implemented." } }, - "summary": "Get answers to a question", + "summary": "Query Genetics Provider TRAPI API as KP", "tags": [ - "Query" + "query", + "1.0.0" ], - "x-accessRestriction": "none" + "x-swagger-router-controller": "swagger_server.controllers.query_controller" } } }, "servers": [ { - "description": "Production Server", - "url": "https://explanatory-agent.azurewebsites.net/v1.0/" + "url": "https://translator.broadinstitute.org/genetics_provider/trapi/v1.0" } ], "tags": [ { - "name": "explanatory" + "name": "1.0.0" }, { "name": "translator" }, { - "name": "1.0.0" + "name": "x-translator" + }, + { + "name": "reasoner" + }, + { + "name": "metadata" + }, + { + "name": "query" } ] }, { - "_id": "da159a55e799a163ee23783edcb11725", + "_id": "855adaa128ce5aa58a091d99e520d396", "_meta": { - "date_created": "2021-01-28T00:01:40.994577+00:00", - "last_updated": "2021-03-05T08:01:14.220549+00:00", - "url": "https://raw.githubusercontent.com/di2ag/chp_metadata/testingCORSsupport/smartapi.yaml", + "date_created": "2021-01-28T00:00:54.028991+00:00", + "last_updated": "2021-03-21T07:00:41.706363+00:00", + "url": "https://raw.githubusercontent.com/di2ag/chp_metadata/master/smartapi.yaml", "username": "veenhouse" }, - "_score": 0.6048277, + "_score": 0.6217669, "info": { "contact": { "email": "luke.j.veenhuis@dartmouth.edu", @@ -23249,7 +22510,7 @@ "termsOfService": "https://github.com/di2ag/chp_api/blob/master/terms%20of%20service", "title": "Connections Hypothesis Provider API", "version": "2.0", - "x-reasoner_standard_version": 1.0, + "x-reasoner_standard_version": 1, "x-translator": { "component": "KP", "team": [ @@ -23481,7 +22742,7 @@ "servers": [ { "description": "Production Server", - "url": "chp.thayer.dartmouth.edu/" + "url": "http://chp.thayer.dartmouth.edu/" } ], "tags": [ @@ -23504,7 +22765,7 @@ "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/indigo/openapi.yml", "username": "vdancik" }, - "_score": 0.6048277, + "_score": 0.6217669, "info": { "contact": { "email": "translator@broadinstitute.org", @@ -23603,240 +22864,351 @@ ] }, { - "_id": "9df83f691d5fa0d8eb9c9f5f6b6ebb39", + "_id": "20051e07e2e70ecba18e6bf8f2ca680b", "_meta": { - "date_created": "2021-01-30T21:31:39.801826+00:00", - "last_updated": "2021-03-05T08:01:21.747151+00:00", - "url": "https://bl-lookup-sri.renci.org/apidocs/openapi.yml", - "username": "kshefchek" + "date_created": "2021-01-23T22:44:15.777639+00:00", + "last_updated": "2021-03-29T07:01:49.920221+00:00", + "url": "https://raw.githubusercontent.com/NCATSTranslator/Explanatory-Agent/master/Agent/smart-api.yaml", + "username": "tziomics" }, - "_score": 0.6048277, + "_score": 0.6217669, "info": { "contact": { - "email": "bizon@renci.org", - "name": "Chris Bizon", - "x-id": "https://github.com/cbizon", + "email": "rw37@drexel.edu", + "name": "Rosina Weber", + "x-id": "RosinaWeber", "x-role": "responsible developer" }, - "description": "The Biolink Model defines a set of common concepts for use in Translator. These include semantic types for entities, as well as the relations between them. These concepts are organized into an inheritance hierarchy capturing different granularities of description. Furthermore, each concept contains metadata relating the concept to ontologies.\nThe Biolink Lookup Service provides a computational interface to the model, including access to previous versions. When the service is deployed, it queries the Biolink Github repository, and updates itself to access the latest version.", + "description": "A Translator Reasoner API for the Explanatory Agent", "license": { - "name": "MIT", - "url": "https://opensource.org/licenses/MIT" + "name": "To Be Determined", + "url": "TBD" }, - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Biolink+Model+Lookup&provider_long=the+Translator+Consortium", - "title": "Biolink Model Lookup", - "version": "1.0.0", + "termsOfService": "TBD", + "title": "Explanatory Agent API", + "version": "1.0", + "x-reasoner_standard_version": "1.0.0", "x-translator": { - "component": "Utility", + "component": "ARA", "team": [ - "Standards Reference Implementation Team" + "Explanatory Agent" ] } }, "paths": { - "/bl/{concept}/ancestors": { + "/predicates/": { "get": { - "description": "", - "parameters": [ - { - "default": "chemical_substance", - "in": "path", - "name": "concept", - "required": true - }, - { - "default": "latest", - "in": "query", - "name": "version" - } - ], "responses": { "200": { "content": { "application/json": { "schema": { - "items": { - "type": "string" + "additionalProperties": { + "additionalProperties": { + "description": "Array of predicates", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": "Target map", + "type": "object" }, - "type": "array" + "description": "Source map", + "example": { + "biolink:Disease": { + "biolink:Gene": [ + "biolink:condition_associated_with_gene" + ] + } + }, + "type": "object" } } }, - "description": "successful operation" + "description": "Predicates by source and target" } }, - "summary": "Return all ancestors (superclasses or superproperties) of concept, based on the BioLink Model YAML.", + "summary": "Get supported relationships by source and target", "tags": [ - "lookup" - ] + "Predicates" + ], + "x-accessRestriction": "none" } }, - "/bl/{concept}/descendants": { - "get": { - "description": "", - "parameters": [ - { - "default": "chemical_substance", - "in": "path", - "name": "concept", - "required": true + "/query/": { + "post": { + "externalDocs": { + "url": "https://github.com/NCATSTranslator/Explanatory-Agent/tree/master/Agent" + }, + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Query" + } + } }, - { - "default": "latest", - "in": "query", - "name": "version" - } - ], + "description": "A message with question graph.", + "required": true + }, "responses": { "200": { "content": { "application/json": { "schema": { - "items": { - "type": "string" - }, - "type": "array" + "$ref": "#/components/schemas/Response" } } }, - "description": "successful operation" + "description": "A message with knowledge graph and answers." + }, + "400": { + "description": "The request provided does not conform to the TRAPI standard." + }, + "500": { + "description": "An internal server error has occurred." } }, - "summary": "Return descendants (subclasses or subproperties) of concept, based on the BioLink Model YAML", + "summary": "Get answers to a question", "tags": [ - "lookup" - ] + "Query" + ], + "x-accessRestriction": "none" } + } + }, + "servers": [ + { + "description": "Production Server", + "url": "https://explanatory-agent.azurewebsites.net/v1.0/" + } + ], + "tags": [ + { + "name": "explanatory" }, - "/bl/{concept}/lineage": { - "get": { - "description": "", - "parameters": [ - { - "default": "chemical_substance", - "in": "path", - "name": "concept", - "required": true + { + "name": "translator" + }, + { + "name": "1.0.0" + } + ] + }, + { + "_id": "0a29abdf1b63a762ee93d29f29a8db67", + "_meta": { + "date_created": "2021-01-22T18:08:13.583794+00:00", + "last_updated": "2021-03-29T07:01:50.562624+00:00", + "url": "https://aragorn-ranker.renci.org/openapi.json", + "username": "PhillipsOwen" + }, + "_score": 0.6217669, + "info": { + "contact": { + "email": "patrick@covar.com", + "name": "Patrick Wang", + "x-id": "https://github.com/patrickkwang", + "x-role": "responsible developer" + }, + "description": "ARAGORN Ranker: The ranker used by the ARAGORN ARA, which takes a TRAPI 1.0 message containing answers, and calculates numerical scores for each answer.", + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=ARAGORN Ranker&provider_long=RENCI", + "title": "ARAGORN Ranker", + "version": "2.2.2", + "x-translator": { + "component": "ARA", + "team": [ + "Ranking Agent" + ] + } + }, + "paths": { + "/omnicorp_overlay": { + "post": { + "description": "Add support to message.\n\nAdd support edges to knowledge_graph and bindings to results.", + "operationId": "query_omnicorp_overlay_post", + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Response" + } + } }, - { - "default": "latest", - "in": "query", - "name": "version" - } - ], + "required": true + }, "responses": { "200": { "content": { "application/json": { "schema": { - "items": { - "type": "string" - }, - "type": "array" + "$ref": "#/components/schemas/Response" } } }, - "description": "successful operation" + "description": "Successful Response" + }, + "422": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/HTTPValidationError" + } + } + }, + "description": "Validation Error" } }, - "summary": "Return the ancestors and descendants of concept, based on the BioLink Model YAML", + "summary": "Query", "tags": [ - "lookup" + "ARAGORN-Ranker" ] } }, - "/uri_lookup/{uri}": { - "get": { - "description": "", + "/score": { + "post": { + "description": "Score answers.\n\nThis is mostly glue around the heavy lifting in ranker_obj.Ranker", + "operationId": "query_score_post", "parameters": [ { - "example": "RO:0002606", - "in": "path", - "name": "uri", - "required": true - }, - { - "default": "latest", "in": "query", - "name": "version" + "name": "jaccard_like", + "required": false, + "schema": { + "default": false, + "title": "Jaccard Like", + "type": "boolean" + } } ], + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Response" + } + } + }, + "required": true + }, "responses": { "200": { "content": { "application/json": { "schema": { - "items": { - "type": "string" - }, - "type": "array" + "$ref": "#/components/schemas/Response" } } }, - "description": "successful operation" + "description": "Successful Response" + }, + "422": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/HTTPValidationError" + } + } + }, + "description": "Validation Error" } }, - "summary": "Given the URI for a property, return the corresponding BioLink Model slot. Checks the Biolink Model YAML for both slot_uri and mappings.", + "summary": "Query", "tags": [ - "lookup" + "ARAGORN-Ranker" ] } }, - "/bl/{concept}": { - "get": { - "description": "", + "/weight_correctness": { + "post": { + "description": "Weight kgraph edges based on metadata.\n\n\"19 pubs from CTD is a 1, and 2 should at least be 0.5\"\n - cbizon", + "operationId": "query_weight_correctness_post", "parameters": [ { - "default": "chemical_substance", - "in": "path", - "name": "concept", - "required": true + "description": "Portion of cooccurrence publications relevant to a question", + "in": "query", + "name": "relevance", + "required": false, + "schema": { + "default": 0.0025, + "description": "Portion of cooccurrence publications relevant to a question", + "title": "Relevance", + "type": "number" + } }, { - "default": "latest", + "description": "Minimum weight (at 0 publications)", "in": "query", - "name": "version" + "name": "wt_min", + "required": false, + "schema": { + "default": 0, + "description": "Minimum weight (at 0 publications)", + "title": "Wt Min", + "type": "number" + } + }, + { + "description": "Maximum weight (at inf publications)", + "in": "query", + "name": "wt_max", + "required": false, + "schema": { + "default": 1, + "description": "Maximum weight (at inf publications)", + "title": "Wt Max", + "type": "number" + } + }, + { + "description": "Publications at 50% of wt_max", + "in": "query", + "name": "p50", + "required": false, + "schema": { + "default": 2, + "description": "Publications at 50% of wt_max", + "title": "P50", + "type": "number" + } } ], + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Response" + } + } + }, + "required": true + }, "responses": { "200": { "content": { "application/json": { "schema": { - "type": "object" + "$ref": "#/components/schemas/Response" } } }, - "description": "successful operation" - } - }, - "summary": "Get all properties for concept from the BioLink Model YAML.", - "tags": [ - "lookup" - ] - } - }, - "/versions": { - "get": { - "description": "", - "responses": { - "200": { + "description": "Successful Response" + }, + "422": { "content": { "application/json": { "schema": { - "items": { - "type": "string" - }, - "type": "array" + "$ref": "#/components/schemas/HTTPValidationError" } } }, - "description": "successful operation" + "description": "Validation Error" } }, - "summary": "Get available BioLink Model versions. These values can be used to parameterize other function calls.", + "summary": "Query", "tags": [ - "meta" + "ARAGORN-Ranker" ] } } @@ -23844,7 +23216,7 @@ "servers": [ { "description": "Default server", - "url": "https://bl-lookup-sri.renci.org/" + "url": "https://aragorn-ranker.renci.org" } ], "tags": [ @@ -23852,10 +23224,10 @@ "name": "translator" }, { - "name": "lookup" + "name": "ARAGORN" }, { - "name": "meta" + "name": "ARA" } ] }, @@ -23868,7 +23240,7 @@ "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/robokop/openapi.yml", "username": "patrickkwang" }, - "_score": 0.6048277, + "_score": 0.6217669, "info": { "contact": { "email": "patrick@covar.com", @@ -23995,508 +23367,259 @@ ] }, { - "_id": "855adaa128ce5aa58a091d99e520d396", + "_id": "9df83f691d5fa0d8eb9c9f5f6b6ebb39", "_meta": { - "date_created": "2021-01-28T00:00:54.028991+00:00", - "last_updated": "2021-03-05T08:02:09.858995+00:00", - "url": "https://raw.githubusercontent.com/di2ag/chp_metadata/master/smartapi.yaml", - "username": "veenhouse" + "date_created": "2021-01-30T21:31:39.801826+00:00", + "last_updated": "2021-03-29T07:03:29.076512+00:00", + "url": "https://bl-lookup-sri.renci.org/apidocs/openapi.yml", + "username": "kshefchek" }, - "_score": 0.6048277, + "_score": 0.6217669, "info": { "contact": { - "email": "luke.j.veenhuis@dartmouth.edu", - "name": "Luke Veenhuis", - "x-id": "LukeVeenhuis", + "email": "bizon@renci.org", + "name": "Chris Bizon", + "x-id": "https://github.com/cbizon", "x-role": "responsible developer" }, - "description": "A Translator Reasoner API for the Connections Hypothesis Provider", + "description": "The Biolink Model defines a set of common concepts for use in Translator. These include semantic types for entities, as well as the relations between them. These concepts are organized into an inheritance hierarchy capturing different granularities of description. Furthermore, each concept contains metadata relating the concept to ontologies.\nThe Biolink Lookup Service provides a computational interface to the model, including access to previous versions. When the service is deployed, it queries the Biolink Github repository, and updates itself to access the latest version.", "license": { - "name": "Apache 2.0", - "url": "http://www.apache.org/licenses/LICENSE-2.0.html" + "name": "MIT", + "url": "https://opensource.org/licenses/MIT" }, - "termsOfService": "https://github.com/di2ag/chp_api/blob/master/terms%20of%20service", - "title": "Connections Hypothesis Provider API", - "version": "2.0", - "x-reasoner_standard_version": 1.0, + "termsOfService": "http://robokop.renci.org:7055/tos?service_long=Biolink+Model+Lookup&provider_long=the+Translator+Consortium", + "title": "Biolink Model Lookup", + "version": "1.0.0", "x-translator": { - "component": "KP", + "component": "Utility", "team": [ - "Connections Hypothesis Provider" + "Standards Reference Implementation Team" ] } }, "paths": { - "/predicates": { + "/bl/{concept}/ancestors": { "get": { + "description": "", + "parameters": [ + { + "default": "chemical_substance", + "in": "path", + "name": "concept", + "required": true + }, + { + "default": "latest", + "in": "query", + "name": "version" + } + ], "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:Drug": { - "biolink:Disease": [ - "biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation" - ] - }, - "biolink:Gene": { - "biolink:Disease": [ - "biolink:GeneToDiseaseAssociation" - ] - } + "items": { + "type": "string" }, - "type": "object" + "type": "array" } } }, - "description": "Predicates by source and target" + "description": "successful operation" } }, - "summary": "Get supported relationships by source and target", + "summary": "Return all ancestors (superclasses or superproperties) of concept, based on the BioLink Model YAML.", "tags": [ - "Predicates" - ], - "x-accessRestriction": "none" + "lookup" + ] } }, - "/versions": { + "/bl/{concept}/descendants": { "get": { + "description": "", + "parameters": [ + { + "default": "chemical_substance", + "in": "path", + "name": "concept", + "required": true + }, + { + "default": "latest", + "in": "query", + "name": "version" + } + ], "responses": { "200": { "content": { "application/json": { "schema": { - "additionalProperties": { - "additionalProperties": { - "description": "object of service versions", - "items": { - "type": "string" - }, - "type": "object" - } - }, - "example": { - "chp": "1.1.0", - "chp_client": "0.2.1", - "chp_data": "0.1.1", - "pybkb": "1.1.0" + "items": { + "type": "string" }, - "type": "object" + "type": "array" } } }, - "description": "versions of our service" + "description": "successful operation" } }, - "summary": "Get a list of versions of our service repositories", + "summary": "Return descendants (subclasses or subproperties) of concept, based on the BioLink Model YAML", "tags": [ - "Versions" + "lookup" ] } }, - "/query": { - "post": { - "externalDocs": { - "url": "https://github.com/di2ag/chp_client" + "/bl/{concept}/lineage": { + "get": { + "description": "", + "parameters": [ + { + "default": "chemical_substance", + "in": "path", + "name": "concept", + "required": true + }, + { + "default": "latest", + "in": "query", + "name": "version" + } + ], + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "items": { + "type": "string" + }, + "type": "array" + } + } + }, + "description": "successful operation" + } }, - "requestBody": { - "content": { - "application/json": { - "example": { - "message": { - "query_graph": { - "edges": { - "e0": { - "object": "n2", - "predicate": "biolink:GeneToDiseaseAssociation", - "subject": "n0" - }, - "e1": { - "object": "n2", - "predicate": "biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation", - "subject": "n1" - }, - "e2": { - "object": "n3", - "predicate": "biolink:DiseaseToPhenotypicFeatureAssociation", - "properties": { - "days": 500, - "qualifier": ">=" - }, - "subject": "n2" - } - }, - "nodes": { - "n0": { - "category": "biolink:Gene", - "id": "ENSEMBL:ENSG00000132155" - }, - "n1": { - "category": "biolink:Drug", - "id": "CHEMBL:CHEMBL1201585" - }, - "n2": { - "category": "biolink:Disease", - "id": "MONDO:0007254" - }, - "n3": { - "category": "biolink:PhenotypicFeature", - "id": "EFO:0000714" - } - } - } - } - }, - "schema": { - "$ref": "#/components/schemas/Query" - } - } - }, - "description": "A message with question graph.", - "required": true - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Message" - } - } - }, - "description": "A message with knowledge graph and answers." - } - }, - "summary": "Get answers to a question", + "summary": "Return the ancestors and descendants of concept, based on the BioLink Model YAML", "tags": [ - "Query" - ], - "x-accessRestriction": "none" + "lookup" + ] } }, - "/curies": { + "/uri_lookup/{uri}": { "get": { - "externalDocs": { - "url": "https://github.com/di2ag/chp_client" - }, + "description": "", + "parameters": [ + { + "example": "RO:0002606", + "in": "path", + "name": "uri", + "required": true + }, + { + "default": "latest", + "in": "query", + "name": "version" + } + ], "responses": { "200": { "content": { "application/json": { "schema": { - "additionalProperties": { - "additionalProperties": { - "description": "object of supported curies", - "items": { - "type": "string" - }, - "type": "object" - } - }, - "example": { - "biolink:Disease": [ - { - "id": "MONDO:0007254", - "name": "breast_cancer" - } - ], - "biolink:Drug": [ - { - "id": "CHEMBL:CHEMBL1201247", - "name": "ZOLADEX" - } - ], - "biolink:Gene": [ - { - "id": "ENSEMBL:ENSG00000106665", - "name": "CLIP2" - } - ], - "biolink:PhenotypicFeature": [ - { - "id": "EFO:0000714", - "name": "survival_time" - } - ] + "items": { + "type": "string" }, - "type": "object" + "type": "array" } } }, - "description": "set of curies currently supported by our service" + "description": "successful operation" } }, - "summary": "Get a set of curies currently supported by our service", + "summary": "Given the URI for a property, return the corresponding BioLink Model slot. Checks the Biolink Model YAML for both slot_uri and mappings.", "tags": [ - "Curies" - ], - "x-accessRestriction": "none" - } - } - }, - "servers": [ - { - "description": "Production Server", - "url": "http://chp.thayer.dartmouth.edu/" - } - ], - "tags": [ - { - "name": "bayesian" - }, - { - "name": "translator" - }, - { - "name": "1.0.0" - } - ] - }, - { - "_id": "4692da88e681a6b23e1ea9ed2152bd85", - "_meta": { - "date_created": "2020-03-16T01:42:25.499864+00:00", - "last_updated": "2021-02-17T07:42:17.081228+00:00", - "url": "https://raw.githubusercontent.com/metadatacenter/metadata-provider/master/metadata-provider-api/assets/openapi.yml", - "username": "marcosmro" - }, - "_score": 0.6048277, - "components": { - "x-bte-kgs-operations": { - "biosampleAssociatedWithDisease": { - "inputs": [ - { - "id": "samd", - "semantic": "Biosample" - } - ], - "outputs": [ - { - "id": "mondo", - "semantic": "DiseaseOrPhenotypicFeature" - } - ], - "parameters": { - "sampleid": "{input1}" - }, - "response-mapping": { - "$ref": "#/components/x-bte-response-mapping/biosample" - }, - "supportBatch": false - }, - "clAssociatedWithBiosample": { - "inputs": [ - { - "id": "clo", - "semantic": "CellLine" - } - ], - "outputs": [ - { - "id": "samd", - "semantic": "Biosample" - } - ], - "parameters": { - "q": "biolink:CellLine={input1}" - }, - "response-mapping": { - "$ref": "#/components/x-bte-response-mapping/cellline-biosample" - }, - "supportBatch": false - }, - "diseaseAssociatedWithBiosample": { - "inputs": [ - { - "id": "mondo", - "semantic": "DiseaseOrPhenotypicFeature" - } - ], - "outputs": [ - { - "id": "samd", - "semantic": "Biosample" - } - ], - "parameters": { - "q": "biolink:Disease={input1}" - }, - "response-mapping": { - "$ref": "#/components/x-bte-response-mapping/disease-biosample" - }, - "supportBatch": false - } - }, - "x-bte-response-mapping": { - "biosample": { - "@context": "http://schema.org", - "@type": "Biosample", - "bts:biosampleAssociatedWithDisease": [ - { - "$input": "bts:samd", - "$source": "NCBI Biosample Database", - "@type": "DiseaseOrPhenotypicFeature", - "bts:age": "data.attributes.age", - "bts:cellline": "data.attributes.cell_line.name", - "bts:mondo": "data.attributes.Disease.mondo", - "bts:organism": "data.attributes.organism", - "bts:sex": "data.attributes.sex.name" - } - ], - "bts:samd": "samd" - }, - "cellline-biosample": { - "@context": "http://schema.org", - "@type": "CellLine", - "bts:clAssociatedWithBiosample": [ - { - "$input": "bts:clo", - "$source": "NCBI Biosample Database", - "@type": "Biosample", - "bts:age": "data.attributes.age", - "bts:cellline": "data.attributes.cell_line.name", - "bts:organism": "data.oorganism", - "bts:samd": "data.biosampleAccession", - "bts:sex": "data.attributes.sex.name" - } - ], - "bts:clo": "clo" - }, - "disease-biosample": { - "@context": "http://schema.org", - "@type": "DiseaseOrPhenotypicFeature", - "bts:diseaseAssociatedWithBiosample": [ - { - "$input": "bts:mondo", - "$source": "NCBI Biosample Database", - "@type": "Biosample", - "bts:age": "data.attributes.age", - "bts:cellline": "data.attributes.cell_line.name", - "bts:organism": "data.oorganism", - "bts:samd": "data.biosampleAccession", - "bts:sex": "data.attributes.sex.name" - } - ], - "bts:mondo": "mondo" + "lookup" + ] } - } - }, - "info": { - "contact": { - "email": "marcosmr@stanford.edu", - "name": " " }, - "description": "Prototype utilities to query a subset of NCBI BioSample metadata records that were processed using semantic technology.\n\nThe current database contains 4,346 records for three diseases: hepatocellular carcinoma, myelodysplasia, and systemic lupus erythematosus. The original records were downloaded on February 2, 2020 from the NCBI's FTP server (https://ftp.ncbi.nih.gov/biosample).", - "termsOfService": "http://api.kp.metadatacenter.org/biosample/tos", - "title": "Metadata Provider API", - "version": "prototype" - }, - "paths": { - "/biosample/search": { + "/bl/{concept}": { "get": { + "description": "", "parameters": [ { - "description": "query", - "example": "biolink:Disease=MONDO:0007256", - "in": "query", - "name": "q", - "required": true, - "schema": { - "type": "string" - } + "default": "chemical_substance", + "in": "path", + "name": "concept", + "required": true }, { - "description": "size of the output", - "example": 200, + "default": "latest", "in": "query", - "name": "limit", - "schema": { - "type": "integer" - } + "name": "version" } ], "responses": { "200": { - "description": "A biosample object", - "x-bte-response-mapping": [ - { - "$ref": "#/components/x-bte-response-mapping/disease-biosample" - }, - { - "$ref": "#/components/x-bte-response-mapping/cellline-biosample" + "content": { + "application/json": { + "schema": { + "type": "object" + } } - ] + }, + "description": "successful operation" } }, - "summary": "retrieve biosample information", - "x-bte-kgs-operations": { - "clAssociatedWithBiosample": { - "$ref": "#/components/x-bte-kgs-operations/clAssociatedWithBiosample" - }, - "diseaseAssociatedWithBiosample": { - "$ref": "#/components/x-bte-kgs-operations/diseaseAssociatedWithBiosample" - } - } + "summary": "Get all properties for concept from the BioLink Model YAML.", + "tags": [ + "lookup" + ] } }, - "/biosample/{sampleid}": { + "/versions": { "get": { - "parameters": [ - { - "description": "the SAMD biosample ID", - "example": "SAMD00005006", - "in": "path", - "name": "sampleid", - "required": true, - "schema": { - "type": "string" - } - } - ], + "description": "", "responses": { "200": { - "description": "A biosample object", - "x-bte-response-mapping": { - "$ref": "#/components/x-bte-response-mapping/biosample" - } + "content": { + "application/json": { + "schema": { + "items": { + "type": "string" + }, + "type": "array" + } + } + }, + "description": "successful operation" } }, - "summary": "retrieve biosample information", - "x-bte-kgs-operations": { - "biosampleAssociatedWithDisease": { - "$ref": "#/components/x-bte-kgs-operations/biosampleAssociatedWithDisease" - } - } + "summary": "Get available BioLink Model versions. These values can be used to parameterize other function calls.", + "tags": [ + "meta" + ] } } }, "servers": [ { - "url": "http://api.kp.metadatacenter.org/" + "description": "Default server", + "url": "https://bl-lookup-sri.renci.org/" } ], "tags": [ { - "name": "metadata" + "name": "translator" }, { - "name": "biosample" + "name": "lookup" }, { - "name": "translator" + "name": "meta" } ] }, @@ -24504,11 +23627,11 @@ "_id": "a8463805ce36964733414a6aaf820cb7", "_meta": { "date_created": "2021-01-28T21:32:46.391247+00:00", - "last_updated": "2021-03-05T08:03:36.091955+00:00", + "last_updated": "2021-03-29T07:04:32.669467+00:00", "url": "https://answercoalesce.renci.org/openapi.json", "username": "PhillipsOwen" }, - "_score": 0.6048277, + "_score": 0.6217669, "info": { "contact": { "email": "patrick@covar.com", @@ -24600,433 +23723,234 @@ ] }, { - "_id": "0a29abdf1b63a762ee93d29f29a8db67", + "_id": "ec6d76016ef40f284359d17fbf78df20", "_meta": { - "date_created": "2021-01-22T18:08:13.583794+00:00", - "last_updated": "2021-03-05T08:03:41.595454+00:00", - "url": "https://aragorn-ranker.renci.org/openapi.json", - "username": "PhillipsOwen" - }, - "_score": 0.6048277, - "info": { - "contact": { - "email": "patrick@covar.com", - "name": "Patrick Wang", - "x-id": "https://github.com/patrickkwang", - "x-role": "responsible developer" - }, - "description": "ARAGORN Ranker: The ranker used by the ARAGORN ARA, which takes a TRAPI 1.0 message containing answers, and calculates numerical scores for each answer.", - "termsOfService": "http://robokop.renci.org:7055/tos?service_long=ARAGORN Ranker&provider_long=RENCI", - "title": "ARAGORN Ranker", - "version": "2.2.2", - "x-translator": { - "component": "ARA", - "team": [ - "Ranking Agent" - ] - } + "date_created": "2020-12-07T23:01:49.428353+00:00", + "last_updated": "2021-03-29T07:01:11.572243+00:00", + "slug": "uberon", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/uberon/smartapi.yaml", + "username": "kevinxin90" }, - "paths": { - "/omnicorp_overlay": { - "post": { - "description": "Add support to message.\n\nAdd support edges to knowledge_graph and bindings to results.", - "operationId": "query_omnicorp_overlay_post", - "requestBody": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Response" - } + "_score": 0.5682892, + "components": { + "x-bte-kgs-operations": { + "developes_from": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UBERON", + "semantic": "AnatomicalEntity" } + ], + "outputs": [ + { + "id": "UBERON", + "semantic": "AnatomicalEntity" + } + ], + "parameters": { + "fields": "developes_from.uberon" }, - "required": true - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Response" - } - } + "predicate": "developes_from", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "_id" }, - "description": "Successful Response" + "header": "application/x-www-form-urlencoded" }, - "422": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/HTTPValidationError" - } - } - }, - "description": "Validation Error" - } - }, - "summary": "Query", - "tags": [ - "ARAGORN-Ranker" - ] - } - }, - "/score": { - "post": { - "description": "Score answers.\n\nThis is mostly glue around the heavy lifting in ranker_obj.Ranker", - "operationId": "query_score_post", - "parameters": [ - { - "in": "query", - "name": "jaccard_like", - "required": false, - "schema": { - "default": false, - "title": "Jaccard Like", - "type": "boolean" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/developes_from" + }, + "source": "UBERON Ontology", + "supportBatch": true + } + ], + "has_part": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UBERON", + "semantic": "AnatomicalEntity" } - } - ], - "requestBody": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Response" - } + ], + "outputs": [ + { + "id": "UBERON", + "semantic": "AnatomicalEntity" } + ], + "parameters": { + "fields": "_id" }, - "required": true - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Response" - } - } + "predicate": "has_part", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "part_of.uberon" }, - "description": "Successful Response" + "header": "application/x-www-form-urlencoded" }, - "422": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/HTTPValidationError" - } - } - }, - "description": "Validation Error" - } - }, - "summary": "Query", - "tags": [ - "ARAGORN-Ranker" - ] - } - }, - "/weight_correctness": { - "post": { - "description": "Weight kgraph edges based on metadata.\n\n\"19 pubs from CTD is a 1, and 2 should at least be 0.5\"\n - cbizon", - "operationId": "query_weight_correctness_post", - "parameters": [ - { - "description": "Portion of cooccurrence publications relevant to a question", - "in": "query", - "name": "relevance", - "required": false, - "schema": { - "default": 0.0025, - "description": "Portion of cooccurrence publications relevant to a question", - "title": "Relevance", - "type": "number" - } + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/has_part" }, - { - "description": "Minimum weight (at 0 publications)", - "in": "query", - "name": "wt_min", - "required": false, - "schema": { - "default": 0.0, - "description": "Minimum weight (at 0 publications)", - "title": "Wt Min", - "type": "number" + "source": "UBERON Ontology", + "supportBatch": true + } + ], + "has_subclass": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UBERON", + "semantic": "AnatomicalEntity" + } + ], + "outputs": [ + { + "id": "UBERON", + "semantic": "AnatomicalEntity" } + ], + "parameters": { + "fields": "children" }, - { - "description": "Maximum weight (at inf publications)", - "in": "query", - "name": "wt_max", - "required": false, - "schema": { - "default": 1.0, - "description": "Maximum weight (at inf publications)", - "title": "Wt Max", - "type": "number" - } + "predicate": "has_subclass", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "_id" + }, + "header": "application/x-www-form-urlencoded" }, - { - "description": "Publications at 50% of wt_max", - "in": "query", - "name": "p50", - "required": false, - "schema": { - "default": 2.0, - "description": "Publications at 50% of wt_max", - "title": "P50", - "type": "number" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/has_subclass" + }, + "source": "UBERON Ontology", + "supportBatch": true + } + ], + "located_in": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UBERON", + "semantic": "AnatomicalEntity" } - } - ], - "requestBody": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Response" - } + ], + "outputs": [ + { + "id": "UBERON", + "semantic": "AnatomicalEntity" } + ], + "parameters": { + "fields": "located_in.uberon" }, - "required": true - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Response" - } - } + "predicate": "located_in", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "_id" }, - "description": "Successful Response" + "header": "application/x-www-form-urlencoded" }, - "422": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/HTTPValidationError" - } - } - }, - "description": "Validation Error" - } - }, - "summary": "Query", - "tags": [ - "ARAGORN-Ranker" - ] - } - } - }, - "servers": [ - { - "description": "Default server", - "url": "https://aragorn-ranker.renci.org" - } - ], - "tags": [ - { - "name": "translator" - }, - { - "name": "ARAGORN" - }, - { - "name": "ARA" - } - ] - }, - { - "_id": "912372f46127b79fb387cd2397203709", - "_meta": { - "date_created": "2021-01-30T00:03:58.007471+00:00", - "last_updated": "2021-03-05T08:01:06.030004+00:00", - "slug": "molecular_kp", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/molecular_data_provider/smartapi.yaml", - "username": "kevinxin90" - }, - "_score": 0.5520779, - "info": { - "contact": { - "email": "translator@broadinstitute.org", - "name": "Molecular Data Provider", - "x-role": "responsible organization" - }, - "description": "Molecular Data Provider for NCATS Biomedical Translator Reasoners", - "license": { - "name": "MIT License", - "url": "https://github.com/broadinstitute/molecular-data-provider/blob/master/LICENSE" - }, - "termsOfService": "https://github.com/broadinstitute/molecular-data-provider/blob/master/terms_of_service.md", - "title": "Molecular Data Provider for NCATS Biomedical Translator Reasoners", - "version": "1.0.0", - "x-translator": { - "component": "KP", - "team": [ - "Molecular Data Provider" - ] - }, - "x-trapi": { - "version": "1.0.0" - } - }, - "paths": { - "/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": [ - "predicates" - ] - } - }, - "/query": { - "post": { - "description": "", - "operationId": "query", - "requestBody": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Query" - } + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/located_in" + }, + "source": "UBERON Ontology", + "supportBatch": true + } + ], + "location_of": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UBERON", + "semantic": "AnatomicalEntity" + } + ], + "outputs": [ + { + "id": "UBERON", + "semantic": "AnatomicalEntity" } + ], + "parameters": { + "fields": "_id" }, - "description": "Query information to be submitted", - "required": true - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Response" - } - } + "predicate": "location_of", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "_id" }, - "description": "OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized." + "header": "application/x-www-form-urlencoded" }, - "400": { - "content": { - "application/json": { - "schema": { - "type": "string" - } - } - }, - "description": "Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)." + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/location_of" }, - "500": { - "content": { - "application/json": { - "schema": { - "type": "string" - } - } - }, - "description": "Internal server error." + "source": "UBERON Ontology", + "supportBatch": true + } + ], + "part_of": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UBERON", + "semantic": "AnatomicalEntity" + } + ], + "outputs": [ + { + "id": "UBERON", + "semantic": "AnatomicalEntity" + } + ], + "parameters": { + "fields": "part_of.uberon" }, - "501": { - "content": { - "application/json": { - "schema": { - "type": "string" - } - } + "predicate": "part_of", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "_id" }, - "description": "Not implemented." - } - }, - "summary": "Query reasoner via one of several inputs", - "tags": [ - "query" - ], - "x-swagger-router-controller": "swagger_server.controllers.query_controller" - } - } - }, - "servers": [ - { - "url": "https://translator.broadinstitute.org/molepro/trapi/v1.0" - } - ], - "tags": [ - { - "description": "Get supported relationships by source and target", - "name": "predicates" - }, - { - "description": "Query reasoner using a predefined question type", - "name": "query" - }, - { - "name": "translator" - }, - { - "name": "reasoner" - } - ] - }, - { - "_id": "a5b0ec6bfde5008984d4b6cde402d61f", - "_meta": { - "date_created": "2020-12-07T23:00:57.213020+00:00", - "last_updated": "2021-03-05T08:01:17.722818+00:00", - "slug": "hpontology", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/hpo/smartapi.yaml", - "username": "kevinxin90" - }, - "_score": 0.5520779, - "components": { - "x-bte-kgs-operations": { - "has_subclass": [ + "header": "application/x-www-form-urlencoded" + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/part_of" + }, + "source": "UBERON Ontology", + "supportBatch": true + } + ], + "produced_by": [ { "inputSeparator": ",", "inputs": [ { - "id": "HP", - "semantic": "PhenotypicFeature" + "id": "UBERON", + "semantic": "AnatomicalEntity" } ], "outputs": [ { - "id": "HP", - "semantic": "PhenotypicFeature" + "id": "UBERON", + "semantic": "AnatomicalEntity" } ], "parameters": { - "fields": "children" + "fields": "produced_by.uberon" }, - "predicate": "has_subclass", + "predicate": "produced_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -25035,9 +23959,42 @@ "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/has_subclass" + "$ref": "#/components/x-bte-response-mapping/produced_by" }, - "source": "Human Phenotype Ontology", + "source": "UBERON Ontology", + "supportBatch": true + } + ], + "produces": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UBERON", + "semantic": "AnatomicalEntity" + } + ], + "outputs": [ + { + "id": "UBERON", + "semantic": "AnatomicalEntity" + } + ], + "parameters": { + "fields": "_id" + }, + "predicate": "produces", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "produced_by.uberon" + }, + "header": "application/x-www-form-urlencoded" + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/produces" + }, + "source": "UBERON Ontology", "supportBatch": true } ], @@ -25046,14 +24003,14 @@ "inputSeparator": ",", "inputs": [ { - "id": "HP", - "semantic": "PhenotypicFeature" + "id": "UBERON", + "semantic": "AnatomicalEntity" } ], "outputs": [ { - "id": "HP", - "semantic": "PhenotypicFeature" + "id": "UBERON", + "semantic": "AnatomicalEntity" } ], "parameters": { @@ -25070,17 +24027,38 @@ "response_mapping": { "$ref": "#/components/x-bte-response-mapping/subclass_of" }, - "source": "Human Phenotype Ontology", + "source": "UBERON Ontology", "supportBatch": true } ] }, "x-bte-response-mapping": { + "developes_from": { + "UBERON": "developes_from.uberon" + }, + "has_part": { + "UBERON": "_id" + }, "has_subclass": { - "HP": "children" + "UBERON": "children" + }, + "located_in": { + "UBERON": "located_in.uberon" + }, + "location_of": { + "UBERON": "_id" + }, + "part_of": { + "UBERON": "part_of.uberon" + }, + "produced_by": { + "UBERON": "produced_by.uberon" + }, + "produces": { + "UBERON": "_id" }, "subclass_of": { - "HP": "parents" + "UBERON": "parents" } } }, @@ -25091,9 +24069,9 @@ "x-id": "https://github.com/kevinxin90", "x-role": "responsible developer" }, - "description": "Documentation of the HPO query web services.", + "description": "Documentation of the UBERON query web services.", "termsOfService": "https://biothings.io/about", - "title": "Human Phenotype Ontology API", + "title": "UBERON Ontology API", "version": "1.0", "x-translator": { "component": "KP", @@ -25103,7 +24081,7 @@ } }, "paths": { - "/phenotype": { + "/anatomy": { "post": { "parameters": [ { @@ -25129,7 +24107,7 @@ "schema": { "properties": { "ids": { - "description": "multiple HPO phenotype IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", + "description": "multiple UBERON anatomy IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", "type": "string" } }, @@ -25152,7 +24130,7 @@ } } }, - "description": "A list of matching phenotype objects" + "description": "A list of matching anatomy objects" }, "400": { "content": { @@ -25165,20 +24143,20 @@ "description": "A response indicating an improperly formatted query" } }, - "summary": "For a list of phenotype IDs, return the matching phenotype object", + "summary": "For a list of anatomy IDs, return the matching anatomy object", "tags": [ - "phenotype" + "anatomy" ] } }, - "/phenotype/{phenotypeid}": { + "/anatomy/{anatomyid}": { "get": { "parameters": [ { - "description": "Retrieve phenotype objects based on HPO phenotype ID Supports JSONP and CORS as well.", - "example": "HP:0000791", + "description": "Retrieve anatomy objects based on UBERON anatomy ID Supports JSONP and CORS as well.", + "example": "UBERON:2002108", "in": "path", - "name": "phenotypeid", + "name": "anatomyid", "required": true, "schema": { "type": "string" @@ -25214,15 +24192,15 @@ } } }, - "description": "A matching phenotype object" + "description": "A matching anatomy object" }, "404": { - "description": "A response indicating an unknown phenotype ID" + "description": "A response indicating an unknown anatomy ID" } }, - "summary": "Retrieve phenotype objects based on ID", + "summary": "Retrieve anatomy objects based on ID", "tags": [ - "phenotype" + "anatomy" ] } }, @@ -25237,10 +24215,10 @@ ], "responses": { "200": { - "description": "DISEASES metadata object" + "description": "UBERON metadata object" } }, - "summary": "Get metadata about the data available from DISEASES", + "summary": "Get metadata about the data available from UBERON", "tags": [ "metadata" ] @@ -25268,7 +24246,7 @@ ], "responses": { "200": { - "description": "DISEASES metadata fields object" + "description": "UBERON metadata fields object" } }, "summary": "Get metadata about the data fields available object", @@ -25282,7 +24260,7 @@ "parameters": [ { "description": "Query string.", - "example": "parents:\"HP:0000787\"", + "example": "parents:\"UBERON:2001995\"", "in": "query", "name": "q", "required": true, @@ -25353,7 +24331,7 @@ "description": "A response indicating an improperly formatted query" } }, - "summary": "Make queries and return matching phenotype hits. Supports JSONP and CORS as well.", + "summary": "Make queries and return matching anatomy hits. Supports JSONP and CORS as well.", "tags": [ "query" ] @@ -25421,7 +24399,7 @@ "description": "A response indicating an improperly formatted query" } }, - "summary": "Make batch phenotype queries and return matching phenotype hits", + "summary": "Make batch anatomy queries and return matching anatomy hits", "tags": [ "query" ], @@ -25431,6 +24409,27 @@ }, { "$ref": "#/components/x-bte-kgs-operations/subclass_of" + }, + { + "$ref": "#/components/x-bte-kgs-operations/part_of" + }, + { + "$ref": "#/components/x-bte-kgs-operations/has_part" + }, + { + "$ref": "#/components/x-bte-kgs-operations/developes_from" + }, + { + "$ref": "#/components/x-bte-kgs-operations/located_in" + }, + { + "$ref": "#/components/x-bte-kgs-operations/location_of" + }, + { + "$ref": "#/components/x-bte-kgs-operations/produced_by" + }, + { + "$ref": "#/components/x-bte-kgs-operations/produces" } ] } @@ -25439,16 +24438,16 @@ "servers": [ { "description": "Encrypted Production server", - "url": "https://biothings.ncats.io/hpo" + "url": "https://biothings.ncats.io/uberon" }, { "description": "Production server", - "url": "http://biothings.ncats.io/hpo" + "url": "http://biothings.ncats.io/uberon" } ], "tags": [ { - "name": "phenotype" + "name": "anatomy" }, { "name": "query" @@ -25462,434 +24461,198 @@ ] }, { - "_id": "27a5b60716c3a401f2c021a5b718c5b1", + "_id": "912372f46127b79fb387cd2397203709", "_meta": { - "date_created": "2021-03-02T21:16:25.421365+00:00", - "last_updated": "2021-03-05T08:01:12.374164+00:00", - "url": "https://raw.githubusercontent.com/SmartAPI/smartapi_registry/master/SmartAPI/smartapi_openapi.yml", - "username": "newgene" + "date_created": "2021-01-30T00:03:58.007471+00:00", + "last_updated": "2021-03-29T07:01:48.696264+00:00", + "slug": "molecular_kp", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/molecular_data_provider/smartapi.yaml", + "username": "kevinxin90" }, - "_score": 0.5520779, + "_score": 0.5682892, "info": { "contact": { - "email": "cwu@scripps.edu", - "name": "Chunlei Wu", - "url": "https://github.com/newgene", - "x-id": "https://orcid.org/0000-0002-2629-6124", - "x-role": "responsible developer" + "email": "translator@broadinstitute.org", + "name": "Molecular Data Provider", + "x-role": "responsible organization" }, - "description": "This is the API provided from [SmartAPI](https://smart-api.info) application.", - "termsOfService": "https://creativecommons.org/licenses/by/4.0/", - "title": "SmartAPI API", - "version": "1.0", - "x-implementationLanguage": "Python", - "x-maturity": "production", + "description": "Molecular Data Provider for NCATS Biomedical Translator Reasoners", + "license": { + "name": "MIT License", + "url": "https://github.com/broadinstitute/molecular-data-provider/blob/master/LICENSE" + }, + "termsOfService": "https://github.com/broadinstitute/molecular-data-provider/blob/master/terms_of_service.md", + "title": "Molecular Data Provider for NCATS Biomedical Translator Reasoners", + "version": "1.0.0", "x-translator": { - "component": "Utility", + "component": "KP", "team": [ - "Service Provider" + "Molecular Data Provider" ] + }, + "x-trapi": { + "version": "1.0.0" } }, "paths": { - "/metadata/{api_id}": { + "/predicates": { "get": { - "description": "Return matching API metadata", - "operationId": "", - "parameters": [ - { - "description": "The value can be either the API id (e.g. \"27a5b60716c3a401f2c021a5b718c5b1\")\n or the slug name (e.g. \"mygene\"). You can also pass \"all\" to get a list of\n all API metadata (using \"from\" and \"size\" for pagination).", - "in": "path", - "name": "api_id", - "required": true, - "schema": { - "type": "string" - } - }, - { - "description": "include \"_meta\" and \"_id\" fields in the response if passed \"1\" or \"true\". Default is \"false\".", - "in": "query", - "name": "meta", - "schema": { - "type": "string" - } - }, - { - "description": "return raw metadata document if passed \"1\" or \"true\". Default is \"false\".", - "in": "query", - "name": "raw", - "schema": { - "type": "string" - } - }, - { - "description": "You can use this parameter to filter the fields returned from the raw metadata document. Only effective when \"raw=1\" is passed. E.g. \"info.contact.name,servers\". Nested fields are supported via dot notation, and multiple fields can be passed as a comma-separated string.", - "in": "query", - "name": "fields", - "schema": { - "type": "string" - } - }, - { - "description": "Output format for the return API metadata. The value can be \"json\" or \"yaml\". Default is \"json\".", - "in": "query", - "name": "format", - "schema": { - "type": "string" - } - }, - { - "description": "Number of items to be skipped. Combining with \"size\" parameter, this can be used for the pagination of the long result.", - "in": "query", - "name": "from", - "schema": { - "type": "string" - } - }, - { - "description": "The number of items returned in one request. Combining with \"from\" parameter, this can be used for the pagination of the long result.", - "in": "query", - "name": "size", - "schema": { - "type": "string" - } - } - ], "responses": { "200": { - "description": "successful response" + "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": "Return matching API metadata", + "summary": "Get supported relationships by source and target", "tags": [ - "metadata" + "predicates" ] } }, - "/query/": { - "get": { - "description": "Query metadata for matching APIs.", - "parameters": [ - { - "description": "Can pass any string as the query term to match any field, e.g. \"mygene.info\", or pass a fielded query term like \"info.contact.name:wu\".", - "in": "query", - "name": "q", - "required": true, - "schema": { - "type": "string" - } - }, - { - "description": "You can use this parameter to filter the fields returned from the raw metadata document. Only effective when \"raw=1\" is passed. E.g. \"info.contact.name,servers\". Nested fields are supported via dot notation, and multiple fields can be passed as a comma-separated string.", - "in": "query", - "name": "fields", - "schema": { - "type": "string" - } - }, - { - "description": "return raw metadata document if passed \"1\" or \"true\". Default is \"false\".", - "in": "query", - "name": "raw", - "schema": { - "type": "string" - } - }, - { - "description": "Number of items to be skipped. Combining with \"size\" parameter, this can be used for the pagination of the long result.", - "in": "query", - "name": "from", - "schema": { - "type": "string" + "/query": { + "post": { + "description": "", + "operationId": "query", + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Query" + } } }, - { - "description": "The number of items returned in one request. Combining with \"from\" parameter, this can be used for the pagination of the long result.", - "in": "query", - "name": "size", - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "default response" - } + "description": "Query information to be submitted", + "required": true }, - "summary": "Query metadata for matching APIs." - } - }, - "/validate": { - "get": { - "description": "Validate input SmartAPI metadata", - "operationId": "", - "parameters": [ - { - "description": "The full URL of an input SmartAPI metadata to validate. The file format can be either JSON or YAML.", - "in": "query", - "name": "url", - "required": true, - "schema": { - "type": "string" - } - } - ], "responses": { "200": { - "description": "default response" - } - }, - "summary": "Validate input SmartAPI metadata" - } - }, - "/suggestion": { - "get": { - "description": "Return suggested values from the existing APIs in the registry for a given field.", - "operationId": "", - "parameters": [ - { - "description": "An input field to return the suggested values and their occurrence numbers.", - "in": "query", - "name": "field", - "schema": { - "type": "string" - } - }, - { - "description": "The maximum number of suggested values to return", - "in": "query", - "name": "size", - "schema": { - "type": "string" - } - } - ], - "responses": { - "default": { - "description": "Default response" - } - }, - "summary": "Return suggested values for a give field." - } - }, - "/metakg": { - "get": { - "parameters": [ - { - "description": "The subject type of the association, e.g. Gene", - "example": "Gene", - "in": "query", - "name": "subject", - "schema": { - "type": "string" - } - }, - { - "description": "The object type of the association, e.g. ChemicalSubstance", - "example": "ChemicalSubstance", - "in": "query", - "name": "object", - "schema": { - "type": "string" - } + "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." }, - { - "description": "The predicate of the association, e.g. Gene", - "example": "physically_interacts_with", - "in": "query", - "name": "predicate", - "schema": { - "type": "string" - } + "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)." }, - { - "description": "The API providing the association, e.g. MyChem.info API", - "example": "MyChem.info API", - "in": "query", - "name": "api", - "schema": { - "type": "string" - } + "500": { + "content": { + "application/json": { + "schema": { + "type": "string" + } + } + }, + "description": "Internal server error." }, - { - "description": "The data source providing the association, e.g. drugbank", - "example": "drugbank", - "in": "query", - "name": "provided_by", - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { + "501": { "content": { "application/json": { "schema": { - "description": "Array of all associations", - "items": { - "properties": { - "api": { - "description": "The api providing the association, e.g. MyChem.info", - "properties": { - "name": { - "description": "The api providing the association, e.g. MyChem.info", - "example": "MyChem.info API", - "type": "string" - }, - "smartapi": { - "description": "smartapi related data", - "properties": { - "id": { - "description": "unique smartapi id for the api", - "example": "8f08d1446e0bb9c2b323713ce83e2bd3", - "type": "string" - }, - "metadata": { - "description": "the url for smartapi specification", - "example": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/mychem.info/openapi_full.yml", - "type": "string" - }, - "ui": { - "description": "the web UI url for the API", - "example": "https://smart-api.info/ui/8f08d1446e0bb9c2b323713ce83e2bd3", - "type": "string" - } - }, - "type": "object" - } - }, - "type": "object" - }, - "object": { - "description": "The object type of the association, e.g. ChemicalSubstance", - "example": "ChemicalSubstance", - "type": "string" - }, - "predicate": { - "description": "The predicate of the association, e.g. physically_interacts_with", - "example": "physically_interacts_with", - "type": "string" - }, - "provided_by": { - "description": "The data source providing the association, e.g. ChEMBL", - "example": "ChEMBL", - "type": "string" - }, - "subject": { - "description": "The subject type of the association, e.g. Gene", - "example": "Gene", - "type": "string" - } - }, - "type": "object" - }, - "type": "array" + "type": "string" } } }, - "description": "Association information including subject, object, predicate, api, provided_by and smartapi info." + "description": "Not implemented." } }, - "summary": "retrieve associations within smartapi, if no parameters provided, will return all associations" + "summary": "Query reasoner via one of several inputs", + "tags": [ + "query" + ], + "x-swagger-router-controller": "swagger_server.controllers.query_controller" } } }, "servers": [ { - "description": "Production server", - "url": "https://smart-api.info/api" - }, - { - "description": "Development server", - "url": "http://dev.smart-api.info/api" + "url": "https://translator.broadinstitute.org/molepro/trapi/v1.0" } ], "tags": [ { - "name": "api" + "description": "Get supported relationships by source and target", + "name": "predicates" }, { - "name": "metadata" + "description": "Query reasoner using a predefined question type", + "name": "query" }, { - "name": "openapi" + "name": "translator" }, { - "name": "translator" + "name": "trapi" } ] }, { - "_id": "89054eff6ee6d91641d278d9ffdb3993", + "_id": "b0ead2b28cfe5794e24845661ba45897", "_meta": { - "date_created": "2021-01-20T00:00:12.144499+00:00", - "last_updated": "2021-03-05T08:02:07.441566+00:00", - "url": "https://api.collaboratory.semanticscience.org/openapi.json", - "username": "vemonet" + "date_created": "2021-03-17T22:53:48.733473+00:00", + "last_updated": "2021-03-23T19:27:00.319896+00:00", + "url": "https://raw.githubusercontent.com/jeffhhk/mediKanren/tweak-openapi/biolink/open-api/TranslatorReasonersAPI.yaml", + "username": "jeffhhk" }, - "_score": 0.5520779, + "_score": 0.5682892, "info": { "contact": { - "email": "vincent.emonet@maastrichtuniversity.nl" + "email": "edeutsch@systemsbiology.org" }, - "description": "Translator Reasoner API for the Knowledge Collaboratory, hosted on the [Nanopublications network](http://nanopub.org/wordpress/), for annotated drug indications or any other BioLink-compliant claims. \n\n This Open API supports [Translator Reasoner API](https://github.com/NCATSTranslator/ReasonerAPI) version `1.0.0-beta` queries and the [`KGX`](https://github.com/biolink/kgx) format \n\nSee the API GitHub repository: [github.com/MaastrichtU-IDS/knowledge-collaboratory-api](https://github.com/MaastrichtU-IDS/knowledge-collaboratory-api) \n\nThis service is supported by the [NCATS Translator project](https://ncats.nih.gov/translator/about)", + "description": "OpenAPI for NCATS Biomedical Translator Reasoners", "license": { - "name": "MIT license", - "url": "https://opensource.org/licenses/MIT" + "name": "Apache 2.0", + "url": "http://www.apache.org/licenses/LICENSE-2.0.html" }, - "termsOfService": "https://github.com/MaastrichtU-IDS/knowledge-collaboratory-api/blob/master/LICENSE", - "title": "Translator Knowledge Collaboratory API", - "version": "1.0.0", + "termsOfService": "INSERT-URL-HERE", + "title": "OpenAPI for NCATS Biomedical Translator Reasoners", + "version": "1.0.0-beta", "x-translator": { - "component": "KP", + "component": "ARA", "team": [ - "Clinical Data Provider" + "Unsecret Agent" ] } }, "paths": { - "/kgx": { - "get": { - "operationId": "api.get_kgx", - "parameters": [ - { - "description": "Get drug indications from which KG", - "in": "query", - "name": "from_kg", - "schema": { - "default": "NeuroDKG", - "enum": [ - "NeuroDKG", - "Nanopublications" - ], - "type": "string" - } - } - ], - "responses": { - "200": { - "content": { - "application/zip": { - "schema": { - "format": "binary", - "type": "string" - } - } - }, - "description": "Zip file with nodes and edges files in KGX TSV format" - } - }, - "summary": "Get the Knowledge Collaboratory drug indications in KGX TSV format (TSV files in a .zip)", - "tags": [ - "translator" - ] - } - }, "/predicates": { "get": { - "operationId": "api.get_predicates", "responses": { "200": { "content": { @@ -25930,8 +24693,8 @@ }, "/query": { "post": { - "description": "Send a [ReasonerAPI](https://github.com/NCATSTranslator/ReasonerAPI) query to request the predicted targets given: a source node, and the relation to predict. Use classes and relations from the [BioLink model](https://biolink.github.io/biolink-model)", - "operationId": "api.post_reasoner_query", + "description": "", + "operationId": "query", "requestBody": { "content": { "application/json": { @@ -25993,18 +24756,21 @@ } } }, - "servers": [ - { - "url": "https://api.collaboratory.semanticscience.org" - } - ], "tags": [ { "description": "Get supported relationships by source and target", + "externalDocs": { + "description": "Documentation for the reasoner predicates function", + "url": "http://unsecret.ncats.io/overview.html#predicates" + }, "name": "predicates" }, { "description": "Query reasoner using a predefined question type", + "externalDocs": { + "description": "Documentation for the reasoner query function", + "url": "http://unsecret.ncats.io/overview.html#query" + }, "name": "query" }, { @@ -26016,234 +24782,197 @@ ] }, { - "_id": "ec6d76016ef40f284359d17fbf78df20", + "_id": "a37a3502ce5210b06dc2f830ac2663ad", "_meta": { - "date_created": "2020-12-07T23:01:49.428353+00:00", - "last_updated": "2021-03-05T08:02:26.692600+00:00", - "slug": "uberon", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/uberon/smartapi.yaml", - "username": "kevinxin90" + "date_created": "2021-03-23T18:53:20.187390+00:00", + "last_updated": "2021-03-29T07:02:07.324995+00:00", + "url": "https://raw.githubusercontent.com/jeffhhk/mediKanren/tweak2-openapi/medikanren/open-api/TranslatorReasonersAPI.yaml", + "username": "jeffhhk" }, - "_score": 0.5520779, - "components": { - "x-bte-kgs-operations": { - "developes_from": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UBERON", - "semantic": "AnatomicalEntity" - } - ], - "outputs": [ - { - "id": "UBERON", - "semantic": "AnatomicalEntity" - } - ], - "parameters": { - "fields": "developes_from.uberon" - }, - "predicate": "developes_from", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "_id" - }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/developes_from" - }, - "source": "UBERON Ontology", - "supportBatch": true - } - ], - "has_part": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UBERON", - "semantic": "AnatomicalEntity" - } - ], - "outputs": [ - { - "id": "UBERON", - "semantic": "AnatomicalEntity" - } - ], - "parameters": { - "fields": "_id" - }, - "predicate": "has_part", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "part_of.uberon" + "_score": 0.5682892, + "info": { + "contact": { + "email": "webyrd@gmail.com", + "name": "William E. Byrd", + "url": "https://github.com/webyrd" + }, + "description": "OpenAPI for NCATS Biomedical Translator Reasoners", + "license": { + "name": "Apache 2.0", + "url": "http://www.apache.org/licenses/LICENSE-2.0.html" + }, + "termsOfService": "INSERT-URL-HERE", + "title": "OpenAPI for NCATS Biomedical Translator Reasoners", + "version": "1.0.0-beta", + "x-translator": { + "component": "ARA", + "team": [ + "Unsecret Agent" + ] + } + }, + "paths": { + "/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" + } + } }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/has_part" - }, - "source": "UBERON Ontology", - "supportBatch": true - } - ], - "has_subclass": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UBERON", - "semantic": "AnatomicalEntity" - } - ], - "outputs": [ - { - "id": "UBERON", - "semantic": "AnatomicalEntity" + "description": "Predicates by source and target" + } + }, + "summary": "Get supported relationships by source and target", + "tags": [ + "predicates" + ] + } + }, + "/query": { + "post": { + "description": "", + "operationId": "query", + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Query" + } } - ], - "parameters": { - "fields": "children" }, - "predicate": "has_subclass", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "_id" + "description": "Query information to be submitted", + "required": true + }, + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Response" + } + } }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/has_subclass" - }, - "source": "UBERON Ontology", - "supportBatch": true - } - ], - "located_in": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UBERON", - "semantic": "AnatomicalEntity" - } - ], - "outputs": [ - { - "id": "UBERON", - "semantic": "AnatomicalEntity" - } - ], - "parameters": { - "fields": "located_in.uberon" + "description": "OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized." }, - "predicate": "located_in", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "_id" + "400": { + "content": { + "application/json": { + "schema": { + "type": "string" + } + } }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/located_in" - }, - "source": "UBERON Ontology", - "supportBatch": true - } - ], - "location_of": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UBERON", - "semantic": "AnatomicalEntity" - } - ], - "outputs": [ - { - "id": "UBERON", - "semantic": "AnatomicalEntity" - } - ], - "parameters": { - "fields": "_id" + "description": "Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)." }, - "predicate": "location_of", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "_id" + "500": { + "content": { + "application/json": { + "schema": { + "type": "string" + } + } }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/location_of" - }, - "source": "UBERON Ontology", - "supportBatch": true - } - ], - "part_of": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UBERON", - "semantic": "AnatomicalEntity" - } - ], - "outputs": [ - { - "id": "UBERON", - "semantic": "AnatomicalEntity" - } - ], - "parameters": { - "fields": "part_of.uberon" + "description": "Internal server error." }, - "predicate": "part_of", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "_id" + "501": { + "content": { + "application/json": { + "schema": { + "type": "string" + } + } }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/part_of" - }, - "source": "UBERON Ontology", - "supportBatch": true - } - ], - "produced_by": [ + "description": "Not implemented." + } + }, + "summary": "Query reasoner via one of several inputs", + "tags": [ + "query" + ], + "x-swagger-router-controller": "swagger_server.controllers.query_controller" + } + } + }, + "tags": [ + { + "description": "Get supported relationships by source and target", + "externalDocs": { + "description": "Documentation for the reasoner predicates function", + "url": "http://unsecret.ncats.io/overview.html#predicates" + }, + "name": "predicates" + }, + { + "description": "Query reasoner using a predefined question type", + "externalDocs": { + "description": "Documentation for the reasoner query function", + "url": "http://unsecret.ncats.io/overview.html#query" + }, + "name": "query" + }, + { + "name": "translator" + }, + { + "name": "reasoner" + } + ] + }, + { + "_id": "a5b0ec6bfde5008984d4b6cde402d61f", + "_meta": { + "date_created": "2020-12-07T23:00:57.213020+00:00", + "last_updated": "2021-03-29T07:02:47.676460+00:00", + "slug": "hpontology", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/hpo/smartapi.yaml", + "username": "kevinxin90" + }, + "_score": 0.5682892, + "components": { + "x-bte-kgs-operations": { + "has_subclass": [ { "inputSeparator": ",", "inputs": [ { - "id": "UBERON", - "semantic": "AnatomicalEntity" + "id": "HP", + "semantic": "PhenotypicFeature" } ], "outputs": [ { - "id": "UBERON", - "semantic": "AnatomicalEntity" + "id": "HP", + "semantic": "PhenotypicFeature" } ], "parameters": { - "fields": "produced_by.uberon" + "fields": "children" }, - "predicate": "produced_by", + "predicate": "has_subclass", "requestBody": { "body": { "q": "{inputs[0]}", @@ -26252,42 +24981,9 @@ "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/produced_by" - }, - "source": "UBERON Ontology", - "supportBatch": true - } - ], - "produces": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UBERON", - "semantic": "AnatomicalEntity" - } - ], - "outputs": [ - { - "id": "UBERON", - "semantic": "AnatomicalEntity" - } - ], - "parameters": { - "fields": "_id" - }, - "predicate": "produces", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "produced_by.uberon" - }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/produces" + "$ref": "#/components/x-bte-response-mapping/has_subclass" }, - "source": "UBERON Ontology", + "source": "Human Phenotype Ontology", "supportBatch": true } ], @@ -26296,14 +24992,14 @@ "inputSeparator": ",", "inputs": [ { - "id": "UBERON", - "semantic": "AnatomicalEntity" + "id": "HP", + "semantic": "PhenotypicFeature" } ], "outputs": [ { - "id": "UBERON", - "semantic": "AnatomicalEntity" + "id": "HP", + "semantic": "PhenotypicFeature" } ], "parameters": { @@ -26320,38 +25016,17 @@ "response_mapping": { "$ref": "#/components/x-bte-response-mapping/subclass_of" }, - "source": "UBERON Ontology", + "source": "Human Phenotype Ontology", "supportBatch": true } ] }, "x-bte-response-mapping": { - "developes_from": { - "UBERON": "developes_from.uberon" - }, - "has_part": { - "UBERON": "_id" - }, "has_subclass": { - "UBERON": "children" - }, - "located_in": { - "UBERON": "located_in.uberon" - }, - "location_of": { - "UBERON": "_id" - }, - "part_of": { - "UBERON": "part_of.uberon" - }, - "produced_by": { - "UBERON": "produced_by.uberon" - }, - "produces": { - "UBERON": "_id" + "HP": "children" }, "subclass_of": { - "UBERON": "parents" + "HP": "parents" } } }, @@ -26362,9 +25037,9 @@ "x-id": "https://github.com/kevinxin90", "x-role": "responsible developer" }, - "description": "Documentation of the UBERON query web services.", + "description": "Documentation of the HPO query web services.", "termsOfService": "https://biothings.io/about", - "title": "UBERON Ontology API", + "title": "Human Phenotype Ontology API", "version": "1.0", "x-translator": { "component": "KP", @@ -26374,7 +25049,7 @@ } }, "paths": { - "/anatomy": { + "/phenotype": { "post": { "parameters": [ { @@ -26400,7 +25075,7 @@ "schema": { "properties": { "ids": { - "description": "multiple UBERON anatomy IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", + "description": "multiple HPO phenotype IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", "type": "string" } }, @@ -26423,7 +25098,7 @@ } } }, - "description": "A list of matching anatomy objects" + "description": "A list of matching phenotype objects" }, "400": { "content": { @@ -26436,20 +25111,20 @@ "description": "A response indicating an improperly formatted query" } }, - "summary": "For a list of anatomy IDs, return the matching anatomy object", + "summary": "For a list of phenotype IDs, return the matching phenotype object", "tags": [ - "anatomy" + "phenotype" ] } }, - "/anatomy/{anatomyid}": { + "/phenotype/{phenotypeid}": { "get": { "parameters": [ { - "description": "Retrieve anatomy objects based on UBERON anatomy ID Supports JSONP and CORS as well.", - "example": "UBERON:2002108", + "description": "Retrieve phenotype objects based on HPO phenotype ID Supports JSONP and CORS as well.", + "example": "HP:0000791", "in": "path", - "name": "anatomyid", + "name": "phenotypeid", "required": true, "schema": { "type": "string" @@ -26485,15 +25160,15 @@ } } }, - "description": "A matching anatomy object" + "description": "A matching phenotype object" }, "404": { - "description": "A response indicating an unknown anatomy ID" + "description": "A response indicating an unknown phenotype ID" } }, - "summary": "Retrieve anatomy objects based on ID", + "summary": "Retrieve phenotype objects based on ID", "tags": [ - "anatomy" + "phenotype" ] } }, @@ -26508,10 +25183,10 @@ ], "responses": { "200": { - "description": "UBERON metadata object" + "description": "DISEASES metadata object" } }, - "summary": "Get metadata about the data available from UBERON", + "summary": "Get metadata about the data available from DISEASES", "tags": [ "metadata" ] @@ -26539,7 +25214,7 @@ ], "responses": { "200": { - "description": "UBERON metadata fields object" + "description": "DISEASES metadata fields object" } }, "summary": "Get metadata about the data fields available object", @@ -26553,7 +25228,7 @@ "parameters": [ { "description": "Query string.", - "example": "parents:\"UBERON:2001995\"", + "example": "parents:\"HP:0000787\"", "in": "query", "name": "q", "required": true, @@ -26624,7 +25299,7 @@ "description": "A response indicating an improperly formatted query" } }, - "summary": "Make queries and return matching anatomy hits. Supports JSONP and CORS as well.", + "summary": "Make queries and return matching phenotype hits. Supports JSONP and CORS as well.", "tags": [ "query" ] @@ -26692,7 +25367,7 @@ "description": "A response indicating an improperly formatted query" } }, - "summary": "Make batch anatomy queries and return matching anatomy hits", + "summary": "Make batch phenotype queries and return matching phenotype hits", "tags": [ "query" ], @@ -26702,27 +25377,6 @@ }, { "$ref": "#/components/x-bte-kgs-operations/subclass_of" - }, - { - "$ref": "#/components/x-bte-kgs-operations/part_of" - }, - { - "$ref": "#/components/x-bte-kgs-operations/has_part" - }, - { - "$ref": "#/components/x-bte-kgs-operations/developes_from" - }, - { - "$ref": "#/components/x-bte-kgs-operations/located_in" - }, - { - "$ref": "#/components/x-bte-kgs-operations/location_of" - }, - { - "$ref": "#/components/x-bte-kgs-operations/produced_by" - }, - { - "$ref": "#/components/x-bte-kgs-operations/produces" } ] } @@ -26731,16 +25385,16 @@ "servers": [ { "description": "Encrypted Production server", - "url": "https://biothings.ncats.io/uberon" + "url": "https://biothings.ncats.io/hpo" }, { "description": "Production server", - "url": "http://biothings.ncats.io/uberon" + "url": "http://biothings.ncats.io/hpo" } ], "tags": [ { - "name": "anatomy" + "name": "phenotype" }, { "name": "query" @@ -26754,246 +25408,359 @@ ] }, { - "_id": "94cb5d61356b04e0be1c51c70945918b", + "_id": "27a5b60716c3a401f2c021a5b718c5b1", "_meta": { - "date_created": "2021-01-27T00:00:58.335234+00:00", - "last_updated": "2021-03-05T08:02:27.253760+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/myvariant.info/openapi_minimum.yml", - "username": "oldray" + "date_created": "2021-03-02T21:16:25.421365+00:00", + "last_updated": "2021-03-29T07:04:45.302428+00:00", + "url": "https://raw.githubusercontent.com/SmartAPI/smartapi_registry/master/SmartAPI/smartapi_openapi.yml", + "username": "newgene" }, - "_score": 0.5520779, + "_score": 0.5682892, "info": { "contact": { - "email": "help@myvariant.info", + "email": "cwu@scripps.edu", "name": "Chunlei Wu", - "x-id": "https://github.com/newgene", + "url": "https://github.com/newgene", + "x-id": "https://orcid.org/0000-0002-2629-6124", "x-role": "responsible developer" }, - "description": "Documentation of the MyVariant.info Variant Query web services. Learn more about [MyVariant.info](http://myvariant.info/)", - "termsOfService": "http://myvariant.info/terms/", - "title": "MyVariant.info API", + "description": "This is the API provided from [SmartAPI](https://smart-api.info) application.", + "termsOfService": "https://creativecommons.org/licenses/by/4.0/", + "title": "SmartAPI API", "version": "1.0", + "x-implementationLanguage": "Python", + "x-maturity": "production", "x-translator": { - "component": "KP", + "component": "Utility", "team": [ "Service Provider" ] } }, "paths": { - "/query": { + "/metadata/{api_id}": { "get": { + "description": "Return matching API metadata", + "operationId": "", "parameters": [ { - "description": "Query string. Examples \"rs752396467\", \"possibly_damaging\", \"CDK7\".", - "in": "query", - "name": "q", + "description": "The value can be either the API id (e.g. \"27a5b60716c3a401f2c021a5b718c5b1\")\n or the slug name (e.g. \"mygene\"). You can also pass \"all\" to get a list of\n all API metadata (using \"from\" and \"size\" for pagination).", + "in": "path", + "name": "api_id", "required": true, "schema": { "type": "string" - }, - "x-valueType": [ - "http://identifiers.org/hgnc.symbol/", - "http://identifiers.org/dbsnp/", - "http://identifiers.org/ensembl.gene/", - "http://identifiers.org/ensembl.transcript/", - "http://identifiers.org/ensembl.protein/", - "http://identifiers.org/ccds/", - "http://identifiers.org/uniprot/", - "http://identifiers.org/clinvar/", - "http://identifiers.org/omim/", - "http://identifiers.org/efo/", - "http://identifiers.org/orphanet/", - "http://identifiers.org/hgnc/", - "http://identifiers.org/pubmed/", - "http://identifiers.org/refseq/", - "http://identifiers.org/clinicalsignificance/" - ] + } + }, + { + "description": "include \"_meta\" and \"_id\" fields in the response if passed \"1\" or \"true\". Default is \"false\".", + "in": "query", + "name": "meta", + "schema": { + "type": "string" + } + }, + { + "description": "return raw metadata document if passed \"1\" or \"true\". Default is \"false\".", + "in": "query", + "name": "raw", + "schema": { + "type": "string" + } + }, + { + "description": "You can use this parameter to filter the fields returned from the raw metadata document. Only effective when \"raw=1\" is passed. E.g. \"info.contact.name,servers\". Nested fields are supported via dot notation, and multiple fields can be passed as a comma-separated string.", + "in": "query", + "name": "fields", + "schema": { + "type": "string" + } + }, + { + "description": "Output format for the return API metadata. The value can be \"json\" or \"yaml\". Default is \"json\".", + "in": "query", + "name": "format", + "schema": { + "type": "string" + } + }, + { + "description": "Number of items to be skipped. Combining with \"size\" parameter, this can be used for the pagination of the long result.", + "in": "query", + "name": "from", + "schema": { + "type": "string" + } + }, + { + "description": "The number of items returned in one request. Combining with \"from\" parameter, this can be used for the pagination of the long result.", + "in": "query", + "name": "size", + "schema": { + "type": "string" + } } ], "responses": { "200": { - "description": "A query response object with \"hits\" property", - "x-JSONLDContext": "https://github.com/NCATS-Tangerine/translator-api-registry/blob/master/myvariant.info/jsonld_context/myvariant_context.json", - "x-responseValueType": [ - { - "path": "_id", - "valueType": "http://identifiers.org/hgvs/" - }, - { - "path": "cadd.gene.genename", - "valueType": "http://identifiers.org/hgnc.symbol/" - }, - { - "path": "clinvar.rsid", - "valueType": "http://identifiers.org/dbsnp/" - }, - { - "path": "cadd.gene.gene_id", - "valueType": "http://identifiers.org/ensembl.gene/" - }, - { - "path": "cadd.gene.feature_id", - "valueType": "http://identifiers.org/ensembl.transcript/" - }, - { - "path": "cadd.gene.ccds_id", - "valueType": "http://identifiers.org/ccds/" - }, - { - "path": "clinvar.uniprot", - "valueType": "http://identifiers.org/uniprot/" - }, - { - "path": "clinvar.omim", - "valueType": "http://identifiers.org/omim/" - }, - { - "path": "clinvar.rcv.accession", - "valueType": "http://identifiers.org/clinvar/" - }, - { - "path": "clinvar.rcv.conditions.identifiers.omim", - "valueType": "http://identifiers.org/omim/" - }, - { - "path": "clinvar.rcv.conditions.identifiers.efo", - "valueType": "http://identifiers.org/efo/" - }, - { - "path": "clinvar.rcv.conditions.identifiers.orphanet", - "valueType": "http://identifiers.org/orphanet/" - }, - { - "path": "clinvar.gene.id", - "valueType": "http://identifiers.org/hgnc/" - }, - { - "path": "dbnsfp.ensembl.proteinid", - "valueType": "http://identifiers.org/ensembl.protein/" - }, - { - "path": "docm.pubmed_id", - "valueType": "http://identifiers.org/pubmed/" - }, - { - "path": "evs.gene.accession", - "valueType": "http://identifiers.org/refseq/" - }, - { - "path": "clinvar.rcv.clinical_significance", - "valueType": "http://identifiers.org/clinicalsignificance/" - } - ] + "description": "successful response" } }, - "summary": "Make variant query and return matching variant hits" + "summary": "Return matching API metadata", + "tags": [ + "metadata" + ] } }, - "/variant/{variantid}": { + "/query/": { "get": { + "description": "Query metadata for matching APIs.", "parameters": [ { - "description": "Variant HGVS ID, dbSNP ID", - "in": "path", - "name": "variantid", + "description": "Can pass any string as the query term to match any field, e.g. \"mygene.info\", or pass a fielded query term like \"info.contact.name:wu\".", + "in": "query", + "name": "q", "required": true, "schema": { "type": "string" - }, - "x-valueType": [ - "http://identifiers.org/hgvs/", - "http://identifiers.org/dbsnp/" - ] + } + }, + { + "description": "You can use this parameter to filter the fields returned from the raw metadata document. Only effective when \"raw=1\" is passed. E.g. \"info.contact.name,servers\". Nested fields are supported via dot notation, and multiple fields can be passed as a comma-separated string.", + "in": "query", + "name": "fields", + "schema": { + "type": "string" + } + }, + { + "description": "return raw metadata document if passed \"1\" or \"true\". Default is \"false\".", + "in": "query", + "name": "raw", + "schema": { + "type": "string" + } + }, + { + "description": "Number of items to be skipped. Combining with \"size\" parameter, this can be used for the pagination of the long result.", + "in": "query", + "name": "from", + "schema": { + "type": "string" + } + }, + { + "description": "The number of items returned in one request. Combining with \"from\" parameter, this can be used for the pagination of the long result.", + "in": "query", + "name": "size", + "schema": { + "type": "string" + } } ], "responses": { "200": { - "description": "A variant object", - "x-JSONLDContext": "https://github.com/NCATS-Tangerine/translator-api-registry/blob/master/myvariant.info/jsonld_context/myvariant_context.json", - "x-responseValueType": [ - { - "path": "cadd.gene.genename", - "valueType": "http://identifiers.org/hgnc.symbol/" - }, - { - "path": "clinvar.rsid", - "valueType": "http://identifiers.org/dbsnp/" - }, - { - "path": "cadd.gene.gene_id", - "valueType": "http://identifiers.org/ensembl.gene/" - }, - { - "path": "cadd.gene.feature_id", - "valueType": "http://identifiers.org/ensembl.transcript/" - }, - { - "path": "cadd.gene.ccds_id", - "valueType": "http://identifiers.org/ccds/" - }, - { - "path": "clinvar.uniprot", - "valueType": "http://identifiers.org/uniprot/" - }, - { - "path": "clinvar.rcv.accession", - "valueType": "http://identifiers.org/clinvar/" - }, - { - "path": "clinvar.rcv.conditions.identifiers.omim", - "valueType": "http://identifiers.org/omim/" - }, - { - "path": "clinvar.rcv.conditions.identifiers.efo", - "valueType": "http://identifiers.org/efo/" - }, - { - "path": "clinvar.rcv.conditions.identifiers.orphanet", - "valueType": "http://identifiers.org/orphanet/" - }, - { - "path": "clinvar.gene.id", - "valueType": "http://identifiers.org/hgnc/" - }, - { - "path": "dbnsfp.ensembl.proteinid", - "valueType": "http://identifiers.org/ensembl.protein/" - }, - { - "path": "docm.pubmed_id", - "valueType": "http://identifiers.org/pubmed/" - }, - { - "path": "evs.gene.accession", - "valueType": "http://identifiers.org/refseq/" - }, - { - "path": "clinvar.rcv.clinical_significance", - "valueType": "http://identifiers.org/clinicalsignificance/" + "description": "default response" + } + }, + "summary": "Query metadata for matching APIs." + } + }, + "/validate": { + "get": { + "description": "Validate input SmartAPI metadata", + "operationId": "", + "parameters": [ + { + "description": "The full URL of an input SmartAPI metadata to validate. The file format can be either JSON or YAML.", + "in": "query", + "name": "url", + "required": true, + "schema": { + "type": "string" + } + } + ], + "responses": { + "200": { + "description": "default response" + } + }, + "summary": "Validate input SmartAPI metadata" + } + }, + "/suggestion": { + "get": { + "description": "Return suggested values from the existing APIs in the registry for a given field.", + "operationId": "", + "parameters": [ + { + "description": "An input field to return the suggested values and their occurrence numbers.", + "in": "query", + "name": "field", + "schema": { + "type": "string" + } + }, + { + "description": "The maximum number of suggested values to return", + "in": "query", + "name": "size", + "schema": { + "type": "string" + } + } + ], + "responses": { + "default": { + "description": "Default response" + } + }, + "summary": "Return suggested values for a give field." + } + }, + "/metakg": { + "get": { + "parameters": [ + { + "description": "The subject type of the association, e.g. Gene", + "example": "Gene", + "in": "query", + "name": "subject", + "schema": { + "type": "string" + } + }, + { + "description": "The object type of the association, e.g. ChemicalSubstance", + "example": "ChemicalSubstance", + "in": "query", + "name": "object", + "schema": { + "type": "string" + } + }, + { + "description": "The predicate of the association, e.g. Gene", + "example": "physically_interacts_with", + "in": "query", + "name": "predicate", + "schema": { + "type": "string" + } + }, + { + "description": "The API providing the association, e.g. MyChem.info API", + "example": "MyChem.info API", + "in": "query", + "name": "api", + "schema": { + "type": "string" + } + }, + { + "description": "The data source providing the association, e.g. drugbank", + "example": "drugbank", + "in": "query", + "name": "provided_by", + "schema": { + "type": "string" + } + } + ], + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "description": "Array of all associations", + "items": { + "properties": { + "api": { + "description": "The api providing the association, e.g. MyChem.info", + "properties": { + "name": { + "description": "The api providing the association, e.g. MyChem.info", + "example": "MyChem.info API", + "type": "string" + }, + "smartapi": { + "description": "smartapi related data", + "properties": { + "id": { + "description": "unique smartapi id for the api", + "example": "8f08d1446e0bb9c2b323713ce83e2bd3", + "type": "string" + }, + "metadata": { + "description": "the url for smartapi specification", + "example": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/mychem.info/openapi_full.yml", + "type": "string" + }, + "ui": { + "description": "the web UI url for the API", + "example": "https://smart-api.info/ui/8f08d1446e0bb9c2b323713ce83e2bd3", + "type": "string" + } + }, + "type": "object" + } + }, + "type": "object" + }, + "object": { + "description": "The object type of the association, e.g. ChemicalSubstance", + "example": "ChemicalSubstance", + "type": "string" + }, + "predicate": { + "description": "The predicate of the association, e.g. physically_interacts_with", + "example": "physically_interacts_with", + "type": "string" + }, + "provided_by": { + "description": "The data source providing the association, e.g. ChEMBL", + "example": "ChEMBL", + "type": "string" + }, + "subject": { + "description": "The subject type of the association, e.g. Gene", + "example": "Gene", + "type": "string" + } + }, + "type": "object" + }, + "type": "array" + } } - ] + }, + "description": "Association information including subject, object, predicate, api, provided_by and smartapi info." } }, - "summary": "For a given variant id, return the matching variant object" + "summary": "retrieve associations within smartapi, if no parameters provided, will return all associations" } } }, "servers": [ { "description": "Production server", - "url": "http://myvariant.info/v1" + "url": "https://smart-api.info/api" + }, + { + "description": "Development server", + "url": "http://dev.smart-api.info/api" } ], "tags": [ { - "name": "variant" + "name": "api" }, { - "name": "annotation" + "name": "metadata" }, { - "name": "query" + "name": "openapi" }, { "name": "translator" @@ -27001,131 +25768,533 @@ ] }, { - "_id": "671b45c0301c8624abbd26ae78449ca2", + "_id": "415c3b1a85ead4ceb58caf00dee9b24e", "_meta": { - "date_created": "2021-02-10T05:26:25.703523+00:00", - "last_updated": "2021-03-05T08:00:59.514607+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/mydisease.info/smartapi.yaml", - "username": "kevinxin90" + "date_created": "2021-02-02T02:37:11.215923+00:00", + "last_updated": "2021-03-08T20:59:28.486729+00:00", + "url": "https://raw.githubusercontent.com/suihuanglab/improving-agent/main/app/improving-agent.yaml", + "username": "brettasmi" }, - "_score": 0.5077911, - "components": { - "x-bte-kgs-operations": { - "bp-disease": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "GO", - "semantic": "BiologicalProcess" - } - ], - "method": "post", - "outputs": [ - { - "id": "MESH", - "semantic": "Disease" - } - ], - "parameters": { - "fields": "ctd.mesh", - "size": "250" - }, - "path": "/query", - "predicate": "related_to", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "ctd.bp_related_to_disease.go_id" + "_score": 0.5232822, + "info": { + "contact": { + "email": "brett.smith@isbscience.org", + "x-role": "responsible developer" + }, + "description": "imProving Agent OpenAPI TRAPI Specification", + "license": { + "name": "Apache 2.0", + "url": "http://www.apache.org/licenses/LICENSE-2.0.html" + }, + "termsOfService": "https://spoke.rbvi.ucsf.edu/license.html", + "title": "imProving Agent", + "version": "1.0.0", + "x-translator": { + "component": "ARA", + "team": [ + "imProving Agent" + ] + }, + "x-trapi": { + "version": "1.0.0" + } + }, + "paths": { + "/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" + } + } }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/bp-disease" - }, - "source": "CTD", - "supportBatch": true - } - ], - "chemical-disease": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "MESH", - "semantic": "ChemicalSubstance" - } - ], - "method": "post", - "outputs": [ - { - "id": "MESH", - "semantic": "Disease" + "description": "Predicates by source and target" + } + }, + "summary": "Get supported relationships by source and target", + "tags": [ + "predicates" + ] + } + }, + "/query": { + "post": { + "description": "", + "operationId": "query", + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Query" + } } - ], - "parameters": { - "fields": "disgenet.xrefs.mesh", - "size": "250" }, - "path": "/query", - "predicate": "related_to", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "ctd.chemical_related_to_disease.mesh_chemical_id" + "description": "Query information to be submitted", + "required": true + }, + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Response" + } + } }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/mesh" - }, - "source": "hpo", - "supportBatch": true - } - ], - "disease-bp": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "MESH", - "semantic": "Disease" - } - ], - "outputs": [ - { - "id": "GO", - "semantic": "BiologicalProcess" - } - ], - "parameters": { - "fields": "ctd.bp_related_to_disease" + "description": "OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized." }, - "predicate": "related_to", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "mondo.xrefs.mesh, disgenet.xrefs.mesh" + "400": { + "content": { + "application/json": { + "schema": { + "type": "string" + } + } }, - "header": "application/x-www-form-urlencoded" + "description": "Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)." }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/disease-bp" + "500": { + "content": { + "application/json": { + "schema": { + "type": "string" + } + } + }, + "description": "Internal server error." }, - "source": "CTD", - "supportBatch": true - } - ], - "disease-chemical": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "MESH", - "semantic": "Disease" - } - ], - "method": "post", + "501": { + "content": { + "application/json": { + "schema": { + "type": "string" + } + } + }, + "description": "Not implemented." + } + }, + "summary": "Query reasoner via one of several inputs", + "tags": [ + "query" + ], + "x-swagger-router-controller": "swagger_server.controllers.query_controller" + } + } + }, + "servers": [ + { + "url": "https://evidara.healthdatascience.cloud/api/v1/" + } + ], + "tags": [ + { + "description": "Get supported relationships by source and target", + "name": "predicates" + }, + { + "description": "Query reasoner using a predefined question type", + "name": "query" + }, + { + "name": "translator" + }, + { + "name": "reasoner" + }, + { + "externalDocs": { + "description": "Documentation of SPOKE data", + "url": "https://spoke.rbvi.ucsf.edu/docs/index.html" + }, + "name": "SPOKE" + } + ] + }, + { + "_id": "00bab7d59abe031098d5cb1597f7f1c4", + "_meta": { + "date_created": "2021-03-02T03:45:02.003694+00:00", + "last_updated": "2021-03-08T17:40:01.860482+00:00", + "url": "https://arax.ncats.io/kg2/api/rtxkg2/v1.0/openapi.json", + "username": "edeutsch" + }, + "_score": 0.5232822, + "info": { + "contact": { + "email": "edeutsch@systemsbiology.org" + }, + "description": "TRAPI 1.0 endpoint for the NCATS Biomedical Translator KP called RTX KG2", + "license": { + "name": "Apache 2.0", + "url": "http://www.apache.org/licenses/LICENSE-2.0.html" + }, + "termsOfService": "https://github.com/RTXteam/RTX/blob/master/LICENSE", + "title": "RTX KG2", + "version": "2.3.4", + "x-translator": { + "component": "ARA", + "team": "Expander Agent" + }, + "x-trapi": { + "version": "1.0.0" + } + }, + "paths": { + "/entity": { + "get": { + "operationId": "get_entity", + "parameters": [ + { + "description": "A string to search by (name, abbreviation, CURIE, etc.). The parameter may be repeated for multiple search strings.", + "explode": true, + "in": "query", + "name": "q", + "required": true, + "schema": { + "example": [ + "MESH:D014867", + "NCIT:C34373" + ], + "items": { + "type": "string" + }, + "type": "array" + }, + "style": "form" + } + ], + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "type": "object" + } + } + }, + "description": "successful operation" + }, + "404": { + "description": "Entity not found" + } + }, + "summary": "Obtain CURIE and synonym information about a search term", + "tags": [ + "entity" + ], + "x-openapi-router-controller": "openapi_server.controllers.entity_controller" + } + }, + "/predicates": { + "get": { + "operationId": "predicates", + "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" + ], + "x-openapi-router-controller": "openapi_server.controllers.predicates_controller" + } + }, + "/query": { + "post": { + "operationId": "query", + "parameters": [ + { + "description": "Set to true in order to bypass any possible cached response and try to answer the query over again\n", + "explode": true, + "in": "query", + "name": "bypass_cache", + "required": false, + "schema": { + "default": false, + "type": "boolean" + }, + "style": "form" + } + ], + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Query" + } + } + }, + "description": "Query information to be submitted", + "required": true + }, + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Response" + } + } + }, + "description": "OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized." + }, + "400": { + "content": { + "application/json": { + "schema": { + "type": "string" + } + } + }, + "description": "Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)." + }, + "500": { + "content": { + "application/json": { + "schema": { + "type": "string" + } + } + }, + "description": "Internal server error." + }, + "501": { + "content": { + "application/json": { + "schema": { + "type": "string" + } + } + }, + "description": "Not implemented." + } + }, + "summary": "Query reasoner via one of several inputs", + "tags": [ + "query" + ], + "x-openapi-router-controller": "openapi_server.controllers.query_controller" + } + } + }, + "servers": [ + { + "url": "https://arax.ncats.io/api/rtxkg2/v1.0" + } + ], + "tags": [ + { + "description": "Get all supported relationships by source and target", + "externalDocs": { + "description": "Documentation for the reasoner predicates function", + "url": "http://arax.ncats.io/overview.html#predicates" + }, + "name": "predicates" + }, + { + "description": "Query reasoner using a predefined question type", + "externalDocs": { + "description": "Documentation for the reasoner query function", + "url": "http://arax.ncats.io/overview.html#query" + }, + "name": "query" + }, + { + "name": "translator" + }, + { + "name": "trapi" + }, + { + "description": "Return extensive information about entities in the knowledge graph", + "externalDocs": { + "description": "Documentation for the reasoner entity function", + "url": "https://arax.ncats.io/overview.html#entity" + }, + "name": "entity" + } + ] + }, + { + "_id": "671b45c0301c8624abbd26ae78449ca2", + "_meta": { + "date_created": "2021-02-10T05:26:25.703523+00:00", + "last_updated": "2021-03-29T07:02:17.504416+00:00", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/mydisease.info/smartapi.yaml", + "username": "kevinxin90" + }, + "_score": 0.5232822, + "components": { + "x-bte-kgs-operations": { + "chemical-disease": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "MESH", + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ + { + "id": "MESH", + "semantic": "Disease" + } + ], + "parameters": { + "fields": "ctd.mesh", + "size": "1000" + }, + "path": "/query", + "predicate": "related_to", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "ctd.chemical_related_to_disease.mesh_chemical_id" + }, + "header": "application/x-www-form-urlencoded" + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ctd-mesh-disease" + }, + "source": "CTD", + "supportBatch": true + } + ], + "chemical-disease2": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "MESH", + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ + { + "id": "OMIM", + "semantic": "Disease" + } + ], + "parameters": { + "fields": "ctd.omim", + "size": "1000" + }, + "path": "/query", + "predicate": "related_to", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "ctd.chemical_related_to_disease.mesh_chemical_id" + }, + "header": "application/x-www-form-urlencoded" + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ctd-omim-disease" + }, + "source": "CTD", + "supportBatch": true + } + ], + "disease-chemical": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "MESH", + "semantic": "Disease" + } + ], + "method": "post", + "outputs": [ + { + "id": "MESH", + "semantic": "ChemicalSubstance" + } + ], + "parameters": { + "fields": "ctd.chemical_related_to_disease" + }, + "path": "/query", + "predicate": "related_to", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "ctd.mesh" + }, + "header": "application/x-www-form-urlencoded" + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/disease-chemical" + }, + "source": "CTD", + "supportBatch": true + } + ], + "disease-chemical2": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "OMIM", + "semantic": "Disease" + } + ], + "method": "post", "outputs": [ { "id": "MESH", @@ -27140,7 +26309,7 @@ "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "mondo.xrefs.mesh, disgenet.xrefs.mesh" + "scopes": "ctd.omim" }, "header": "application/x-www-form-urlencoded" }, @@ -27167,7 +26336,7 @@ } ], "parameters": { - "fields": "disgenet.genes_related_to_disease.gene_id" + "fields": "disgenet.genes_related_to_disease" }, "predicate": "related_to", "requestBody": { @@ -27180,7 +26349,7 @@ "response_mapping": { "$ref": "#/components/x-bte-response-mapping/disease-gene" }, - "source": "disgenet", + "source": "DisGeNET", "supportBatch": true } ], @@ -27213,7 +26382,7 @@ "response_mapping": { "$ref": "#/components/x-bte-response-mapping/disease-phenotype" }, - "source": "Human Phenotype Ontology", + "source": "HPO Annotations", "supportBatch": true } ], @@ -27235,7 +26404,7 @@ "parameters": { "fields": "hpo.phenotype_related_to_disease" }, - "predicate": "related_to", + "predicate": "has_phenotype", "requestBody": { "body": { "q": "{inputs[0]}", @@ -27246,7 +26415,7 @@ "response_mapping": { "$ref": "#/components/x-bte-response-mapping/disease-phenotype" }, - "source": "Human Phenotype Ontology", + "source": "HPO Annotations", "supportBatch": true } ], @@ -27268,7 +26437,7 @@ "parameters": { "fields": "covid_phenotypes.hp" }, - "predicate": "related_to", + "predicate": "has_phenotype", "requestBody": { "body": { "q": "{inputs[0]}", @@ -27279,7 +26448,7 @@ "response_mapping": { "$ref": "#/components/x-bte-response-mapping/disease-phenotype2" }, - "source": "covid_phenotypes", + "source": "Automat covid_phenotypes", "supportBatch": true } ], @@ -27312,7 +26481,7 @@ "response_mapping": { "$ref": "#/components/x-bte-response-mapping/disease-variant" }, - "source": "disgenet", + "source": "DisGeNET", "supportBatch": true } ], @@ -27333,7 +26502,7 @@ ], "parameters": { "fields": "disgenet.xrefs.umls", - "size": "250" + "size": "1000" }, "predicate": "related_to", "requestBody": { @@ -27346,7 +26515,7 @@ "response_mapping": { "$ref": "#/components/x-bte-response-mapping/umls" }, - "source": "disgenet", + "source": "DisGeNET", "supportBatch": true } ], @@ -27367,7 +26536,8 @@ } ], "parameters": { - "fields": "mondo.descendants" + "fields": "mondo.descendants", + "size": "1000" }, "path": "/query", "predicate": "superclass_of", @@ -27381,7 +26551,7 @@ "response_mapping": { "$ref": "#/components/x-bte-response-mapping/has_subclass" }, - "source": "mondo", + "source": "MONDO", "supportBatch": true } ], @@ -27402,8 +26572,8 @@ } ], "parameters": { - "fields": "mondo.xrefs.omim", - "size": "250" + "fields": "hpo.omim", + "size": "1000" }, "path": "/query", "predicate": "related_to", @@ -27417,7 +26587,78 @@ "response_mapping": { "$ref": "#/components/x-bte-response-mapping/omim" }, - "source": "Human Phenotype Ontology", + "source": "HPO Annotations", + "supportBatch": true + } + ], + "phenotype-disease2": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "HP", + "semantic": "PhenotypicFeature" + } + ], + "method": "post", + "outputs": [ + { + "id": "ORPHANET", + "semantic": "Disease" + } + ], + "parameters": { + "fields": "hpo.orphanet", + "size": "1000" + }, + "path": "/query", + "predicate": "related_to", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "hpo.phenotype_related_to_disease.hpo_id" + }, + "header": "application/x-www-form-urlencoded" + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/orphanet" + }, + "source": "HPO Annotations", + "supportBatch": true + } + ], + "phenotype-disease3": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "HP", + "semantic": "PhenotypicFeature" + } + ], + "method": "post", + "outputs": [ + { + "id": "MONDO", + "semantic": "Disease" + } + ], + "parameters": { + "fields": "mondo.mondo" + }, + "path": "/query", + "predicate": "related_to", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "covid_phenotypes.hp" + }, + "header": "application/x-www-form-urlencoded" + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/mondo" + }, + "source": "Automat covid_phenotypes", "supportBatch": true } ], @@ -27438,7 +26679,8 @@ } ], "parameters": { - "fields": "mondo.parents" + "fields": "mondo.parents", + "size": "1000" }, "path": "/query", "predicate": "subclass_of", @@ -27452,7 +26694,7 @@ "response_mapping": { "$ref": "#/components/x-bte-response-mapping/subclass_of" }, - "source": "mondo", + "source": "MONDO", "supportBatch": true } ], @@ -27473,7 +26715,7 @@ ], "parameters": { "fields": "disgenet.xrefs.umls", - "size": "250" + "size": "1000" }, "predicate": "related_to", "requestBody": { @@ -27486,30 +26728,32 @@ "response_mapping": { "$ref": "#/components/x-bte-response-mapping/umls" }, - "source": "disgenet", + "source": "DisGeNET", "supportBatch": true } ] }, "x-bte-response-mapping": { - "bp-disease": { + "ctd-mesh-disease": { "MESH": "ctd.mesh" }, - "disease-bp": { - "GO": "ctd.bp_related_to_disease.go_id", - "name": "ctd.bp_related_to_disease.go_name" + "ctd-omim-disease": { + "OMIM": "ctd.omim" }, "disease-chemical": { "MESH": "ctd.chemical_related_to_disease.mesh_chemical_id", + "evidence": "ctd.chemical_related_to_disease.direct_evidence", "pubmed": "ctd.chemical_related_to_disease.pubmed" }, "disease-gene": { - "NCBIGENE": "disgenet.genes_related_to_disease.gene_id" + "NCBIGENE": "disgenet.genes_related_to_disease.gene_id", + "pubmed": "disgenet.genes_related_to_disease.pubmed" }, "disease-phenotype": { "HP": "hpo.phenotype_related_to_disease.hpo_id", "evidence": "hpo.phenotype_related_to_disease.evidence", - "frequency": "hpo.phenotype_related_to_disease.frequency" + "frequency": "hpo.phenotype_related_to_disease.numeric_freq", + "pubmed": "hpo.phenotype_related_to_disease.pmid_refs" }, "disease-phenotype2": { "HP": "covid_phenotypes.hp" @@ -27521,11 +26765,14 @@ "has_subclass": { "MONDO": "mondo.descendants" }, - "mesh": { - "MESH": "disgenet.xrefs.mesh" + "mondo": { + "MONDO": "mondo.mondo" }, "omim": { - "OMIM": "mondo.xrefs.omim" + "OMIM": "hpo.omim" + }, + "orphanet": { + "ORPHANET": "hpo.orphanet" }, "subclass_of": { "MONDO": "mondo.parents" @@ -27889,11 +27136,14 @@ { "$ref": "#/components/x-bte-kgs-operations/disease-phenotype2" }, + { + "$ref": "#/components/x-bte-kgs-operations/disease-phenotype3" + }, { "$ref": "#/components/x-bte-kgs-operations/disease-chemical" }, { - "$ref": "#/components/x-bte-kgs-operations/disease-bp" + "$ref": "#/components/x-bte-kgs-operations/disease-chemical2" }, { "$ref": "#/components/x-bte-kgs-operations/gene-disease" @@ -27904,11 +27154,17 @@ { "$ref": "#/components/x-bte-kgs-operations/phenotype-disease" }, + { + "$ref": "#/components/x-bte-kgs-operations/phenotype-disease2" + }, + { + "$ref": "#/components/x-bte-kgs-operations/phenotype-disease3" + }, { "$ref": "#/components/x-bte-kgs-operations/chemical-disease" }, { - "$ref": "#/components/x-bte-kgs-operations/bp-disease" + "$ref": "#/components/x-bte-kgs-operations/chemical-disease2" }, { "$ref": "#/components/x-bte-kgs-operations/has_subclass" @@ -27945,125 +27201,128 @@ ] }, { - "_id": "09c8782d9f4027712e65b95424adba79", + "_id": "59dce17363dce279d389100834e43648", "_meta": { - "date_created": "2020-12-08T00:04:53.736889+00:00", - "last_updated": "2021-03-05T08:00:59.906727+00:00", - "slug": "myvariant", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/myvariant.info/openapi_full.yml", + "date_created": "2020-12-16T00:00:51.690125+00:00", + "last_updated": "2021-03-29T07:02:09.028444+00:00", + "slug": "mygene", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/mygene.info/openapi_full.yml", "username": "newgene" }, - "_score": 0.5077911, + "_score": 0.5232822, "components": { "x-bte-kgs-operations": { - "conditionAssociatedWithVariant": [ + "BPToGene": [ { "inputSeparator": ",", "inputs": [ { - "id": "OMIM", - "semantic": "Disease" + "id": "GO", + "semantic": "BiologicalProcess" } ], "outputs": [ { - "id": "DBSNP", - "semantic": "SequenceVariant" + "id": "NCBIGENE", + "semantic": "Gene" } ], "parameters": { - "fields": "dbsnp.rsid", - "size": "250" + "fields": "entrezgene", + "species": "human" }, - "predicate": "related_to", + "predicate": "has_participant", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "clinvar.rcv.conditions.identifiers.omim" + "scopes": "go.BP.id", + "size": 1000 }, "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/dbsnp" + "$ref": "#/components/x-bte-response-mapping/entrezgene" }, - "source": "clinvar", + "source": "NCBI Gene", "supportBatch": true } ], - "variantAffectDrugResponse": [ + "CCToGene": [ { "inputSeparator": ",", "inputs": [ { - "id": "DBSNP", - "semantic": "SequenceVariant" + "id": "GO", + "semantic": "CellularComponent" } ], "outputs": [ { - "id": "name", - "semantic": "ChemicalSubstance" + "id": "NCBIGENE", + "semantic": "Gene" } ], "parameters": { - "fields": "civic.evidence_items", - "size": "1000" + "fields": "entrezgene", + "species": "human" }, - "predicate": "variant_affect_drug_response", + "predicate": "expresses", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "dbsnp.rsid" + "scopes": "go.CC.id", + "size": 1000 }, "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/variant_affect_drug_response" + "$ref": "#/components/x-bte-response-mapping/entrezgene" }, - "source": "civic", + "source": "NCBI Gene", "supportBatch": true } ], - "variantAssociatedWithCondition": [ + "GeneToProtein": [ { "inputSeparator": ",", "inputs": [ { - "id": "DBSNP", - "semantic": "SequenceVariant" + "id": "ENSEMBL", + "semantic": "Gene" } ], "outputs": [ { - "id": "OMIM", - "semantic": "Disease" + "id": "UniProtKB", + "semantic": "Protein" } ], "parameters": { - "fields": "clinvar.rcv" + "fields": "uniprot.Swiss-Prot", + "species": "human" }, - "predicate": "related_to", + "predicate": "has_gene_product", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "dbsnp.rsid" + "scopes": "ensembl.gene" }, "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/variant-disease-omim" + "$ref": "#/components/x-bte-response-mapping/uniprotProtein" }, - "source": "clinvar", + "source": "UniprotKB", "supportBatch": true } ], - "variantAssociatedWithGene": [ + "MFToGene": [ { "inputSeparator": ",", "inputs": [ { - "id": "DBSNP", - "semantic": "SequenceVariant" + "id": "GO", + "semantic": "MolecularActivity" } ], "outputs": [ @@ -28073,873 +27332,299 @@ } ], "parameters": { - "fields": "dbsnp.gene.geneid" + "fields": "entrezgene", + "species": "human" }, - "predicate": "located_in", + "predicate": "enabled_by", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "dbsnp.rsid" + "scopes": "go.MF.id", + "size": 1000 }, "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/variant-gene" + "$ref": "#/components/x-bte-response-mapping/entrezgene" }, - "source": "dbsnp", + "source": "NCBI Gene", "supportBatch": true } - ] - }, - "x-bte-response-mapping": { - "dbsnp": { - "DBSNP": "dbsnp.rsid" - }, - "variant-disease-omim": { - "OMIM": "clinvar.rcv.conditions.identifiers.omim", - "clinicalsignificance": "clinvar.rcv.clinical_significance", - "name": "clinvar.rcv.conditions.name" - }, - "variant-gene": { - "NCBIGENE": "dbsnp.gene.geneid" - }, - "variant_affect_drug_response": { - "clinical_significance": "civic.evidence_items.clinical_significance", - "evidence_level": "civic.evidence_items.evidence_level", - "evidence_type": "civic.evidence_items.evidence_type", - "name": "civic.evidence_items.drugs.name", - "pubmed": "civic.evidence_items.source.pubmed" - } - } - }, - "info": { - "contact": { - "email": "help@myvariant.info", - "name": "Chunlei Wu", - "x-id": "https://github.com/newgene", - "x-role": "responsible developer" - }, - "description": "Documentation of the MyVariant.info Variant Query web services. Learn more about [MyVariant.info](http://myvariant.info/)", - "termsOfService": "http://myvariant.info/terms/", - "title": "MyVariant.info API", - "version": "1.0", - "x-translator": { - "component": "KP", - "team": [ - "Service Provider" - ] - } - }, - "paths": { - "/metadata": { - "get": { - "parameters": [ - { - "$ref": "#/components/parameters/callback", - "in": "query", - "name": "callback" - } - ], - "responses": { - "200": { - "description": "MyVariant.info metadata object" - } - }, - "summary": "Get metadata about the data available from MyVariant.info.", - "tags": [ - "metadata" - ] - } - }, - "/metadata/fields": { - "get": { - "parameters": [ - { - "description": "Pass a search term to filter the available fields, e.g. \"search=clinvar\".", - "in": "query", - "name": "search", - "schema": { - "type": "string" + ], + "PathwayHasGene": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "REACT", + "semantic": "Pathway" } - }, - { - "description": "Pass a prefix string to filter the available fields, e.g. \"prefix=refseq\".", - "in": "query", - "name": "prefix", - "schema": { - "type": "string" + ], + "method": "post", + "outputs": [ + { + "id": "NCBIGENE", + "semantic": "Gene" } + ], + "parameters": { + "fields": "entrezgene", + "species": "human" }, - { - "$ref": "#/components/parameters/callback", - "in": "query", - "name": "callback" - } - ], - "responses": { - "200": { - "description": "MyVariant.info metadata fields object" - } - }, - "summary": "Get metadata about the data fields available from MyVariant.info.", - "tags": [ - "metadata" - ] - } - }, - "/query": { - "get": { - "parameters": [ - { - "description": "Query string. Examples \"rs752396467\", \"possibly_damaging\", \"CDK7\". The detailed query syntax can be found from our [docs](http://docs.myvariant.info/en/latest/doc/variant_query_service.html).", - "example": "CDK7", - "in": "query", - "name": "q", - "required": true, - "schema": { - "type": "string" - } + "predicate": "has_participant", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "pathway.reactome.id", + "size": 1000 + }, + "header": "application/x-www-form-urlencoded" }, - { - "$ref": "#/components/parameters/fields", - "1": "query", - "name": "fields" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/entrezgene" }, - { - "$ref": "#/components/parameters/size", - "in": "query", - "name": "size" + "source": "Reactome", + "supportBatch": true + }, + { + "inputSeparator": ",", + "inputs": [ + { + "id": "KEGG", + "semantic": "Pathway" + } + ], + "method": "post", + "outputs": [ + { + "id": "NCBIGENE", + "semantic": "Gene" + } + ], + "parameters": { + "fields": "entrezgene", + "species": "human" }, - { - "$ref": "#/components/parameters/from", - "in": "query", - "name": "from" + "predicate": "has_participant", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "pathway.kegg.id", + "size": 1000 + }, + "header": "application/x-www-form-urlencoded" }, - { - "$ref": "#/components/parameters/sort", - "in": "query", - "name": "sort" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/entrezgene" }, - { - "description": "a single field or comma-separated fields to return facets, for example, \"facets=clinvar.gene.id\", \"facets=clinvar.gene.id,dbnsfp.uniprot.acc\".", - "in": "query", - "name": "facets", - "schema": { - "type": "string" + "source": "ConsensusPathDB", + "supportBatch": true + }, + { + "inputSeparator": ",", + "inputs": [ + { + "id": "WIKIPATHWAYS", + "semantic": "Pathway" + } + ], + "method": "post", + "outputs": [ + { + "id": "NCBIGENE", + "semantic": "Gene" } + ], + "parameters": { + "fields": "entrezgene", + "species": "human" }, - { - "$ref": "#/components/parameters/callback", - "in": "query", - "name": "callback" + "predicate": "has_participant", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "pathway.wikipathways.id", + "size": 1000 + }, + "header": "application/x-www-form-urlencoded" }, - { - "$ref": "#/components/parameters/dotfield", - "in": "query", - "name": "dotfield" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/entrezgene" }, - { - "$ref": "#/components/parameters/email", - "in": "query", - "name": "email" - } - ], - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/QueryResult" - } - } - }, - "description": "A query response object with \"hits\" property" + "source": "ConsensusPathDB", + "supportBatch": true + }, + { + "inputSeparator": ",", + "inputs": [ + { + "id": "BIOCARTA", + "semantic": "Pathway" + } + ], + "method": "post", + "outputs": [ + { + "id": "NCBIGENE", + "semantic": "Gene" + } + ], + "parameters": { + "fields": "entrezgene", + "species": "human" }, - "400": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResult" - } - } + "predicate": "has_participant", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "pathway.biocarta.id", + "size": 1000 }, - "description": "A response indicating an improperly formatted query" - } - }, - "summary": "Make variant query and return matching variant list. Support JSONP and CORS as well.", - "tags": [ - "query" - ] - }, - "post": { - "parameters": [ - { - "$ref": "#/components/parameters/fields", - "in": "query", - "name": "fields" + "header": "application/x-www-form-urlencoded" }, - { - "$ref": "#/components/parameters/dotfield", - "in": "query", - "name": "dotfield" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/entrezgene" }, - { - "$ref": "#/components/parameters/email", - "in": "query", - "name": "email" - } - ], - "requestBody": { - "content": { - "application/x-www-form-urlencoded": { - "schema": { - "properties": { - "q": { - "description": "multiple query terms seperated by comma (also support \"+\" or white space), but no wildcard, e.g., \"q=rs58991260,rs2500\" or \"q=rs58991260+rs2500\"", - "type": "string" - }, - "scopes": { - "description": "Specify one or more fields (separated by comma) as the search \"scopes\", e.g., \"scopes=dbsnp.rsid\". The available \"fields\" that can be passed to \"scopes\" parameter are listed [here](http://docs.myvariant.info/en/latest/doc/data.html#available-fields). Default: \"scopes=_id\" (HGVS id).", - "type": "string" - } - }, - "required": [ - "q" - ] - } + "source": "ConsensusPathDB", + "supportBatch": true + } + ], + "ProteinToGene": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UniProtKB", + "semantic": "Protein" } - } - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/QueryPOSTResult" - } - } - }, - "description": "Query response objects with \"hits\" property" + ], + "outputs": [ + { + "id": "ENSEMBL", + "semantic": "Gene" + } + ], + "parameters": { + "fields": "ensembl.gene", + "species": "human" }, - "400": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResult" - } - } + "predicate": "related_to", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "uniprot.Swiss-Prot" }, - "description": "A response indicating an improperly formatted query" - } - }, - "summary": "Make variant batch query and return matching variant hits", - "tags": [ - "query" - ], - "x-bte-kgs-operations": [ - { - "$ref": "#/components/x-bte-kgs-operations/variantAssociatedWithGene" + "header": "application/x-www-form-urlencoded" }, - { - "$ref": "#/components/x-bte-kgs-operations/variantAssociatedWithCondition" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ensemblGene" }, - { - "$ref": "#/components/x-bte-kgs-operations/conditionAssociatedWithVariant" + "source": "UniprotKB", + "supportBatch": true + } + ], + "enablesMF": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "NCBIGENE", + "semantic": "Gene" + } + ], + "outputs": [ + { + "id": "GO", + "semantic": "MolecularActivity" + } + ], + "parameters": { + "fields": "go.MF", + "species": "human" }, - { - "$ref": "#/components/x-bte-kgs-operations/variantAffectDrugResponse" - } - ] - } - }, - "/variant": { - "post": { - "parameters": [ - { - "$ref": "#/components/parameters/fields", - "in": "query", - "name": "fields" + "predicate": "enables", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "entrezgene" + }, + "header": "application/x-www-form-urlencoded" }, - { - "$ref": "#/components/parameters/dotfield", - "in": "query", - "name": "dotfield" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/molecularFunction" }, - { - "$ref": "#/components/parameters/email", - "in": "query", - "name": "email" - } - ], - "requestBody": { - "content": { - "application/x-www-form-urlencoded": { - "schema": { - "properties": { - "ids": { - "description": "multiple variant ids seperated by comma, e.g., \"ids=chr6:g.152708291G>A,chr1:g.35367G>A\" or \"ids=rs5882,rs12190874\". Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted.", - "type": "string" - } - }, - "required": [ - "ids" - ] - } + "source": "NCBI Gene", + "supportBatch": true + } + ], + "hasHomolog": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "NCBIGENE", + "semantic": "Gene" } - } - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "items": { - "$ref": "#/components/schemas/Variant" - }, - "type": "array" - } - } - }, - "description": "a list of matching variant objects" - } - }, - "summary": "For a list of variant ids, return the matching variant objects", - "tags": [ - "variant" - ] - } - }, - "/variant/{variantid}": { - "get": { - "parameters": [ - { - "description": "HGVS or rsid, e.g., chr6:g.152708291G>A, rs12190874", - "example": "chr6:g.152708291G>A", - "in": "path", - "name": "variantid", - "required": true, - "schema": { - "type": "string" + ], + "outputs": [ + { + "id": "MGI", + "semantic": "Gene" } + ], + "parameters": { + "fields": "pantherdb.ortholog" }, - { - "$ref": "#/components/parameters/fields", - "in": "query", - "name": "fields" - }, - { - "$ref": "#/components/parameters/dotfield", - "in": "query", - "name": "dotfield" - }, - { - "$ref": "#/components/parameters/callback", - "in": "query", - "name": "callback" - }, - { - "$ref": "#/components/parameters/email", - "in": "query", - "name": "email" - } - ], - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Variant" - } - } - }, - "description": "A matching variant object" - }, - "404": { - "description": "A response indicating an unknown variant id" - } - }, - "summary": "Retrieve variant annotation object based on HGVS or rsid, support JSONP and CORS as well.", - "tags": [ - "variant" - ] - } - } - }, - "servers": [ - { - "description": "Encrypted Production server", - "url": "https://myvariant.info/v1" - }, - { - "description": "Production server", - "url": "http://myvariant.info/v1" - } - ], - "tags": [ - { - "name": "variant" - }, - { - "name": "query" - }, - { - "name": "metadata" - }, - { - "name": "translator" - }, - { - "name": "biothings" - } - ] - }, - { - "_id": "415c3b1a85ead4ceb58caf00dee9b24e", - "_meta": { - "date_created": "2021-02-02T02:37:11.215923+00:00", - "last_updated": "2021-03-05T08:01:09.477002+00:00", - "url": "https://raw.githubusercontent.com/suihuanglab/improving-agent/main/app/improving-agent.yaml", - "username": "brettasmi" - }, - "_score": 0.5077911, - "info": { - "contact": { - "email": "brett.smith@isbscience.org", - "x-role": "responsible developer" - }, - "description": "imProving Agent OpenAPI TRAPI Specification", - "license": { - "name": "Apache 2.0", - "url": "http://www.apache.org/licenses/LICENSE-2.0.html" - }, - "termsOfService": "https://spoke.rbvi.ucsf.edu/license.html", - "title": "imProving Agent", - "version": "1.0.0", - "x-translator": { - "component": "ARA", - "team": [ - "imProving Agent" - ] - }, - "x-trapi": { - "version": "1.0.0" - } - }, - "paths": { - "/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": [ - "predicates" - ] - } - }, - "/query": { - "post": { - "description": "", - "operationId": "query", - "requestBody": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Query" - } - } - }, - "description": "Query information to be submitted", - "required": true - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Response" - } - } - }, - "description": "OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized." - }, - "400": { - "content": { - "application/json": { - "schema": { - "type": "string" - } - } - }, - "description": "Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)." - }, - "500": { - "content": { - "application/json": { - "schema": { - "type": "string" - } - } - }, - "description": "Internal server error." - }, - "501": { - "content": { - "application/json": { - "schema": { - "type": "string" - } - } - }, - "description": "Not implemented." - } - }, - "summary": "Query reasoner via one of several inputs", - "tags": [ - "query" - ], - "x-swagger-router-controller": "swagger_server.controllers.query_controller" - } - } - }, - "servers": [ - { - "url": "https://evidara.healthdatascience.cloud/api/v1/" - } - ], - "tags": [ - { - "description": "Get supported relationships by source and target", - "name": "predicates" - }, - { - "description": "Query reasoner using a predefined question type", - "name": "query" - }, - { - "name": "translator" - }, - { - "name": "reasoner" - }, - { - "externalDocs": { - "description": "Documentation of SPOKE data", - "url": "https://spoke.rbvi.ucsf.edu/docs/index.html" - }, - "name": "SPOKE" - } - ] - }, - { - "_id": "00bab7d59abe031098d5cb1597f7f1c4", - "_meta": { - "date_created": "2021-03-02T03:45:02.003694+00:00", - "last_updated": "2021-03-05T08:05:14.763224+00:00", - "url": "https://arax.ncats.io/kg2/api/rtxkg2/v1.0/openapi.json", - "username": "edeutsch" - }, - "_score": 0.5077911, - "info": { - "contact": { - "email": "edeutsch@systemsbiology.org" - }, - "description": "TRAPI 1.0 endpoint for the NCATS Biomedical Translator KP called RTX KG2", - "license": { - "name": "Apache 2.0", - "url": "http://www.apache.org/licenses/LICENSE-2.0.html" - }, - "termsOfService": "https://github.com/RTXteam/RTX/blob/master/LICENSE", - "title": "RTX KG2", - "version": "2.3.4", - "x-translator": { - "component": "ARA", - "team": "Expander Agent" - }, - "x-trapi": { - "version": "1.0.0" - } - }, - "paths": { - "/entity": { - "get": { - "operationId": "get_entity", - "parameters": [ - { - "description": "A string to search by (name, abbreviation, CURIE, etc.). The parameter may be repeated for multiple search strings.", - "explode": true, - "in": "query", - "name": "q", - "required": true, - "schema": { - "example": [ - "MESH:D014867", - "NCIT:C34373" - ], - "items": { - "type": "string" - }, - "type": "array" - }, - "style": "form" - } - ], - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "type": "object" - } - } - }, - "description": "successful operation" - }, - "404": { - "description": "Entity not found" - } - }, - "summary": "Obtain CURIE and synonym information about a search term", - "tags": [ - "entity" - ], - "x-openapi-router-controller": "openapi_server.controllers.entity_controller" - } - }, - "/predicates": { - "get": { - "operationId": "predicates", - "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" - ], - "x-openapi-router-controller": "openapi_server.controllers.predicates_controller" - } - }, - "/query": { - "post": { - "operationId": "query", - "parameters": [ - { - "description": "Set to true in order to bypass any possible cached response and try to answer the query over again\n", - "explode": true, - "in": "query", - "name": "bypass_cache", - "required": false, - "schema": { - "default": false, - "type": "boolean" - }, - "style": "form" - } - ], - "requestBody": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Query" - } - } - }, - "description": "Query information to be submitted", - "required": true - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Response" - } - } - }, - "description": "OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized." - }, - "400": { - "content": { - "application/json": { - "schema": { - "type": "string" - } - } + "predicate": "homologous_to", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "entrezgene" }, - "description": "Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)." + "header": "application/x-www-form-urlencoded" }, - "500": { - "content": { - "application/json": { - "schema": { - "type": "string" - } - } - }, - "description": "Internal server error." + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/pantherMGI" }, - "501": { - "content": { - "application/json": { - "schema": { - "type": "string" - } - } - }, - "description": "Not implemented." - } - }, - "summary": "Query reasoner via one of several inputs", - "tags": [ - "query" - ], - "x-openapi-router-controller": "openapi_server.controllers.query_controller" - } - } - }, - "servers": [ - { - "url": "https://arax.ncats.io/api/rtxkg2/v1.0" - } - ], - "tags": [ - { - "description": "Get supported relationships by source and target", - "externalDocs": { - "description": "Documentation for the reasoner predicates function", - "url": "http://arax.ncats.io/overview.html#predicates" - }, - "name": "predicates" - }, - { - "description": "Query reasoner using a predefined question type", - "externalDocs": { - "description": "Documentation for the reasoner query function", - "url": "http://arax.ncats.io/overview.html#query" - }, - "name": "query" - }, - { - "name": "translator" - }, - { - "name": "reasoner" - }, - { - "description": "Return identifier and type of some entity in the knowledge graph", - "externalDocs": { - "description": "Documentation for the reasoner entity function", - "url": "https://arax.ncats.io/overview.html#entity" - }, - "name": "entity" - } - ] - }, - { - "_id": "59dce17363dce279d389100834e43648", - "_meta": { - "date_created": "2020-12-16T00:00:51.690125+00:00", - "last_updated": "2021-03-05T08:01:46.298836+00:00", - "slug": "mygene", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/mygene.info/openapi_full.yml", - "username": "newgene" - }, - "_score": 0.5077911, - "components": { - "x-bte-kgs-operations": { - "PathwayHasGene": [ + "source": "PANTHER", + "supportBatch": true + } + ], + "hasTranscript": [ { "inputSeparator": ",", "inputs": [ { - "id": "REACT", - "semantic": "Pathway" + "id": "ENSEMBL", + "semantic": "Gene" } ], - "method": "post", "outputs": [ { - "id": "NCBIGENE", - "semantic": "Gene" + "id": "ENSEMBL", + "semantic": "Transcript" } ], "parameters": { - "fields": "entrezgene", - "size": 1000, + "fields": "ensembl.transcript", "species": "human" }, - "predicate": "functional_association", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "pathway.reactome.id" + "scopes": "ensembl.gene" }, "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/functional_association_reactome_gene" + "$ref": "#/components/x-bte-response-mapping/ensemblTranscript" }, - "source": "CPDB", + "source": "Ensembl", "supportBatch": true - }, + } + ], + "involvedInBP": [ { "inputSeparator": ",", "inputs": [ @@ -28948,18 +27633,17 @@ "semantic": "Gene" } ], - "method": "post", "outputs": [ { - "id": "REACT", - "semantic": "Pathway" + "id": "GO", + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "pathway.reactome", + "fields": "go.BP", "species": "human" }, - "predicate": "functional_association", + "predicate": "participates_in", "requestBody": { "body": { "q": "{inputs[0]}", @@ -28968,13 +27652,13 @@ "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/functional_association_reactome" + "$ref": "#/components/x-bte-response-mapping/biologicalProcess" }, - "source": "CPDB", + "source": "NCBI Gene", "supportBatch": true } ], - "enablesMF": [ + "involvedInCC": [ { "inputSeparator": ",", "inputs": [ @@ -28986,13 +27670,14 @@ "outputs": [ { "id": "GO", - "semantic": "MolecularActivity" + "semantic": "CellularComponent" } ], "parameters": { - "fields": "go.MF" + "fields": "go.CC", + "species": "human" }, - "predicate": "functional_association", + "predicate": "expressed_in", "requestBody": { "body": { "q": "{inputs[0]}", @@ -29001,75 +27686,13 @@ "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/functional_association_mf" - }, - "source": "entrez", - "supportBatch": true - } - ], - "hasGeneProduct": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "ENSEMBL", - "semantic": "Gene" - } - ], - "outputs": [ - { - "id": "UNIPROTKB", - "semantic": "Protein" - } - ], - "parameters": { - "fields": "uniprot.Swiss-Prot" - }, - "predicate": "has_gene_product", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "ensembl.gene" - }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/has_gene_product" - }, - "supportBatch": true - }, - { - "inputSeparator": ",", - "inputs": [ - { - "id": "ENSEMBL", - "semantic": "Gene" - } - ], - "outputs": [ - { - "id": "ENSEMBL", - "semantic": "Protein" - } - ], - "parameters": { - "fields": "ensembl.protein" - }, - "predicate": "has_gene_product", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "ensembl.gene" - }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/has_gene_product" + "$ref": "#/components/x-bte-response-mapping/cellularComponent" }, + "source": "NCBI Gene", "supportBatch": true } ], - "hasHomolog": [ + "involvedInPathway": [ { "inputSeparator": ",", "inputs": [ @@ -29078,16 +27701,18 @@ "semantic": "Gene" } ], + "method": "post", "outputs": [ { - "id": "MGI", - "semantic": "Gene" + "id": "REACT", + "semantic": "Pathway" } ], "parameters": { - "fields": "pantherdb.ortholog" + "fields": "pathway.reactome", + "species": "human" }, - "predicate": "homologous_to", + "predicate": "participates_in", "requestBody": { "body": { "q": "{inputs[0]}", @@ -29096,44 +27721,11 @@ "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/homologous_to" - }, - "supportBatch": true - } - ], - "hasTranscript": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "ENSEMBL", - "semantic": "Gene" - } - ], - "outputs": [ - { - "id": "ENSEMBL", - "semantic": "Transcript" - } - ], - "parameters": { - "fields": "ensembl.transcript" - }, - "predicate": "gene_to_transcript_relationship", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "ensembl.gene" - }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/gene_to_transcript_relationship" + "$ref": "#/components/x-bte-response-mapping/reactomePathway" }, + "source": "Reactome", "supportBatch": true - } - ], - "involvedInBP": [ + }, { "inputSeparator": ",", "inputs": [ @@ -29142,16 +27734,18 @@ "semantic": "Gene" } ], + "method": "post", "outputs": [ { - "id": "GO", - "semantic": "BiologicalProcess" + "id": "KEGG", + "semantic": "Pathway" } ], "parameters": { - "fields": "go.BP" + "fields": "pathway.kegg", + "species": "human" }, - "predicate": "functional_association", + "predicate": "participates_in", "requestBody": { "body": { "q": "{inputs[0]}", @@ -29160,13 +27754,11 @@ "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/functional_association_bp" + "$ref": "#/components/x-bte-response-mapping/keggPathway" }, - "source": "entrez", + "source": "ConsensusPathDB", "supportBatch": true - } - ], - "involvedInCC": [ + }, { "inputSeparator": ",", "inputs": [ @@ -29175,16 +27767,18 @@ "semantic": "Gene" } ], + "method": "post", "outputs": [ { - "id": "GO", - "semantic": "CellularComponent" + "id": "WIKIPATHWAYS", + "semantic": "Pathway" } ], "parameters": { - "fields": "go.CC" + "fields": "pathway.wikipathways", + "species": "human" }, - "predicate": "functional_association", + "predicate": "participates_in", "requestBody": { "body": { "q": "{inputs[0]}", @@ -29193,13 +27787,11 @@ "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/functional_association_cc" + "$ref": "#/components/x-bte-response-mapping/wikipathway" }, - "source": "entrez", + "source": "ConsensusPathDB", "supportBatch": true - } - ], - "involvedInPathway": [ + }, { "inputSeparator": ",", "inputs": [ @@ -29211,14 +27803,15 @@ "method": "post", "outputs": [ { - "id": "WIKIPATHWAYS", + "id": "BIOCARTA", "semantic": "Pathway" } ], "parameters": { - "fields": "pathway.wikipathways" + "fields": "pathway.biocarta", + "species": "human" }, - "predicate": "functional_association", + "predicate": "participates_in", "requestBody": { "body": { "q": "{inputs[0]}", @@ -29227,77 +27820,70 @@ "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/functional_association_wikipathways" + "$ref": "#/components/x-bte-response-mapping/biocarta" }, - "source": "CPDB", + "source": "ConsensusPathDB", "supportBatch": true } ] }, "x-bte-response-mapping": { - "ENSEMBL": "ensembl.gene", - "HGNC": "HGNC", - "NCBIGENE": "entrezgene", - "OMIM": "MIM", - "PHARMGKB": "pharmgkb", - "PHAROS": "pahros.target_id", - "SYMBOL": "symbol", - "UMLS": "umls.cui", - "description": "summary", - "functional_association_bp": { + "biocarta": { + "BIOCARTA": "pathway.biocarta.id", + "name": "pathway.biocarta.name" + }, + "biologicalProcess": { "GO": "go.BP.id", "evidence": "go.BP.evidence", + "name": "go.BP.term", "pubmed": "go.BP.pubmed", - "term": "go.BP.term" + "qualifiers": "go.BP.qualifier" }, - "functional_association_cc": { + "cellularComponent": { "GO": "go.CC.id", "evidence": "go.CC.evidence", + "name": "go.CC.term", "pubmed": "go.CC.pubmed", - "term": "go.CC.term" + "qualifiers": "go.CC.qualifier" + }, + "ensemblGene": { + "ENSEMBL": "ensembl.gene" + }, + "ensemblProtein": { + "ENSEMBL": "ensembl.protein" + }, + "ensemblTranscript": { + "ENSEMBL": "ensembl.transcript" }, - "functional_association_mf": { + "entrezgene": { + "NCBIGENE": "entrezgene" + }, + "keggPathway": { + "KEGG": "pathway.kegg.id", + "name": "pathway.kegg.name" + }, + "molecularFunction": { "GO": "go.MF.id", "evidence": "go.MF.evidence", + "name": "go.MF.term", "pubmed": "go.MF.pubmed", - "term": "go.MF.term" + "qualifiers": "go.MF.qualifier" + }, + "pantherMGI": { + "MGI": "pantherdb.ortholog.MGI", + "inTaxon": "pantherdb.ortholog.taxid" }, - "functional_association_reactome": { + "reactomePathway": { "REACT": "pathway.reactome.id", "name": "pathway.reactome.name" }, - "functional_association_reactome_gene": { - "NCBIGENE": "entrezgene" + "uniprotProtein": { + "UniProtKB": "uniprot.Swiss-Prot" }, - "functional_association_wikipathways": { + "wikipathway": { "WIKIPATHWAYS": "pathway.wikipathways.id", "name": "pathway.wikipathways.name" - }, - "gene_to_transcript_relationship": { - "ENSEMBL": "ensembl.transcript" - }, - "has_gene_product": { - "ENSEMBL": "ensembl.protein", - "UNIPROTKB": "uniprot.Swiss-Prot" - }, - "homologous_to": { - "ENSEMBL": "pantherdb.ortholog.Ensembl", - "FlyBase": "pantherdb.ortholog.FlyBase", - "HGNC": "pantherdb.ortholog.HGNC", - "MGI": "pantherdb.ortholog.MGI", - "POMBASE": "pantherdb.ortholog.PomBase", - "RGD": "pantherdb.ortholog.RGD", - "SGD": "pantherdb.ortholog.SGD", - "TAIR": "pantherdb.ortholog.TAIR", - "ZFIN": "pantherdb.ortholog.ZFIN", - "dictyBase": "pantherdb.ortholog.dictyBase", - "inTaxon": "pantherdb.ortholog.taxid" - }, - "inTaxon": "taxid", - "name": [ - "name", - "other_names" - ] + } } }, "info": { @@ -29515,7 +28101,7 @@ } }, { - "description": "relevant when faceting on species (i.e., \u201cfacets=taxid\u201d are passed). It\u2019s used to pass species filter without changing the scope of faceting, so that the returned facet counts won\u2019t change. Either species name or taxonomy id can be used, just like \u201cspecies\u201d parameter.", + "description": "relevant when faceting on species (i.e., “facets=taxid” are passed). It’s used to pass species filter without changing the scope of faceting, so that the returned facet counts won’t change. Either species name or taxonomy id can be used, just like “species” parameter.", "in": "query", "name": "species_facet_filter", "schema": { @@ -29523,7 +28109,7 @@ } }, { - "description": "when passed as \u201cTrue\u201d or \u201c1\u201d, the query returns only the hits with valid Entrez gene ids. Default: False.", + "description": "when passed as “True” or “1”, the query returns only the hits with valid Entrez gene ids. Default: False.", "in": "query", "name": "entrezonly", "schema": { @@ -29531,7 +28117,7 @@ } }, { - "description": "when passed as \u201cTrue\u201d or \u201c1\u201d, the query returns only the hits with valid Ensembl gene ids. Default: False.", + "description": "when passed as “True” or “1”, the query returns only the hits with valid Ensembl gene ids. Default: False.", "in": "query", "name": "ensemblonly", "schema": { @@ -29628,12 +28214,21 @@ { "$ref": "#/components/x-bte-kgs-operations/enablesMF" }, + { + "$ref": "#/components/x-bte-kgs-operations/MFToGene" + }, { "$ref": "#/components/x-bte-kgs-operations/involvedInBP" }, + { + "$ref": "#/components/x-bte-kgs-operations/BPToGene" + }, { "$ref": "#/components/x-bte-kgs-operations/involvedInCC" }, + { + "$ref": "#/components/x-bte-kgs-operations/CCToGene" + }, { "$ref": "#/components/x-bte-kgs-operations/involvedInPathway" }, @@ -29641,7 +28236,10 @@ "$ref": "#/components/x-bte-kgs-operations/hasTranscript" }, { - "$ref": "#/components/x-bte-kgs-operations/hasGeneProduct" + "$ref": "#/components/x-bte-kgs-operations/GeneToProtein" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ProteinToGene" }, { "$ref": "#/components/x-bte-kgs-operations/hasHomolog" @@ -29682,289 +28280,567 @@ ] }, { - "_id": "ed0ee52921c7cbce24033ffd1369922e", + "_id": "09c8782d9f4027712e65b95424adba79", "_meta": { - "date_created": "2020-12-07T23:03:08.522992+00:00", - "last_updated": "2021-03-05T08:01:07.297170+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/semmed/semmed_disease.yaml", - "username": "kevinxin90" + "date_created": "2020-12-08T00:04:53.736889+00:00", + "last_updated": "2021-03-29T07:02:19.472958+00:00", + "slug": "myvariant", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/myvariant.info/openapi_full.yml", + "username": "newgene" }, - "_score": 0.47008187, + "_score": 0.5232822, "components": { "x-bte-kgs-operations": { - "Disease-affected_by-AnatomicalEntity": [ + "conditionAssociatedWithVariant": [ { "inputSeparator": ",", "inputs": [ { - "id": "UMLS", + "id": "OMIM", "semantic": "Disease" } ], - "method": "post", "outputs": [ { - "id": "UMLS", - "semantic": "AnatomicalEntity" + "id": "DBSNP", + "semantic": "SequenceVariant" } ], "parameters": { - "fields": "affected_by" + "fields": "dbsnp.rsid", + "size": "250" }, - "path": "/query", - "predicate": "affected_by", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" - } + "scopes": "clinvar.rcv.conditions.identifiers.omim" + }, + "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-affected_by-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/dbsnp" }, - "source": "SEMMED", + "source": "clinvar", "supportBatch": true } ], - "Disease-affected_by-BiologicalProcess": [ + "variantAffectDrugResponse": [ { "inputSeparator": ",", "inputs": [ { - "id": "UMLS", - "semantic": "Disease" + "id": "DBSNP", + "semantic": "SequenceVariant" } ], - "method": "post", "outputs": [ { - "id": "UMLS", - "semantic": "BiologicalProcess" + "id": "name", + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "affected_by" + "fields": "civic.evidence_items", + "size": "1000" }, - "path": "/query", - "predicate": "affected_by", + "predicate": "variant_affect_drug_response", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" - } + "scopes": "dbsnp.rsid" + }, + "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-affected_by-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/variant_affect_drug_response" }, - "source": "SEMMED", + "source": "civic", "supportBatch": true } ], - "Disease-affected_by-Cell": [ + "variantAssociatedWithCondition": [ { "inputSeparator": ",", "inputs": [ { - "id": "UMLS", - "semantic": "Disease" + "id": "DBSNP", + "semantic": "SequenceVariant" } ], - "method": "post", "outputs": [ { - "id": "UMLS", - "semantic": "Cell" - } - ], - "parameters": { - "fields": "affected_by" - }, - "path": "/query", - "predicate": "affected_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-affected_by-Cell" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-affected_by-CellularComponent": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", + "id": "OMIM", "semantic": "Disease" } ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "CellularComponent" - } - ], "parameters": { - "fields": "affected_by" + "fields": "clinvar.rcv" }, - "path": "/query", - "predicate": "affected_by", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" - } + "scopes": "dbsnp.rsid" + }, + "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-affected_by-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/variant-disease-omim" }, - "source": "SEMMED", + "source": "clinvar", "supportBatch": true } ], - "Disease-affected_by-ChemicalSubstance": [ + "variantAssociatedWithGene": [ { "inputSeparator": ",", "inputs": [ { - "id": "UMLS", - "semantic": "Disease" + "id": "DBSNP", + "semantic": "SequenceVariant" } ], - "method": "post", "outputs": [ { - "id": "UMLS", - "semantic": "ChemicalSubstance" + "id": "NCBIGENE", + "semantic": "Gene" } ], "parameters": { - "fields": "affected_by" + "fields": "dbsnp.gene.geneid" }, - "path": "/query", - "predicate": "affected_by", + "predicate": "located_in", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" - } + "scopes": "dbsnp.rsid" + }, + "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-affected_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/variant-gene" }, - "source": "SEMMED", + "source": "dbsnp", "supportBatch": true } - ], - "Disease-affected_by-Disease": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Disease" + ] + }, + "x-bte-response-mapping": { + "dbsnp": { + "DBSNP": "dbsnp.rsid" + }, + "variant-disease-omim": { + "OMIM": "clinvar.rcv.conditions.identifiers.omim", + "clinicalsignificance": "clinvar.rcv.clinical_significance", + "name": "clinvar.rcv.conditions.name" + }, + "variant-gene": { + "NCBIGENE": "dbsnp.gene.geneid" + }, + "variant_affect_drug_response": { + "clinical_significance": "civic.evidence_items.clinical_significance", + "evidence_level": "civic.evidence_items.evidence_level", + "evidence_type": "civic.evidence_items.evidence_type", + "name": "civic.evidence_items.drugs.name", + "pubmed": "civic.evidence_items.source.pubmed" + } + } + }, + "info": { + "contact": { + "email": "help@myvariant.info", + "name": "Chunlei Wu", + "x-id": "https://github.com/newgene", + "x-role": "responsible developer" + }, + "description": "Documentation of the MyVariant.info Variant Query web services. Learn more about [MyVariant.info](http://myvariant.info/)", + "termsOfService": "http://myvariant.info/terms/", + "title": "MyVariant.info API", + "version": "1.0", + "x-translator": { + "component": "KP", + "team": [ + "Service Provider" + ] + } + }, + "paths": { + "/metadata": { + "get": { + "parameters": [ + { + "$ref": "#/components/parameters/callback", + "in": "query", + "name": "callback" + } + ], + "responses": { + "200": { + "description": "MyVariant.info metadata object" + } + }, + "summary": "Get metadata about the data available from MyVariant.info.", + "tags": [ + "metadata" + ] + } + }, + "/metadata/fields": { + "get": { + "parameters": [ + { + "description": "Pass a search term to filter the available fields, e.g. \"search=clinvar\".", + "in": "query", + "name": "search", + "schema": { + "type": "string" } - ], - "parameters": { - "fields": "affected_by" }, - "path": "/query", - "predicate": "affected_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" + { + "description": "Pass a prefix string to filter the available fields, e.g. \"prefix=refseq\".", + "in": "query", + "name": "prefix", + "schema": { + "type": "string" } }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-affected_by-Disease" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-affected_by-Gene": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Gene" + { + "$ref": "#/components/parameters/callback", + "in": "query", + "name": "callback" + } + ], + "responses": { + "200": { + "description": "MyVariant.info metadata fields object" + } + }, + "summary": "Get metadata about the data fields available from MyVariant.info.", + "tags": [ + "metadata" + ] + } + }, + "/query": { + "get": { + "parameters": [ + { + "description": "Query string. Examples \"rs752396467\", \"possibly_damaging\", \"CDK7\". The detailed query syntax can be found from our [docs](http://docs.myvariant.info/en/latest/doc/variant_query_service.html).", + "example": "CDK7", + "in": "query", + "name": "q", + "required": true, + "schema": { + "type": "string" } - ], - "parameters": { - "fields": "affected_by" }, - "path": "/query", - "predicate": "affected_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } + { + "1": "query", + "$ref": "#/components/parameters/fields", + "name": "fields" }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-affected_by-Gene" + { + "$ref": "#/components/parameters/size", + "in": "query", + "name": "size" }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-affected_by-PhenotypicFeature": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "PhenotypicFeature" - } - ], - "parameters": { - "fields": "affected_by" + { + "$ref": "#/components/parameters/from", + "in": "query", + "name": "from" }, - "path": "/query", - "predicate": "affected_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" + { + "$ref": "#/components/parameters/sort", + "in": "query", + "name": "sort" + }, + { + "description": "a single field or comma-separated fields to return facets, for example, \"facets=clinvar.gene.id\", \"facets=clinvar.gene.id,dbnsfp.uniprot.acc\".", + "in": "query", + "name": "facets", + "schema": { + "type": "string" } }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-affected_by-PhenotypicFeature" + { + "$ref": "#/components/parameters/callback", + "in": "query", + "name": "callback" }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-affects-AnatomicalEntity": [ + { + "$ref": "#/components/parameters/dotfield", + "in": "query", + "name": "dotfield" + }, + { + "$ref": "#/components/parameters/email", + "in": "query", + "name": "email" + } + ], + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/QueryResult" + } + } + }, + "description": "A query response object with \"hits\" property" + }, + "400": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResult" + } + } + }, + "description": "A response indicating an improperly formatted query" + } + }, + "summary": "Make variant query and return matching variant list. Support JSONP and CORS as well.", + "tags": [ + "query" + ] + }, + "post": { + "parameters": [ + { + "$ref": "#/components/parameters/fields", + "in": "query", + "name": "fields" + }, + { + "$ref": "#/components/parameters/dotfield", + "in": "query", + "name": "dotfield" + }, + { + "$ref": "#/components/parameters/email", + "in": "query", + "name": "email" + } + ], + "requestBody": { + "content": { + "application/x-www-form-urlencoded": { + "schema": { + "properties": { + "q": { + "description": "multiple query terms seperated by comma (also support \"+\" or white space), but no wildcard, e.g., \"q=rs58991260,rs2500\" or \"q=rs58991260+rs2500\"", + "type": "string" + }, + "scopes": { + "description": "Specify one or more fields (separated by comma) as the search \"scopes\", e.g., \"scopes=dbsnp.rsid\". The available \"fields\" that can be passed to \"scopes\" parameter are listed [here](http://docs.myvariant.info/en/latest/doc/data.html#available-fields). Default: \"scopes=_id\" (HGVS id).", + "type": "string" + } + }, + "required": [ + "q" + ] + } + } + } + }, + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/QueryPOSTResult" + } + } + }, + "description": "Query response objects with \"hits\" property" + }, + "400": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResult" + } + } + }, + "description": "A response indicating an improperly formatted query" + } + }, + "summary": "Make variant batch query and return matching variant hits", + "tags": [ + "query" + ], + "x-bte-kgs-operations": [ + { + "$ref": "#/components/x-bte-kgs-operations/variantAssociatedWithGene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/variantAssociatedWithCondition" + }, + { + "$ref": "#/components/x-bte-kgs-operations/conditionAssociatedWithVariant" + }, + { + "$ref": "#/components/x-bte-kgs-operations/variantAffectDrugResponse" + } + ] + } + }, + "/variant": { + "post": { + "parameters": [ + { + "$ref": "#/components/parameters/fields", + "in": "query", + "name": "fields" + }, + { + "$ref": "#/components/parameters/dotfield", + "in": "query", + "name": "dotfield" + }, + { + "$ref": "#/components/parameters/email", + "in": "query", + "name": "email" + } + ], + "requestBody": { + "content": { + "application/x-www-form-urlencoded": { + "schema": { + "properties": { + "ids": { + "description": "multiple variant ids seperated by comma, e.g., \"ids=chr6:g.152708291G>A,chr1:g.35367G>A\" or \"ids=rs5882,rs12190874\". Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted.", + "type": "string" + } + }, + "required": [ + "ids" + ] + } + } + } + }, + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "items": { + "$ref": "#/components/schemas/Variant" + }, + "type": "array" + } + } + }, + "description": "a list of matching variant objects" + } + }, + "summary": "For a list of variant ids, return the matching variant objects", + "tags": [ + "variant" + ] + } + }, + "/variant/{variantid}": { + "get": { + "parameters": [ + { + "description": "HGVS or rsid, e.g., chr6:g.152708291G>A, rs12190874", + "example": "chr6:g.152708291G>A", + "in": "path", + "name": "variantid", + "required": true, + "schema": { + "type": "string" + } + }, + { + "$ref": "#/components/parameters/fields", + "in": "query", + "name": "fields" + }, + { + "$ref": "#/components/parameters/dotfield", + "in": "query", + "name": "dotfield" + }, + { + "$ref": "#/components/parameters/callback", + "in": "query", + "name": "callback" + }, + { + "$ref": "#/components/parameters/email", + "in": "query", + "name": "email" + } + ], + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Variant" + } + } + }, + "description": "A matching variant object" + }, + "404": { + "description": "A response indicating an unknown variant id" + } + }, + "summary": "Retrieve variant annotation object based on HGVS or rsid, support JSONP and CORS as well.", + "tags": [ + "variant" + ] + } + } + }, + "servers": [ + { + "description": "Encrypted Production server", + "url": "https://myvariant.info/v1" + }, + { + "description": "Production server", + "url": "http://myvariant.info/v1" + } + ], + "tags": [ + { + "name": "variant" + }, + { + "name": "query" + }, + { + "name": "metadata" + }, + { + "name": "translator" + }, + { + "name": "biothings" + } + ] + }, + { + "_id": "8f08d1446e0bb9c2b323713ce83e2bd3", + "_meta": { + "date_created": "2021-02-02T00:00:20.885951+00:00", + "last_updated": "2021-03-29T07:01:46.578639+00:00", + "slug": "mychem", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/mychem.info/openapi_full.yml", + "username": "newgene" + }, + "_score": 0.4848808, + "components": { + "x-bte-kgs-operations": { + "contraindicatedBy": [ { "inputSeparator": ",", "inputs": [ @@ -29973,270 +28849,262 @@ "semantic": "Disease" } ], - "method": "post", "outputs": [ { - "id": "UMLS", - "semantic": "AnatomicalEntity" + "id": "CHEMBL.COMPOUND", + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "affects" + "fields": "chembl.molecule_chembl_id", + "size": "1000" }, - "path": "/query", - "predicate": "affects", + "predicate": "is_contraindication_for", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" - } + "scopes": "drugcentral.drug_use.contraindication.umls_cui" + }, + "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-affects-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/chembl" }, - "source": "SEMMED", + "source": "drugcentral", "supportBatch": true } ], - "Disease-affects-BiologicalProcess": [ + "contraindication": [ { "inputSeparator": ",", "inputs": [ { - "id": "UMLS", - "semantic": "Disease" + "id": "CHEMBL.COMPOUND", + "semantic": "ChemicalSubstance" } ], - "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "Disease" } ], "parameters": { - "fields": "affects" + "fields": "drugcentral.drug_use.contraindication" }, - "path": "/query", - "predicate": "affects", + "predicate": "contraindicated_for", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" - } + "scopes": "chembl.molecule_chembl_id" + }, + "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-affects-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/contraindication" }, - "source": "SEMMED", + "source": "drugcentral", "supportBatch": true } ], - "Disease-affects-Cell": [ + "metabolize": [ { "inputSeparator": ",", "inputs": [ { - "id": "UMLS", - "semantic": "Disease" + "id": "SYMBOL", + "semantic": "Gene" } ], - "method": "post", "outputs": [ { - "id": "UMLS", - "semantic": "Cell" + "id": "DRUGBANK", + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "affects" + "fields": "drugbank.id", + "size": "1000" }, - "path": "/query", - "predicate": "affects", + "predicate": "affects_metabolic_processing_of", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" - } + "scopes": "drugbank.enzymes.gene_name" + }, + "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-affects-Cell" + "$ref": "#/components/x-bte-response-mapping/drugbank" }, - "source": "SEMMED", + "source": "drugbank", "supportBatch": true } ], - "Disease-affects-CellularComponent": [ + "metabolizedBy": [ { "inputSeparator": ",", "inputs": [ { - "id": "UMLS", - "semantic": "Disease" + "id": "DRUGBANK", + "semantic": "ChemicalSubstance" } ], - "method": "post", "outputs": [ { - "id": "UMLS", - "semantic": "CellularComponent" + "id": "SYMBOL", + "semantic": "Gene" } ], "parameters": { - "fields": "affects" + "fields": "drugbank.enzymes" }, - "path": "/query", - "predicate": "affects", + "predicate": "metabolic_processing_affected_by", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" - } + "scopes": "drugbank.id" + }, + "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-affects-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/metabolizedBy" }, - "source": "SEMMED", + "source": "drugbank", "supportBatch": true } ], - "Disease-affects-ChemicalSubstance": [ + "target": [ { "inputSeparator": ",", "inputs": [ { - "id": "UMLS", - "semantic": "Disease" + "id": "DRUGBANK", + "semantic": "ChemicalSubstance" } ], - "method": "post", "outputs": [ { - "id": "UMLS", - "semantic": "ChemicalSubstance" + "id": "SYMBOL", + "semantic": "Gene" } ], "parameters": { - "fields": "affects" + "fields": "drugbank.targets" }, - "path": "/query", - "predicate": "affects", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" - } + "scopes": "drugbank.id" + }, + "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-affects-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/target-drugbank" }, - "source": "SEMMED", + "source": "drugbank", "supportBatch": true - } - ], - "Disease-affects-Disease": [ + }, { "inputSeparator": ",", "inputs": [ { - "id": "UMLS", - "semantic": "Disease" + "id": "CHEMBL.COMPOUND", + "semantic": "ChemicalSubstance" } ], - "method": "post", "outputs": [ { - "id": "UMLS", - "semantic": "Disease" + "id": "SYMBOL", + "semantic": "Gene" } ], "parameters": { - "fields": "affects" + "fields": "drugcentral.bioactivity" }, - "path": "/query", - "predicate": "affects", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" - } + "scopes": "chembl.molecule_chembl_id" + }, + "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-affects-Disease" + "$ref": "#/components/x-bte-response-mapping/target-drugcentral" }, - "source": "SEMMED", + "source": "drugcentral", "supportBatch": true } ], - "Disease-affects-Gene": [ + "targetedBy": [ { "inputSeparator": ",", "inputs": [ { - "id": "UMLS", - "semantic": "Disease" + "id": "SYMBOL", + "semantic": "Gene" } ], - "method": "post", "outputs": [ { - "id": "UMLS", - "semantic": "Gene" + "id": "DRUGBANK", + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "affects" + "fields": "drugbank.id", + "size": "1000" }, - "path": "/query", - "predicate": "affects", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" - } + "scopes": "drugbank.targets.gene_name" + }, + "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-affects-Gene" + "$ref": "#/components/x-bte-response-mapping/drugbank" }, - "source": "SEMMED", + "source": "drugbank", "supportBatch": true - } - ], - "Disease-affects-PhenotypicFeature": [ + }, { "inputSeparator": ",", "inputs": [ { - "id": "UMLS", - "semantic": "Disease" + "id": "SYMBOL", + "semantic": "Gene" } ], - "method": "post", "outputs": [ { - "id": "UMLS", - "semantic": "PhenotypicFeature" + "id": "CHEMBL.COMPOUND", + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "affects" + "fields": "chembl.molecule_chembl_id", + "size": "1000" }, - "path": "/query", - "predicate": "affects", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" - } + "scopes": "drugcentral.bioactivity.uniprot.gene_symbol" + }, + "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-affects-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/chembl" }, - "source": "SEMMED", + "source": "drugcentral", "supportBatch": true } ], - "Disease-caused_by-AnatomicalEntity": [ + "treatedBy": [ { "inputSeparator": ",", "inputs": [ @@ -30245,460 +29113,2032 @@ "semantic": "Disease" } ], - "method": "post", "outputs": [ { - "id": "UMLS", - "semantic": "AnatomicalEntity" + "id": "CHEMBL.COMPOUND", + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "caused_by" + "fields": "chembl.molecule_chembl_id", + "size": "1000" }, - "path": "/query", - "predicate": "caused_by", + "predicate": "approved_for_treatment_by", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" - } + "scopes": "drugcentral.drug_use.indication.umls_cui" + }, + "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-caused_by-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/chembl" }, - "source": "SEMMED", + "source": "drugcentral", "supportBatch": true } ], - "Disease-caused_by-BiologicalProcess": [ + "treats": [ { "inputSeparator": ",", "inputs": [ { - "id": "UMLS", - "semantic": "Disease" + "id": "CHEMBL.COMPOUND", + "semantic": "ChemicalSubstance" } ], - "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "Disease" } ], "parameters": { - "fields": "caused_by" + "fields": "drugcentral.drug_use.indication" }, - "path": "/query", - "predicate": "caused_by", + "predicate": "approved_to_treat", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-caused_by-BiologicalProcess" + "scopes": "chembl.molecule_chembl_id" + }, + "header": "application/x-www-form-urlencoded" }, - "source": "SEMMED", + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/treats" + }, + "source": "drugcentral", "supportBatch": true } - ], - "Disease-caused_by-Cell": [ + ] + }, + "x-bte-response-mapping": { + "chembl": { + "CHEMBL.COMPOUND": "chembl.molecule_chembl_id" + }, + "contraindication": { + "SNOMED": "drugcentral.drug_use.contraindication.snomed_concept_id", + "UMLS": "drugcentral.drug_use.contraindication.umls_cui", + "name": "drugcentral.drug_use.contraindication.concept_name" + }, + "drugbank": { + "DRUGBANK": "drugbank.id" + }, + "metabolizedBy": { + "SYMBOL": "drugbank.enzymes.gene_name", + "action": "drugbank.enzymes.actions", + "function": "drugbank.enzymes.general_function", + "name": "drugbank.enzymes.name", + "pubmed": "drugbank.enzymes.pmids" + }, + "target-drugbank": { + "SYMBOL": "drugbank.targets.gene_name", + "action": "drugbank.targets.actions", + "function": "drugbank.targets.general_function", + "name": "drugbank.targets.name", + "pubmed": "drugbank.targets.pmids" + }, + "target-drugcentral": { + "SYMBOL": "drugcentral.bioactivity.uniprot.gene_symbol", + "action": "drugcentral.bioactivity.action_type", + "name": "drugcentral.bioactivity.target_name" + }, + "treats": { + "SNOMED": "drugcentral.drug_use.indication.snomed_concept_id", + "UMLS": "drugcentral.drug_use.indication.umls_cui", + "name": "drugcentral.drug_use.indication.concept_name" + } + } + }, + "info": { + "contact": { + "email": "help@biothings.io", + "name": "Chunlei Wu", + "x-id": "https://github.com/newgene", + "x-role": "responsible developer" + }, + "description": "Documentation of the MyChem.info chem query web services. Learn more about [MyChem.info](http://MyChem.info/)", + "termsOfService": "http://MyChem.info/terms", + "title": "MyChem.info API", + "version": "1.0", + "x-translator": { + "component": "KP", + "team": [ + "Service Provider" + ] + } + }, + "paths": { + "/chem": { + "post": { + "parameters": [ + { + "$ref": "#/components/parameters/dotfield", + "name": "dotfield" + }, + { + "$ref": "#/components/parameters/fields", + "name": "fields" + }, + { + "$ref": "#/components/parameters/email", + "name": "email" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" + } + ], + "requestBody": { + "content": { + "application/x-www-form-urlencoded": { + "schema": { + "properties": { + "ids": { + "description": "multiple chemical IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", + "type": "string" + } + }, + "required": [ + "ids" + ] + } + } + } + }, + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "items": { + "$ref": "#/components/schemas/Chem" + }, + "type": "array" + } + } + }, + "description": "A list of matching chemical objects" + }, + "400": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResult" + } + } + }, + "description": "A response indicating an improperly formatted query" + } + }, + "summary": "For a list of chemical IDs, return the matching chemical object", + "tags": [ + "chemical" + ] + } + }, + "/chem/{chemid}": { + "get": { + "parameters": [ + { + "description": "Retrieve chemical objects based on ID - currently one of: [InChiKey](https://en.wikipedia.org/wiki/International_Chemical_Identifier#InChIKey), [DrugBank accession number](https://www.drugbank.ca/documentation), [ChEMBLID](https://www.ebi.ac.uk/chembl/faq#faq40), [ChEBI identifier](http://www.ebi.ac.uk/chebi/aboutChebiForward.do), [PubChem CID](https://pubchem.ncbi.nlm.nih.gov/search/help_search.html#Cid), [UNII](https://www.fda.gov/ForIndustry/DataStandards/SubstanceRegistrationSystem-UniqueIngredientIdentifierUNII/). Supports JSONP and CORS as well.", + "example": "USNINKBPBVKHHZ-CYUUQNCZSA-L", + "in": "path", + "name": "chemid", + "required": true, + "schema": { + "type": "string" + } + }, + { + "$ref": "#/components/parameters/dotfield", + "name": "dotfield" + }, + { + "$ref": "#/components/parameters/callback", + "name": "callback" + }, + { + "$ref": "#/components/parameters/fields", + "name": "fields" + }, + { + "$ref": "#/components/parameters/email", + "name": "email" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" + } + ], + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Chem" + } + } + }, + "description": "A matching chemical object" + }, + "404": { + "description": "A response indicating an unknown chemical ID" + } + }, + "summary": "Retrieve chemical objects based on ID", + "tags": [ + "chemical" + ] + } + }, + "/metadata": { + "get": { + "parameters": [ + { + "$ref": "#/components/parameters/callback", + "in": "query", + "name": "callback" + } + ], + "responses": { + "200": { + "description": "MyChem.info metadata object" + } + }, + "summary": "Get metadata about the data available from MyChem.info", + "tags": [ + "metadata" + ] + } + }, + "/metadata/fields": { + "get": { + "parameters": [ + { + "$ref": "#/components/parameters/search", + "name": "search" + }, + { + "$ref": "#/components/parameters/callback", + "name": "callback" + }, + { + "$ref": "#/components/parameters/prefix", + "name": "prefix" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" + } + ], + "responses": { + "200": { + "description": "MyChem.info metadata fields object" + } + }, + "summary": "Get metadata about the data fields available from a MyChem.info chem object", + "tags": [ + "metadata" + ] + } + }, + "/query": { + "get": { + "parameters": [ + { + "description": "Query string. The detailed query syntax can be found from our [docs](http://MyChem.info). Examples: \"Fludara\", \"CHEMBI:63599\", \"DB01073\".", + "example": "Fludara", + "in": "query", + "name": "q", + "required": true, + "schema": { + "type": "string" + } + }, + { + "$ref": "#/components/parameters/dotfield", + "name": "dotfield" + }, + { + "$ref": "#/components/parameters/fields", + "name": "fields" + }, + { + "$ref": "#/components/parameters/facet_size", + "name": "facet_size" + }, + { + "$ref": "#/components/parameters/sort", + "name": "sort" + }, + { + "$ref": "#/components/parameters/callback", + "name": "callback" + }, + { + "$ref": "#/components/parameters/email", + "name": "email" + }, + { + "$ref": "#/components/parameters/facets", + "name": "facets" + }, + { + "$ref": "#/components/parameters/size", + "name": "size" + }, + { + "$ref": "#/components/parameters/from", + "name": "from" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" + } + ], + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/QueryResult" + } + } + }, + "description": "A query response with the \"hits\" property" + }, + "400": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResult" + } + } + }, + "description": "A response indicating an improperly formatted query" + } + }, + "summary": "Make chemical queries and return matching chemical hits. Supports JSONP and CORS as well.", + "tags": [ + "query" + ] + }, + "post": { + "parameters": [ + { + "$ref": "#/components/parameters/dotfield", + "name": "dotfield" + }, + { + "$ref": "#/components/parameters/email", + "name": "email" + }, + { + "$ref": "#/components/parameters/fields", + "name": "fields" + }, + { + "$ref": "#/components/parameters/size", + "name": "size" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" + } + ], + "requestBody": { + "content": { + "application/x-www-form-urlencoded": { + "schema": { + "properties": { + "q": { + "description": "multiple 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 chemical queries and return matching chemical hits", + "tags": [ + "query" + ], + "x-bte-kgs-operations": [ + { + "$ref": "#/components/x-bte-kgs-operations/metabolizedBy" + }, + { + "$ref": "#/components/x-bte-kgs-operations/target" + }, + { + "$ref": "#/components/x-bte-kgs-operations/treats" + }, + { + "$ref": "#/components/x-bte-kgs-operations/contraindication" + }, + { + "$ref": "#/components/x-bte-kgs-operations/metabolize" + }, + { + "$ref": "#/components/x-bte-kgs-operations/targetedBy" + }, + { + "$ref": "#/components/x-bte-kgs-operations/treatedBy" + }, + { + "$ref": "#/components/x-bte-kgs-operations/contraindicatedBy" + } + ] + } + } + }, + "servers": [ + { + "description": "Encrypted Production server", + "url": "https://mychem.info/v1" + }, + { + "description": "Production server", + "url": "http://mychem.info/v1" + } + ], + "tags": [ + { + "name": "chemical" + }, + { + "name": "drug" + }, + { + "name": "annotation" + }, + { + "name": "query" + }, + { + "name": "translator" + }, + { + "name": "biothings" + } + ] + }, + { + "_id": "a7f784626a426d054885a5f33f17d3f8", + "_meta": { + "date_created": "2020-12-07T23:02:08.115894+00:00", + "last_updated": "2021-03-29T07:02:16.952134+00:00", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/DISEASES/smartapi.yaml", + "username": "kevinxin90" + }, + "_score": 0.4848808, + "components": { + "x-bte-kgs-operations": { + "disease-gene": [ { "inputSeparator": ",", "inputs": [ { - "id": "UMLS", + "id": "DOID", "semantic": "Disease" } ], - "method": "post", "outputs": [ { - "id": "UMLS", - "semantic": "Cell" + "id": "SYMBOL", + "semantic": "Gene" } ], "parameters": { - "fields": "caused_by" + "fields": "DISEASES.associatedWith" }, - "path": "/query", - "predicate": "caused_by", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" - } + "scopes": "DISEASES.doid" + }, + "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-caused_by-Cell" + "$ref": "#/components/x-bte-response-mapping/disease-gene" }, - "source": "SEMMED", + "source": "DISEASES", "supportBatch": true } ], - "Disease-caused_by-CellularComponent": [ + "gene-disease": [ { "inputSeparator": ",", "inputs": [ { - "id": "UMLS", - "semantic": "Disease" + "id": "SYMBOL", + "semantic": "Gene" } ], - "method": "post", "outputs": [ { - "id": "UMLS", - "semantic": "CellularComponent" + "id": "DOID", + "semantic": "Disease" } ], "parameters": { - "fields": "caused_by" + "fields": "DISEASES.doid", + "size": "250" }, - "path": "/query", - "predicate": "caused_by", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" - } + "scopes": "DISEASES.associatedWith.symbol" + }, + "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-caused_by-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/gene-disease" }, - "source": "SEMMED", + "source": "DISEASES", "supportBatch": true } - ], - "Disease-caused_by-ChemicalSubstance": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "ChemicalSubstance" + ] + }, + "x-bte-response-mapping": { + "disease-gene": { + "SYMBOL": "DISEASES.associatedWith.symbol", + "category": "DISEASES.associatedWith.category" + }, + "gene-disease": { + "DOID": "DISEASES.doid" + } + } + }, + "info": { + "contact": { + "email": "help@biothings.io", + "name": "JIWEN XIN", + "x-id": "https://github.com/kevinxin90", + "x-role": "responsible developer" + }, + "description": "Documentation of the DISEASES query web services.", + "termsOfService": "https://biothings.io/about", + "title": "DISEASES API", + "version": "1.0", + "x-translator": { + "component": "KP", + "team": [ + "Service Provider" + ] + } + }, + "paths": { + "/disease": { + "post": { + "parameters": [ + { + "$ref": "#/components/parameters/dotfield", + "name": "dotfield" + }, + { + "$ref": "#/components/parameters/fields", + "name": "fields" + }, + { + "$ref": "#/components/parameters/email", + "name": "email" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" + } + ], + "requestBody": { + "content": { + "application/x-www-form-urlencoded": { + "schema": { + "properties": { + "ids": { + "description": "multiple MONDO Disease IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", + "type": "string" + } + }, + "required": [ + "ids" + ] + } } - ], - "parameters": { - "fields": "caused_by" + } + }, + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "items": { + "$ref": "#/components/schemas/Disease" + }, + "type": "array" + } + } + }, + "description": "A list of matching disease objects" }, - "path": "/query", - "predicate": "caused_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" + "400": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResult" + } + } + }, + "description": "A response indicating an improperly formatted query" + } + }, + "summary": "For a list of disease IDs, return the matching disease object", + "tags": [ + "disease" + ] + } + }, + "/disease/{diseaseid}": { + "get": { + "parameters": [ + { + "description": "Retrieve disease objects based on MONDO disease ID Supports JSONP and CORS as well.", + "example": "MONDO:0016537", + "in": "path", + "name": "diseaseid", + "required": true, + "schema": { + "type": "string" } }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-caused_by-ChemicalSubstance" + { + "$ref": "#/components/parameters/dotfield", + "name": "dotfield" }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-caused_by-Disease": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Disease" + { + "$ref": "#/components/parameters/callback", + "name": "callback" + }, + { + "$ref": "#/components/parameters/fields", + "name": "fields" + }, + { + "$ref": "#/components/parameters/email", + "name": "email" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" + } + ], + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Disease" + } + } + }, + "description": "A matching disease object" + }, + "404": { + "description": "A response indicating an unknown disease ID" + } + }, + "summary": "Retrieve disease objects based on ID", + "tags": [ + "disease" + ] + } + }, + "/metadata": { + "get": { + "parameters": [ + { + "$ref": "#/components/parameters/callback", + "in": "query", + "name": "callback" + } + ], + "responses": { + "200": { + "description": "DISEASES metadata object" + } + }, + "summary": "Get metadata about the data available from DISEASES", + "tags": [ + "metadata" + ] + } + }, + "/metadata/fields": { + "get": { + "parameters": [ + { + "$ref": "#/components/parameters/search", + "name": "search" + }, + { + "$ref": "#/components/parameters/callback", + "name": "callback" + }, + { + "$ref": "#/components/parameters/prefix", + "name": "prefix" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" + } + ], + "responses": { + "200": { + "description": "DISEASES metadata fields object" + } + }, + "summary": "Get metadata about the data fields available from a DISEASES disease object", + "tags": [ + "metadata" + ] + } + }, + "/query": { + "get": { + "parameters": [ + { + "description": "Query string.", + "example": "DISEASES.doid:\"DOID:0110389\"", + "in": "query", + "name": "q", + "required": true, + "schema": { + "type": "string" } - ], - "parameters": { - "fields": "caused_by" }, - "path": "/query", - "predicate": "caused_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" + { + "$ref": "#/components/parameters/dotfield", + "name": "dotfield" + }, + { + "$ref": "#/components/parameters/fields", + "name": "fields" + }, + { + "$ref": "#/components/parameters/facet_size", + "name": "facet_size" + }, + { + "$ref": "#/components/parameters/sort", + "name": "sort" + }, + { + "$ref": "#/components/parameters/callback", + "name": "callback" + }, + { + "$ref": "#/components/parameters/email", + "name": "email" + }, + { + "$ref": "#/components/parameters/facets", + "name": "facets" + }, + { + "$ref": "#/components/parameters/size", + "name": "size" + }, + { + "$ref": "#/components/parameters/from", + "name": "from" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" + } + ], + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/QueryResult" + } + } + }, + "description": "A query response with the \"hits\" property" + }, + "400": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResult" + } + } + }, + "description": "A response indicating an improperly formatted query" + } + }, + "summary": "Make queries and return matching disease hits. Supports JSONP and CORS as well.", + "tags": [ + "query" + ] + }, + "post": { + "parameters": [ + { + "$ref": "#/components/parameters/dotfield", + "name": "dotfield" + }, + { + "$ref": "#/components/parameters/email", + "name": "email" + }, + { + "$ref": "#/components/parameters/fields", + "name": "fields" + }, + { + "$ref": "#/components/parameters/size", + "name": "size" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" + } + ], + "requestBody": { + "content": { + "application/x-www-form-urlencoded": { + "schema": { + "properties": { + "q": { + "description": "multiple query terms separated by comma (also \"+\" or whitespace). Does not support wildcard queries", + "type": "string" + }, + "scopes": { + "description": "a comma-separated list of fields as the search \"scopes\" (fields to search through for query term). The available \"fields\" that can be passed to the \"scopes\" parameter are listed in the **/metadata/fields** endpoint.string Default: \"scopes=_id\".", + "type": "string" + } + } + } + } + } + }, + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/QueryPOSTResult" + } + } + }, + "description": "Query response objects with the \"hits\" property", + "x-bte-response-mapping": { + "$ref": "#/components/x-bte-response-mapping/query-post" } }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-caused_by-Disease" + "400": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResult" + } + } + }, + "description": "A response indicating an improperly formatted query" + } + }, + "summary": "Make batch disease queries and return matching disease hits", + "tags": [ + "query" + ], + "x-bte-kgs-operations": [ + { + "$ref": "#/components/x-bte-kgs-operations/disease-gene" }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-caused_by-Gene": [ + { + "$ref": "#/components/x-bte-kgs-operations/gene-disease" + } + ] + } + } + }, + "servers": [ + { + "description": "Encrypted Production server", + "url": "https://biothings.ncats.io/DISEASES" + }, + { + "description": "Production server", + "url": "http://biothings.ncats.io/DISEASES" + } + ], + "tags": [ + { + "name": "gene" + }, + { + "name": "disease" + }, + { + "name": "annotation" + }, + { + "name": "query" + }, + { + "name": "translator" + }, + { + "name": "biothings" + } + ] + }, + { + "_id": "1f47552dabd67351d4c625adb0a10d00", + "_meta": { + "date_created": "2020-12-07T23:04:37.029674+00:00", + "last_updated": "2021-03-29T07:01:51.219780+00:00", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/EBIgene2phenotype/smartapi.yaml", + "username": "kevinxin90" + }, + "_score": 0.4848808, + "components": { + "x-bte-kgs-operations": { + "gene_related_to_phenotype": [ { "inputSeparator": ",", "inputs": [ { - "id": "UMLS", - "semantic": "Disease" + "id": "HGNC", + "semantic": "Gene" } ], - "method": "post", "outputs": [ { - "id": "UMLS", - "semantic": "Gene" + "id": "HP", + "semantic": "PhenotypicFeature" } ], "parameters": { - "fields": "caused_by" + "fields": "gene2phenotype" }, - "path": "/query", - "predicate": "caused_by", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" - } + "scopes": "_id" + }, + "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-caused_by-Gene" + "$ref": "#/components/x-bte-response-mapping/gene_related_to_phenotype" }, - "source": "SEMMED", + "source": "EBI", "supportBatch": true } ], - "Disease-caused_by-PhenotypicFeature": [ + "phenotype_related_to_gene": [ { "inputSeparator": ",", "inputs": [ { - "id": "UMLS", - "semantic": "Disease" + "id": "HP", + "semantic": "PhenotypicFeature" } ], - "method": "post", "outputs": [ { - "id": "UMLS", - "semantic": "PhenotypicFeature" + "id": "HGNC", + "semantic": "Gene" } ], "parameters": { - "fields": "caused_by" + "fields": "_id", + "size": "350" }, - "path": "/query", - "predicate": "caused_by", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" - } + "scopes": "gene2phenotype.phenotypes" + }, + "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-caused_by-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/phenotype_related_to_gene" }, - "source": "SEMMED", + "source": "EBI", "supportBatch": true } - ], - "Disease-causes-BiologicalProcess": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "BiologicalProcess" + ] + }, + "x-bte-response-mapping": { + "gene_related_to_phenotype": { + "HP": "gene2phenotype.phenotypes", + "probability": "gene2phenotype.DDD_category", + "pubmed": "gene2phenotype.pmids" + }, + "phenotype_related_to_gene": { + "HGNC": "_id" + } + } + }, + "info": { + "contact": { + "email": "help@biothings.io", + "name": "JIWEN XIN", + "x-id": "https://github.com/kevinxin90", + "x-role": "responsible developer" + }, + "description": "Documentation of the EBIgene2phenotype query web services.", + "termsOfService": "https://biothings.io/about", + "title": "EBIgene2phenotype API", + "version": "1.0", + "x-translator": { + "component": "KP", + "team": [ + "Service Provider" + ] + } + }, + "paths": { + "/gene": { + "post": { + "parameters": [ + { + "$ref": "#/components/parameters/dotfield", + "name": "dotfield" + }, + { + "$ref": "#/components/parameters/fields", + "name": "fields" + }, + { + "$ref": "#/components/parameters/email", + "name": "email" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" + } + ], + "requestBody": { + "content": { + "application/x-www-form-urlencoded": { + "schema": { + "properties": { + "ids": { + "description": "multiple HGNC Gene IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", + "type": "string" + } + }, + "required": [ + "ids" + ] + } } - ], - "parameters": { - "fields": "causes" + } + }, + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "items": { + "$ref": "#/components/schemas/Gene" + }, + "type": "array" + } + } + }, + "description": "A list of matching gene objects" }, - "path": "/query", - "predicate": "causes", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" + "400": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResult" + } + } + }, + "description": "A response indicating an improperly formatted query" + } + }, + "summary": "For a list of chemical IDs, return the matching gene object", + "tags": [ + "gene" + ] + } + }, + "/gene/{geneid}": { + "get": { + "parameters": [ + { + "description": "Retrieve gene objects based on HGNC Gene ID Supports JSONP and CORS as well.", + "example": 851, + "in": "path", + "name": "geneid", + "required": true, + "schema": { + "type": "string" } }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-causes-BiologicalProcess" + { + "$ref": "#/components/parameters/dotfield", + "name": "dotfield" }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-causes-Disease": [ + { + "$ref": "#/components/parameters/callback", + "name": "callback" + }, + { + "$ref": "#/components/parameters/fields", + "name": "fields" + }, + { + "$ref": "#/components/parameters/email", + "name": "email" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" + } + ], + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Gene" + } + } + }, + "description": "A matching gene object" + }, + "404": { + "description": "A response indicating an unknown gene ID" + } + }, + "summary": "Retrieve gene objects based on ID", + "tags": [ + "gene" + ] + } + }, + "/metadata": { + "get": { + "parameters": [ + { + "$ref": "#/components/parameters/callback", + "in": "query", + "name": "callback" + } + ], + "responses": { + "200": { + "description": "EBIgene2phenotype metadata object" + } + }, + "summary": "Get metadata about the data available from EBIgene2phenotype", + "tags": [ + "metadata" + ] + } + }, + "/metadata/fields": { + "get": { + "parameters": [ + { + "$ref": "#/components/parameters/search", + "name": "search" + }, + { + "$ref": "#/components/parameters/callback", + "name": "callback" + }, + { + "$ref": "#/components/parameters/prefix", + "name": "prefix" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" + } + ], + "responses": { + "200": { + "description": "EBIgene2phenotype metadata fields object" + } + }, + "summary": "Get metadata about the data fields available from a EBIgene2phenotype gene object", + "tags": [ + "metadata" + ] + } + }, + "/query": { + "get": { + "parameters": [ + { + "description": "Query string.", + "example": "gene2phenotype.mutation_consequence:\"loss of function\"", + "in": "query", + "name": "q", + "required": true, + "schema": { + "type": "string" + } + }, + { + "$ref": "#/components/parameters/dotfield", + "name": "dotfield" + }, + { + "$ref": "#/components/parameters/fields", + "name": "fields" + }, + { + "$ref": "#/components/parameters/facet_size", + "name": "facet_size" + }, + { + "$ref": "#/components/parameters/sort", + "name": "sort" + }, + { + "$ref": "#/components/parameters/callback", + "name": "callback" + }, + { + "$ref": "#/components/parameters/email", + "name": "email" + }, + { + "$ref": "#/components/parameters/facets", + "name": "facets" + }, + { + "$ref": "#/components/parameters/size", + "name": "size" + }, + { + "$ref": "#/components/parameters/from", + "name": "from" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" + } + ], + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/QueryResult" + } + } + }, + "description": "A query response with the \"hits\" property" + }, + "400": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResult" + } + } + }, + "description": "A response indicating an improperly formatted query" + } + }, + "summary": "Make queries and return matching gene hits. Supports JSONP and CORS as well.", + "tags": [ + "query" + ] + }, + "post": { + "parameters": [ + { + "$ref": "#/components/parameters/dotfield", + "name": "dotfield" + }, + { + "$ref": "#/components/parameters/email", + "name": "email" + }, + { + "$ref": "#/components/parameters/fields", + "name": "fields" + }, + { + "$ref": "#/components/parameters/size", + "name": "size" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" + } + ], + "requestBody": { + "content": { + "application/x-www-form-urlencoded": { + "schema": { + "properties": { + "q": { + "description": "multiple 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 gene queries and return matching gene hits", + "tags": [ + "query" + ], + "x-bte-kgs-operations": [ + { + "$ref": "#/components/x-bte-kgs-operations/gene_related_to_phenotype" + }, + { + "$ref": "#/components/x-bte-kgs-operations/phenotype_related_to_gene" + } + ] + } + } + }, + "servers": [ + { + "description": "Encrypted Production server", + "url": "https://biothings.ncats.io/ebigene2phenotype" + }, + { + "description": "Production server", + "url": "http://biothings.ncats.io/ebigene2phenotype" + } + ], + "tags": [ + { + "name": "gene" + }, + { + "name": "phenotype" + }, + { + "name": "annotation" + }, + { + "name": "query" + }, + { + "name": "translator" + }, + { + "name": "biothings" + } + ] + }, + { + "_id": "77ed27f111262d0289ed4f4071faa619", + "_meta": { + "date_created": "2020-12-07T23:05:24.514205+00:00", + "last_updated": "2021-03-29T07:02:55.505067+00:00", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/MGIgene2phenotype/smartapi.yaml", + "username": "kevinxin90" + }, + "_score": 0.4848808, + "components": { + "x-bte-kgs-operations": { + "disease_related_to_gene": [ { "inputSeparator": ",", "inputs": [ { - "id": "UMLS", + "id": "DOID", "semantic": "Disease" } ], - "method": "post", "outputs": [ { - "id": "UMLS", - "semantic": "Disease" + "id": "MGI", + "semantic": "Gene" } ], "parameters": { - "fields": "causes" + "fields": "_id", + "size": "300" }, - "path": "/query", - "predicate": "causes", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" - } + "scopes": "mgi.associated_with_disease.doid" + }, + "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-causes-Disease" + "$ref": "#/components/x-bte-response-mapping/mgi" }, - "source": "SEMMED", + "source": "mgi_gene2phenotype", "supportBatch": true } ], - "Disease-coexists_with-AnatomicalEntity": [ + "gene_related_to_disease": [ { "inputSeparator": ",", "inputs": [ { - "id": "UMLS", - "semantic": "Disease" + "id": "MGI", + "semantic": "Gene" } ], - "method": "post", "outputs": [ { - "id": "UMLS", - "semantic": "AnatomicalEntity" + "id": "DOID", + "semantic": "Disease" } ], "parameters": { - "fields": "coexists_with" + "fields": "mgi.associated_with_disease" }, - "path": "/query", - "predicate": "coexists_with", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" - } + "scopes": "_id" + }, + "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-coexists_with-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/gene_related_to_disease" }, - "source": "SEMMED", + "source": "mgi_gene2phenotype", "supportBatch": true } ], - "Disease-coexists_with-BiologicalProcess": [ + "gene_related_to_phenotype": [ { "inputSeparator": ",", "inputs": [ { - "id": "UMLS", - "semantic": "Disease" + "id": "MGI", + "semantic": "Gene" } ], - "method": "post", "outputs": [ { - "id": "UMLS", - "semantic": "BiologicalProcess" + "id": "MP", + "semantic": "PhenotypicFeature" } ], "parameters": { - "fields": "coexists_with" + "fields": "mgi.associated_with_phenotype" }, - "path": "/query", - "predicate": "coexists_with", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" - } + "scopes": "_id" + }, + "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-coexists_with-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/gene_related_to_phenotype" }, - "source": "SEMMED", + "source": "mgi_gene2phenotype", "supportBatch": true } ], - "Disease-coexists_with-Cell": [ + "phenotype_related_to_gene": [ { "inputSeparator": ",", "inputs": [ { - "id": "UMLS", - "semantic": "Disease" + "id": "MP", + "semantic": "PhenotypicFeature" } ], - "method": "post", "outputs": [ { - "id": "UMLS", - "semantic": "Cell" + "id": "MGI", + "semantic": "Gene" } ], "parameters": { - "fields": "coexists_with" + "fields": "_id", + "size": "300" }, - "path": "/query", - "predicate": "coexists_with", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "umls" + "scopes": "mgi.associated_with_phenotype.mp" } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-coexists_with-Cell" + "$ref": "#/components/x-bte-response-mapping/mgi" }, - "source": "SEMMED", + "source": "mgi_gene2phenotype", "supportBatch": true } - ], - "Disease-coexists_with-CellularComponent": [ + ] + }, + "x-bte-response-mapping": { + "gene_related_to_disease": { + "DOID": "mgi.associated_with_disease.doid", + "name": "mgi.associated_with_disease.name" + }, + "gene_related_to_phenotype": { + "MP": "mgi.associated_with_phenotype.mp", + "pubmed": "mgi.associated_with_phenotype.pubmed" + }, + "mgi": { + "MGI": "_id" + } + } + }, + "info": { + "contact": { + "email": "help@biothings.io", + "name": "JIWEN XIN", + "x-id": "https://github.com/kevinxin90", + "x-role": "responsible developer" + }, + "description": "Documentation of the MGIgene2phenotype query web services.", + "termsOfService": "https://biothings.io/about", + "title": "MGIgene2phenotype API", + "version": "1.0", + "x-translator": { + "component": "KP", + "team": [ + "Service Provider" + ] + } + }, + "paths": { + "/gene": { + "post": { + "parameters": [ + { + "$ref": "#/components/parameters/dotfield", + "name": "dotfield" + }, + { + "$ref": "#/components/parameters/fields", + "name": "fields" + }, + { + "$ref": "#/components/parameters/email", + "name": "email" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" + } + ], + "requestBody": { + "content": { + "application/x-www-form-urlencoded": { + "schema": { + "properties": { + "ids": { + "description": "multiple MGI Gene IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", + "type": "string" + } + }, + "required": [ + "ids" + ] + } + } + } + }, + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "items": { + "$ref": "#/components/schemas/Gene" + }, + "type": "array" + } + } + }, + "description": "A list of matching gene objects" + }, + "400": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResult" + } + } + }, + "description": "A response indicating an improperly formatted query" + } + }, + "summary": "For a list of chemical IDs, return the matching gene object", + "tags": [ + "gene" + ] + } + }, + "/gene/{geneid}": { + "get": { + "parameters": [ + { + "description": "Retrieve gene objects based on MGI Gene ID Supports JSONP and CORS as well.", + "example": "MGI:101864", + "in": "path", + "name": "geneid", + "required": true, + "schema": { + "type": "string" + } + }, + { + "$ref": "#/components/parameters/dotfield", + "name": "dotfield" + }, + { + "$ref": "#/components/parameters/callback", + "name": "callback" + }, + { + "$ref": "#/components/parameters/fields", + "name": "fields" + }, + { + "$ref": "#/components/parameters/email", + "name": "email" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" + } + ], + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Gene" + } + } + }, + "description": "A matching gene object" + }, + "404": { + "description": "A response indicating an unknown gene ID" + } + }, + "summary": "Retrieve gene objects based on ID", + "tags": [ + "gene" + ] + } + }, + "/metadata": { + "get": { + "parameters": [ + { + "$ref": "#/components/parameters/callback", + "in": "query", + "name": "callback" + } + ], + "responses": { + "200": { + "description": "MGIgene2phenotype metadata object" + } + }, + "summary": "Get metadata about the data available from MGIgene2phenotype", + "tags": [ + "metadata" + ] + } + }, + "/metadata/fields": { + "get": { + "parameters": [ + { + "$ref": "#/components/parameters/search", + "name": "search" + }, + { + "$ref": "#/components/parameters/callback", + "name": "callback" + }, + { + "$ref": "#/components/parameters/prefix", + "name": "prefix" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" + } + ], + "responses": { + "200": { + "description": "MGIgene2phenotype metadata fields object" + } + }, + "summary": "Get metadata about the data fields available from a MGIgene2phenotype gene object", + "tags": [ + "metadata" + ] + } + }, + "/query": { + "get": { + "parameters": [ + { + "description": "Query string.", + "example": "mgi.associated_with_disease.doid:\"DOID:0110293\"", + "in": "query", + "name": "q", + "required": true, + "schema": { + "type": "string" + } + }, + { + "$ref": "#/components/parameters/dotfield", + "name": "dotfield" + }, + { + "$ref": "#/components/parameters/fields", + "name": "fields" + }, + { + "$ref": "#/components/parameters/facet_size", + "name": "facet_size" + }, + { + "$ref": "#/components/parameters/sort", + "name": "sort" + }, + { + "$ref": "#/components/parameters/callback", + "name": "callback" + }, + { + "$ref": "#/components/parameters/email", + "name": "email" + }, + { + "$ref": "#/components/parameters/facets", + "name": "facets" + }, + { + "$ref": "#/components/parameters/size", + "name": "size" + }, + { + "$ref": "#/components/parameters/from", + "name": "from" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" + } + ], + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/QueryResult" + } + } + }, + "description": "A query response with the \"hits\" property" + }, + "400": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResult" + } + } + }, + "description": "A response indicating an improperly formatted query" + } + }, + "summary": "Make queries and return matching gene hits. Supports JSONP and CORS as well.", + "tags": [ + "query" + ] + }, + "post": { + "parameters": [ + { + "$ref": "#/components/parameters/dotfield", + "name": "dotfield" + }, + { + "$ref": "#/components/parameters/email", + "name": "email" + }, + { + "$ref": "#/components/parameters/fields", + "name": "fields" + }, + { + "$ref": "#/components/parameters/size", + "name": "size" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" + } + ], + "requestBody": { + "content": { + "application/x-www-form-urlencoded": { + "schema": { + "properties": { + "q": { + "description": "multiple 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 gene queries and return matching gene hits", + "tags": [ + "query" + ], + "x-bte-kgs-operations": [ + { + "$ref": "#/components/x-bte-kgs-operations/gene_related_to_phenotype" + }, + { + "$ref": "#/components/x-bte-kgs-operations/gene_related_to_disease" + }, + { + "$ref": "#/components/x-bte-kgs-operations/phenotype_related_to_gene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/disease_related_to_gene" + } + ] + } + } + }, + "servers": [ + { + "description": "Encrypted Production server", + "url": "https://biothings.ncats.io/mgigene2phenotype" + }, + { + "description": "Production server", + "url": "http://biothings.ncats.io/mgigene2phenotype" + } + ], + "tags": [ + { + "name": "gene" + }, + { + "name": "phenotype" + }, + { + "name": "annotation" + }, + { + "name": "query" + }, + { + "name": "translator" + }, + { + "name": "biothings" + } + ] + }, + { + "_id": "0c9f1154a1986f1774057af4c1caa5b2", + "_meta": { + "date_created": "2020-12-07T23:01:40.279745+00:00", + "last_updated": "2021-03-29T07:03:35.282572+00:00", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/semmed/semmed_anatomy.yaml", + "username": "kevinxin90" + }, + "_score": 0.4848808, + "components": { + "x-bte-kgs-operations": { + "AnatomicalEntity-affected_by-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "CellularComponent" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "coexists_with" + "fields": "affected_by" }, "path": "/query", - "predicate": "coexists_with", + "predicate": "affected_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -30706,33 +31146,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-coexists_with-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-affected_by-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-coexists_with-ChemicalSubstance": [ + "AnatomicalEntity-affected_by-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "CellularComponent" } ], "parameters": { - "fields": "coexists_with" + "fields": "affected_by" }, "path": "/query", - "predicate": "coexists_with", + "predicate": "affected_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -30740,33 +31180,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-coexists_with-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-affected_by-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-coexists_with-Disease": [ + "AnatomicalEntity-affected_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "coexists_with" + "fields": "affected_by" }, "path": "/query", - "predicate": "coexists_with", + "predicate": "affected_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -30774,33 +31214,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-coexists_with-Disease" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-affected_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-coexists_with-Gene": [ + "AnatomicalEntity-affected_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "Disease" } ], "parameters": { - "fields": "coexists_with" + "fields": "affected_by" }, "path": "/query", - "predicate": "coexists_with", + "predicate": "affected_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -30808,33 +31248,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-coexists_with-Gene" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-affected_by-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-coexists_with-PhenotypicFeature": [ + "AnatomicalEntity-affected_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "Gene" } ], "parameters": { - "fields": "coexists_with" + "fields": "affected_by" }, "path": "/query", - "predicate": "coexists_with", + "predicate": "affected_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -30842,33 +31282,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-coexists_with-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-affected_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-derives_from-ChemicalSubstance": [ + "AnatomicalEntity-affects-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "derives_from" + "fields": "affects" }, "path": "/query", - "predicate": "derives_from", + "predicate": "affects", "requestBody": { "body": { "q": "{inputs[0]}", @@ -30876,33 +31316,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-derives_from-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-affects-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-derives_from-Gene": [ + "AnatomicalEntity-affects-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "Disease" } ], "parameters": { - "fields": "derives_from" + "fields": "affects" }, "path": "/query", - "predicate": "derives_from", + "predicate": "affects", "requestBody": { "body": { "q": "{inputs[0]}", @@ -30910,33 +31350,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-derives_from-Gene" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-affects-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-derives_info-ChemicalSubstance": [ + "AnatomicalEntity-causes-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "derives_info" + "fields": "causes" }, "path": "/query", - "predicate": "derives_info", + "predicate": "causes", "requestBody": { "body": { "q": "{inputs[0]}", @@ -30944,33 +31384,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-derives_info-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-causes-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-disrupted_by-BiologicalProcess": [ + "AnatomicalEntity-causes-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "Disease" } ], "parameters": { - "fields": "disrupted_by" + "fields": "causes" }, "path": "/query", - "predicate": "disrupted_by", + "predicate": "causes", "requestBody": { "body": { "q": "{inputs[0]}", @@ -30978,26 +31418,26 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-disrupted_by-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-causes-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-disrupted_by-CellularComponent": [ + "AnatomicalEntity-disrupted_by-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "CellularComponent" + "semantic": "BiologicalProcess" } ], "parameters": { @@ -31012,19 +31452,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-disrupted_by-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-disrupted_by-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-disrupted_by-ChemicalSubstance": [ + "AnatomicalEntity-disrupted_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", @@ -31046,19 +31486,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-disrupted_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-disrupted_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-disrupted_by-Disease": [ + "AnatomicalEntity-disrupted_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", @@ -31080,19 +31520,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-disrupted_by-Disease" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-disrupted_by-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-disrupted_by-Gene": [ + "AnatomicalEntity-disrupted_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", @@ -31114,89 +31554,21 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-disrupted_by-Gene" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-disrupted_by-PhenotypicFeature": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "PhenotypicFeature" - } - ], - "parameters": { - "fields": "disrupted_by" - }, - "path": "/query", - "predicate": "disrupted_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-disrupted_by-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-disrupted_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-disrupts-AnatomicalEntity": [ + "AnatomicalEntity-manifestation_of-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ { "id": "UMLS", "semantic": "AnatomicalEntity" } ], - "parameters": { - "fields": "disrupts" - }, - "path": "/query", - "predicate": "disrupts", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-disrupts-AnatomicalEntity" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-disrupts-BiologicalProcess": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], "method": "post", "outputs": [ { @@ -31205,10 +31577,10 @@ } ], "parameters": { - "fields": "disrupts" + "fields": "manifestation_of" }, "path": "/query", - "predicate": "disrupts", + "predicate": "manifestation_of", "requestBody": { "body": { "q": "{inputs[0]}", @@ -31216,33 +31588,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-disrupts-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-manifestation_of-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-disrupts-Cell": [ + "AnatomicalEntity-manifested_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Cell" + "semantic": "Disease" } ], "parameters": { - "fields": "disrupts" + "fields": "manifested_by" }, "path": "/query", - "predicate": "disrupts", + "predicate": "manifested_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -31250,33 +31622,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-disrupts-Cell" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-manifested_by-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-disrupts-CellularComponent": [ + "AnatomicalEntity-negatively_regulated_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "CellularComponent" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "disrupts" + "fields": "negatively_regulated_by" }, "path": "/query", - "predicate": "disrupts", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -31284,33 +31656,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-disrupts-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-negatively_regulated_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-disrupts-Disease": [ + "AnatomicalEntity-negatively_regulates-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "disrupts" + "fields": "negatively_regulates" }, "path": "/query", - "predicate": "disrupts", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -31318,19 +31690,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-disrupts-Disease" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-negatively_regulates-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-disrupts-Gene": [ + "AnatomicalEntity-negatively_regulates-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", @@ -31341,10 +31713,10 @@ } ], "parameters": { - "fields": "disrupts" + "fields": "negatively_regulates" }, "path": "/query", - "predicate": "disrupts", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -31352,33 +31724,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-disrupts-Gene" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-negatively_regulates-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-disrupts-PhenotypicFeature": [ + "AnatomicalEntity-physically_interacts_with-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "disrupts" + "fields": "physically_interacts_with" }, "path": "/query", - "predicate": "disrupts", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -31386,33 +31758,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-disrupts-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-physically_interacts_with-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-negatively_regulated_by-BiologicalProcess": [ + "AnatomicalEntity-physically_interacts_with-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "Gene" } ], "parameters": { - "fields": "negatively_regulated_by" + "fields": "physically_interacts_with" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -31420,19 +31792,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-negatively_regulated_by-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-physically_interacts_with-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-negatively_regulated_by-ChemicalSubstance": [ + "AnatomicalEntity-positively_regulated_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", @@ -31443,44 +31815,10 @@ } ], "parameters": { - "fields": "negatively_regulated_by" - }, - "path": "/query", - "predicate": "negatively_regulated_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-negatively_regulated_by-ChemicalSubstance" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-negatively_regulated_by-Disease": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "parameters": { - "fields": "negatively_regulated_by" + "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -31488,19 +31826,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-negatively_regulated_by-Disease" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-positively_regulated_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-negatively_regulated_by-Gene": [ + "AnatomicalEntity-positively_regulated_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", @@ -31511,10 +31849,10 @@ } ], "parameters": { - "fields": "negatively_regulated_by" + "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -31522,33 +31860,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-negatively_regulated_by-Gene" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-positively_regulated_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-negatively_regulated_by-PhenotypicFeature": [ + "AnatomicalEntity-positively_regulates-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "negatively_regulated_by" + "fields": "positively_regulates" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "entity_positively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -31556,33 +31894,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-negatively_regulated_by-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-positively_regulates-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-negatively_regulates-BiologicalProcess": [ + "AnatomicalEntity-positively_regulates-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "Gene" } ], "parameters": { - "fields": "negatively_regulates" + "fields": "positively_regulates" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "entity_positively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -31590,33 +31928,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-negatively_regulates-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-positively_regulates-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-negatively_regulates-ChemicalSubstance": [ + "AnatomicalEntity-preceded_by-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "negatively_regulates" + "fields": "preceded_by" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "preceded_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -31624,19 +31962,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-negatively_regulates-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-preceded_by-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-negatively_regulates-Disease": [ + "AnatomicalEntity-preceded_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", @@ -31647,44 +31985,10 @@ } ], "parameters": { - "fields": "negatively_regulates" - }, - "path": "/query", - "predicate": "negatively_regulates", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-negatively_regulates-Disease" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-negatively_regulates-Gene": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Gene" - } - ], - "parameters": { - "fields": "negatively_regulates" + "fields": "preceded_by" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "preceded_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -31692,19 +31996,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-negatively_regulates-Gene" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-preceded_by-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-physically_interacts_with-BiologicalProcess": [ + "AnatomicalEntity-precedes-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", @@ -31715,10 +32019,10 @@ } ], "parameters": { - "fields": "physically_interacts_with" + "fields": "precedes" }, "path": "/query", - "predicate": "physically_interacts_with", + "predicate": "precedes", "requestBody": { "body": { "q": "{inputs[0]}", @@ -31726,67 +32030,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-physically_interacts_with-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-precedes-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-physically_interacts_with-CellularComponent": [ + "AnatomicalEntity-precedes-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ - { - "id": "UMLS", - "semantic": "CellularComponent" - } - ], - "parameters": { - "fields": "physically_interacts_with" - }, - "path": "/query", - "predicate": "physically_interacts_with", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-physically_interacts_with-CellularComponent" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-physically_interacts_with-ChemicalSubstance": [ - { - "inputSeparator": ",", - "inputs": [ { "id": "UMLS", "semantic": "Disease" } ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "ChemicalSubstance" - } - ], "parameters": { - "fields": "physically_interacts_with" + "fields": "precedes" }, "path": "/query", - "predicate": "physically_interacts_with", + "predicate": "precedes", "requestBody": { "body": { "q": "{inputs[0]}", @@ -31794,19 +32064,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-physically_interacts_with-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-precedes-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-physically_interacts_with-Disease": [ + "AnatomicalEntity-predisposes-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", @@ -31817,10 +32087,10 @@ } ], "parameters": { - "fields": "physically_interacts_with" + "fields": "predisposes" }, "path": "/query", - "predicate": "physically_interacts_with", + "predicate": "predisposes", "requestBody": { "body": { "q": "{inputs[0]}", @@ -31828,67 +32098,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-physically_interacts_with-Disease" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-predisposes-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-physically_interacts_with-Gene": [ + "AnatomicalEntity-prevents-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ - { - "id": "UMLS", - "semantic": "Gene" - } - ], - "parameters": { - "fields": "physically_interacts_with" - }, - "path": "/query", - "predicate": "physically_interacts_with", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-physically_interacts_with-Gene" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-physically_interacts_with-PhenotypicFeature": [ - { - "inputSeparator": ",", - "inputs": [ { "id": "UMLS", "semantic": "Disease" } ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "PhenotypicFeature" - } - ], "parameters": { - "fields": "physically_interacts_with" + "fields": "prevents" }, "path": "/query", - "predicate": "physically_interacts_with", + "predicate": "prevents", "requestBody": { "body": { "q": "{inputs[0]}", @@ -31896,33 +32132,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-physically_interacts_with-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-prevents-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-positively_regulated_by-ChemicalSubstance": [ + "AnatomicalEntity-related_to-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "AnatomicalEntity" } ], "parameters": { - "fields": "positively_regulated_by" + "fields": "related_to" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -31930,33 +32166,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-positively_regulated_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-related_to-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-positively_regulated_by-Disease": [ + "AnatomicalEntity-related_to-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "positively_regulated_by" + "fields": "related_to" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -31964,33 +32200,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-positively_regulated_by-Disease" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-related_to-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-positively_regulated_by-Gene": [ + "AnatomicalEntity-related_to-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "CellularComponent" } ], "parameters": { - "fields": "positively_regulated_by" + "fields": "related_to" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -31998,33 +32234,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-positively_regulated_by-Gene" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-related_to-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-positively_regulates-BiologicalProcess": [ + "AnatomicalEntity-related_to-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "positively_regulates" + "fields": "related_to" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -32032,33 +32268,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-positively_regulates-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-related_to-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-positively_regulates-ChemicalSubstance": [ + "AnatomicalEntity-related_to-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "parameters": { - "fields": "positively_regulates" + "fields": "related_to" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -32066,33 +32302,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-positively_regulates-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-related_to-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-positively_regulates-Disease": [ + "AnatomicalEntity-related_to-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "Gene" } ], "parameters": { - "fields": "positively_regulates" + "fields": "related_to" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -32100,33 +32336,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-positively_regulates-Disease" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-related_to-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "Disease-positively_regulates-Gene": [ + "AnatomicalEntity-related_to-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "parameters": { - "fields": "positively_regulates" + "fields": "related_to" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -32134,823 +32370,7 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-positively_regulates-Gene" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-prevented_by-AnatomicalEntity": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "AnatomicalEntity" - } - ], - "parameters": { - "fields": "prevented_by" - }, - "path": "/query", - "predicate": "prevented_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-prevented_by-AnatomicalEntity" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-prevented_by-BiologicalProcess": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "BiologicalProcess" - } - ], - "parameters": { - "fields": "prevented_by" - }, - "path": "/query", - "predicate": "prevented_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-prevented_by-BiologicalProcess" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-prevented_by-ChemicalSubstance": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "ChemicalSubstance" - } - ], - "parameters": { - "fields": "prevented_by" - }, - "path": "/query", - "predicate": "prevented_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-prevented_by-ChemicalSubstance" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-prevented_by-Disease": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "parameters": { - "fields": "prevented_by" - }, - "path": "/query", - "predicate": "prevented_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-prevented_by-Disease" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-prevented_by-Gene": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Gene" - } - ], - "parameters": { - "fields": "prevented_by" - }, - "path": "/query", - "predicate": "prevented_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-prevented_by-Gene" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-prevented_by-PhenotypicFeature": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "PhenotypicFeature" - } - ], - "parameters": { - "fields": "prevented_by" - }, - "path": "/query", - "predicate": "prevented_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-prevented_by-PhenotypicFeature" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-prevents-Disease": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "parameters": { - "fields": "prevents" - }, - "path": "/query", - "predicate": "prevents", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-prevents-Disease" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-related_to-AnatomicalEntity": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "AnatomicalEntity" - } - ], - "parameters": { - "fields": "related_to" - }, - "path": "/query", - "predicate": "related_to", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-related_to-AnatomicalEntity" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-related_to-BiologicalProcess": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "BiologicalProcess" - } - ], - "parameters": { - "fields": "related_to" - }, - "path": "/query", - "predicate": "related_to", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-related_to-BiologicalProcess" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-related_to-Cell": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Cell" - } - ], - "parameters": { - "fields": "related_to" - }, - "path": "/query", - "predicate": "related_to", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-related_to-Cell" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-related_to-CellularComponent": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "CellularComponent" - } - ], - "parameters": { - "fields": "related_to" - }, - "path": "/query", - "predicate": "related_to", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-related_to-CellularComponent" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-related_to-ChemicalSubstance": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "ChemicalSubstance" - } - ], - "parameters": { - "fields": "related_to" - }, - "path": "/query", - "predicate": "related_to", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-related_to-ChemicalSubstance" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-related_to-Disease": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "parameters": { - "fields": "related_to" - }, - "path": "/query", - "predicate": "related_to", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-related_to-Disease" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-related_to-Gene": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Gene" - } - ], - "parameters": { - "fields": "related_to" - }, - "path": "/query", - "predicate": "related_to", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-related_to-Gene" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-related_to-PhenotypicFeature": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "PhenotypicFeature" - } - ], - "parameters": { - "fields": "related_to" - }, - "path": "/query", - "predicate": "related_to", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-related_to-PhenotypicFeature" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-treated_by-AnatomicalEntity": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "AnatomicalEntity" - } - ], - "parameters": { - "fields": "treated_by" - }, - "path": "/query", - "predicate": "treated_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-treated_by-AnatomicalEntity" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-treated_by-BiologicalProcess": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "BiologicalProcess" - } - ], - "parameters": { - "fields": "treated_by" - }, - "path": "/query", - "predicate": "treated_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-treated_by-BiologicalProcess" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-treated_by-Cell": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Cell" - } - ], - "parameters": { - "fields": "treated_by" - }, - "path": "/query", - "predicate": "treated_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-treated_by-Cell" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-treated_by-CellularComponent": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "CellularComponent" - } - ], - "parameters": { - "fields": "treated_by" - }, - "path": "/query", - "predicate": "treated_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-treated_by-CellularComponent" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-treated_by-ChemicalSubstance": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "ChemicalSubstance" - } - ], - "parameters": { - "fields": "treated_by" - }, - "path": "/query", - "predicate": "treated_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-treated_by-ChemicalSubstance" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-treated_by-Disease": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "parameters": { - "fields": "treated_by" - }, - "path": "/query", - "predicate": "treated_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-treated_by-Disease" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-treated_by-Gene": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Gene" - } - ], - "parameters": { - "fields": "treated_by" - }, - "path": "/query", - "predicate": "treated_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-treated_by-Gene" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-treated_by-PhenotypicFeature": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "PhenotypicFeature" - } - ], - "parameters": { - "fields": "treated_by" - }, - "path": "/query", - "predicate": "treated_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-treated_by-PhenotypicFeature" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Disease-treats-Disease": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "parameters": { - "fields": "treats" - }, - "path": "/query", - "predicate": "treats", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Disease-treats-Disease" + "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-related_to-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true @@ -32958,389 +32378,153 @@ ] }, "x-bte-response-mapping": { - "Disease-affected_by-AnatomicalEntity": { - "pmid": "affected_by.pmid", - "umls": "affected_by.umls" - }, - "Disease-affected_by-BiologicalProcess": { - "pmid": "affected_by.pmid", - "umls": "affected_by.umls" - }, - "Disease-affected_by-Cell": { - "pmid": "affected_by.pmid", - "umls": "affected_by.umls" - }, - "Disease-affected_by-CellularComponent": { + "AnatomicalEntity-affected_by-BiologicalProcess": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "Disease-affected_by-ChemicalSubstance": { + "AnatomicalEntity-affected_by-CellularComponent": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "Disease-affected_by-Disease": { + "AnatomicalEntity-affected_by-ChemicalSubstance": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "Disease-affected_by-Gene": { + "AnatomicalEntity-affected_by-Disease": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "Disease-affected_by-PhenotypicFeature": { + "AnatomicalEntity-affected_by-Gene": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "Disease-affects-AnatomicalEntity": { - "pmid": "affects.pmid", - "umls": "affects.umls" - }, - "Disease-affects-BiologicalProcess": { - "pmid": "affects.pmid", - "umls": "affects.umls" - }, - "Disease-affects-Cell": { - "pmid": "affects.pmid", - "umls": "affects.umls" - }, - "Disease-affects-CellularComponent": { - "pmid": "affects.pmid", - "umls": "affects.umls" - }, - "Disease-affects-ChemicalSubstance": { - "pmid": "affects.pmid", - "umls": "affects.umls" - }, - "Disease-affects-Disease": { - "pmid": "affects.pmid", - "umls": "affects.umls" - }, - "Disease-affects-Gene": { + "AnatomicalEntity-affects-BiologicalProcess": { "pmid": "affects.pmid", "umls": "affects.umls" }, - "Disease-affects-PhenotypicFeature": { + "AnatomicalEntity-affects-Disease": { "pmid": "affects.pmid", "umls": "affects.umls" }, - "Disease-caused_by-AnatomicalEntity": { - "pmid": "caused_by.pmid", - "umls": "caused_by.umls" - }, - "Disease-caused_by-BiologicalProcess": { - "pmid": "caused_by.pmid", - "umls": "caused_by.umls" - }, - "Disease-caused_by-Cell": { - "pmid": "caused_by.pmid", - "umls": "caused_by.umls" - }, - "Disease-caused_by-CellularComponent": { - "pmid": "caused_by.pmid", - "umls": "caused_by.umls" - }, - "Disease-caused_by-ChemicalSubstance": { - "pmid": "caused_by.pmid", - "umls": "caused_by.umls" - }, - "Disease-caused_by-Disease": { - "pmid": "caused_by.pmid", - "umls": "caused_by.umls" - }, - "Disease-caused_by-Gene": { - "pmid": "caused_by.pmid", - "umls": "caused_by.umls" - }, - "Disease-caused_by-PhenotypicFeature": { - "pmid": "caused_by.pmid", - "umls": "caused_by.umls" - }, - "Disease-causes-BiologicalProcess": { + "AnatomicalEntity-causes-BiologicalProcess": { "pmid": "causes.pmid", "umls": "causes.umls" }, - "Disease-causes-Disease": { + "AnatomicalEntity-causes-Disease": { "pmid": "causes.pmid", "umls": "causes.umls" }, - "Disease-coexists_with-AnatomicalEntity": { - "pmid": "coexists_with.pmid", - "umls": "coexists_with.umls" - }, - "Disease-coexists_with-BiologicalProcess": { - "pmid": "coexists_with.pmid", - "umls": "coexists_with.umls" - }, - "Disease-coexists_with-Cell": { - "pmid": "coexists_with.pmid", - "umls": "coexists_with.umls" - }, - "Disease-coexists_with-CellularComponent": { - "pmid": "coexists_with.pmid", - "umls": "coexists_with.umls" - }, - "Disease-coexists_with-ChemicalSubstance": { - "pmid": "coexists_with.pmid", - "umls": "coexists_with.umls" - }, - "Disease-coexists_with-Disease": { - "pmid": "coexists_with.pmid", - "umls": "coexists_with.umls" - }, - "Disease-coexists_with-Gene": { - "pmid": "coexists_with.pmid", - "umls": "coexists_with.umls" - }, - "Disease-coexists_with-PhenotypicFeature": { - "pmid": "coexists_with.pmid", - "umls": "coexists_with.umls" - }, - "Disease-derives_from-ChemicalSubstance": { - "pmid": "derives_from.pmid", - "umls": "derives_from.umls" - }, - "Disease-derives_from-Gene": { - "pmid": "derives_from.pmid", - "umls": "derives_from.umls" - }, - "Disease-derives_info-ChemicalSubstance": { - "pmid": "derives_info.pmid", - "umls": "derives_info.umls" - }, - "Disease-disrupted_by-BiologicalProcess": { - "pmid": "disrupted_by.pmid", - "umls": "disrupted_by.umls" - }, - "Disease-disrupted_by-CellularComponent": { - "pmid": "disrupted_by.pmid", - "umls": "disrupted_by.umls" - }, - "Disease-disrupted_by-ChemicalSubstance": { + "AnatomicalEntity-disrupted_by-BiologicalProcess": { "pmid": "disrupted_by.pmid", "umls": "disrupted_by.umls" }, - "Disease-disrupted_by-Disease": { + "AnatomicalEntity-disrupted_by-ChemicalSubstance": { "pmid": "disrupted_by.pmid", "umls": "disrupted_by.umls" }, - "Disease-disrupted_by-Gene": { + "AnatomicalEntity-disrupted_by-Disease": { "pmid": "disrupted_by.pmid", "umls": "disrupted_by.umls" }, - "Disease-disrupted_by-PhenotypicFeature": { + "AnatomicalEntity-disrupted_by-Gene": { "pmid": "disrupted_by.pmid", "umls": "disrupted_by.umls" }, - "Disease-disrupts-AnatomicalEntity": { - "pmid": "disrupts.pmid", - "umls": "disrupts.umls" - }, - "Disease-disrupts-BiologicalProcess": { - "pmid": "disrupts.pmid", - "umls": "disrupts.umls" - }, - "Disease-disrupts-Cell": { - "pmid": "disrupts.pmid", - "umls": "disrupts.umls" - }, - "Disease-disrupts-CellularComponent": { - "pmid": "disrupts.pmid", - "umls": "disrupts.umls" - }, - "Disease-disrupts-Disease": { - "pmid": "disrupts.pmid", - "umls": "disrupts.umls" - }, - "Disease-disrupts-Gene": { - "pmid": "disrupts.pmid", - "umls": "disrupts.umls" - }, - "Disease-disrupts-PhenotypicFeature": { - "pmid": "disrupts.pmid", - "umls": "disrupts.umls" - }, - "Disease-negatively_regulated_by-BiologicalProcess": { - "pmid": "negatively_regulated_by.pmid", - "umls": "negatively_regulated_by.umls" - }, - "Disease-negatively_regulated_by-ChemicalSubstance": { - "pmid": "negatively_regulated_by.pmid", - "umls": "negatively_regulated_by.umls" - }, - "Disease-negatively_regulated_by-Disease": { - "pmid": "negatively_regulated_by.pmid", - "umls": "negatively_regulated_by.umls" - }, - "Disease-negatively_regulated_by-Gene": { - "pmid": "negatively_regulated_by.pmid", - "umls": "negatively_regulated_by.umls" + "AnatomicalEntity-manifestation_of-BiologicalProcess": { + "pmid": "manifestation_of.pmid", + "umls": "manifestation_of.umls" }, - "Disease-negatively_regulated_by-PhenotypicFeature": { + "AnatomicalEntity-manifested_by-Disease": { + "pmid": "manifested_by.pmid", + "umls": "manifested_by.umls" + }, + "AnatomicalEntity-negatively_regulated_by-ChemicalSubstance": { "pmid": "negatively_regulated_by.pmid", "umls": "negatively_regulated_by.umls" }, - "Disease-negatively_regulates-BiologicalProcess": { - "pmid": "negatively_regulates.pmid", - "umls": "negatively_regulates.umls" - }, - "Disease-negatively_regulates-ChemicalSubstance": { - "pmid": "negatively_regulates.pmid", - "umls": "negatively_regulates.umls" - }, - "Disease-negatively_regulates-Disease": { + "AnatomicalEntity-negatively_regulates-ChemicalSubstance": { "pmid": "negatively_regulates.pmid", "umls": "negatively_regulates.umls" }, - "Disease-negatively_regulates-Gene": { + "AnatomicalEntity-negatively_regulates-Gene": { "pmid": "negatively_regulates.pmid", "umls": "negatively_regulates.umls" }, - "Disease-physically_interacts_with-BiologicalProcess": { - "pmid": "physically_interacts_with.pmid", - "umls": "physically_interacts_with.umls" - }, - "Disease-physically_interacts_with-CellularComponent": { - "pmid": "physically_interacts_with.pmid", - "umls": "physically_interacts_with.umls" - }, - "Disease-physically_interacts_with-ChemicalSubstance": { - "pmid": "physically_interacts_with.pmid", - "umls": "physically_interacts_with.umls" - }, - "Disease-physically_interacts_with-Disease": { - "pmid": "physically_interacts_with.pmid", - "umls": "physically_interacts_with.umls" - }, - "Disease-physically_interacts_with-Gene": { + "AnatomicalEntity-physically_interacts_with-ChemicalSubstance": { "pmid": "physically_interacts_with.pmid", "umls": "physically_interacts_with.umls" }, - "Disease-physically_interacts_with-PhenotypicFeature": { + "AnatomicalEntity-physically_interacts_with-Gene": { "pmid": "physically_interacts_with.pmid", "umls": "physically_interacts_with.umls" }, - "Disease-positively_regulated_by-ChemicalSubstance": { - "pmid": "positively_regulated_by.pmid", - "umls": "positively_regulated_by.umls" - }, - "Disease-positively_regulated_by-Disease": { + "AnatomicalEntity-positively_regulated_by-ChemicalSubstance": { "pmid": "positively_regulated_by.pmid", "umls": "positively_regulated_by.umls" }, - "Disease-positively_regulated_by-Gene": { + "AnatomicalEntity-positively_regulated_by-Gene": { "pmid": "positively_regulated_by.pmid", "umls": "positively_regulated_by.umls" }, - "Disease-positively_regulates-BiologicalProcess": { - "pmid": "positively_regulates.pmid", - "umls": "positively_regulates.umls" - }, - "Disease-positively_regulates-ChemicalSubstance": { - "pmid": "positively_regulates.pmid", - "umls": "positively_regulates.umls" - }, - "Disease-positively_regulates-Disease": { + "AnatomicalEntity-positively_regulates-ChemicalSubstance": { "pmid": "positively_regulates.pmid", "umls": "positively_regulates.umls" }, - "Disease-positively_regulates-Gene": { + "AnatomicalEntity-positively_regulates-Gene": { "pmid": "positively_regulates.pmid", "umls": "positively_regulates.umls" }, - "Disease-prevented_by-AnatomicalEntity": { - "pmid": "prevented_by.pmid", - "umls": "prevented_by.umls" - }, - "Disease-prevented_by-BiologicalProcess": { - "pmid": "prevented_by.pmid", - "umls": "prevented_by.umls" + "AnatomicalEntity-preceded_by-BiologicalProcess": { + "pmid": "preceded_by.pmid", + "umls": "preceded_by.umls" }, - "Disease-prevented_by-ChemicalSubstance": { - "pmid": "prevented_by.pmid", - "umls": "prevented_by.umls" + "AnatomicalEntity-preceded_by-Disease": { + "pmid": "preceded_by.pmid", + "umls": "preceded_by.umls" }, - "Disease-prevented_by-Disease": { - "pmid": "prevented_by.pmid", - "umls": "prevented_by.umls" + "AnatomicalEntity-precedes-BiologicalProcess": { + "pmid": "precedes.pmid", + "umls": "precedes.umls" }, - "Disease-prevented_by-Gene": { - "pmid": "prevented_by.pmid", - "umls": "prevented_by.umls" + "AnatomicalEntity-precedes-Disease": { + "pmid": "precedes.pmid", + "umls": "precedes.umls" }, - "Disease-prevented_by-PhenotypicFeature": { - "pmid": "prevented_by.pmid", - "umls": "prevented_by.umls" + "AnatomicalEntity-predisposes-Disease": { + "pmid": "predisposes.pmid", + "umls": "predisposes.umls" }, - "Disease-prevents-Disease": { + "AnatomicalEntity-prevents-Disease": { "pmid": "prevents.pmid", "umls": "prevents.umls" }, - "Disease-related_to-AnatomicalEntity": { - "pmid": "related_to.pmid", - "umls": "related_to.umls" - }, - "Disease-related_to-BiologicalProcess": { + "AnatomicalEntity-related_to-AnatomicalEntity": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "Disease-related_to-Cell": { + "AnatomicalEntity-related_to-BiologicalProcess": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "Disease-related_to-CellularComponent": { + "AnatomicalEntity-related_to-CellularComponent": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "Disease-related_to-ChemicalSubstance": { + "AnatomicalEntity-related_to-ChemicalSubstance": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "Disease-related_to-Disease": { + "AnatomicalEntity-related_to-Disease": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "Disease-related_to-Gene": { + "AnatomicalEntity-related_to-Gene": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "Disease-related_to-PhenotypicFeature": { + "AnatomicalEntity-related_to-PhenotypicFeature": { "pmid": "related_to.pmid", "umls": "related_to.umls" - }, - "Disease-treated_by-AnatomicalEntity": { - "pmid": "treated_by.pmid", - "umls": "treated_by.umls" - }, - "Disease-treated_by-BiologicalProcess": { - "pmid": "treated_by.pmid", - "umls": "treated_by.umls" - }, - "Disease-treated_by-Cell": { - "pmid": "treated_by.pmid", - "umls": "treated_by.umls" - }, - "Disease-treated_by-CellularComponent": { - "pmid": "treated_by.pmid", - "umls": "treated_by.umls" - }, - "Disease-treated_by-ChemicalSubstance": { - "pmid": "treated_by.pmid", - "umls": "treated_by.umls" - }, - "Disease-treated_by-Disease": { - "pmid": "treated_by.pmid", - "umls": "treated_by.umls" - }, - "Disease-treated_by-Gene": { - "pmid": "treated_by.pmid", - "umls": "treated_by.umls" - }, - "Disease-treated_by-PhenotypicFeature": { - "pmid": "treated_by.pmid", - "umls": "treated_by.umls" - }, - "Disease-treats-Disease": { - "pmid": "treats.pmid", - "umls": "treats.umls" } } }, @@ -33351,9 +32535,9 @@ "x-id": "https://github.com/newgene", "x-role": "responsible developer" }, - "description": "Documentation of the SEMMED disease query web services. Learn more about [semmed disease](http://pending.biothings.io/semmed)", + "description": "Documentation of the SEMMED disease query web services. Learn more about [mydisease.info](http://pending.biothings.io/semmed)", "termsOfService": "http://biothings.ncats.io", - "title": "SEMMED Disease API", + "title": "SEMMED Anatomy API", "version": "1.0", "x-translator": { "component": "KP", @@ -33363,7 +32547,7 @@ } }, "paths": { - "/disease": { + "/anatomy": { "post": { "parameters": [ { @@ -33431,14 +32615,14 @@ ] } }, - "/disease/{diseaseid}": { + "/anatomy/{anatomyid}": { "get": { "parameters": [ { "description": "Retrieve disease objects based on ID", "example": "C0004096", "in": "path", - "name": "diseaseid", + "name": "anatomyid", "required": true, "schema": { "type": "string" @@ -33687,1124 +32871,1355 @@ ], "x-bte-kgs-operations": [ { - "$ref": "#/components/x-bte-kgs-operations/Disease-affected_by-AnatomicalEntity" - }, - { - "$ref": "#/components/x-bte-kgs-operations/Disease-affected_by-Cell" - }, - { - "$ref": "#/components/x-bte-kgs-operations/Disease-affected_by-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-affected_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-affected_by-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-affected_by-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-affected_by-Disease" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-affected_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-affected_by-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-affected_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-affected_by-Gene" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-affected_by-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-affected_by-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-affects-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-affects-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-affects-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-affects-Cell" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-causes-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-affects-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-causes-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-affects-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-disrupted_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-affects-Disease" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-disrupted_by-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-affects-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-disrupted_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-affects-Gene" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-disrupted_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-affects-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-manifestation_of-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-caused_by-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-manifested_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-caused_by-Cell" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-negatively_regulated_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-caused_by-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-negatively_regulates-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-caused_by-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-negatively_regulates-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-caused_by-Disease" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-physically_interacts_with-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-caused_by-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-physically_interacts_with-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-caused_by-Gene" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-positively_regulated_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-caused_by-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-positively_regulated_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-causes-Disease" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-positively_regulates-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-causes-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-positively_regulates-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-coexists_with-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-preceded_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-coexists_with-Cell" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-preceded_by-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-coexists_with-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-precedes-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-coexists_with-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-precedes-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-coexists_with-Disease" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-predisposes-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-coexists_with-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-prevents-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-coexists_with-Gene" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-related_to-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-coexists_with-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-related_to-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-derives_from-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-related_to-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-derives_from-Gene" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-related_to-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-derives_info-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-related_to-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-disrupted_by-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-related_to-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/Disease-disrupted_by-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-related_to-CellularComponent" + } + ] + } + } + }, + "servers": [ + { + "description": "Production server", + "url": "https://biothings.ncats.io/semmed_anatomy" + } + ], + "tags": [ + { + "name": "anatomicalentity" + }, + { + "name": "annotation" + }, + { + "name": "query" + }, + { + "name": "translator" + }, + { + "name": "biothings" + }, + { + "name": "semmed" + } + ] + }, + { + "_id": "81955d376a10505c1c69cd06dbda3047", + "_meta": { + "date_created": "2020-12-07T23:01:45.135044+00:00", + "last_updated": "2021-03-29T07:03:34.694078+00:00", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/semmed/semmed_gene.yaml", + "username": "kevinxin90" + }, + "_score": 0.4848808, + "components": { + "x-bte-kgs-operations": { + "Gene-affected_by-BiologicalProcess": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "Gene" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "BiologicalProcess" + } + ], + "parameters": { + "fields": "affected_by" }, - 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"username": "newgene" - }, - "_score": 0.47008187, - "components": { - "x-bte-kgs-operations": { - "contraindicatedBy": [ + "source": "SEMMED", + "supportBatch": true + } + ], + "Gene-disrupts-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "Gene" } ], + "method": "post", "outputs": [ { - "id": "CHEMBL.COMPOUND", - "semantic": "ChemicalSubstance" + "id": "UMLS", + "semantic": "AnatomicalEntity" } ], "parameters": { - "fields": "chembl.molecule_chembl_id", - "size": "250" + "fields": "disrupts" }, - "predicate": "contraindicated_for", + "path": "/query", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "drugcentral.drug_use.contraindication.umls_cui" - }, - "header": "application/x-www-form-urlencoded" + "scopes": "umls" + } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/chembl" + "$ref": "#/components/x-bte-response-mapping/Gene-disrupts-AnatomicalEntity" }, - "source": "drugcentral", + "source": "SEMMED", "supportBatch": true } ], - "contraindication": [ + "Gene-disrupts-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { - "id": "CHEMBL.COMPOUND", - "semantic": "ChemicalSubstance" + "id": "UMLS", + "semantic": "Gene" } ], + "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "drugcentral.drug_use.contraindication" + "fields": "disrupts" }, - "predicate": "contraindication", + "path": "/query", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "chembl.molecule_chembl_id" - }, - "header": "application/x-www-form-urlencoded" + "scopes": "umls" + } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/contraindication" + "$ref": "#/components/x-bte-response-mapping/Gene-disrupts-BiologicalProcess" }, - "source": "drugcentral", + "source": "SEMMED", "supportBatch": true } ], - "metabolize": [ + "Gene-disrupts-Cell": [ { "inputSeparator": ",", "inputs": [ { - "id": "SYMBOL", + "id": "UMLS", "semantic": "Gene" } ], + "method": "post", "outputs": [ { - "id": "DRUGBANK", - "semantic": "ChemicalSubstance" + "id": "UMLS", + "semantic": "Cell" } ], "parameters": { - "fields": "drugbank.id", - "size": "250" + "fields": "disrupts" }, - "predicate": "metabolize", + "path": "/query", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "drugbank.enzymes.gene_name" - }, - "header": "application/x-www-form-urlencoded" + "scopes": "umls" + } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/drugbank" + "$ref": "#/components/x-bte-response-mapping/Gene-disrupts-Cell" }, - "source": "drugbank", + "source": "SEMMED", "supportBatch": true } ], - "metabolizedBy": [ + "Gene-disrupts-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { - "id": "DRUGBANK", - "semantic": "ChemicalSubstance" + "id": "UMLS", + "semantic": "Gene" } ], + "method": "post", "outputs": [ { - "id": "SYMBOL", - "semantic": "Gene" + "id": "UMLS", + "semantic": "CellularComponent" } ], "parameters": { - "fields": "drugbank.enzymes" + "fields": "disrupts" }, - "predicate": "metabolic_processing_affected_by", + "path": "/query", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "drugbank.id" - }, - "header": "application/x-www-form-urlencoded" + "scopes": "umls" + } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/metabolizedBy" + "$ref": "#/components/x-bte-response-mapping/Gene-disrupts-CellularComponent" }, - "source": "drugbank", + "source": "SEMMED", "supportBatch": true } ], - "target": [ + "Gene-disrupts-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { - "id": "DRUGBANK", - "semantic": "ChemicalSubstance" + "id": "UMLS", + "semantic": "Gene" } ], + "method": "post", "outputs": [ { - "id": "SYMBOL", - "semantic": "Gene" + "id": "UMLS", + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "drugbank.targets" + "fields": "disrupts" }, - "predicate": "physically_interacts_with", + "path": "/query", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "drugbank.id" - }, - "header": "application/x-www-form-urlencoded" + "scopes": "umls" + } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/target-drugbank" + "$ref": "#/components/x-bte-response-mapping/Gene-disrupts-ChemicalSubstance" }, - "source": "drugbank", + "source": "SEMMED", "supportBatch": true - }, + } + ], + "Gene-disrupts-Disease": [ { "inputSeparator": ",", "inputs": [ { - "id": "CHEMBL.COMPOUND", - "semantic": "ChemicalSubstance" + "id": "UMLS", + "semantic": "Gene" } ], + "method": "post", "outputs": [ { - "id": "SYMBOL", - "semantic": "Gene" + "id": "UMLS", + "semantic": "Disease" } ], "parameters": { - "fields": "drugcentral.bioactivity" + "fields": "disrupts" }, - "predicate": "physically_interacts_with", + "path": "/query", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "chembl.molecule_chembl_id" - }, - "header": "application/x-www-form-urlencoded" + "scopes": "umls" + } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/target-drugcentral" + "$ref": "#/components/x-bte-response-mapping/Gene-disrupts-Disease" }, - "source": "drugcentral", + "source": "SEMMED", "supportBatch": true } ], - "targetedBy": [ + "Gene-disrupts-Gene": [ { "inputSeparator": ",", "inputs": [ { - "id": "SYMBOL", + "id": "UMLS", "semantic": "Gene" } ], + "method": "post", "outputs": [ { - "id": "DRUGBANK", - "semantic": "ChemicalSubstance" + "id": "UMLS", + "semantic": "Gene" } ], "parameters": { - "fields": "drugbank.id", - "size": "250" + "fields": "disrupts" }, - "predicate": "physically_interacts_with", + "path": "/query", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "drugbank.targets.gene_name" - }, - "header": "application/x-www-form-urlencoded" + "scopes": "umls" + } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/drugbank" + "$ref": "#/components/x-bte-response-mapping/Gene-disrupts-Gene" }, - "source": "drugbank", + "source": "SEMMED", "supportBatch": true - }, + } + ], + "Gene-disrupts-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { - "id": "SYMBOL", + "id": "UMLS", "semantic": "Gene" } ], + "method": "post", "outputs": [ { - "id": "CHEMBL.COMPOUND", - "semantic": "ChemicalSubstance" + "id": "UMLS", + "semantic": "PhenotypicFeature" } ], "parameters": { - "fields": "chembl.molecule_chembl_id", - "size": "250" + "fields": "disrupts" }, - "predicate": "physically_interacts_with", + "path": "/query", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "drugcentral.bioactivity.uniprot.gene_symbol" - }, - "header": "application/x-www-form-urlencoded" + "scopes": "umls" + } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/chembl" + "$ref": "#/components/x-bte-response-mapping/Gene-disrupts-PhenotypicFeature" }, - "source": "drugcentral", + "source": "SEMMED", "supportBatch": true } ], - "treatedBy": [ + "Gene-negatively_regulated_by-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "Gene" } ], + "method": "post", "outputs": [ { - "id": "CHEMBL.COMPOUND", - "semantic": "ChemicalSubstance" + "id": "UMLS", + "semantic": "AnatomicalEntity" } ], "parameters": { - "fields": "chembl.molecule_chembl_id", - "size": "250" + "fields": "negatively_regulated_by" }, - "predicate": "treated_by", + "path": "/query", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "drugcentral.drug_use.indication.umls_cui" - }, - "header": "application/x-www-form-urlencoded" + "scopes": "umls" + } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/chembl" + "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulated_by-AnatomicalEntity" }, - "source": "drugcentral", + "source": "SEMMED", "supportBatch": true } ], - "treats": [ + "Gene-negatively_regulated_by-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { - "id": "CHEMBL.COMPOUND", - "semantic": "ChemicalSubstance" + "id": "UMLS", + "semantic": "Gene" } ], + "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "drugcentral.drug_use.indication" + "fields": "negatively_regulated_by" }, - "predicate": "treats", + "path": "/query", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "chembl.molecule_chembl_id" - }, - "header": "application/x-www-form-urlencoded" + "scopes": "umls" + } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/treats" + "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulated_by-BiologicalProcess" }, - "source": "drugcentral", + "source": "SEMMED", "supportBatch": true } - ] - }, - "x-bte-response-mapping": { - "chembl": { - "CHEMBL.COMPOUND": "chembl.molecule_chembl_id" - }, - "contraindication": { - "SNOMED": "drugcentral.drug_use.contraindication.snomed_concept_id", - "UMLS": "drugcentral.drug_use.contraindication.umls_cui", - "name": "drugcentral.drug_use.contraindication.concept_name" - }, - "drugbank": { - "DRUGBANK": "drugbank.id" - }, - "metabolizedBy": { - "SYMBOL": "drugbank.enzymes.gene_name", - "action": "drugbank.enzymes.actions", - "function": "drugbank.enzymes.general_function", - "name": "drugbank.enzymes.name" - }, - "target-drugbank": { - "SYMBOL": "drugbank.targets.gene_name", - "action": "drugbank.targets.actions", - "function": "drugbank.targets.general_function", - "name": "drugbank.targets.name", - "pubmed": "drugbank.targets.pmids" - }, - "target-drugcentral": { - "SYMBOL": "drugcentral.bioactivity.uniprot.gene_symbol", - "action": "drugcentral.bioactivity.action_type", - "name": "drugcentral.bioactivity.target_name" - }, - "treats": { - "SNOMED": "drugcentral.drug_use.indication.snomed_concept_id", - "UMLS": "drugcentral.drug_use.indication.umls_cui", - "name": "drugcentral.drug_use.indication.concept_name" - } - } - }, - "info": { - "contact": { - "email": "help@biothings.io", - "name": "Chunlei Wu", - "x-id": "https://github.com/newgene", - "x-role": "responsible developer" - }, - "description": "Documentation of the MyChem.info chem query web services. Learn more about [MyChem.info](http://MyChem.info/)", - "termsOfService": "http://MyChem.info/terms", - "title": "MyChem.info API", - "version": "1.0", - "x-translator": { - "component": "KP", - "team": [ - "Service Provider" - ] - } - }, - "paths": { - "/chem": { - "post": { - "parameters": [ - { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" - }, - { - "$ref": "#/components/parameters/fields", - "name": "fields" - }, - { - "$ref": "#/components/parameters/email", - "name": "email" - }, - { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "requestBody": { - "content": { - "application/x-www-form-urlencoded": { - "schema": { - "properties": { - "ids": { - "description": "multiple chemical IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", - "type": "string" - } - }, - "required": [ - "ids" - ] - } - } - } - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "items": { - "$ref": "#/components/schemas/Chem" - }, - "type": "array" - } - } - }, - "description": "A list of matching chemical objects" - }, - "400": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResult" - } - } - }, - "description": "A response indicating an improperly formatted query" - } - }, - "summary": "For a list of chemical IDs, return the matching chemical object", - "tags": [ - "chemical" - ] - } - }, - "/chem/{chemid}": { - "get": { - "parameters": [ - { - "description": "Retrieve chemical objects based on ID - currently one of: [InChiKey](https://en.wikipedia.org/wiki/International_Chemical_Identifier#InChIKey), [DrugBank accession number](https://www.drugbank.ca/documentation), [ChEMBLID](https://www.ebi.ac.uk/chembl/faq#faq40), [ChEBI identifier](http://www.ebi.ac.uk/chebi/aboutChebiForward.do), [PubChem CID](https://pubchem.ncbi.nlm.nih.gov/search/help_search.html#Cid), [UNII](https://www.fda.gov/ForIndustry/DataStandards/SubstanceRegistrationSystem-UniqueIngredientIdentifierUNII/). Supports JSONP and CORS as well.", - "example": "USNINKBPBVKHHZ-CYUUQNCZSA-L", - "in": "path", - "name": "chemid", - "required": true, - "schema": { - "type": "string" - } - }, - { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" - }, - { - "$ref": "#/components/parameters/callback", - "name": "callback" - }, - { - "$ref": "#/components/parameters/fields", - "name": "fields" - }, - { - "$ref": "#/components/parameters/email", - "name": "email" - }, - { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Chem" - } - } - }, - "description": "A matching chemical object" - }, - "404": { - "description": "A response indicating an unknown chemical ID" - } - }, - "summary": "Retrieve chemical objects based on ID", - "tags": [ - "chemical" - ] - } - }, - "/metadata": { - "get": { - "parameters": [ - { - "$ref": "#/components/parameters/callback", - "in": "query", - "name": "callback" - } - ], - "responses": { - "200": { - "description": "MyChem.info metadata object" - } - }, - "summary": "Get metadata about the data available from MyChem.info", - "tags": [ - "metadata" - ] - } - }, - "/metadata/fields": { - "get": { - "parameters": [ - { - "$ref": "#/components/parameters/search", - "name": "search" - }, - { - "$ref": "#/components/parameters/callback", - "name": "callback" - }, - { - "$ref": "#/components/parameters/prefix", - "name": "prefix" - }, - { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "responses": { - "200": { - "description": "MyChem.info metadata fields object" - } - }, - "summary": "Get metadata about the data fields available from a MyChem.info chem object", - "tags": [ - "metadata" - ] - } - }, - "/query": { - "get": { - "parameters": [ - { - "description": "Query string. The detailed query syntax can be found from our [docs](http://MyChem.info). Examples: \"Fludara\", \"CHEMBI:63599\", \"DB01073\".", - "example": "Fludara", - "in": "query", - "name": "q", - "required": true, - "schema": { - "type": "string" + ], + "Gene-negatively_regulated_by-Cell": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "Gene" } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "Cell" + } + ], + "parameters": { + "fields": "negatively_regulated_by" }, - { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" - }, - { - "$ref": "#/components/parameters/fields", - "name": "fields" - }, - { - "$ref": "#/components/parameters/facet_size", - "name": "facet_size" - }, - { - "$ref": "#/components/parameters/sort", - "name": "sort" - }, - { - "$ref": "#/components/parameters/callback", - "name": "callback" - }, - { - "$ref": "#/components/parameters/email", - "name": "email" + "path": "/query", + "predicate": "entity_negatively_regulated_by_entity", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } }, - { - "$ref": "#/components/parameters/facets", - "name": "facets" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulated_by-Cell" }, - { - "$ref": "#/components/parameters/size", - "name": "size" + "source": "SEMMED", + "supportBatch": true + } + ], + "Gene-negatively_regulated_by-CellularComponent": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "Gene" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "CellularComponent" + } + ], + "parameters": { + "fields": "negatively_regulated_by" }, - { - "$ref": "#/components/parameters/from", - "name": "from" + "path": "/query", + "predicate": "entity_negatively_regulated_by_entity", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } }, - { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/QueryResult" - } - } - }, - "description": "A query response with the \"hits\" property" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulated_by-CellularComponent" }, - "400": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResult" - } - } - }, - "description": "A response indicating an improperly formatted query" - } - }, - "summary": "Make chemical queries and return matching chemical hits. Supports JSONP and CORS as well.", - "tags": [ - "query" - ] - }, - "post": { - "parameters": [ - { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" + "source": "SEMMED", + "supportBatch": true + } + ], + "Gene-negatively_regulated_by-ChemicalSubstance": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "Gene" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "parameters": { + "fields": "negatively_regulated_by" }, - { - "$ref": "#/components/parameters/email", - "name": "email" + "path": "/query", + "predicate": "entity_negatively_regulated_by_entity", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } }, - { - "$ref": "#/components/parameters/fields", - "name": "fields" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulated_by-ChemicalSubstance" }, - { - "$ref": "#/components/parameters/size", - "name": "size" + "source": "SEMMED", + "supportBatch": true + } + ], + "Gene-negatively_regulated_by-Disease": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "Gene" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "Disease" + } + ], + "parameters": { + "fields": "negatively_regulated_by" }, - { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "requestBody": { - "content": { - "application/x-www-form-urlencoded": { - "schema": { - "properties": { - "q": { - "description": "multiple query terms separated by comma (also \"+\" or whitespace). Does not support wildcard queries", - "type": "string" - }, - "scopes": { - "description": "a comma-separated list of fields as the search \"scopes\" (fields to search through for query term). The available \"fields\" that can be passed to the \"scopes\" parameter are listed in the **/metadata/fields** endpoint.string Default: \"scopes=_id\".", - "type": "string" - } - } - } + "path": "/query", + "predicate": "entity_negatively_regulated_by_entity", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" } - } - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/QueryPOSTResult" - } - } - }, - "description": "Query response objects with the \"hits\" property" }, - "400": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResult" - } - } - }, - "description": "A response indicating an improperly formatted query" - } - }, - "summary": "Make batch chemical queries and return matching chemical hits", - "tags": [ - "query" - ], - "x-bte-kgs-operations": [ - { - "$ref": "#/components/x-bte-kgs-operations/metabolizedBy" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulated_by-Disease" }, - { - "$ref": "#/components/x-bte-kgs-operations/target" + "source": "SEMMED", + "supportBatch": true + } + ], + "Gene-negatively_regulated_by-Gene": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "Gene" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "Gene" + } + ], + "parameters": { + "fields": "negatively_regulated_by" }, - { - "$ref": "#/components/x-bte-kgs-operations/treats" + "path": "/query", + "predicate": "entity_negatively_regulated_by_entity", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } }, - { - "$ref": "#/components/x-bte-kgs-operations/contraindication" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulated_by-Gene" }, - { - "$ref": "#/components/x-bte-kgs-operations/metabolize" + "source": "SEMMED", + "supportBatch": true + } + ], + "Gene-negatively_regulated_by-PhenotypicFeature": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "Gene" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "PhenotypicFeature" + } + ], + "parameters": { + "fields": "negatively_regulated_by" }, - { - "$ref": "#/components/x-bte-kgs-operations/targetedBy" + "path": "/query", + "predicate": "entity_negatively_regulated_by_entity", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } }, - { - "$ref": "#/components/x-bte-kgs-operations/treatedBy" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulated_by-PhenotypicFeature" }, - { - "$ref": "#/components/x-bte-kgs-operations/contraindicatedBy" - } - ] - } - } - }, - "servers": [ - { - "description": "Encrypted Production server", - "url": "https://mychem.info/v1" - }, - { - "description": "Production server", - "url": "http://mychem.info/v1" - } - ], - "tags": [ - { - "name": "chemical" - }, - { - "name": "drug" - }, - { - "name": "annotation" - }, - { - "name": "query" - }, - { - "name": "translator" - }, - { - "name": "biothings" - } - ] - }, - { - "_id": "0c9f1154a1986f1774057af4c1caa5b2", - "_meta": { - "date_created": "2020-12-07T23:01:40.279745+00:00", - "last_updated": "2021-03-05T08:01:28.012456+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/semmed/semmed_anatomy.yaml", - "username": "kevinxin90" - }, - "_score": 0.47008187, - "components": { - "x-bte-kgs-operations": { - "AnatomicalEntity-affected_by-BiologicalProcess": [ + "source": "SEMMED", + "supportBatch": true + } + ], + "Gene-negatively_regulates-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", @@ -34815,10 +34230,10 @@ } ], "parameters": { - "fields": "affected_by" + "fields": "negatively_regulates" }, "path": "/query", - "predicate": "affected_by", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -34826,19 +34241,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-affected_by-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulates-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-affected_by-CellularComponent": [ + "Gene-negatively_regulates-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", @@ -34849,10 +34264,10 @@ } ], "parameters": { - "fields": "affected_by" + "fields": "negatively_regulates" }, "path": "/query", - "predicate": "affected_by", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -34860,19 +34275,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-affected_by-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulates-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-affected_by-ChemicalSubstance": [ + "Gene-negatively_regulates-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", @@ -34883,10 +34298,10 @@ } ], "parameters": { - "fields": "affected_by" + "fields": "negatively_regulates" }, "path": "/query", - "predicate": "affected_by", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -34894,19 +34309,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-affected_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulates-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-affected_by-Disease": [ + "Gene-negatively_regulates-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", @@ -34917,10 +34332,10 @@ } ], "parameters": { - "fields": "affected_by" + "fields": "negatively_regulates" }, "path": "/query", - "predicate": "affected_by", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -34928,19 +34343,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-affected_by-Disease" + "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulates-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-affected_by-Gene": [ + "Gene-negatively_regulates-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", @@ -34951,10 +34366,10 @@ } ], "parameters": { - "fields": "affected_by" + "fields": "negatively_regulates" }, "path": "/query", - "predicate": "affected_by", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -34962,33 +34377,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-affected_by-Gene" + "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulates-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-affects-BiologicalProcess": [ + "Gene-negatively_regulates-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "PhenotypicFeature" } ], "parameters": { - "fields": "affects" + "fields": "negatively_regulates" }, "path": "/query", - "predicate": "affects", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -34996,33 +34411,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-affects-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulates-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-affects-Disease": [ + "Gene-physically_interacts_with-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "parameters": { - "fields": "affects" + "fields": "physically_interacts_with" }, "path": "/query", - "predicate": "affects", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35030,19 +34445,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-affects-Disease" + "$ref": "#/components/x-bte-response-mapping/Gene-physically_interacts_with-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-causes-BiologicalProcess": [ + "Gene-physically_interacts_with-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", @@ -35053,10 +34468,10 @@ } ], "parameters": { - "fields": "causes" + "fields": "physically_interacts_with" }, "path": "/query", - "predicate": "causes", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35064,33 +34479,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-causes-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/Gene-physically_interacts_with-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-causes-Disease": [ + "Gene-physically_interacts_with-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "Cell" } ], "parameters": { - "fields": "causes" + "fields": "physically_interacts_with" }, "path": "/query", - "predicate": "causes", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35098,33 +34513,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-causes-Disease" + "$ref": "#/components/x-bte-response-mapping/Gene-physically_interacts_with-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-disrupted_by-BiologicalProcess": [ + "Gene-physically_interacts_with-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "CellularComponent" } ], "parameters": { - "fields": "disrupted_by" + "fields": "physically_interacts_with" }, "path": "/query", - "predicate": "disrupted_by", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35132,19 +34547,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-disrupted_by-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/Gene-physically_interacts_with-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-disrupted_by-ChemicalSubstance": [ + "Gene-physically_interacts_with-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", @@ -35155,10 +34570,78 @@ } ], "parameters": { - "fields": "disrupted_by" + "fields": "physically_interacts_with" + }, + "path": "/query", + "predicate": "physically_interacts_with", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/Gene-physically_interacts_with-ChemicalSubstance" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "Gene-physically_interacts_with-Disease": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "Gene" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "Disease" + } + ], + "parameters": { + "fields": "physically_interacts_with" + }, + "path": "/query", + "predicate": "physically_interacts_with", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/Gene-physically_interacts_with-Disease" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "Gene-physically_interacts_with-Gene": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "Gene" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "Gene" + } + ], + "parameters": { + "fields": "physically_interacts_with" }, "path": "/query", - "predicate": "disrupted_by", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35166,33 +34649,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-disrupted_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/Gene-physically_interacts_with-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-disrupted_by-Disease": [ + "Gene-physically_interacts_with-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "PhenotypicFeature" } ], "parameters": { - "fields": "disrupted_by" + "fields": "physically_interacts_with" }, "path": "/query", - "predicate": "disrupted_by", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35200,33 +34683,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-disrupted_by-Disease" + "$ref": "#/components/x-bte-response-mapping/Gene-physically_interacts_with-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-disrupted_by-Gene": [ + "Gene-positively_regulated_by-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "AnatomicalEntity" } ], "parameters": { - "fields": "disrupted_by" + "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "disrupted_by", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35234,19 +34717,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-disrupted_by-Gene" + "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulated_by-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-manifestation_of-BiologicalProcess": [ + "Gene-positively_regulated_by-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", @@ -35257,10 +34740,10 @@ } ], "parameters": { - "fields": "manifestation_of" + "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "manifestation_of", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35268,33 +34751,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-manifestation_of-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulated_by-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-manifested_by-Disease": [ + "Gene-positively_regulated_by-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "Cell" } ], "parameters": { - "fields": "manifested_by" + "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "manifested_by", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35302,33 +34785,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-manifested_by-Disease" + "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulated_by-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-negatively_regulated_by-ChemicalSubstance": [ + "Gene-positively_regulated_by-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "CellularComponent" } ], "parameters": { - "fields": "negatively_regulated_by" + "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35336,19 +34819,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-negatively_regulated_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulated_by-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-negatively_regulates-ChemicalSubstance": [ + "Gene-positively_regulated_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", @@ -35359,10 +34842,10 @@ } ], "parameters": { - "fields": "negatively_regulates" + "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35370,33 +34853,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-negatively_regulates-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulated_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-negatively_regulates-Gene": [ + "Gene-positively_regulated_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "Disease" } ], "parameters": { - "fields": "negatively_regulates" + "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35404,33 +34887,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-negatively_regulates-Gene" + "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulated_by-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-physically_interacts_with-ChemicalSubstance": [ + "Gene-positively_regulated_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Gene" } ], "parameters": { - "fields": "physically_interacts_with" + "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "physically_interacts_with", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35438,33 +34921,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-physically_interacts_with-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulated_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-physically_interacts_with-Gene": [ + "Gene-positively_regulated_by-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "parameters": { - "fields": "physically_interacts_with" + "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "physically_interacts_with", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35472,33 +34955,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-physically_interacts_with-Gene" + "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulated_by-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-positively_regulated_by-ChemicalSubstance": [ + "Gene-positively_regulates-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "AnatomicalEntity" } ], "parameters": { - "fields": "positively_regulated_by" + "fields": "positively_regulates" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "entity_positively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35506,33 +34989,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-positively_regulated_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulates-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-positively_regulated_by-Gene": [ + "Gene-positively_regulates-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "positively_regulated_by" + "fields": "positively_regulates" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "entity_positively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35540,33 +35023,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-positively_regulated_by-Gene" + "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulates-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-positively_regulates-ChemicalSubstance": [ + "Gene-positively_regulates-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Cell" } ], "parameters": { "fields": "positively_regulates" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "entity_positively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35574,33 +35057,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-positively_regulates-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulates-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-positively_regulates-Gene": [ + "Gene-positively_regulates-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "CellularComponent" } ], "parameters": { "fields": "positively_regulates" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "entity_positively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35608,33 +35091,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-positively_regulates-Gene" + "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulates-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-preceded_by-BiologicalProcess": [ + "Gene-positively_regulates-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "preceded_by" + "fields": "positively_regulates" }, "path": "/query", - "predicate": "preceded_by", + "predicate": "entity_positively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35642,19 +35125,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-preceded_by-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulates-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-preceded_by-Disease": [ + "Gene-positively_regulates-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", @@ -35665,10 +35148,10 @@ } ], "parameters": { - "fields": "preceded_by" + "fields": "positively_regulates" }, "path": "/query", - "predicate": "preceded_by", + "predicate": "entity_positively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35676,33 +35159,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-preceded_by-Disease" + "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulates-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-precedes-BiologicalProcess": [ + "Gene-positively_regulates-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "Gene" } ], "parameters": { - "fields": "precedes" + "fields": "positively_regulates" }, "path": "/query", - "predicate": "precedes", + "predicate": "entity_positively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35710,33 +35193,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-precedes-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulates-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-precedes-Disease": [ + "Gene-positively_regulates-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "PhenotypicFeature" } ], "parameters": { - "fields": "precedes" + "fields": "positively_regulates" }, "path": "/query", - "predicate": "precedes", + "predicate": "entity_positively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35744,19 +35227,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-precedes-Disease" + "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulates-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-predisposes-Disease": [ + "Gene-prevents-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", @@ -35767,10 +35250,10 @@ } ], "parameters": { - "fields": "predisposes" + "fields": "prevents" }, "path": "/query", - "predicate": "predisposes", + "predicate": "prevents", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35778,33 +35261,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-predisposes-Disease" + "$ref": "#/components/x-bte-response-mapping/Gene-prevents-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-prevents-Disease": [ + "Gene-related_to-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "AnatomicalEntity" } ], "parameters": { - "fields": "prevents" + "fields": "related_to" }, "path": "/query", - "predicate": "prevents", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -35812,26 +35295,26 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-prevents-Disease" + "$ref": "#/components/x-bte-response-mapping/Gene-related_to-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-related_to-AnatomicalEntity": [ + "Gene-related_to-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "BiologicalProcess" } ], "parameters": { @@ -35846,26 +35329,26 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-related_to-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/Gene-related_to-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-related_to-BiologicalProcess": [ + "Gene-related_to-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "Cell" } ], "parameters": { @@ -35880,26 +35363,26 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-related_to-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/Gene-related_to-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-related_to-CellularComponent": [ + "Gene-related_to-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "CellularComponent" + "semantic": "ChemicalSubstance" } ], "parameters": { @@ -35914,26 +35397,26 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-related_to-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/Gene-related_to-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-related_to-ChemicalSubstance": [ + "Gene-related_to-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "parameters": { @@ -35948,26 +35431,26 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-related_to-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/Gene-related_to-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-related_to-Disease": [ + "Gene-related_to-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "Gene" } ], "parameters": { @@ -35982,26 +35465,26 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-related_to-Disease" + "$ref": "#/components/x-bte-response-mapping/Gene-related_to-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-related_to-Gene": [ + "Gene-related_to-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "parameters": { @@ -36016,33 +35499,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-related_to-Gene" + "$ref": "#/components/x-bte-response-mapping/Gene-related_to-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "AnatomicalEntity-related_to-PhenotypicFeature": [ + "Gene-treats-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "Disease" } ], "parameters": { - "fields": "related_to" + "fields": "treats" }, "path": "/query", - "predicate": "related_to", + "predicate": "treats", "requestBody": { "body": { "q": "{inputs[0]}", @@ -36050,7 +35533,7 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/AnatomicalEntity-related_to-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/Gene-treats-Disease" }, "source": "SEMMED", "supportBatch": true @@ -36058,153 +35541,301 @@ ] }, "x-bte-response-mapping": { - "AnatomicalEntity-affected_by-BiologicalProcess": { + "Gene-affected_by-BiologicalProcess": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "AnatomicalEntity-affected_by-CellularComponent": { + "Gene-affected_by-CellularComponent": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "AnatomicalEntity-affected_by-ChemicalSubstance": { + "Gene-affected_by-ChemicalSubstance": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "AnatomicalEntity-affected_by-Disease": { + "Gene-affected_by-Disease": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "AnatomicalEntity-affected_by-Gene": { + "Gene-affected_by-Gene": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "AnatomicalEntity-affects-BiologicalProcess": { + "Gene-affects-AnatomicalEntity": { "pmid": "affects.pmid", "umls": "affects.umls" }, - "AnatomicalEntity-affects-Disease": { + "Gene-affects-BiologicalProcess": { "pmid": "affects.pmid", "umls": "affects.umls" }, - "AnatomicalEntity-causes-BiologicalProcess": { + "Gene-affects-Cell": { + "pmid": "affects.pmid", + "umls": "affects.umls" + }, + "Gene-affects-CellularComponent": { + "pmid": "affects.pmid", + "umls": "affects.umls" + }, + "Gene-affects-ChemicalSubstance": { + "pmid": "affects.pmid", + "umls": "affects.umls" + }, + "Gene-affects-Disease": { + "pmid": "affects.pmid", + "umls": "affects.umls" + }, + "Gene-affects-Gene": { + "pmid": "affects.pmid", + "umls": "affects.umls" + }, + "Gene-affects-PhenotypicFeature": { + "pmid": "affects.pmid", + "umls": "affects.umls" + }, + "Gene-causes-BiologicalProcess": { "pmid": "causes.pmid", "umls": "causes.umls" }, - "AnatomicalEntity-causes-Disease": { + "Gene-causes-Disease": { "pmid": "causes.pmid", "umls": "causes.umls" }, - "AnatomicalEntity-disrupted_by-BiologicalProcess": { + "Gene-disrupted_by-BiologicalProcess": { "pmid": "disrupted_by.pmid", "umls": "disrupted_by.umls" }, - "AnatomicalEntity-disrupted_by-ChemicalSubstance": { + "Gene-disrupted_by-ChemicalSubstance": { "pmid": "disrupted_by.pmid", "umls": "disrupted_by.umls" }, - "AnatomicalEntity-disrupted_by-Disease": { + "Gene-disrupted_by-Disease": { "pmid": "disrupted_by.pmid", "umls": "disrupted_by.umls" }, - "AnatomicalEntity-disrupted_by-Gene": { + "Gene-disrupted_by-Gene": { "pmid": "disrupted_by.pmid", "umls": "disrupted_by.umls" }, - "AnatomicalEntity-manifestation_of-BiologicalProcess": { - "pmid": "manifestation_of.pmid", - "umls": "manifestation_of.umls" + "Gene-disrupts-AnatomicalEntity": { + "pmid": "disrupts.pmid", + "umls": "disrupts.umls" }, - "AnatomicalEntity-manifested_by-Disease": { - "pmid": "manifested_by.pmid", - "umls": "manifested_by.umls" + "Gene-disrupts-BiologicalProcess": { + "pmid": "disrupts.pmid", + "umls": "disrupts.umls" }, - "AnatomicalEntity-negatively_regulated_by-ChemicalSubstance": { + "Gene-disrupts-Cell": { + "pmid": "disrupts.pmid", + "umls": "disrupts.umls" + }, + "Gene-disrupts-CellularComponent": { + "pmid": "disrupts.pmid", + "umls": "disrupts.umls" + }, + "Gene-disrupts-ChemicalSubstance": { + "pmid": "disrupts.pmid", + "umls": "disrupts.umls" + }, + "Gene-disrupts-Disease": { + "pmid": "disrupts.pmid", + "umls": "disrupts.umls" + }, + "Gene-disrupts-Gene": { + "pmid": "disrupts.pmid", + "umls": "disrupts.umls" + }, + "Gene-disrupts-PhenotypicFeature": { + "pmid": "disrupts.pmid", + "umls": "disrupts.umls" + }, + "Gene-negatively_regulated_by-AnatomicalEntity": { "pmid": "negatively_regulated_by.pmid", "umls": "negatively_regulated_by.umls" }, - "AnatomicalEntity-negatively_regulates-ChemicalSubstance": { + "Gene-negatively_regulated_by-BiologicalProcess": { + "pmid": "negatively_regulated_by.pmid", + "umls": "negatively_regulated_by.umls" + }, + "Gene-negatively_regulated_by-Cell": { + "pmid": "negatively_regulated_by.pmid", + "umls": "negatively_regulated_by.umls" + }, + "Gene-negatively_regulated_by-CellularComponent": { + "pmid": "negatively_regulated_by.pmid", + "umls": "negatively_regulated_by.umls" + }, + "Gene-negatively_regulated_by-ChemicalSubstance": { + "pmid": "negatively_regulated_by.pmid", + "umls": "negatively_regulated_by.umls" + }, + "Gene-negatively_regulated_by-Disease": { + "pmid": "negatively_regulated_by.pmid", + "umls": "negatively_regulated_by.umls" + }, + "Gene-negatively_regulated_by-Gene": { + "pmid": "negatively_regulated_by.pmid", + "umls": "negatively_regulated_by.umls" + }, + "Gene-negatively_regulated_by-PhenotypicFeature": { + "pmid": "negatively_regulated_by.pmid", + "umls": "negatively_regulated_by.umls" + }, + "Gene-negatively_regulates-BiologicalProcess": { "pmid": "negatively_regulates.pmid", "umls": "negatively_regulates.umls" }, - "AnatomicalEntity-negatively_regulates-Gene": { + "Gene-negatively_regulates-CellularComponent": { "pmid": "negatively_regulates.pmid", "umls": "negatively_regulates.umls" }, - "AnatomicalEntity-physically_interacts_with-ChemicalSubstance": { + "Gene-negatively_regulates-ChemicalSubstance": { + "pmid": "negatively_regulates.pmid", + "umls": "negatively_regulates.umls" + }, + "Gene-negatively_regulates-Disease": { + "pmid": "negatively_regulates.pmid", + "umls": "negatively_regulates.umls" + }, + "Gene-negatively_regulates-Gene": { + "pmid": "negatively_regulates.pmid", + "umls": "negatively_regulates.umls" + }, + "Gene-negatively_regulates-PhenotypicFeature": { + "pmid": "negatively_regulates.pmid", + "umls": "negatively_regulates.umls" + }, + "Gene-physically_interacts_with-AnatomicalEntity": { "pmid": "physically_interacts_with.pmid", "umls": "physically_interacts_with.umls" }, - "AnatomicalEntity-physically_interacts_with-Gene": { + "Gene-physically_interacts_with-BiologicalProcess": { "pmid": "physically_interacts_with.pmid", "umls": "physically_interacts_with.umls" }, - "AnatomicalEntity-positively_regulated_by-ChemicalSubstance": { + "Gene-physically_interacts_with-Cell": { + "pmid": "physically_interacts_with.pmid", + "umls": "physically_interacts_with.umls" + }, + "Gene-physically_interacts_with-CellularComponent": { + "pmid": "physically_interacts_with.pmid", + "umls": "physically_interacts_with.umls" + }, + "Gene-physically_interacts_with-ChemicalSubstance": { + "pmid": "physically_interacts_with.pmid", + "umls": "physically_interacts_with.umls" + }, + "Gene-physically_interacts_with-Disease": { + "pmid": "physically_interacts_with.pmid", + "umls": "physically_interacts_with.umls" + }, + "Gene-physically_interacts_with-Gene": { + "pmid": "physically_interacts_with.pmid", + "umls": "physically_interacts_with.umls" + }, + "Gene-physically_interacts_with-PhenotypicFeature": { + "pmid": "physically_interacts_with.pmid", + "umls": "physically_interacts_with.umls" + }, + "Gene-positively_regulated_by-AnatomicalEntity": { "pmid": "positively_regulated_by.pmid", "umls": "positively_regulated_by.umls" }, - "AnatomicalEntity-positively_regulated_by-Gene": { + "Gene-positively_regulated_by-BiologicalProcess": { "pmid": "positively_regulated_by.pmid", "umls": "positively_regulated_by.umls" }, - "AnatomicalEntity-positively_regulates-ChemicalSubstance": { + "Gene-positively_regulated_by-Cell": { + "pmid": "positively_regulated_by.pmid", + "umls": "positively_regulated_by.umls" + }, + "Gene-positively_regulated_by-CellularComponent": { + "pmid": "positively_regulated_by.pmid", + "umls": "positively_regulated_by.umls" + }, + "Gene-positively_regulated_by-ChemicalSubstance": { + "pmid": "positively_regulated_by.pmid", + "umls": "positively_regulated_by.umls" + }, + "Gene-positively_regulated_by-Disease": { + "pmid": "positively_regulated_by.pmid", + "umls": "positively_regulated_by.umls" + }, + "Gene-positively_regulated_by-Gene": { + "pmid": "positively_regulated_by.pmid", + "umls": "positively_regulated_by.umls" + }, + "Gene-positively_regulated_by-PhenotypicFeature": { + "pmid": "positively_regulated_by.pmid", + "umls": "positively_regulated_by.umls" + }, + "Gene-positively_regulates-AnatomicalEntity": { "pmid": "positively_regulates.pmid", "umls": "positively_regulates.umls" }, - "AnatomicalEntity-positively_regulates-Gene": { + "Gene-positively_regulates-BiologicalProcess": { "pmid": "positively_regulates.pmid", "umls": "positively_regulates.umls" }, - "AnatomicalEntity-preceded_by-BiologicalProcess": { - "pmid": "preceded_by.pmid", - "umls": "preceded_by.umls" + "Gene-positively_regulates-Cell": { + "pmid": "positively_regulates.pmid", + "umls": "positively_regulates.umls" }, - "AnatomicalEntity-preceded_by-Disease": { - "pmid": "preceded_by.pmid", - "umls": "preceded_by.umls" + "Gene-positively_regulates-CellularComponent": { + "pmid": "positively_regulates.pmid", + "umls": "positively_regulates.umls" }, - "AnatomicalEntity-precedes-BiologicalProcess": { - "pmid": "precedes.pmid", - "umls": "precedes.umls" + "Gene-positively_regulates-ChemicalSubstance": { + "pmid": "positively_regulates.pmid", + "umls": "positively_regulates.umls" }, - "AnatomicalEntity-precedes-Disease": { - "pmid": "precedes.pmid", - "umls": "precedes.umls" + "Gene-positively_regulates-Disease": { + "pmid": "positively_regulates.pmid", + "umls": "positively_regulates.umls" }, - "AnatomicalEntity-predisposes-Disease": { - "pmid": "predisposes.pmid", - "umls": "predisposes.umls" + "Gene-positively_regulates-Gene": { + "pmid": "positively_regulates.pmid", + "umls": "positively_regulates.umls" }, - "AnatomicalEntity-prevents-Disease": { + "Gene-positively_regulates-PhenotypicFeature": { + "pmid": "positively_regulates.pmid", + "umls": "positively_regulates.umls" + }, + "Gene-prevents-Disease": { "pmid": "prevents.pmid", "umls": "prevents.umls" }, - "AnatomicalEntity-related_to-AnatomicalEntity": { + "Gene-related_to-AnatomicalEntity": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "AnatomicalEntity-related_to-BiologicalProcess": { + "Gene-related_to-BiologicalProcess": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "AnatomicalEntity-related_to-CellularComponent": { + "Gene-related_to-Cell": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "AnatomicalEntity-related_to-ChemicalSubstance": { + "Gene-related_to-ChemicalSubstance": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "AnatomicalEntity-related_to-Disease": { + "Gene-related_to-Disease": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "AnatomicalEntity-related_to-Gene": { + "Gene-related_to-Gene": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "AnatomicalEntity-related_to-PhenotypicFeature": { + "Gene-related_to-PhenotypicFeature": { "pmid": "related_to.pmid", "umls": "related_to.umls" + }, + "Gene-treats-Disease": { + "pmid": "treats.pmid", + "umls": "treats.umls" } } }, @@ -36217,7 +35848,7 @@ }, "description": "Documentation of the SEMMED disease query web services. Learn more about [mydisease.info](http://pending.biothings.io/semmed)", "termsOfService": "http://biothings.ncats.io", - "title": "SEMMED Anatomy API", + "title": "SEMMED Gene API", "version": "1.0", "x-translator": { "component": "KP", @@ -36227,7 +35858,7 @@ } }, "paths": { - "/anatomy": { + "/gene": { "post": { "parameters": [ { @@ -36295,14 +35926,14 @@ ] } }, - "/anatomy/{anatomyid}": { + "/gene/{geneid}": { "get": { "parameters": [ { "description": "Retrieve disease objects based on ID", "example": "C0004096", "in": "path", - "name": "anatomyid", + "name": "geneid", "required": true, "schema": { "type": "string" @@ -36532,7 +36163,10 @@ } } }, - "description": "Query response objects with the \"hits\" property" + "description": "Query response objects with the \"hits\" property", + "x-bte-response-mapping": { + "$ref": "#/components/x-bte-response-mapping/query-post" + } }, "400": { "content": { @@ -36551,115 +36185,226 @@ ], "x-bte-kgs-operations": [ { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-affected_by-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/Gene-affected_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-affected_by-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/Gene-affected_by-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-affected_by-Disease" + "$ref": "#/components/x-bte-kgs-operations/Gene-affected_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-affected_by-Gene" + "$ref": "#/components/x-bte-kgs-operations/Gene-affected_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-affected_by-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/Gene-affected_by-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-affects-Disease" + "$ref": "#/components/x-bte-kgs-operations/Gene-affects-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-affects-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/Gene-affects-Cell" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-causes-Disease" + "$ref": "#/components/x-bte-kgs-operations/Gene-affects-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-causes-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/Gene-affects-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-disrupted_by-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/Gene-affects-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-disrupted_by-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/Gene-affects-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-disrupted_by-Disease" + "$ref": "#/components/x-bte-kgs-operations/Gene-affects-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-disrupted_by-Gene" + "$ref": "#/components/x-bte-kgs-operations/Gene-affects-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-manifestation_of-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/Gene-causes-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-manifested_by-Disease" + "$ref": "#/components/x-bte-kgs-operations/Gene-causes-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-negatively_regulated_by-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/Gene-disrupted_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-negatively_regulates-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/Gene-disrupted_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-negatively_regulates-Gene" + "$ref": "#/components/x-bte-kgs-operations/Gene-disrupted_by-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-physically_interacts_with-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/Gene-disrupted_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-physically_interacts_with-Gene" + "$ref": "#/components/x-bte-kgs-operations/Gene-disrupts-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-positively_regulated_by-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/Gene-disrupts-Cell" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-positively_regulated_by-Gene" + "$ref": "#/components/x-bte-kgs-operations/Gene-disrupts-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-positively_regulates-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/Gene-disrupts-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-positively_regulates-Gene" + "$ref": "#/components/x-bte-kgs-operations/Gene-disrupts-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-preceded_by-Disease" + "$ref": "#/components/x-bte-kgs-operations/Gene-disrupts-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-preceded_by-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/Gene-disrupts-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-precedes-Disease" + "$ref": "#/components/x-bte-kgs-operations/Gene-disrupts-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-precedes-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulated_by-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-predisposes-Disease" + "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulated_by-Cell" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-prevents-Disease" + "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulated_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-related_to-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulated_by-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-related_to-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulated_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-related_to-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulated_by-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-related_to-Disease" + "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulated_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-related_to-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulated_by-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-related_to-Gene" + "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulates-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-related_to-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulates-BiologicalProcess" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulates-Disease" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulates-PhenotypicFeature" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulates-Gene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulates-CellularComponent" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-physically_interacts_with-AnatomicalEntity" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-physically_interacts_with-Cell" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-physically_interacts_with-ChemicalSubstance" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-physically_interacts_with-BiologicalProcess" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-physically_interacts_with-Disease" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-physically_interacts_with-PhenotypicFeature" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-physically_interacts_with-Gene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-physically_interacts_with-CellularComponent" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulated_by-AnatomicalEntity" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulated_by-Cell" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulated_by-ChemicalSubstance" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulated_by-BiologicalProcess" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulated_by-Disease" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulated_by-PhenotypicFeature" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulated_by-Gene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulated_by-CellularComponent" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulates-AnatomicalEntity" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulates-Cell" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulates-ChemicalSubstance" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulates-BiologicalProcess" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulates-Disease" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulates-PhenotypicFeature" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulates-Gene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulates-CellularComponent" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-prevents-Disease" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-related_to-AnatomicalEntity" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-related_to-Cell" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-related_to-ChemicalSubstance" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-related_to-BiologicalProcess" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-related_to-Disease" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-related_to-PhenotypicFeature" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-related_to-Gene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Gene-treats-Disease" } ] } @@ -36668,12 +36413,12 @@ "servers": [ { "description": "Production server", - "url": "https://biothings.ncats.io/semmed_anatomy" + "url": "https://biothings.ncats.io/semmedgene" } ], "tags": [ { - "name": "anatomicalentity" + "name": "disease" }, { "name": "annotation" @@ -36693,23 +36438,23 @@ ] }, { - "_id": "81955d376a10505c1c69cd06dbda3047", + "_id": "2dffb89df7f970b6a07e816e255d33ec", "_meta": { - "date_created": "2020-12-07T23:01:45.135044+00:00", - "last_updated": "2021-03-05T08:01:19.453211+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/semmed/semmed_gene.yaml", + "date_created": "2020-12-07T22:59:15.759070+00:00", + "last_updated": "2021-03-29T07:03:52.883430+00:00", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/semmed/semmed_phenotype.yaml", "username": "kevinxin90" }, - "_score": 0.47008187, + "_score": 0.4848808, "components": { "x-bte-kgs-operations": { - "Gene-affected_by-BiologicalProcess": [ + "PhenotypicFeature-affected_by-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -36731,53 +36476,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-affected_by-BiologicalProcess" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Gene-affected_by-CellularComponent": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Gene" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "CellularComponent" - } - ], - "parameters": { - "fields": "affected_by" - }, - "path": "/query", - "predicate": "affected_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-affected_by-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-affected_by-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-affected_by-ChemicalSubstance": [ + "PhenotypicFeature-affected_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -36799,19 +36510,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-affected_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-affected_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-affected_by-Disease": [ + "PhenotypicFeature-affected_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -36833,19 +36544,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-affected_by-Disease" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-affected_by-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-affected_by-Gene": [ + "PhenotypicFeature-affected_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -36867,53 +36578,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-affected_by-Gene" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Gene-affects-AnatomicalEntity": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Gene" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "AnatomicalEntity" - } - ], - "parameters": { - "fields": "affects" - }, - "path": "/query", - "predicate": "affects", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-affects-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-affected_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-affects-BiologicalProcess": [ + "PhenotypicFeature-affects-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -36935,19 +36612,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-affects-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-affects-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-affects-Cell": [ + "PhenotypicFeature-affects-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -36969,19 +36646,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-affects-Cell" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-affects-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-affects-CellularComponent": [ + "PhenotypicFeature-affects-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -37003,53 +36680,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-affects-CellularComponent" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Gene-affects-ChemicalSubstance": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Gene" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "ChemicalSubstance" - } - ], - "parameters": { - "fields": "affects" - }, - "path": "/query", - "predicate": "affects", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-affects-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-affects-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-affects-Disease": [ + "PhenotypicFeature-affects-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -37071,89 +36714,21 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-affects-Disease" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Gene-affects-Gene": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Gene" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Gene" - } - ], - "parameters": { - "fields": "affects" - }, - "path": "/query", - "predicate": "affects", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-affects-Gene" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-affects-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-affects-PhenotypicFeature": [ + "PhenotypicFeature-causes-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ - { - "id": "UMLS", - "semantic": "Gene" - } - ], - "method": "post", - "outputs": [ { "id": "UMLS", "semantic": "PhenotypicFeature" } ], - "parameters": { - "fields": "affects" - }, - "path": "/query", - "predicate": "affects", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-affects-PhenotypicFeature" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Gene-causes-BiologicalProcess": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Gene" - } - ], "method": "post", "outputs": [ { @@ -37173,19 +36748,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-causes-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-causes-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-causes-Disease": [ + "PhenotypicFeature-causes-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -37207,53 +36782,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-causes-Disease" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "Gene-disrupted_by-BiologicalProcess": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "Gene" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "BiologicalProcess" - } - ], - "parameters": { - "fields": "disrupted_by" - }, - "path": "/query", - "predicate": "disrupted_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-disrupted_by-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-causes-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-disrupted_by-ChemicalSubstance": [ + "PhenotypicFeature-disrupted_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -37275,19 +36816,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-disrupted_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-disrupted_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-disrupted_by-Disease": [ + "PhenotypicFeature-disrupted_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -37309,19 +36850,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-disrupted_by-Disease" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-disrupted_by-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-disrupted_by-Gene": [ + "PhenotypicFeature-disrupted_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -37343,26 +36884,26 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-disrupted_by-Gene" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-disrupted_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-disrupts-AnatomicalEntity": [ + "PhenotypicFeature-disrupts-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "BiologicalProcess" } ], "parameters": { @@ -37377,26 +36918,26 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-disrupts-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-disrupts-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-disrupts-BiologicalProcess": [ + "PhenotypicFeature-disrupts-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "Cell" } ], "parameters": { @@ -37411,26 +36952,26 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-disrupts-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-disrupts-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-disrupts-Cell": [ + "PhenotypicFeature-disrupts-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Cell" + "semantic": "CellularComponent" } ], "parameters": { @@ -37445,26 +36986,26 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-disrupts-Cell" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-disrupts-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-disrupts-CellularComponent": [ + "PhenotypicFeature-disrupts-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "CellularComponent" + "semantic": "Disease" } ], "parameters": { @@ -37479,19 +37020,53 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-disrupts-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-disrupts-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-disrupts-ChemicalSubstance": [ + "PhenotypicFeature-has_part-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "CellularComponent" + } + ], + "parameters": { + "fields": "has_part" + }, + "path": "/query", + "predicate": "has_part", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-has_part-CellularComponent" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "PhenotypicFeature-has_part-ChemicalSubstance": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -37502,10 +37077,10 @@ } ], "parameters": { - "fields": "disrupts" + "fields": "has_part" }, "path": "/query", - "predicate": "disrupts", + "predicate": "has_part", "requestBody": { "body": { "q": "{inputs[0]}", @@ -37513,19 +37088,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-disrupts-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-has_part-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-disrupts-Disease": [ + "PhenotypicFeature-has_part-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -37536,10 +37111,10 @@ } ], "parameters": { - "fields": "disrupts" + "fields": "has_part" }, "path": "/query", - "predicate": "disrupts", + "predicate": "has_part", "requestBody": { "body": { "q": "{inputs[0]}", @@ -37547,19 +37122,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-disrupts-Disease" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-has_part-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-disrupts-Gene": [ + "PhenotypicFeature-has_part-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -37570,10 +37145,10 @@ } ], "parameters": { - "fields": "disrupts" + "fields": "has_part" }, "path": "/query", - "predicate": "disrupts", + "predicate": "has_part", "requestBody": { "body": { "q": "{inputs[0]}", @@ -37581,33 +37156,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-disrupts-Gene" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-has_part-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-disrupts-PhenotypicFeature": [ + "PhenotypicFeature-has_subclass-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "Disease" } ], "parameters": { - "fields": "disrupts" + "fields": "has_subclass" }, "path": "/query", - "predicate": "disrupts", + "predicate": "has_subclass", "requestBody": { "body": { "q": "{inputs[0]}", @@ -37615,33 +37190,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-disrupts-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-has_subclass-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-negatively_regulated_by-AnatomicalEntity": [ + "PhenotypicFeature-has_subclass-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "PhenotypicFeature" } ], "parameters": { - "fields": "negatively_regulated_by" + "fields": "has_subclass" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "has_subclass", "requestBody": { "body": { "q": "{inputs[0]}", @@ -37649,33 +37224,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulated_by-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-has_subclass-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-negatively_regulated_by-BiologicalProcess": [ + "PhenotypicFeature-located_in-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "AnatomicalEntity" } ], "parameters": { - "fields": "negatively_regulated_by" + "fields": "located_in" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "located_in", "requestBody": { "body": { "q": "{inputs[0]}", @@ -37683,19 +37258,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulated_by-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-located_in-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-negatively_regulated_by-Cell": [ + "PhenotypicFeature-located_in-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -37706,10 +37281,10 @@ } ], "parameters": { - "fields": "negatively_regulated_by" + "fields": "located_in" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "located_in", "requestBody": { "body": { "q": "{inputs[0]}", @@ -37717,19 +37292,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulated_by-Cell" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-located_in-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-negatively_regulated_by-CellularComponent": [ + "PhenotypicFeature-located_in-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -37740,10 +37315,10 @@ } ], "parameters": { - "fields": "negatively_regulated_by" + "fields": "located_in" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "located_in", "requestBody": { "body": { "q": "{inputs[0]}", @@ -37751,33 +37326,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulated_by-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-located_in-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-negatively_regulated_by-ChemicalSubstance": [ + "PhenotypicFeature-manifestation_of-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "negatively_regulated_by" + "fields": "manifestation_of" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "manifestation_of", "requestBody": { "body": { "q": "{inputs[0]}", @@ -37785,19 +37360,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulated_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-manifestation_of-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-negatively_regulated_by-Disease": [ + "PhenotypicFeature-manifestation_of-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -37808,10 +37383,10 @@ } ], "parameters": { - "fields": "negatively_regulated_by" + "fields": "manifestation_of" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "manifestation_of", "requestBody": { "body": { "q": "{inputs[0]}", @@ -37819,19 +37394,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulated_by-Disease" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-manifestation_of-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-negatively_regulated_by-Gene": [ + "PhenotypicFeature-manifestation_of-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -37842,10 +37417,10 @@ } ], "parameters": { - "fields": "negatively_regulated_by" + "fields": "manifestation_of" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "manifestation_of", "requestBody": { "body": { "q": "{inputs[0]}", @@ -37853,33 +37428,67 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulated_by-Gene" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-manifestation_of-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-negatively_regulated_by-PhenotypicFeature": [ + "PhenotypicFeature-manifested_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ + { + "id": "UMLS", + "semantic": "Disease" + } + ], + "parameters": { + "fields": "manifested_by" + }, + "path": "/query", + "predicate": "manifested_by", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-manifested_by-Disease" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "PhenotypicFeature-negatively_regulated_by-ChemicalSubstance": [ + { + "inputSeparator": ",", + "inputs": [ { "id": "UMLS", "semantic": "PhenotypicFeature" } ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], "parameters": { "fields": "negatively_regulated_by" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -37887,33 +37496,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulated_by-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-negatively_regulated_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-negatively_regulates-BiologicalProcess": [ + "PhenotypicFeature-negatively_regulated_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "Gene" } ], "parameters": { - "fields": "negatively_regulates" + "fields": "negatively_regulated_by" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -37921,33 +37530,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulates-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-negatively_regulated_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-negatively_regulates-CellularComponent": [ + "PhenotypicFeature-negatively_regulates-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "CellularComponent" + "semantic": "BiologicalProcess" } ], "parameters": { "fields": "negatively_regulates" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -37955,19 +37564,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulates-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-negatively_regulates-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-negatively_regulates-ChemicalSubstance": [ + "PhenotypicFeature-negatively_regulates-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -37981,7 +37590,7 @@ "fields": "negatively_regulates" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -37989,19 +37598,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulates-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-negatively_regulates-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-negatively_regulates-Disease": [ + "PhenotypicFeature-negatively_regulates-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -38015,7 +37624,7 @@ "fields": "negatively_regulates" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38023,19 +37632,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulates-Disease" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-negatively_regulates-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-negatively_regulates-Gene": [ + "PhenotypicFeature-negatively_regulates-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -38049,7 +37658,7 @@ "fields": "negatively_regulates" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38057,33 +37666,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulates-Gene" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-negatively_regulates-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-negatively_regulates-PhenotypicFeature": [ + "PhenotypicFeature-part_of-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "AnatomicalEntity" } ], "parameters": { - "fields": "negatively_regulates" + "fields": "part_of" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "part_of", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38091,33 +37700,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-negatively_regulates-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-part_of-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-physically_interacts_with-AnatomicalEntity": [ + "PhenotypicFeature-part_of-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Cell" } ], "parameters": { - "fields": "physically_interacts_with" + "fields": "part_of" }, "path": "/query", - "predicate": "physically_interacts_with", + "predicate": "part_of", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38125,33 +37734,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-physically_interacts_with-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-part_of-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-physically_interacts_with-BiologicalProcess": [ + "PhenotypicFeature-part_of-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "CellularComponent" } ], "parameters": { - "fields": "physically_interacts_with" + "fields": "part_of" }, "path": "/query", - "predicate": "physically_interacts_with", + "predicate": "part_of", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38159,33 +37768,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-physically_interacts_with-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-part_of-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-physically_interacts_with-Cell": [ + "PhenotypicFeature-part_of-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Cell" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "physically_interacts_with" + "fields": "part_of" }, "path": "/query", - "predicate": "physically_interacts_with", + "predicate": "part_of", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38193,33 +37802,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-physically_interacts_with-Cell" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-part_of-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-physically_interacts_with-CellularComponent": [ + "PhenotypicFeature-part_of-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "CellularComponent" + "semantic": "Disease" } ], "parameters": { - "fields": "physically_interacts_with" + "fields": "part_of" }, "path": "/query", - "predicate": "physically_interacts_with", + "predicate": "part_of", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38227,19 +37836,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-physically_interacts_with-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-part_of-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-physically_interacts_with-ChemicalSubstance": [ + "PhenotypicFeature-physically_interacts_with-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -38261,19 +37870,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-physically_interacts_with-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-physically_interacts_with-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-physically_interacts_with-Disease": [ + "PhenotypicFeature-physically_interacts_with-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -38295,19 +37904,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-physically_interacts_with-Disease" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-physically_interacts_with-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-physically_interacts_with-Gene": [ + "PhenotypicFeature-physically_interacts_with-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -38329,33 +37938,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-physically_interacts_with-Gene" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-physically_interacts_with-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-physically_interacts_with-PhenotypicFeature": [ + "PhenotypicFeature-positively_regulated_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "physically_interacts_with" + "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "physically_interacts_with", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38363,33 +37972,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-physically_interacts_with-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-positively_regulated_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-positively_regulated_by-AnatomicalEntity": [ + "PhenotypicFeature-positively_regulated_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "parameters": { "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38397,33 +38006,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulated_by-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-positively_regulated_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-positively_regulated_by-BiologicalProcess": [ + "PhenotypicFeature-positively_regulates-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "positively_regulated_by" + "fields": "positively_regulates" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "entity_positively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38431,33 +38040,67 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulated_by-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-positively_regulates-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-positively_regulated_by-Cell": [ + "PhenotypicFeature-positively_regulates-Gene": [ { "inputSeparator": ",", "inputs": [ + { + "id": "UMLS", + "semantic": "PhenotypicFeature" + } + ], + "method": "post", + "outputs": [ { "id": "UMLS", "semantic": "Gene" } ], + "parameters": { + "fields": "positively_regulates" + }, + "path": "/query", + "predicate": "entity_positively_regulates_entity", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-positively_regulates-Gene" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "PhenotypicFeature-preceded_by-BiologicalProcess": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "PhenotypicFeature" + } + ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Cell" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "positively_regulated_by" + "fields": "preceded_by" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "preceded_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38465,33 +38108,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulated_by-Cell" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-preceded_by-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-positively_regulated_by-CellularComponent": [ + "PhenotypicFeature-preceded_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "CellularComponent" + "semantic": "Disease" } ], "parameters": { - "fields": "positively_regulated_by" + "fields": "preceded_by" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "preceded_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38499,33 +38142,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulated_by-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-preceded_by-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-positively_regulated_by-ChemicalSubstance": [ + "PhenotypicFeature-precedes-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "positively_regulated_by" + "fields": "precedes" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "precedes", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38533,19 +38176,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulated_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-precedes-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-positively_regulated_by-Disease": [ + "PhenotypicFeature-predisposes-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -38556,10 +38199,10 @@ } ], "parameters": { - "fields": "positively_regulated_by" + "fields": "predisposes" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "predisposes", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38567,33 +38210,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulated_by-Disease" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-predisposes-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-positively_regulated_by-Gene": [ + "PhenotypicFeature-prevents-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "Disease" } ], "parameters": { - "fields": "positively_regulated_by" + "fields": "prevents" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "prevents", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38601,33 +38244,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulated_by-Gene" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-prevents-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-positively_regulated_by-PhenotypicFeature": [ + "PhenotypicFeature-produced_by-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "positively_regulated_by" + "fields": "produced_by" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "produced_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38635,33 +38278,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulated_by-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-produced_by-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-positively_regulates-AnatomicalEntity": [ + "PhenotypicFeature-produced_by-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Cell" } ], "parameters": { - "fields": "positively_regulates" + "fields": "produced_by" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "produced_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38669,33 +38312,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulates-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-produced_by-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-positively_regulates-BiologicalProcess": [ + "PhenotypicFeature-produced_by-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "CellularComponent" } ], "parameters": { - "fields": "positively_regulates" + "fields": "produced_by" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "produced_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38703,33 +38346,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulates-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-produced_by-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-positively_regulates-Cell": [ + "PhenotypicFeature-produced_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Cell" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "positively_regulates" + "fields": "produced_by" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "produced_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38737,33 +38380,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulates-Cell" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-produced_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-positively_regulates-CellularComponent": [ + "PhenotypicFeature-produced_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "CellularComponent" + "semantic": "Disease" } ], "parameters": { - "fields": "positively_regulates" + "fields": "produced_by" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "produced_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38771,33 +38414,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulates-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-produced_by-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-positively_regulates-ChemicalSubstance": [ + "PhenotypicFeature-produced_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Gene" } ], "parameters": { - "fields": "positively_regulates" + "fields": "produced_by" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "produced_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38805,33 +38448,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulates-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-produced_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-positively_regulates-Disease": [ + "PhenotypicFeature-produces-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "positively_regulates" + "fields": "produces" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "produces", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38839,19 +38482,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulates-Disease" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-produces-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-positively_regulates-Gene": [ + "PhenotypicFeature-produces-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -38862,10 +38505,10 @@ } ], "parameters": { - "fields": "positively_regulates" + "fields": "produces" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "produces", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38873,33 +38516,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulates-Gene" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-produces-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-positively_regulates-PhenotypicFeature": [ + "PhenotypicFeature-related_to-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "AnatomicalEntity" } ], "parameters": { - "fields": "positively_regulates" + "fields": "related_to" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38907,33 +38550,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-positively_regulates-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-related_to-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-prevents-Disease": [ + "PhenotypicFeature-related_to-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "prevents" + "fields": "related_to" }, "path": "/query", - "predicate": "prevents", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -38941,26 +38584,26 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-prevents-Disease" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-related_to-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-related_to-AnatomicalEntity": [ + "PhenotypicFeature-related_to-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "ChemicalSubstance" } ], "parameters": { @@ -38975,26 +38618,26 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-related_to-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-related_to-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-related_to-BiologicalProcess": [ + "PhenotypicFeature-related_to-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "Disease" } ], "parameters": { @@ -39009,26 +38652,26 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-related_to-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-related_to-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-related_to-Cell": [ + "PhenotypicFeature-related_to-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Cell" + "semantic": "Gene" } ], "parameters": { @@ -39043,19 +38686,87 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-related_to-Cell" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-related_to-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-related_to-ChemicalSubstance": [ + "PhenotypicFeature-subclass_of-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "AnatomicalEntity" + } + ], + "parameters": { + "fields": "subclass_of" + }, + "path": "/query", + "predicate": "subclass_of", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-subclass_of-AnatomicalEntity" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "PhenotypicFeature-subclass_of-BiologicalProcess": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "PhenotypicFeature" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "BiologicalProcess" + } + ], + "parameters": { + "fields": "subclass_of" + }, + "path": "/query", + "predicate": "subclass_of", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-subclass_of-BiologicalProcess" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "PhenotypicFeature-subclass_of-ChemicalSubstance": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -39066,10 +38777,10 @@ } ], "parameters": { - "fields": "related_to" + "fields": "subclass_of" }, "path": "/query", - "predicate": "related_to", + "predicate": "subclass_of", "requestBody": { "body": { "q": "{inputs[0]}", @@ -39077,19 +38788,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-related_to-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-subclass_of-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-related_to-Disease": [ + "PhenotypicFeature-subclass_of-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -39100,10 +38811,10 @@ } ], "parameters": { - "fields": "related_to" + "fields": "subclass_of" }, "path": "/query", - "predicate": "related_to", + "predicate": "subclass_of", "requestBody": { "body": { "q": "{inputs[0]}", @@ -39111,19 +38822,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-related_to-Disease" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-subclass_of-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-related_to-Gene": [ + "PhenotypicFeature-subclass_of-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -39134,10 +38845,10 @@ } ], "parameters": { - "fields": "related_to" + "fields": "subclass_of" }, "path": "/query", - "predicate": "related_to", + "predicate": "subclass_of", "requestBody": { "body": { "q": "{inputs[0]}", @@ -39145,19 +38856,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-related_to-Gene" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-subclass_of-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-related_to-PhenotypicFeature": [ + "PhenotypicFeature-subclass_of-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -39168,10 +38879,10 @@ } ], "parameters": { - "fields": "related_to" + "fields": "subclass_of" }, "path": "/query", - "predicate": "related_to", + "predicate": "subclass_of", "requestBody": { "body": { "q": "{inputs[0]}", @@ -39179,19 +38890,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-related_to-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-subclass_of-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "Gene-treats-Disease": [ + "PhenotypicFeature-treats-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "PhenotypicFeature" } ], "method": "post", @@ -39213,7 +38924,7 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/Gene-treats-Disease" + "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-treats-Disease" }, "source": "SEMMED", "supportBatch": true @@ -39221,299 +38932,295 @@ ] }, "x-bte-response-mapping": { - "Gene-affected_by-BiologicalProcess": { - "pmid": "affected_by.pmid", - "umls": "affected_by.umls" - }, - "Gene-affected_by-CellularComponent": { + "PhenotypicFeature-affected_by-BiologicalProcess": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "Gene-affected_by-ChemicalSubstance": { + "PhenotypicFeature-affected_by-ChemicalSubstance": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "Gene-affected_by-Disease": { + "PhenotypicFeature-affected_by-Disease": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "Gene-affected_by-Gene": { + "PhenotypicFeature-affected_by-Gene": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "Gene-affects-AnatomicalEntity": { - "pmid": "affects.pmid", - "umls": "affects.umls" - }, - "Gene-affects-BiologicalProcess": { - "pmid": "affects.pmid", - "umls": "affects.umls" - }, - "Gene-affects-Cell": { - "pmid": "affects.pmid", - "umls": "affects.umls" - }, - "Gene-affects-CellularComponent": { - "pmid": "affects.pmid", - "umls": "affects.umls" - }, - "Gene-affects-ChemicalSubstance": { + "PhenotypicFeature-affects-BiologicalProcess": { "pmid": "affects.pmid", "umls": "affects.umls" }, - "Gene-affects-Disease": { + "PhenotypicFeature-affects-Cell": { "pmid": "affects.pmid", "umls": "affects.umls" }, - "Gene-affects-Gene": { + "PhenotypicFeature-affects-CellularComponent": { "pmid": "affects.pmid", "umls": "affects.umls" }, - "Gene-affects-PhenotypicFeature": { + "PhenotypicFeature-affects-Disease": { "pmid": "affects.pmid", "umls": "affects.umls" }, - "Gene-causes-BiologicalProcess": { + "PhenotypicFeature-causes-BiologicalProcess": { "pmid": "causes.pmid", "umls": "causes.umls" }, - "Gene-causes-Disease": { + "PhenotypicFeature-causes-Disease": { "pmid": "causes.pmid", "umls": "causes.umls" }, - "Gene-disrupted_by-BiologicalProcess": { - "pmid": "disrupted_by.pmid", - "umls": "disrupted_by.umls" - }, - "Gene-disrupted_by-ChemicalSubstance": { + "PhenotypicFeature-disrupted_by-ChemicalSubstance": { "pmid": "disrupted_by.pmid", "umls": "disrupted_by.umls" }, - "Gene-disrupted_by-Disease": { + "PhenotypicFeature-disrupted_by-Disease": { "pmid": "disrupted_by.pmid", "umls": "disrupted_by.umls" }, - "Gene-disrupted_by-Gene": { + "PhenotypicFeature-disrupted_by-Gene": { "pmid": "disrupted_by.pmid", "umls": "disrupted_by.umls" }, - "Gene-disrupts-AnatomicalEntity": { + "PhenotypicFeature-disrupts-BiologicalProcess": { "pmid": "disrupts.pmid", "umls": "disrupts.umls" }, - "Gene-disrupts-BiologicalProcess": { + "PhenotypicFeature-disrupts-Cell": { "pmid": "disrupts.pmid", "umls": "disrupts.umls" }, - "Gene-disrupts-Cell": { + "PhenotypicFeature-disrupts-CellularComponent": { "pmid": "disrupts.pmid", "umls": "disrupts.umls" }, - "Gene-disrupts-CellularComponent": { + "PhenotypicFeature-disrupts-Disease": { "pmid": "disrupts.pmid", "umls": "disrupts.umls" }, - "Gene-disrupts-ChemicalSubstance": { - "pmid": "disrupts.pmid", - "umls": "disrupts.umls" + "PhenotypicFeature-has_part-CellularComponent": { + "pmid": "has_part.pmid", + "umls": "has_part.umls" }, - "Gene-disrupts-Disease": { - "pmid": "disrupts.pmid", - "umls": "disrupts.umls" + "PhenotypicFeature-has_part-ChemicalSubstance": { + "pmid": "has_part.pmid", + "umls": "has_part.umls" }, - "Gene-disrupts-Gene": { - "pmid": "disrupts.pmid", - "umls": "disrupts.umls" + "PhenotypicFeature-has_part-Disease": { + "pmid": "has_part.pmid", + "umls": "has_part.umls" }, - "Gene-disrupts-PhenotypicFeature": { - "pmid": "disrupts.pmid", - "umls": "disrupts.umls" + "PhenotypicFeature-has_part-Gene": { + "pmid": "has_part.pmid", + "umls": "has_part.umls" }, - "Gene-negatively_regulated_by-AnatomicalEntity": { - "pmid": "negatively_regulated_by.pmid", - "umls": "negatively_regulated_by.umls" + "PhenotypicFeature-has_subclass-Disease": { + "pmid": "has_subclass.pmid", + "umls": "has_subclass.umls" }, - "Gene-negatively_regulated_by-BiologicalProcess": { - "pmid": "negatively_regulated_by.pmid", - "umls": "negatively_regulated_by.umls" + "PhenotypicFeature-has_subclass-PhenotypicFeature": { + "pmid": "has_subclass.pmid", + "umls": "has_subclass.umls" + }, + "PhenotypicFeature-located_in-AnatomicalEntity": { + "pmid": "located_in.pmid", + "umls": "located_in.umls" + }, + "PhenotypicFeature-located_in-Cell": { + "pmid": "located_in.pmid", + "umls": "located_in.umls" + }, + "PhenotypicFeature-located_in-CellularComponent": { + "pmid": "located_in.pmid", + "umls": "located_in.umls" }, - "Gene-negatively_regulated_by-Cell": { - "pmid": "negatively_regulated_by.pmid", - "umls": "negatively_regulated_by.umls" + "PhenotypicFeature-manifestation_of-BiologicalProcess": { + "pmid": "manifestation_of.pmid", + "umls": "manifestation_of.umls" }, - "Gene-negatively_regulated_by-CellularComponent": { - "pmid": "negatively_regulated_by.pmid", - "umls": "negatively_regulated_by.umls" + "PhenotypicFeature-manifestation_of-Disease": { + "pmid": "manifestation_of.pmid", + "umls": "manifestation_of.umls" }, - "Gene-negatively_regulated_by-ChemicalSubstance": { - "pmid": "negatively_regulated_by.pmid", - "umls": "negatively_regulated_by.umls" + "PhenotypicFeature-manifestation_of-Gene": { + "pmid": "manifestation_of.pmid", + "umls": "manifestation_of.umls" }, - "Gene-negatively_regulated_by-Disease": { - "pmid": "negatively_regulated_by.pmid", - "umls": "negatively_regulated_by.umls" + "PhenotypicFeature-manifested_by-Disease": { + "pmid": "manifested_by.pmid", + "umls": "manifested_by.umls" }, - "Gene-negatively_regulated_by-Gene": { + "PhenotypicFeature-negatively_regulated_by-ChemicalSubstance": { "pmid": "negatively_regulated_by.pmid", "umls": "negatively_regulated_by.umls" }, - "Gene-negatively_regulated_by-PhenotypicFeature": { + "PhenotypicFeature-negatively_regulated_by-Gene": { "pmid": "negatively_regulated_by.pmid", "umls": "negatively_regulated_by.umls" }, - "Gene-negatively_regulates-BiologicalProcess": { - "pmid": "negatively_regulates.pmid", - "umls": "negatively_regulates.umls" - }, - "Gene-negatively_regulates-CellularComponent": { - "pmid": "negatively_regulates.pmid", - "umls": "negatively_regulates.umls" - }, - "Gene-negatively_regulates-ChemicalSubstance": { + "PhenotypicFeature-negatively_regulates-BiologicalProcess": { "pmid": "negatively_regulates.pmid", "umls": "negatively_regulates.umls" }, - "Gene-negatively_regulates-Disease": { + "PhenotypicFeature-negatively_regulates-ChemicalSubstance": { "pmid": "negatively_regulates.pmid", "umls": "negatively_regulates.umls" }, - "Gene-negatively_regulates-Gene": { + "PhenotypicFeature-negatively_regulates-Disease": { "pmid": "negatively_regulates.pmid", "umls": "negatively_regulates.umls" }, - "Gene-negatively_regulates-PhenotypicFeature": { + "PhenotypicFeature-negatively_regulates-Gene": { "pmid": "negatively_regulates.pmid", "umls": "negatively_regulates.umls" }, - "Gene-physically_interacts_with-AnatomicalEntity": { - "pmid": "physically_interacts_with.pmid", - "umls": "physically_interacts_with.umls" + "PhenotypicFeature-part_of-AnatomicalEntity": { + "pmid": "part_of.pmid", + "umls": "part_of.umls" }, - "Gene-physically_interacts_with-BiologicalProcess": { - "pmid": "physically_interacts_with.pmid", - "umls": "physically_interacts_with.umls" + "PhenotypicFeature-part_of-Cell": { + "pmid": "part_of.pmid", + "umls": "part_of.umls" }, - "Gene-physically_interacts_with-Cell": { - "pmid": "physically_interacts_with.pmid", - "umls": "physically_interacts_with.umls" + "PhenotypicFeature-part_of-CellularComponent": { + "pmid": "part_of.pmid", + "umls": "part_of.umls" }, - "Gene-physically_interacts_with-CellularComponent": { - "pmid": "physically_interacts_with.pmid", - "umls": "physically_interacts_with.umls" + "PhenotypicFeature-part_of-ChemicalSubstance": { + "pmid": "part_of.pmid", + "umls": "part_of.umls" }, - "Gene-physically_interacts_with-ChemicalSubstance": { - "pmid": "physically_interacts_with.pmid", - "umls": "physically_interacts_with.umls" + "PhenotypicFeature-part_of-Disease": { + "pmid": "part_of.pmid", + "umls": "part_of.umls" }, - "Gene-physically_interacts_with-Disease": { + "PhenotypicFeature-physically_interacts_with-ChemicalSubstance": { "pmid": "physically_interacts_with.pmid", "umls": "physically_interacts_with.umls" }, - "Gene-physically_interacts_with-Gene": { + "PhenotypicFeature-physically_interacts_with-Disease": { "pmid": "physically_interacts_with.pmid", "umls": "physically_interacts_with.umls" }, - "Gene-physically_interacts_with-PhenotypicFeature": { + "PhenotypicFeature-physically_interacts_with-Gene": { "pmid": "physically_interacts_with.pmid", "umls": "physically_interacts_with.umls" }, - "Gene-positively_regulated_by-AnatomicalEntity": { + "PhenotypicFeature-positively_regulated_by-ChemicalSubstance": { "pmid": "positively_regulated_by.pmid", "umls": "positively_regulated_by.umls" }, - "Gene-positively_regulated_by-BiologicalProcess": { + "PhenotypicFeature-positively_regulated_by-Gene": { "pmid": "positively_regulated_by.pmid", "umls": "positively_regulated_by.umls" }, - "Gene-positively_regulated_by-Cell": { - "pmid": "positively_regulated_by.pmid", - "umls": "positively_regulated_by.umls" + "PhenotypicFeature-positively_regulates-ChemicalSubstance": { + "pmid": "positively_regulates.pmid", + "umls": "positively_regulates.umls" }, - "Gene-positively_regulated_by-CellularComponent": { - "pmid": "positively_regulated_by.pmid", - "umls": "positively_regulated_by.umls" + "PhenotypicFeature-positively_regulates-Gene": { + "pmid": "positively_regulates.pmid", + "umls": "positively_regulates.umls" }, - "Gene-positively_regulated_by-ChemicalSubstance": { - "pmid": "positively_regulated_by.pmid", - "umls": "positively_regulated_by.umls" + "PhenotypicFeature-preceded_by-BiologicalProcess": { + "pmid": "preceded_by.pmid", + "umls": "preceded_by.umls" }, - "Gene-positively_regulated_by-Disease": { - "pmid": "positively_regulated_by.pmid", - "umls": "positively_regulated_by.umls" + "PhenotypicFeature-preceded_by-Disease": { + "pmid": "preceded_by.pmid", + "umls": "preceded_by.umls" }, - "Gene-positively_regulated_by-Gene": { - "pmid": "positively_regulated_by.pmid", - "umls": "positively_regulated_by.umls" + "PhenotypicFeature-precedes-BiologicalProcess": { + "pmid": "precedes.pmid", + "umls": "precedes.umls" }, - "Gene-positively_regulated_by-PhenotypicFeature": { - "pmid": "positively_regulated_by.pmid", - "umls": "positively_regulated_by.umls" + "PhenotypicFeature-predisposes-Disease": { + "pmid": "predisposes.pmid", + "umls": "predisposes.umls" }, - "Gene-positively_regulates-AnatomicalEntity": { - "pmid": "positively_regulates.pmid", - "umls": "positively_regulates.umls" + "PhenotypicFeature-prevents-Disease": { + "pmid": "prevents.pmid", + "umls": "prevents.umls" }, - "Gene-positively_regulates-BiologicalProcess": { - "pmid": "positively_regulates.pmid", - "umls": "positively_regulates.umls" + "PhenotypicFeature-produced_by-BiologicalProcess": { + "pmid": "produced_by.pmid", + "umls": "produced_by.umls" }, - "Gene-positively_regulates-Cell": { - "pmid": "positively_regulates.pmid", - "umls": "positively_regulates.umls" + "PhenotypicFeature-produced_by-Cell": { + "pmid": "produced_by.pmid", + "umls": "produced_by.umls" }, - "Gene-positively_regulates-CellularComponent": { - "pmid": "positively_regulates.pmid", - "umls": "positively_regulates.umls" + "PhenotypicFeature-produced_by-CellularComponent": { + "pmid": "produced_by.pmid", + "umls": "produced_by.umls" }, - "Gene-positively_regulates-ChemicalSubstance": { - "pmid": "positively_regulates.pmid", - "umls": "positively_regulates.umls" + "PhenotypicFeature-produced_by-ChemicalSubstance": { + "pmid": "produced_by.pmid", + "umls": "produced_by.umls" }, - "Gene-positively_regulates-Disease": { - "pmid": "positively_regulates.pmid", - "umls": "positively_regulates.umls" + "PhenotypicFeature-produced_by-Disease": { + "pmid": "produced_by.pmid", + "umls": "produced_by.umls" }, - "Gene-positively_regulates-Gene": { - "pmid": "positively_regulates.pmid", - "umls": "positively_regulates.umls" + "PhenotypicFeature-produced_by-Gene": { + "pmid": "produced_by.pmid", + "umls": "produced_by.umls" }, - "Gene-positively_regulates-PhenotypicFeature": { - "pmid": "positively_regulates.pmid", - "umls": "positively_regulates.umls" + "PhenotypicFeature-produces-ChemicalSubstance": { + "pmid": "produces.pmid", + "umls": "produces.umls" }, - "Gene-prevents-Disease": { - "pmid": "prevents.pmid", - "umls": "prevents.umls" + "PhenotypicFeature-produces-Gene": { + "pmid": "produces.pmid", + "umls": "produces.umls" }, - "Gene-related_to-AnatomicalEntity": { + "PhenotypicFeature-related_to-AnatomicalEntity": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "Gene-related_to-BiologicalProcess": { + "PhenotypicFeature-related_to-BiologicalProcess": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "Gene-related_to-Cell": { + "PhenotypicFeature-related_to-ChemicalSubstance": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "Gene-related_to-ChemicalSubstance": { + "PhenotypicFeature-related_to-Disease": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "Gene-related_to-Disease": { + "PhenotypicFeature-related_to-Gene": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "Gene-related_to-Gene": { - "pmid": "related_to.pmid", - "umls": "related_to.umls" + "PhenotypicFeature-subclass_of-AnatomicalEntity": { + "pmid": "subclass_of.pmid", + "umls": "subclass_of.umls" }, - "Gene-related_to-PhenotypicFeature": { - "pmid": "related_to.pmid", - "umls": "related_to.umls" + "PhenotypicFeature-subclass_of-BiologicalProcess": { + "pmid": "subclass_of.pmid", + "umls": "subclass_of.umls" }, - "Gene-treats-Disease": { + "PhenotypicFeature-subclass_of-ChemicalSubstance": { + "pmid": "subclass_of.pmid", + "umls": "subclass_of.umls" + }, + "PhenotypicFeature-subclass_of-Disease": { + "pmid": "subclass_of.pmid", + "umls": "subclass_of.umls" + }, + "PhenotypicFeature-subclass_of-Gene": { + "pmid": "subclass_of.pmid", + "umls": "subclass_of.umls" + }, + "PhenotypicFeature-subclass_of-PhenotypicFeature": { + "pmid": "subclass_of.pmid", + "umls": "subclass_of.umls" + }, + "PhenotypicFeature-treats-Disease": { "pmid": "treats.pmid", "umls": "treats.umls" } @@ -39528,7 +39235,7 @@ }, "description": "Documentation of the SEMMED disease query web services. Learn more about [mydisease.info](http://pending.biothings.io/semmed)", "termsOfService": "http://biothings.ncats.io", - "title": "SEMMED Gene API", + "title": "SEMMED Phenotype API", "version": "1.0", "x-translator": { "component": "KP", @@ -39538,7 +39245,7 @@ } }, "paths": { - "/gene": { + "/phenotype": { "post": { "parameters": [ { @@ -39606,14 +39313,14 @@ ] } }, - "/gene/{geneid}": { + "/phenotype/{phenotypeid}": { "get": { "parameters": [ { "description": "Retrieve disease objects based on ID", "example": "C0004096", "in": "path", - "name": "geneid", + "name": "phenotypeid", "required": true, "schema": { "type": "string" @@ -39843,10 +39550,7 @@ } } }, - "description": "Query response objects with the \"hits\" property", - "x-bte-response-mapping": { - "$ref": "#/components/x-bte-response-mapping/query-post" - } + "description": "Query response objects with the \"hits\" property" }, "400": { "content": { @@ -39865,226 +39569,223 @@ ], "x-bte-kgs-operations": [ { - "$ref": "#/components/x-bte-kgs-operations/Gene-affected_by-ChemicalSubstance" - }, - { - "$ref": "#/components/x-bte-kgs-operations/Gene-affected_by-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-affected_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-affected_by-Disease" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-affected_by-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-affected_by-Gene" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-affected_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-affected_by-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-affected_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-affects-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-affects-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-affects-Cell" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-affects-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-affects-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-affects-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-affects-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-affects-Cell" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-affects-Disease" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-causes-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-affects-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-causes-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-affects-Gene" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-disrupted_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-affects-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-disrupted_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-causes-Disease" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-disrupted_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-causes-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-disrupts-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-disrupted_by-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-disrupts-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-disrupted_by-Disease" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-disrupts-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-disrupted_by-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-disrupts-Cell" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-disrupted_by-Gene" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-has_part-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-disrupts-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-has_part-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-disrupts-Cell" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-has_part-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-disrupts-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-has_part-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-disrupts-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-has_subclass-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-disrupts-Disease" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-has_subclass-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-disrupts-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-located_in-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-disrupts-Gene" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-located_in-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-disrupts-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-located_in-Cell" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulated_by-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-manifestation_of-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulated_by-Cell" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-manifestation_of-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulated_by-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-manifestation_of-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulated_by-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-manifested_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulated_by-Disease" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-negatively_regulated_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulated_by-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-negatively_regulated_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulated_by-Gene" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-negatively_regulates-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulated_by-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-negatively_regulates-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulates-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-negatively_regulates-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulates-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-negatively_regulates-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulates-Disease" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-part_of-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulates-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-part_of-Cell" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulates-Gene" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-part_of-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-negatively_regulates-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-part_of-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-physically_interacts_with-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-part_of-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-physically_interacts_with-Cell" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-physically_interacts_with-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-physically_interacts_with-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-physically_interacts_with-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-physically_interacts_with-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-physically_interacts_with-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-physically_interacts_with-Disease" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-positively_regulated_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-physically_interacts_with-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-positively_regulated_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-physically_interacts_with-Gene" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-positively_regulates-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-physically_interacts_with-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-positively_regulates-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulated_by-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-preceded_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulated_by-Cell" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-preceded_by-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulated_by-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-precedes-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulated_by-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-predisposes-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulated_by-Disease" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-prevents-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulated_by-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-produced_by-Cell" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulated_by-Gene" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-produced_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulated_by-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-produced_by-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulates-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-produced_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulates-Cell" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-produced_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulates-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-produced_by-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulates-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-produces-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulates-Disease" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-produces-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulates-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-related_to-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulates-Gene" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-related_to-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-positively_regulates-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-related_to-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-prevents-Disease" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-related_to-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-related_to-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-related_to-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-related_to-Cell" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-subclass_of-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-related_to-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-subclass_of-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-related_to-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-subclass_of-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-related_to-Disease" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-subclass_of-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-related_to-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-subclass_of-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-related_to-Gene" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-subclass_of-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/Gene-treats-Disease" + "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-treats-Disease" } ] } @@ -40093,157 +39794,55 @@ "servers": [ { "description": "Production server", - "url": "https://biothings.ncats.io/semmedgene" + "url": "https://biothings.ncats.io/semmedphenotype" } ], "tags": [ { - "name": "disease" - }, - { - "name": "annotation" - }, - { - "name": "query" - }, - { - "name": "translator" - }, - { - "name": "biothings" - }, - { - "name": "semmed" - } - ] - }, - { - "_id": "2dffb89df7f970b6a07e816e255d33ec", - "_meta": { - "date_created": "2020-12-07T22:59:15.759070+00:00", - "last_updated": "2021-03-05T08:01:08.409966+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/semmed/semmed_phenotype.yaml", - "username": "kevinxin90" - }, - "_score": 0.47008187, - "components": { - "x-bte-kgs-operations": { - "PhenotypicFeature-affected_by-BiologicalProcess": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "PhenotypicFeature" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "BiologicalProcess" - } - ], - "parameters": { - "fields": "affected_by" - }, - "path": "/query", - "predicate": "affected_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-affected_by-BiologicalProcess" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "PhenotypicFeature-affected_by-ChemicalSubstance": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "PhenotypicFeature" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "ChemicalSubstance" - } - ], - "parameters": { - "fields": "affected_by" - }, - "path": "/query", - "predicate": "affected_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-affected_by-ChemicalSubstance" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "PhenotypicFeature-affected_by-Disease": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "PhenotypicFeature" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "parameters": { - "fields": "affected_by" - }, - "path": "/query", - "predicate": "affected_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-affected_by-Disease" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "PhenotypicFeature-affected_by-Gene": [ + "name": "phenotype" + }, + { + "name": "annotation" + }, + { + "name": "query" + }, + { + "name": "translator" + }, + { + "name": "biothings" + }, + { + "name": "semmed" + } + ] + }, + { + "_id": "5a7d625d50fc518d33db48cf39ce9b30", + "_meta": { + "date_created": "2020-12-07T23:04:41.049935+00:00", + "last_updated": "2021-03-29T07:03:28.573600+00:00", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/semmed/semmed_biological_process.yaml", + "username": "kevinxin90" + }, + "_score": 0.4848808, + "components": { + "x-bte-kgs-operations": { + "BiologicalProcess-affected_by-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "AnatomicalEntity" } ], "parameters": { @@ -40258,67 +39857,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-affected_by-Gene" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affected_by-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-affects-BiologicalProcess": [ + "BiologicalProcess-affected_by-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ - { - "id": "UMLS", - "semantic": "PhenotypicFeature" - } - ], - "method": "post", - "outputs": [ { "id": "UMLS", "semantic": "BiologicalProcess" } ], - "parameters": { - "fields": "affects" - }, - "path": "/query", - "predicate": "affects", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-affects-BiologicalProcess" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "PhenotypicFeature-affects-Cell": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "PhenotypicFeature" - } - ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Cell" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "affects" + "fields": "affected_by" }, "path": "/query", - "predicate": "affects", + "predicate": "affected_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -40326,19 +39891,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-affects-Cell" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affected_by-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-affects-CellularComponent": [ + "BiologicalProcess-affected_by-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", @@ -40349,10 +39914,10 @@ } ], "parameters": { - "fields": "affects" + "fields": "affected_by" }, "path": "/query", - "predicate": "affects", + "predicate": "affected_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -40360,33 +39925,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-affects-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affected_by-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-affects-Disease": [ + "BiologicalProcess-affected_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "affects" + "fields": "affected_by" }, "path": "/query", - "predicate": "affects", + "predicate": "affected_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -40394,55 +39959,21 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-affects-Disease" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affected_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-causes-BiologicalProcess": [ + "BiologicalProcess-affected_by-Disease": [ { "inputSeparator": ",", "inputs": [ - { - "id": "UMLS", - "semantic": "PhenotypicFeature" - } - ], - "method": "post", - "outputs": [ { "id": "UMLS", "semantic": "BiologicalProcess" } ], - "parameters": { - "fields": "causes" - }, - "path": "/query", - "predicate": "causes", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-causes-BiologicalProcess" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "PhenotypicFeature-causes-Disease": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "PhenotypicFeature" - } - ], "method": "post", "outputs": [ { @@ -40451,10 +39982,10 @@ } ], "parameters": { - "fields": "causes" + "fields": "affected_by" }, "path": "/query", - "predicate": "causes", + "predicate": "affected_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -40462,33 +39993,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-causes-Disease" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affected_by-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-disrupted_by-ChemicalSubstance": [ + "BiologicalProcess-affected_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Gene" } ], "parameters": { - "fields": "disrupted_by" + "fields": "affected_by" }, "path": "/query", - "predicate": "disrupted_by", + "predicate": "affected_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -40496,33 +40027,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-disrupted_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affected_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-disrupted_by-Disease": [ + "BiologicalProcess-affected_by-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "PhenotypicFeature" } ], "parameters": { - "fields": "disrupted_by" + "fields": "affected_by" }, "path": "/query", - "predicate": "disrupted_by", + "predicate": "affected_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -40530,33 +40061,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-disrupted_by-Disease" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affected_by-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-disrupted_by-Gene": [ + "BiologicalProcess-affects-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "AnatomicalEntity" } ], "parameters": { - "fields": "disrupted_by" + "fields": "affects" }, "path": "/query", - "predicate": "disrupted_by", + "predicate": "affects", "requestBody": { "body": { "q": "{inputs[0]}", @@ -40564,19 +40095,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-disrupted_by-Gene" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affects-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-disrupts-BiologicalProcess": [ + "BiologicalProcess-affects-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", @@ -40587,10 +40118,10 @@ } ], "parameters": { - "fields": "disrupts" + "fields": "affects" }, "path": "/query", - "predicate": "disrupts", + "predicate": "affects", "requestBody": { "body": { "q": "{inputs[0]}", @@ -40598,19 +40129,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-disrupts-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affects-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-disrupts-Cell": [ + "BiologicalProcess-affects-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", @@ -40621,10 +40152,10 @@ } ], "parameters": { - "fields": "disrupts" + "fields": "affects" }, "path": "/query", - "predicate": "disrupts", + "predicate": "affects", "requestBody": { "body": { "q": "{inputs[0]}", @@ -40632,19 +40163,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-disrupts-Cell" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affects-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-disrupts-CellularComponent": [ + "BiologicalProcess-affects-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", @@ -40655,10 +40186,10 @@ } ], "parameters": { - "fields": "disrupts" + "fields": "affects" }, "path": "/query", - "predicate": "disrupts", + "predicate": "affects", "requestBody": { "body": { "q": "{inputs[0]}", @@ -40666,33 +40197,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-disrupts-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affects-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-disrupts-Disease": [ + "BiologicalProcess-affects-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "disrupts" + "fields": "affects" }, "path": "/query", - "predicate": "disrupts", + "predicate": "affects", "requestBody": { "body": { "q": "{inputs[0]}", @@ -40700,33 +40231,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-disrupts-Disease" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affects-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-has_part-CellularComponent": [ + "BiologicalProcess-affects-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "CellularComponent" + "semantic": "Disease" } ], "parameters": { - "fields": "has_part" + "fields": "affects" }, "path": "/query", - "predicate": "has_part", + "predicate": "affects", "requestBody": { "body": { "q": "{inputs[0]}", @@ -40734,33 +40265,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-has_part-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affects-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-has_part-ChemicalSubstance": [ + "BiologicalProcess-affects-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Gene" } ], "parameters": { - "fields": "has_part" + "fields": "affects" }, "path": "/query", - "predicate": "has_part", + "predicate": "affects", "requestBody": { "body": { "q": "{inputs[0]}", @@ -40768,33 +40299,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-has_part-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affects-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-has_part-Disease": [ + "BiologicalProcess-affects-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "PhenotypicFeature" } ], "parameters": { - "fields": "has_part" + "fields": "affects" }, "path": "/query", - "predicate": "has_part", + "predicate": "affects", "requestBody": { "body": { "q": "{inputs[0]}", @@ -40802,33 +40333,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-has_part-Disease" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affects-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-has_part-Gene": [ + "BiologicalProcess-caused_by-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "AnatomicalEntity" } ], "parameters": { - "fields": "has_part" + "fields": "caused_by" }, "path": "/query", - "predicate": "has_part", + "predicate": "caused_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -40836,33 +40367,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-has_part-Gene" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-caused_by-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-has_subclass-Disease": [ + "BiologicalProcess-caused_by-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "has_subclass" + "fields": "caused_by" }, "path": "/query", - "predicate": "has_subclass", + "predicate": "caused_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -40870,33 +40401,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-has_subclass-Disease" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-caused_by-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-has_subclass-PhenotypicFeature": [ + "BiologicalProcess-caused_by-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "Cell" } ], "parameters": { - "fields": "has_subclass" + "fields": "caused_by" }, "path": "/query", - "predicate": "has_subclass", + "predicate": "caused_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -40904,33 +40435,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-has_subclass-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-caused_by-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-located_in-AnatomicalEntity": [ + "BiologicalProcess-caused_by-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "CellularComponent" } ], "parameters": { - "fields": "located_in" + "fields": "caused_by" }, "path": "/query", - "predicate": "located_in", + "predicate": "caused_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -40938,33 +40469,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-located_in-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-caused_by-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-located_in-Cell": [ + "BiologicalProcess-caused_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Cell" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "located_in" + "fields": "caused_by" }, "path": "/query", - "predicate": "located_in", + "predicate": "caused_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -40972,33 +40503,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-located_in-Cell" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-caused_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-located_in-CellularComponent": [ + "BiologicalProcess-caused_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "CellularComponent" + "semantic": "Disease" } ], "parameters": { - "fields": "located_in" + "fields": "caused_by" }, "path": "/query", - "predicate": "located_in", + "predicate": "caused_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41006,33 +40537,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-located_in-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-caused_by-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-manifestation_of-BiologicalProcess": [ + "BiologicalProcess-caused_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "Gene" } ], "parameters": { - "fields": "manifestation_of" + "fields": "caused_by" }, "path": "/query", - "predicate": "manifestation_of", + "predicate": "caused_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41040,33 +40571,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-manifestation_of-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-caused_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-manifestation_of-Disease": [ + "BiologicalProcess-caused_by-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "PhenotypicFeature" } ], "parameters": { - "fields": "manifestation_of" + "fields": "caused_by" }, "path": "/query", - "predicate": "manifestation_of", + "predicate": "caused_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41074,33 +40605,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-manifestation_of-Disease" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-caused_by-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-manifestation_of-Gene": [ + "BiologicalProcess-causes-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "manifestation_of" + "fields": "causes" }, "path": "/query", - "predicate": "manifestation_of", + "predicate": "causes", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41108,19 +40639,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-manifestation_of-Gene" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-causes-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-manifested_by-Disease": [ + "BiologicalProcess-causes-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", @@ -41131,10 +40662,10 @@ } ], "parameters": { - "fields": "manifested_by" + "fields": "causes" }, "path": "/query", - "predicate": "manifested_by", + "predicate": "causes", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41142,33 +40673,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-manifested_by-Disease" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-causes-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-negatively_regulated_by-ChemicalSubstance": [ + "BiologicalProcess-disrupted_by-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "negatively_regulated_by" + "fields": "disrupted_by" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "disrupted_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41176,33 +40707,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-negatively_regulated_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupted_by-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-negatively_regulated_by-Gene": [ + "BiologicalProcess-disrupted_by-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "Cell" } ], "parameters": { - "fields": "negatively_regulated_by" + "fields": "disrupted_by" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "disrupted_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41210,33 +40741,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-negatively_regulated_by-Gene" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupted_by-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-negatively_regulates-BiologicalProcess": [ + "BiologicalProcess-disrupted_by-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "CellularComponent" } ], "parameters": { - "fields": "negatively_regulates" + "fields": "disrupted_by" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "disrupted_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41244,19 +40775,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-negatively_regulates-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupted_by-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-negatively_regulates-ChemicalSubstance": [ + "BiologicalProcess-disrupted_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", @@ -41267,10 +40798,10 @@ } ], "parameters": { - "fields": "negatively_regulates" + "fields": "disrupted_by" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "disrupted_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41278,19 +40809,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-negatively_regulates-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupted_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-negatively_regulates-Disease": [ + "BiologicalProcess-disrupted_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", @@ -41301,10 +40832,10 @@ } ], "parameters": { - "fields": "negatively_regulates" + "fields": "disrupted_by" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "disrupted_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41312,19 +40843,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-negatively_regulates-Disease" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupted_by-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-negatively_regulates-Gene": [ + "BiologicalProcess-disrupted_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", @@ -41335,10 +40866,10 @@ } ], "parameters": { - "fields": "negatively_regulates" + "fields": "disrupted_by" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "disrupted_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41346,67 +40877,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-negatively_regulates-Gene" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupted_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-part_of-AnatomicalEntity": [ + "BiologicalProcess-disrupted_by-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ - { - "id": "UMLS", - "semantic": "AnatomicalEntity" - } - ], - "parameters": { - "fields": "part_of" - }, - "path": "/query", - "predicate": "part_of", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-part_of-AnatomicalEntity" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "PhenotypicFeature-part_of-Cell": [ - { - "inputSeparator": ",", - "inputs": [ { "id": "UMLS", "semantic": "PhenotypicFeature" } ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Cell" - } - ], "parameters": { - "fields": "part_of" + "fields": "disrupted_by" }, "path": "/query", - "predicate": "part_of", + "predicate": "disrupted_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41414,33 +40911,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-part_of-Cell" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupted_by-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-part_of-CellularComponent": [ + "BiologicalProcess-disrupts-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "CellularComponent" + "semantic": "AnatomicalEntity" } ], "parameters": { - "fields": "part_of" + "fields": "disrupts" }, "path": "/query", - "predicate": "part_of", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41448,33 +40945,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-part_of-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupts-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-part_of-ChemicalSubstance": [ + "BiologicalProcess-disrupts-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "part_of" + "fields": "disrupts" }, "path": "/query", - "predicate": "part_of", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41482,33 +40979,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-part_of-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupts-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-part_of-Disease": [ + "BiologicalProcess-disrupts-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "Cell" } ], "parameters": { - "fields": "part_of" + "fields": "disrupts" }, "path": "/query", - "predicate": "part_of", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41516,33 +41013,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-part_of-Disease" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupts-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-physically_interacts_with-ChemicalSubstance": [ + "BiologicalProcess-disrupts-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "CellularComponent" } ], "parameters": { - "fields": "physically_interacts_with" + "fields": "disrupts" }, "path": "/query", - "predicate": "physically_interacts_with", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41550,19 +41047,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-physically_interacts_with-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupts-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-physically_interacts_with-Disease": [ + "BiologicalProcess-disrupts-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", @@ -41573,10 +41070,10 @@ } ], "parameters": { - "fields": "physically_interacts_with" + "fields": "disrupts" }, "path": "/query", - "predicate": "physically_interacts_with", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41584,19 +41081,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-physically_interacts_with-Disease" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupts-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-physically_interacts_with-Gene": [ + "BiologicalProcess-disrupts-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", @@ -41607,10 +41104,10 @@ } ], "parameters": { - "fields": "physically_interacts_with" + "fields": "disrupts" }, "path": "/query", - "predicate": "physically_interacts_with", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41618,33 +41115,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-physically_interacts_with-Gene" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupts-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-positively_regulated_by-ChemicalSubstance": [ + "BiologicalProcess-negatively_regulated_by-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "positively_regulated_by" + "fields": "negatively_regulated_by" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41652,33 +41149,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-positively_regulated_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-negatively_regulated_by-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-positively_regulated_by-Gene": [ + "BiologicalProcess-negatively_regulated_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "positively_regulated_by" + "fields": "negatively_regulated_by" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41686,33 +41183,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-positively_regulated_by-Gene" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-negatively_regulated_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-positively_regulates-ChemicalSubstance": [ + "BiologicalProcess-negatively_regulated_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "parameters": { - "fields": "positively_regulates" + "fields": "negatively_regulated_by" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41720,19 +41217,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-positively_regulates-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-negatively_regulated_by-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-positively_regulates-Gene": [ + "BiologicalProcess-negatively_regulated_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", @@ -41743,10 +41240,10 @@ } ], "parameters": { - "fields": "positively_regulates" + "fields": "negatively_regulated_by" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41754,33 +41251,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-positively_regulates-Gene" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-negatively_regulated_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-preceded_by-BiologicalProcess": [ + "BiologicalProcess-negatively_regulated_by-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "PhenotypicFeature" } ], "parameters": { - "fields": "preceded_by" + "fields": "negatively_regulated_by" }, "path": "/query", - "predicate": "preceded_by", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41788,33 +41285,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-preceded_by-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-negatively_regulated_by-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-preceded_by-Disease": [ + "BiologicalProcess-negatively_regulates-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "preceded_by" + "fields": "negatively_regulates" }, "path": "/query", - "predicate": "preceded_by", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41822,33 +41319,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-preceded_by-Disease" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-negatively_regulates-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-precedes-BiologicalProcess": [ + "BiologicalProcess-negatively_regulates-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "precedes" + "fields": "negatively_regulates" }, "path": "/query", - "predicate": "precedes", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41856,19 +41353,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-precedes-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-negatively_regulates-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-predisposes-Disease": [ + "BiologicalProcess-negatively_regulates-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", @@ -41879,10 +41376,10 @@ } ], "parameters": { - "fields": "predisposes" + "fields": "negatively_regulates" }, "path": "/query", - "predicate": "predisposes", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41890,33 +41387,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-predisposes-Disease" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-negatively_regulates-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-prevents-Disease": [ + "BiologicalProcess-negatively_regulates-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "Gene" } ], "parameters": { - "fields": "prevents" + "fields": "negatively_regulates" }, "path": "/query", - "predicate": "prevents", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41924,19 +41421,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-prevents-Disease" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-negatively_regulates-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-produced_by-BiologicalProcess": [ + "BiologicalProcess-physically_interacts_with-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", @@ -41947,10 +41444,10 @@ } ], "parameters": { - "fields": "produced_by" + "fields": "physically_interacts_with" }, "path": "/query", - "predicate": "produced_by", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41958,33 +41455,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-produced_by-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-physically_interacts_with-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-produced_by-Cell": [ + "BiologicalProcess-physically_interacts_with-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Cell" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "produced_by" + "fields": "physically_interacts_with" }, "path": "/query", - "predicate": "produced_by", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -41992,33 +41489,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-produced_by-Cell" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-physically_interacts_with-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-produced_by-CellularComponent": [ + "BiologicalProcess-physically_interacts_with-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "CellularComponent" + "semantic": "Disease" } ], "parameters": { - "fields": "produced_by" + "fields": "physically_interacts_with" }, "path": "/query", - "predicate": "produced_by", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -42026,33 +41523,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-produced_by-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-physically_interacts_with-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-produced_by-ChemicalSubstance": [ + "BiologicalProcess-physically_interacts_with-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Gene" } ], "parameters": { - "fields": "produced_by" + "fields": "physically_interacts_with" }, "path": "/query", - "predicate": "produced_by", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -42060,33 +41557,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-produced_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-physically_interacts_with-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-produced_by-Disease": [ + "BiologicalProcess-positively_regulated_by-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "produced_by" + "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "produced_by", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -42094,33 +41591,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-produced_by-Disease" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-positively_regulated_by-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-produced_by-Gene": [ + "BiologicalProcess-positively_regulated_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "produced_by" + "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "produced_by", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -42128,33 +41625,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-produced_by-Gene" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-positively_regulated_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-produces-ChemicalSubstance": [ + "BiologicalProcess-positively_regulated_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "parameters": { - "fields": "produces" + "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "produces", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -42162,19 +41659,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-produces-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-positively_regulated_by-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-produces-Gene": [ + "BiologicalProcess-positively_regulated_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", @@ -42185,10 +41682,10 @@ } ], "parameters": { - "fields": "produces" + "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "produces", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -42196,33 +41693,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-produces-Gene" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-positively_regulated_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-related_to-AnatomicalEntity": [ + "BiologicalProcess-positively_regulates-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "related_to" + "fields": "positively_regulates" }, "path": "/query", - "predicate": "related_to", + "predicate": "entity_positively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -42230,33 +41727,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-related_to-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-positively_regulates-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-related_to-BiologicalProcess": [ + "BiologicalProcess-positively_regulates-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "related_to" + "fields": "positively_regulates" }, "path": "/query", - "predicate": "related_to", + "predicate": "entity_positively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -42264,33 +41761,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-related_to-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-positively_regulates-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-related_to-ChemicalSubstance": [ + "BiologicalProcess-positively_regulates-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Gene" } ], "parameters": { - "fields": "related_to" + "fields": "positively_regulates" }, "path": "/query", - "predicate": "related_to", + "predicate": "entity_positively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -42298,19 +41795,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-related_to-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-positively_regulates-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-related_to-Disease": [ + "BiologicalProcess-prevents-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", @@ -42321,10 +41818,10 @@ } ], "parameters": { - "fields": "related_to" + "fields": "prevents" }, "path": "/query", - "predicate": "related_to", + "predicate": "prevents", "requestBody": { "body": { "q": "{inputs[0]}", @@ -42332,26 +41829,26 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-related_to-Disease" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-prevents-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-related_to-Gene": [ + "BiologicalProcess-related_to-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "AnatomicalEntity" } ], "parameters": { @@ -42366,33 +41863,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-related_to-Gene" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-related_to-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-subclass_of-AnatomicalEntity": [ + "BiologicalProcess-related_to-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "subclass_of" + "fields": "related_to" }, "path": "/query", - "predicate": "subclass_of", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -42400,33 +41897,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-subclass_of-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-related_to-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-subclass_of-BiologicalProcess": [ + "BiologicalProcess-related_to-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "CellularComponent" } ], "parameters": { - "fields": "subclass_of" + "fields": "related_to" }, "path": "/query", - "predicate": "subclass_of", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -42434,19 +41931,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-subclass_of-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-related_to-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-subclass_of-ChemicalSubstance": [ + "BiologicalProcess-related_to-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", @@ -42457,10 +41954,10 @@ } ], "parameters": { - "fields": "subclass_of" + "fields": "related_to" }, "path": "/query", - "predicate": "subclass_of", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -42468,19 +41965,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-subclass_of-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-related_to-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-subclass_of-Disease": [ + "BiologicalProcess-related_to-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", @@ -42491,10 +41988,10 @@ } ], "parameters": { - "fields": "subclass_of" + "fields": "related_to" }, "path": "/query", - "predicate": "subclass_of", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -42502,19 +41999,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-subclass_of-Disease" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-related_to-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-subclass_of-Gene": [ + "BiologicalProcess-related_to-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", @@ -42525,10 +42022,10 @@ } ], "parameters": { - "fields": "subclass_of" + "fields": "related_to" }, "path": "/query", - "predicate": "subclass_of", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -42536,19 +42033,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-subclass_of-Gene" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-related_to-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-subclass_of-PhenotypicFeature": [ + "BiologicalProcess-related_to-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", @@ -42559,10 +42056,10 @@ } ], "parameters": { - "fields": "subclass_of" + "fields": "related_to" }, "path": "/query", - "predicate": "subclass_of", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -42570,19 +42067,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-subclass_of-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-related_to-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "PhenotypicFeature-treats-Disease": [ + "BiologicalProcess-treats-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "method": "post", @@ -42604,7 +42101,7 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/PhenotypicFeature-treats-Disease" + "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-treats-Disease" }, "source": "SEMMED", "supportBatch": true @@ -42612,295 +42109,271 @@ ] }, "x-bte-response-mapping": { - "PhenotypicFeature-affected_by-BiologicalProcess": { + "BiologicalProcess-affected_by-AnatomicalEntity": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "PhenotypicFeature-affected_by-ChemicalSubstance": { + "BiologicalProcess-affected_by-BiologicalProcess": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "PhenotypicFeature-affected_by-Disease": { + "BiologicalProcess-affected_by-CellularComponent": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "PhenotypicFeature-affected_by-Gene": { + "BiologicalProcess-affected_by-ChemicalSubstance": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "PhenotypicFeature-affects-BiologicalProcess": { + "BiologicalProcess-affected_by-Disease": { + "pmid": "affected_by.pmid", + "umls": "affected_by.umls" + }, + "BiologicalProcess-affected_by-Gene": { + "pmid": "affected_by.pmid", + "umls": "affected_by.umls" + }, + "BiologicalProcess-affected_by-PhenotypicFeature": { + "pmid": "affected_by.pmid", + "umls": "affected_by.umls" + }, + "BiologicalProcess-affects-AnatomicalEntity": { "pmid": "affects.pmid", "umls": "affects.umls" }, - "PhenotypicFeature-affects-Cell": { + "BiologicalProcess-affects-BiologicalProcess": { "pmid": "affects.pmid", "umls": "affects.umls" }, - "PhenotypicFeature-affects-CellularComponent": { + "BiologicalProcess-affects-Cell": { "pmid": "affects.pmid", "umls": "affects.umls" }, - "PhenotypicFeature-affects-Disease": { + "BiologicalProcess-affects-CellularComponent": { "pmid": "affects.pmid", "umls": "affects.umls" }, - "PhenotypicFeature-causes-BiologicalProcess": { + "BiologicalProcess-affects-ChemicalSubstance": { + "pmid": "affects.pmid", + "umls": "affects.umls" + }, + "BiologicalProcess-affects-Disease": { + "pmid": "affects.pmid", + "umls": "affects.umls" + }, + "BiologicalProcess-affects-Gene": { + "pmid": "affects.pmid", + "umls": "affects.umls" + }, + "BiologicalProcess-affects-PhenotypicFeature": { + "pmid": "affects.pmid", + "umls": "affects.umls" + }, + "BiologicalProcess-caused_by-AnatomicalEntity": { + "pmid": "caused_by.pmid", + "umls": "caused_by.umls" + }, + "BiologicalProcess-caused_by-BiologicalProcess": { + "pmid": "caused_by.pmid", + "umls": "caused_by.umls" + }, + "BiologicalProcess-caused_by-Cell": { + "pmid": "caused_by.pmid", + "umls": "caused_by.umls" + }, + "BiologicalProcess-caused_by-CellularComponent": { + "pmid": "caused_by.pmid", + "umls": "caused_by.umls" + }, + "BiologicalProcess-caused_by-ChemicalSubstance": { + "pmid": "caused_by.pmid", + "umls": "caused_by.umls" + }, + "BiologicalProcess-caused_by-Disease": { + "pmid": "caused_by.pmid", + "umls": "caused_by.umls" + }, + "BiologicalProcess-caused_by-Gene": { + "pmid": "caused_by.pmid", + "umls": "caused_by.umls" + }, + "BiologicalProcess-caused_by-PhenotypicFeature": { + "pmid": "caused_by.pmid", + "umls": "caused_by.umls" + }, + "BiologicalProcess-causes-BiologicalProcess": { "pmid": "causes.pmid", "umls": "causes.umls" }, - "PhenotypicFeature-causes-Disease": { + "BiologicalProcess-causes-Disease": { "pmid": "causes.pmid", "umls": "causes.umls" }, - "PhenotypicFeature-disrupted_by-ChemicalSubstance": { + "BiologicalProcess-disrupted_by-BiologicalProcess": { "pmid": "disrupted_by.pmid", "umls": "disrupted_by.umls" }, - "PhenotypicFeature-disrupted_by-Disease": { + "BiologicalProcess-disrupted_by-Cell": { "pmid": "disrupted_by.pmid", "umls": "disrupted_by.umls" }, - "PhenotypicFeature-disrupted_by-Gene": { + "BiologicalProcess-disrupted_by-CellularComponent": { "pmid": "disrupted_by.pmid", "umls": "disrupted_by.umls" }, - "PhenotypicFeature-disrupts-BiologicalProcess": { + "BiologicalProcess-disrupted_by-ChemicalSubstance": { + "pmid": "disrupted_by.pmid", + "umls": "disrupted_by.umls" + }, + "BiologicalProcess-disrupted_by-Disease": { + "pmid": "disrupted_by.pmid", + "umls": "disrupted_by.umls" + }, + "BiologicalProcess-disrupted_by-Gene": { + "pmid": "disrupted_by.pmid", + "umls": "disrupted_by.umls" + }, + "BiologicalProcess-disrupted_by-PhenotypicFeature": { + "pmid": "disrupted_by.pmid", + "umls": "disrupted_by.umls" + }, + "BiologicalProcess-disrupts-AnatomicalEntity": { "pmid": "disrupts.pmid", "umls": "disrupts.umls" }, - "PhenotypicFeature-disrupts-Cell": { + "BiologicalProcess-disrupts-BiologicalProcess": { "pmid": "disrupts.pmid", "umls": "disrupts.umls" }, - "PhenotypicFeature-disrupts-CellularComponent": { + "BiologicalProcess-disrupts-Cell": { "pmid": "disrupts.pmid", "umls": "disrupts.umls" }, - "PhenotypicFeature-disrupts-Disease": { + "BiologicalProcess-disrupts-CellularComponent": { "pmid": "disrupts.pmid", "umls": "disrupts.umls" }, - "PhenotypicFeature-has_part-CellularComponent": { - "pmid": "has_part.pmid", - "umls": "has_part.umls" - }, - "PhenotypicFeature-has_part-ChemicalSubstance": { - "pmid": "has_part.pmid", - "umls": "has_part.umls" - }, - "PhenotypicFeature-has_part-Disease": { - "pmid": "has_part.pmid", - "umls": "has_part.umls" - }, - "PhenotypicFeature-has_part-Gene": { - "pmid": "has_part.pmid", - "umls": "has_part.umls" - }, - "PhenotypicFeature-has_subclass-Disease": { - "pmid": "has_subclass.pmid", - "umls": "has_subclass.umls" - }, - "PhenotypicFeature-has_subclass-PhenotypicFeature": { - "pmid": "has_subclass.pmid", - "umls": "has_subclass.umls" - }, - "PhenotypicFeature-located_in-AnatomicalEntity": { - "pmid": "located_in.pmid", - "umls": "located_in.umls" - }, - "PhenotypicFeature-located_in-Cell": { - "pmid": "located_in.pmid", - "umls": "located_in.umls" - }, - "PhenotypicFeature-located_in-CellularComponent": { - "pmid": "located_in.pmid", - "umls": "located_in.umls" + "BiologicalProcess-disrupts-Disease": { + "pmid": "disrupts.pmid", + "umls": "disrupts.umls" }, - "PhenotypicFeature-manifestation_of-BiologicalProcess": { - "pmid": "manifestation_of.pmid", - "umls": "manifestation_of.umls" + "BiologicalProcess-disrupts-Gene": { + "pmid": "disrupts.pmid", + "umls": "disrupts.umls" }, - "PhenotypicFeature-manifestation_of-Disease": { - "pmid": "manifestation_of.pmid", - "umls": "manifestation_of.umls" + "BiologicalProcess-negatively_regulated_by-BiologicalProcess": { + "pmid": "negatively_regulated_by.pmid", + "umls": "negatively_regulated_by.umls" }, - "PhenotypicFeature-manifestation_of-Gene": { - "pmid": "manifestation_of.pmid", - "umls": "manifestation_of.umls" + "BiologicalProcess-negatively_regulated_by-ChemicalSubstance": { + "pmid": "negatively_regulated_by.pmid", + "umls": "negatively_regulated_by.umls" }, - "PhenotypicFeature-manifested_by-Disease": { - "pmid": "manifested_by.pmid", - "umls": "manifested_by.umls" + "BiologicalProcess-negatively_regulated_by-Disease": { + "pmid": "negatively_regulated_by.pmid", + "umls": "negatively_regulated_by.umls" }, - "PhenotypicFeature-negatively_regulated_by-ChemicalSubstance": { + "BiologicalProcess-negatively_regulated_by-Gene": { "pmid": "negatively_regulated_by.pmid", "umls": "negatively_regulated_by.umls" }, - "PhenotypicFeature-negatively_regulated_by-Gene": { + "BiologicalProcess-negatively_regulated_by-PhenotypicFeature": { "pmid": "negatively_regulated_by.pmid", "umls": "negatively_regulated_by.umls" }, - "PhenotypicFeature-negatively_regulates-BiologicalProcess": { + "BiologicalProcess-negatively_regulates-BiologicalProcess": { "pmid": "negatively_regulates.pmid", "umls": "negatively_regulates.umls" }, - "PhenotypicFeature-negatively_regulates-ChemicalSubstance": { + "BiologicalProcess-negatively_regulates-ChemicalSubstance": { "pmid": "negatively_regulates.pmid", "umls": "negatively_regulates.umls" }, - "PhenotypicFeature-negatively_regulates-Disease": { + "BiologicalProcess-negatively_regulates-Disease": { "pmid": "negatively_regulates.pmid", "umls": "negatively_regulates.umls" }, - "PhenotypicFeature-negatively_regulates-Gene": { + "BiologicalProcess-negatively_regulates-Gene": { "pmid": "negatively_regulates.pmid", "umls": "negatively_regulates.umls" }, - "PhenotypicFeature-part_of-AnatomicalEntity": { - "pmid": "part_of.pmid", - "umls": "part_of.umls" - }, - "PhenotypicFeature-part_of-Cell": { - "pmid": "part_of.pmid", - "umls": "part_of.umls" - }, - "PhenotypicFeature-part_of-CellularComponent": { - "pmid": "part_of.pmid", - "umls": "part_of.umls" - }, - "PhenotypicFeature-part_of-ChemicalSubstance": { - "pmid": "part_of.pmid", - "umls": "part_of.umls" - }, - "PhenotypicFeature-part_of-Disease": { - "pmid": "part_of.pmid", - "umls": "part_of.umls" + "BiologicalProcess-physically_interacts_with-BiologicalProcess": { + "pmid": "physically_interacts_with.pmid", + "umls": "physically_interacts_with.umls" }, - "PhenotypicFeature-physically_interacts_with-ChemicalSubstance": { + "BiologicalProcess-physically_interacts_with-ChemicalSubstance": { "pmid": "physically_interacts_with.pmid", "umls": "physically_interacts_with.umls" }, - "PhenotypicFeature-physically_interacts_with-Disease": { + "BiologicalProcess-physically_interacts_with-Disease": { "pmid": "physically_interacts_with.pmid", "umls": "physically_interacts_with.umls" }, - "PhenotypicFeature-physically_interacts_with-Gene": { + "BiologicalProcess-physically_interacts_with-Gene": { "pmid": "physically_interacts_with.pmid", "umls": "physically_interacts_with.umls" }, - "PhenotypicFeature-positively_regulated_by-ChemicalSubstance": { + "BiologicalProcess-positively_regulated_by-BiologicalProcess": { "pmid": "positively_regulated_by.pmid", "umls": "positively_regulated_by.umls" }, - "PhenotypicFeature-positively_regulated_by-Gene": { + "BiologicalProcess-positively_regulated_by-ChemicalSubstance": { "pmid": "positively_regulated_by.pmid", "umls": "positively_regulated_by.umls" }, - "PhenotypicFeature-positively_regulates-ChemicalSubstance": { + "BiologicalProcess-positively_regulated_by-Disease": { + "pmid": "positively_regulated_by.pmid", + "umls": "positively_regulated_by.umls" + }, + "BiologicalProcess-positively_regulated_by-Gene": { + "pmid": "positively_regulated_by.pmid", + "umls": "positively_regulated_by.umls" + }, + "BiologicalProcess-positively_regulates-BiologicalProcess": { "pmid": "positively_regulates.pmid", "umls": "positively_regulates.umls" }, - "PhenotypicFeature-positively_regulates-Gene": { + "BiologicalProcess-positively_regulates-ChemicalSubstance": { "pmid": "positively_regulates.pmid", "umls": "positively_regulates.umls" }, - "PhenotypicFeature-preceded_by-BiologicalProcess": { - "pmid": "preceded_by.pmid", - "umls": "preceded_by.umls" - }, - "PhenotypicFeature-preceded_by-Disease": { - "pmid": "preceded_by.pmid", - "umls": "preceded_by.umls" - }, - "PhenotypicFeature-precedes-BiologicalProcess": { - "pmid": "precedes.pmid", - "umls": "precedes.umls" - }, - "PhenotypicFeature-predisposes-Disease": { - "pmid": "predisposes.pmid", - "umls": "predisposes.umls" + "BiologicalProcess-positively_regulates-Gene": { + "pmid": "positively_regulates.pmid", + "umls": "positively_regulates.umls" }, - "PhenotypicFeature-prevents-Disease": { + "BiologicalProcess-prevents-Disease": { "pmid": "prevents.pmid", "umls": "prevents.umls" }, - "PhenotypicFeature-produced_by-BiologicalProcess": { - "pmid": "produced_by.pmid", - "umls": "produced_by.umls" - }, - "PhenotypicFeature-produced_by-Cell": { - "pmid": "produced_by.pmid", - "umls": "produced_by.umls" - }, - "PhenotypicFeature-produced_by-CellularComponent": { - "pmid": "produced_by.pmid", - "umls": "produced_by.umls" - }, - "PhenotypicFeature-produced_by-ChemicalSubstance": { - "pmid": "produced_by.pmid", - "umls": "produced_by.umls" - }, - "PhenotypicFeature-produced_by-Disease": { - "pmid": "produced_by.pmid", - "umls": "produced_by.umls" - }, - "PhenotypicFeature-produced_by-Gene": { - "pmid": "produced_by.pmid", - "umls": "produced_by.umls" - }, - "PhenotypicFeature-produces-ChemicalSubstance": { - "pmid": "produces.pmid", - "umls": "produces.umls" - }, - "PhenotypicFeature-produces-Gene": { - "pmid": "produces.pmid", - "umls": "produces.umls" - }, - "PhenotypicFeature-related_to-AnatomicalEntity": { + "BiologicalProcess-related_to-AnatomicalEntity": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "PhenotypicFeature-related_to-BiologicalProcess": { + "BiologicalProcess-related_to-BiologicalProcess": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "PhenotypicFeature-related_to-ChemicalSubstance": { + "BiologicalProcess-related_to-CellularComponent": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "PhenotypicFeature-related_to-Disease": { + "BiologicalProcess-related_to-ChemicalSubstance": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "PhenotypicFeature-related_to-Gene": { + "BiologicalProcess-related_to-Disease": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "PhenotypicFeature-subclass_of-AnatomicalEntity": { - "pmid": "subclass_of.pmid", - "umls": "subclass_of.umls" - }, - "PhenotypicFeature-subclass_of-BiologicalProcess": { - "pmid": "subclass_of.pmid", - "umls": "subclass_of.umls" - }, - "PhenotypicFeature-subclass_of-ChemicalSubstance": { - "pmid": "subclass_of.pmid", - "umls": "subclass_of.umls" - }, - "PhenotypicFeature-subclass_of-Disease": { - "pmid": "subclass_of.pmid", - "umls": "subclass_of.umls" - }, - "PhenotypicFeature-subclass_of-Gene": { - "pmid": "subclass_of.pmid", - "umls": "subclass_of.umls" + "BiologicalProcess-related_to-Gene": { + "pmid": "related_to.pmid", + "umls": "related_to.umls" }, - "PhenotypicFeature-subclass_of-PhenotypicFeature": { - "pmid": "subclass_of.pmid", - "umls": "subclass_of.umls" + "BiologicalProcess-related_to-PhenotypicFeature": { + "pmid": "related_to.pmid", + "umls": "related_to.umls" }, - "PhenotypicFeature-treats-Disease": { + "BiologicalProcess-treats-Disease": { "pmid": "treats.pmid", "umls": "treats.umls" } @@ -42915,7 +42388,7 @@ }, "description": "Documentation of the SEMMED disease query web services. Learn more about [mydisease.info](http://pending.biothings.io/semmed)", "termsOfService": "http://biothings.ncats.io", - "title": "SEMMED Phenotype API", + "title": "SEMMED Biological Process API", "version": "1.0", "x-translator": { "component": "KP", @@ -42925,7 +42398,7 @@ } }, "paths": { - "/phenotype": { + "/geneset": { "post": { "parameters": [ { @@ -42993,14 +42466,14 @@ ] } }, - "/phenotype/{phenotypeid}": { + "/geneset/{genesetid}": { "get": { "parameters": [ { "description": "Retrieve disease objects based on ID", "example": "C0004096", "in": "path", - "name": "phenotypeid", + "name": "genesetid", "required": true, "schema": { "type": "string" @@ -43249,223 +42722,205 @@ ], "x-bte-kgs-operations": [ { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-affected_by-ChemicalSubstance" - }, - { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-affected_by-BiologicalProcess" - }, - { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-affected_by-Disease" - }, - { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-affected_by-Gene" - }, - { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-affects-CellularComponent" - }, - { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-affects-Disease" - }, - { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-affects-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affected_by-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-affects-Cell" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affected_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-causes-Disease" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affected_by-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-causes-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affected_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-disrupted_by-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affected_by-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-disrupted_by-Disease" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affected_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-disrupted_by-Gene" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affected_by-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-disrupts-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affects-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-disrupts-Disease" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affects-Cell" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-disrupts-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affects-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-disrupts-Cell" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affects-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-has_part-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affects-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-has_part-Disease" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affects-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-has_part-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affects-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-has_part-Gene" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affects-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-has_subclass-Disease" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-caused_by-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-has_subclass-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-caused_by-Cell" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-located_in-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-caused_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-located_in-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-caused_by-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-located_in-Cell" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-caused_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-manifestation_of-Disease" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-caused_by-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-manifestation_of-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-caused_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-manifestation_of-Gene" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-caused_by-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-manifested_by-Disease" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-causes-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-negatively_regulated_by-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-causes-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-negatively_regulated_by-Gene" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-disrupted_by-Cell" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-negatively_regulates-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-disrupted_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-negatively_regulates-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-disrupted_by-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-negatively_regulates-Disease" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-disrupted_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-negatively_regulates-Gene" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-disrupted_by-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-part_of-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-disrupted_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-part_of-Cell" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-disrupted_by-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-part_of-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-disrupts-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-part_of-Disease" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-disrupts-Cell" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-part_of-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-disrupts-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-physically_interacts_with-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-disrupts-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-physically_interacts_with-Disease" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-disrupts-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-physically_interacts_with-Gene" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-disrupts-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-positively_regulated_by-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-negatively_regulated_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-positively_regulated_by-Gene" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-negatively_regulated_by-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-positively_regulates-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-negatively_regulated_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-positively_regulates-Gene" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-negatively_regulated_by-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-preceded_by-Disease" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-negatively_regulated_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-preceded_by-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-negatively_regulates-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-precedes-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-negatively_regulates-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-predisposes-Disease" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-negatively_regulates-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-prevents-Disease" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-negatively_regulates-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-produced_by-Cell" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-physically_interacts_with-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-produced_by-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-physically_interacts_with-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-produced_by-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-physically_interacts_with-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-produced_by-Disease" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-physically_interacts_with-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-produced_by-Gene" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-positively_regulated_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-produced_by-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-positively_regulated_by-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-produces-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-positively_regulated_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-produces-Gene" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-positively_regulated_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-related_to-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-positively_regulates-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-related_to-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-positively_regulates-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-related_to-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-positively_regulates-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-related_to-Disease" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-prevents-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-related_to-Gene" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-related_to-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-subclass_of-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-related_to-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-subclass_of-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-related_to-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-subclass_of-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-related_to-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-subclass_of-Disease" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-related_to-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-subclass_of-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-related_to-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-subclass_of-Gene" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-related_to-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/PhenotypicFeature-treats-Disease" + "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-treats-Disease" } ] } @@ -43474,12 +42929,12 @@ "servers": [ { "description": "Production server", - "url": "https://biothings.ncats.io/semmedphenotype" + "url": "https://biothings.ncats.io/semmedbp" } ], "tags": [ { - "name": "phenotype" + "name": "chemical" }, { "name": "annotation" @@ -43499,161 +42954,56 @@ ] }, { - "_id": "77ed27f111262d0289ed4f4071faa619", + "_id": "edeb26858bd27d0322af93e7a9e08761", "_meta": { - "date_created": "2020-12-07T23:05:24.514205+00:00", - "last_updated": "2021-03-05T08:01:20.190945+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/MGIgene2phenotype/smartapi.yaml", + "date_created": "2020-12-07T23:07:08.266867+00:00", + "last_updated": "2021-03-29T07:03:27.712377+00:00", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/pfocr/smartapi.yaml", "username": "kevinxin90" }, - "_score": 0.47008187, + "_score": 0.4848808, "components": { "x-bte-kgs-operations": { - "disease_related_to_gene": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "DOID", - "semantic": "Disease" - } - ], - "outputs": [ - { - "id": "MGI", - "semantic": "Gene" - } - ], - "parameters": { - "fields": "_id", - "size": "300" - }, - "predicate": "related_to", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "mgi.associated_with_disease.doid" - }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/mgi" - }, - "source": "mgi_gene2phenotype", - "supportBatch": true - } - ], - "gene_related_to_disease": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "MGI", - "semantic": "Gene" - } - ], - "outputs": [ - { - "id": "DOID", - "semantic": "Disease" - } - ], - "parameters": { - "fields": "mgi.associated_with_disease" - }, - "predicate": "related_to", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "_id" - }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/gene_related_to_disease" - }, - "source": "mgi_gene2phenotype", - "supportBatch": true - } - ], - "gene_related_to_phenotype": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "MGI", - "semantic": "Gene" - } - ], - "outputs": [ - { - "id": "MP", - "semantic": "PhenotypicFeature" - } - ], - "parameters": { - "fields": "mgi.associated_with_phenotype" - }, - "predicate": "related_to", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "_id" - }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/gene_related_to_phenotype" - }, - "source": "mgi_gene2phenotype", - "supportBatch": true - } - ], - "phenotype_related_to_gene": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "MP", - "semantic": "PhenotypicFeature" - } - ], - "outputs": [ - { - "id": "MGI", - "semantic": "Gene" - } - ], - "parameters": { - "fields": "_id", - "size": "300" - }, - "predicate": "related_to", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "mgi.associated_with_phenotype.mp" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/mgi" + "associatedWith": { + "inputSeparator": ",", + "inputs": [ + { + "id": "pathwayFigureID", + "semantic": "Pathway" + } + ], + "outputs": [ + { + "id": "entrez", + "semantic": "Gene" + } + ], + "parameters": { + "dotfield": false, + "fields": "associatedWith" + }, + "requestBody": { + "body": { + "q": "{input1}", + "scopes": "_id" }, - "source": "mgi_gene2phenotype", - "supportBatch": true - } - ] + "header": "application/x-www-form-urlencoded" + }, + "supportBatch": true + } }, "x-bte-response-mapping": { - "gene_related_to_disease": { - "DOID": "mgi.associated_with_disease.doid", - "name": "mgi.associated_with_disease.name" - }, - "gene_related_to_phenotype": { - "MP": "mgi.associated_with_phenotype.mp", - "pubmed": "mgi.associated_with_phenotype.pubmed" - }, - "mgi": { - "MGI": "_id" + "query-post": { + "@context": "http://schema.org", + "@type": "Pathway", + "bts:associatedWith": { + "$input": "bts:pathwayFigureID", + "$source": "PFOCR", + "@type": "Gene", + "bts:entrez": "associatedWith.genes", + "bts:pmc": "associatedWith.pmc" + }, + "bts:pathwayFigureID": "_id" } } }, @@ -43664,9 +43014,9 @@ "x-id": "https://github.com/kevinxin90", "x-role": "responsible developer" }, - "description": "Documentation of the MGIgene2phenotype query web services.", + "description": "Documentation of the pfocr query web services.", "termsOfService": "https://biothings.io/about", - "title": "MGIgene2phenotype API", + "title": "pfocr API", "version": "1.0", "x-translator": { "component": "KP", @@ -43676,7 +43026,7 @@ } }, "paths": { - "/gene": { + "/geneset": { "post": { "parameters": [ { @@ -43702,7 +43052,7 @@ "schema": { "properties": { "ids": { - "description": "multiple MGI Gene IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", + "description": "multiple geneset IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", "type": "string" } }, @@ -43719,13 +43069,13 @@ "application/json": { "schema": { "items": { - "$ref": "#/components/schemas/Gene" + "$ref": "#/components/schemas/Geneset" }, "type": "array" } } }, - "description": "A list of matching gene objects" + "description": "A list of matching geneset objects" }, "400": { "content": { @@ -43738,20 +43088,20 @@ "description": "A response indicating an improperly formatted query" } }, - "summary": "For a list of chemical IDs, return the matching gene object", + "summary": "For a list of geneset IDs, return the matching geneset object", "tags": [ - "gene" + "geneset" ] } }, - "/gene/{geneid}": { + "/geneset/{genesetid}": { "get": { "parameters": [ { - "description": "Retrieve gene objects based on MGI Gene ID Supports JSONP and CORS as well.", - "example": "MGI:101864", + "description": "Retrieve geneset objects based on geneset ID Supports JSONP and CORS as well.", + "example": "PMC2673547__nihms99366f8.jpg", "in": "path", - "name": "geneid", + "name": "genesetid", "required": true, "schema": { "type": "string" @@ -43783,19 +43133,19 @@ "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Gene" + "$ref": "#/components/schemas/geneset" } } }, - "description": "A matching gene object" + "description": "A matching geneset object" }, "404": { - "description": "A response indicating an unknown gene ID" + "description": "A response indicating an unknown geneset ID" } }, - "summary": "Retrieve gene objects based on ID", + "summary": "Retrieve geneset objects based on ID", "tags": [ - "gene" + "geneset" ] } }, @@ -43810,10 +43160,10 @@ ], "responses": { "200": { - "description": "MGIgene2phenotype metadata object" + "description": "pfocr metadata object" } }, - "summary": "Get metadata about the data available from MGIgene2phenotype", + "summary": "Get metadata about the data available from pfocr", "tags": [ "metadata" ] @@ -43841,10 +43191,10 @@ ], "responses": { "200": { - "description": "MGIgene2phenotype metadata fields object" + "description": "pfocr metadata fields object" } }, - "summary": "Get metadata about the data fields available from a MGIgene2phenotype gene object", + "summary": "Get metadata about the data fields available from a pfocr geneset object", "tags": [ "metadata" ] @@ -43855,7 +43205,7 @@ "parameters": [ { "description": "Query string.", - "example": "mgi.associated_with_disease.doid:\"DOID:0110293\"", + "example": "associatedWith.genes:1378", "in": "query", "name": "q", "required": true, @@ -43926,7 +43276,7 @@ "description": "A response indicating an improperly formatted query" } }, - "summary": "Make queries and return matching gene hits. Supports JSONP and CORS as well.", + "summary": "Make queries and return matching geneset hits. Supports JSONP and CORS as well.", "tags": [ "query" ] @@ -43981,7 +43331,10 @@ } } }, - "description": "Query response objects with the \"hits\" property" + "description": "Query response objects with the \"hits\" property", + "x-bte-response-mapping": { + "$ref": "#/components/x-bte-response-mapping/query-post" + } }, "400": { "content": { @@ -43994,43 +43347,34 @@ "description": "A response indicating an improperly formatted query" } }, - "summary": "Make batch gene queries and return matching gene hits", + "summary": "Make batch geneset queries and return matching geneset hits", "tags": [ "query" ], - "x-bte-kgs-operations": [ - { - "$ref": "#/components/x-bte-kgs-operations/gene_related_to_phenotype" - }, - { - "$ref": "#/components/x-bte-kgs-operations/gene_related_to_disease" - }, - { - "$ref": "#/components/x-bte-kgs-operations/phenotype_related_to_gene" - }, - { - "$ref": "#/components/x-bte-kgs-operations/disease_related_to_gene" + "x-bte-kgs-operations": { + "associatedWith": { + "$ref": "#/components/x-bte-kgs-operations/associatedWith" } - ] + } } } }, "servers": [ { "description": "Encrypted Production server", - "url": "https://biothings.ncats.io/mgigene2phenotype" + "url": "https://pending.biothings.io/pfocr" }, { "description": "Production server", - "url": "http://biothings.ncats.io/mgigene2phenotype" + "url": "http://pending.biothings.io/pfocr" } ], "tags": [ { - "name": "gene" + "name": "geneset" }, { - "name": "phenotype" + "name": "gene" }, { "name": "annotation" @@ -44047,57 +43391,23 @@ ] }, { - "_id": "5a7d625d50fc518d33db48cf39ce9b30", + "_id": "7c07eca4ef5ceb532d06c0180e86aedd", "_meta": { - "date_created": "2020-12-07T23:04:41.049935+00:00", - "last_updated": "2021-03-05T08:01:52.626042+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/semmed/semmed_biological_process.yaml", + "date_created": "2020-12-07T22:59:11.235751+00:00", + "last_updated": "2021-03-29T07:04:20.684290+00:00", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/semmed/semmed_chemical.yaml", "username": "kevinxin90" }, - "_score": 0.47008187, + "_score": 0.4848808, "components": { "x-bte-kgs-operations": { - "BiologicalProcess-affected_by-AnatomicalEntity": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "BiologicalProcess" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "AnatomicalEntity" - } - ], - "parameters": { - "fields": "affected_by" - }, - "path": "/query", - "predicate": "affected_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affected_by-AnatomicalEntity" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "BiologicalProcess-affected_by-BiologicalProcess": [ + "ChemicalSubstance-affected_by-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -44119,53 +43429,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affected_by-BiologicalProcess" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "BiologicalProcess-affected_by-CellularComponent": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "BiologicalProcess" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "CellularComponent" - } - ], - "parameters": { - "fields": "affected_by" - }, - "path": "/query", - "predicate": "affected_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affected_by-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affected_by-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-affected_by-ChemicalSubstance": [ + "ChemicalSubstance-affected_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -44187,19 +43463,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affected_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affected_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-affected_by-Disease": [ + "ChemicalSubstance-affected_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -44221,19 +43497,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affected_by-Disease" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affected_by-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-affected_by-Gene": [ + "ChemicalSubstance-affected_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -44255,53 +43531,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affected_by-Gene" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "BiologicalProcess-affected_by-PhenotypicFeature": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "BiologicalProcess" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "PhenotypicFeature" - } - ], - "parameters": { - "fields": "affected_by" - }, - "path": "/query", - "predicate": "affected_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affected_by-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affected_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-affects-AnatomicalEntity": [ + "ChemicalSubstance-affects-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -44323,19 +43565,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affects-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affects-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-affects-BiologicalProcess": [ + "ChemicalSubstance-affects-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -44357,19 +43599,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affects-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affects-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-affects-Cell": [ + "ChemicalSubstance-affects-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -44391,19 +43633,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affects-Cell" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affects-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-affects-CellularComponent": [ + "ChemicalSubstance-affects-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -44425,19 +43667,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affects-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affects-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-affects-ChemicalSubstance": [ + "ChemicalSubstance-affects-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -44459,19 +43701,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affects-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affects-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-affects-Disease": [ + "ChemicalSubstance-affects-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -44493,19 +43735,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affects-Disease" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affects-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-affects-Gene": [ + "ChemicalSubstance-affects-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -44527,19 +43769,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affects-Gene" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affects-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-affects-PhenotypicFeature": [ + "ChemicalSubstance-affects-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -44561,293 +43803,21 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-affects-PhenotypicFeature" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "BiologicalProcess-caused_by-AnatomicalEntity": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "BiologicalProcess" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "AnatomicalEntity" - } - ], - "parameters": { - "fields": "caused_by" - }, - "path": "/query", - "predicate": "caused_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-caused_by-AnatomicalEntity" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "BiologicalProcess-caused_by-BiologicalProcess": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "BiologicalProcess" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "BiologicalProcess" - } - ], - "parameters": { - "fields": "caused_by" - }, - "path": "/query", - "predicate": "caused_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-caused_by-BiologicalProcess" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "BiologicalProcess-caused_by-Cell": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "BiologicalProcess" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Cell" - } - ], - "parameters": { - "fields": "caused_by" - }, - "path": "/query", - "predicate": "caused_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-caused_by-Cell" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "BiologicalProcess-caused_by-CellularComponent": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "BiologicalProcess" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "CellularComponent" - } - ], - "parameters": { - "fields": "caused_by" - }, - "path": "/query", - "predicate": "caused_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-caused_by-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affects-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-caused_by-ChemicalSubstance": [ + "ChemicalSubstance-causes-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ - { - "id": "UMLS", - "semantic": "BiologicalProcess" - } - ], - "method": "post", - "outputs": [ { "id": "UMLS", "semantic": "ChemicalSubstance" } ], - "parameters": { - "fields": "caused_by" - }, - "path": "/query", - "predicate": "caused_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-caused_by-ChemicalSubstance" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "BiologicalProcess-caused_by-Disease": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "BiologicalProcess" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Disease" - } - ], - "parameters": { - "fields": "caused_by" - }, - "path": "/query", - "predicate": "caused_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-caused_by-Disease" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "BiologicalProcess-caused_by-Gene": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "BiologicalProcess" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Gene" - } - ], - "parameters": { - "fields": "caused_by" - }, - "path": "/query", - "predicate": "caused_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-caused_by-Gene" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "BiologicalProcess-caused_by-PhenotypicFeature": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "BiologicalProcess" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "PhenotypicFeature" - } - ], - "parameters": { - "fields": "caused_by" - }, - "path": "/query", - "predicate": "caused_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-caused_by-PhenotypicFeature" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "BiologicalProcess-causes-BiologicalProcess": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "BiologicalProcess" - } - ], "method": "post", "outputs": [ { @@ -44867,19 +43837,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-causes-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-causes-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-causes-Disease": [ + "ChemicalSubstance-causes-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -44901,33 +43871,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-causes-Disease" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-causes-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-disrupted_by-BiologicalProcess": [ + "ChemicalSubstance-coexists_with-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "AnatomicalEntity" } ], "parameters": { - "fields": "disrupted_by" + "fields": "coexists_with" }, "path": "/query", - "predicate": "disrupted_by", + "predicate": "coexists_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -44935,21 +43905,55 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupted_by-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-coexists_with-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-disrupted_by-Cell": [ + "ChemicalSubstance-coexists_with-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ { "id": "UMLS", "semantic": "BiologicalProcess" } ], + "parameters": { + "fields": "coexists_with" + }, + "path": "/query", + "predicate": "coexists_with", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-coexists_with-BiologicalProcess" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "ChemicalSubstance-coexists_with-Cell": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], "method": "post", "outputs": [ { @@ -44958,10 +43962,10 @@ } ], "parameters": { - "fields": "disrupted_by" + "fields": "coexists_with" }, "path": "/query", - "predicate": "disrupted_by", + "predicate": "coexists_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -44969,19 +43973,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupted_by-Cell" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-coexists_with-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-disrupted_by-CellularComponent": [ + "ChemicalSubstance-coexists_with-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -44992,10 +43996,10 @@ } ], "parameters": { - "fields": "disrupted_by" + "fields": "coexists_with" }, "path": "/query", - "predicate": "disrupted_by", + "predicate": "coexists_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45003,19 +44007,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupted_by-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-coexists_with-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-disrupted_by-ChemicalSubstance": [ + "ChemicalSubstance-coexists_with-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -45026,10 +44030,10 @@ } ], "parameters": { - "fields": "disrupted_by" + "fields": "coexists_with" }, "path": "/query", - "predicate": "disrupted_by", + "predicate": "coexists_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45037,19 +44041,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupted_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-coexists_with-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-disrupted_by-Disease": [ + "ChemicalSubstance-coexists_with-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -45060,10 +44064,10 @@ } ], "parameters": { - "fields": "disrupted_by" + "fields": "coexists_with" }, "path": "/query", - "predicate": "disrupted_by", + "predicate": "coexists_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45071,19 +44075,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupted_by-Disease" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-coexists_with-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-disrupted_by-Gene": [ + "ChemicalSubstance-coexists_with-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -45093,6 +44097,74 @@ "semantic": "Gene" } ], + "parameters": { + "fields": "coexists_with" + }, + "path": "/query", + "predicate": "coexists_with", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-coexists_with-Gene" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "ChemicalSubstance-coexists_with-PhenotypicFeature": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "PhenotypicFeature" + } + ], + "parameters": { + "fields": "coexists_with" + }, + "path": "/query", + "predicate": "coexists_with", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-coexists_with-PhenotypicFeature" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "ChemicalSubstance-disrupted_by-ChemicalSubstance": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], "parameters": { "fields": "disrupted_by" }, @@ -45105,26 +44177,26 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupted_by-Gene" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-disrupted_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-disrupted_by-PhenotypicFeature": [ + "ChemicalSubstance-disrupted_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "Gene" } ], "parameters": { @@ -45139,19 +44211,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupted_by-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-disrupted_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-disrupts-AnatomicalEntity": [ + "ChemicalSubstance-disrupts-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -45173,19 +44245,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupts-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-disrupts-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-disrupts-BiologicalProcess": [ + "ChemicalSubstance-disrupts-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -45207,19 +44279,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupts-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-disrupts-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-disrupts-Cell": [ + "ChemicalSubstance-disrupts-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -45241,19 +44313,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupts-Cell" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-disrupts-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-disrupts-CellularComponent": [ + "ChemicalSubstance-disrupts-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -45275,19 +44347,53 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupts-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-disrupts-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-disrupts-Disease": [ + "ChemicalSubstance-disrupts-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "parameters": { + "fields": "disrupts" + }, + "path": "/query", + "predicate": "disrupts", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-disrupts-ChemicalSubstance" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "ChemicalSubstance-disrupts-Disease": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -45309,19 +44415,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupts-Disease" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-disrupts-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-disrupts-Gene": [ + "ChemicalSubstance-disrupts-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -45343,33 +44449,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-disrupts-Gene" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-disrupts-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-negatively_regulated_by-BiologicalProcess": [ + "ChemicalSubstance-disrupts-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "PhenotypicFeature" } ], "parameters": { - "fields": "negatively_regulated_by" + "fields": "disrupts" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45377,33 +44483,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-negatively_regulated_by-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-disrupts-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-negatively_regulated_by-ChemicalSubstance": [ + "ChemicalSubstance-negatively_regulated_by-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "AnatomicalEntity" } ], "parameters": { "fields": "negatively_regulated_by" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45411,33 +44517,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-negatively_regulated_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulated_by-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-negatively_regulated_by-Disease": [ + "ChemicalSubstance-negatively_regulated_by-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "BiologicalProcess" } ], "parameters": { "fields": "negatively_regulated_by" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45445,33 +44551,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-negatively_regulated_by-Disease" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulated_by-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-negatively_regulated_by-Gene": [ + "ChemicalSubstance-negatively_regulated_by-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "Cell" } ], "parameters": { "fields": "negatively_regulated_by" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45479,33 +44585,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-negatively_regulated_by-Gene" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulated_by-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-negatively_regulated_by-PhenotypicFeature": [ + "ChemicalSubstance-negatively_regulated_by-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "CellularComponent" } ], "parameters": { "fields": "negatively_regulated_by" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45513,33 +44619,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-negatively_regulated_by-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulated_by-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-negatively_regulates-BiologicalProcess": [ + "ChemicalSubstance-negatively_regulated_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "negatively_regulates" + "fields": "negatively_regulated_by" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45547,33 +44653,67 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-negatively_regulates-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulated_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-negatively_regulates-ChemicalSubstance": [ + "ChemicalSubstance-negatively_regulated_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ + { + "id": "UMLS", + "semantic": "Disease" + } + ], + "parameters": { + "fields": "negatively_regulated_by" + }, + "path": "/query", + "predicate": "entity_negatively_regulated_by_entity", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulated_by-Disease" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "ChemicalSubstance-negatively_regulated_by-Gene": [ + { + "inputSeparator": ",", + "inputs": [ { "id": "UMLS", "semantic": "ChemicalSubstance" } ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "Gene" + } + ], "parameters": { - "fields": "negatively_regulates" + "fields": "negatively_regulated_by" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45581,33 +44721,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-negatively_regulates-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulated_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-negatively_regulates-Disease": [ + "ChemicalSubstance-negatively_regulated_by-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "PhenotypicFeature" } ], "parameters": { - "fields": "negatively_regulates" + "fields": "negatively_regulated_by" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45615,33 +44755,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-negatively_regulates-Disease" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulated_by-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-negatively_regulates-Gene": [ + "ChemicalSubstance-negatively_regulates-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "AnatomicalEntity" } ], "parameters": { "fields": "negatively_regulates" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45649,19 +44789,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-negatively_regulates-Gene" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulates-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-physically_interacts_with-BiologicalProcess": [ + "ChemicalSubstance-negatively_regulates-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -45672,10 +44812,10 @@ } ], "parameters": { - "fields": "physically_interacts_with" + "fields": "negatively_regulates" }, "path": "/query", - "predicate": "physically_interacts_with", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45683,33 +44823,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-physically_interacts_with-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulates-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-physically_interacts_with-ChemicalSubstance": [ + "ChemicalSubstance-negatively_regulates-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Cell" } ], "parameters": { - "fields": "physically_interacts_with" + "fields": "negatively_regulates" }, "path": "/query", - "predicate": "physically_interacts_with", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45717,33 +44857,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-physically_interacts_with-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulates-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-physically_interacts_with-Disease": [ + "ChemicalSubstance-negatively_regulates-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "CellularComponent" } ], "parameters": { - "fields": "physically_interacts_with" + "fields": "negatively_regulates" }, "path": "/query", - "predicate": "physically_interacts_with", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45751,33 +44891,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-physically_interacts_with-Disease" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulates-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-physically_interacts_with-Gene": [ + "ChemicalSubstance-negatively_regulates-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "physically_interacts_with" + "fields": "negatively_regulates" }, "path": "/query", - "predicate": "physically_interacts_with", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45785,33 +44925,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-physically_interacts_with-Gene" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulates-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-positively_regulated_by-BiologicalProcess": [ + "ChemicalSubstance-negatively_regulates-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "Disease" } ], "parameters": { - "fields": "positively_regulated_by" + "fields": "negatively_regulates" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45819,33 +44959,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-positively_regulated_by-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulates-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-positively_regulated_by-ChemicalSubstance": [ + "ChemicalSubstance-negatively_regulates-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Gene" } ], "parameters": { - "fields": "positively_regulated_by" + "fields": "negatively_regulates" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45853,33 +44993,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-positively_regulated_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulates-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-positively_regulated_by-Disease": [ + "ChemicalSubstance-negatively_regulates-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "PhenotypicFeature" } ], "parameters": { - "fields": "positively_regulated_by" + "fields": "negatively_regulates" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45887,33 +45027,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-positively_regulated_by-Disease" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulates-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-positively_regulated_by-Gene": [ + "ChemicalSubstance-physically_interacts_with-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "AnatomicalEntity" } ], "parameters": { - "fields": "positively_regulated_by" + "fields": "physically_interacts_with" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45921,19 +45061,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-positively_regulated_by-Gene" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-physically_interacts_with-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-positively_regulates-BiologicalProcess": [ + "ChemicalSubstance-physically_interacts_with-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", @@ -45944,10 +45084,10 @@ } ], "parameters": { - "fields": "positively_regulates" + "fields": "physically_interacts_with" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45955,33 +45095,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-positively_regulates-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-physically_interacts_with-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-positively_regulates-ChemicalSubstance": [ + "ChemicalSubstance-physically_interacts_with-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Cell" } ], "parameters": { - "fields": "positively_regulates" + "fields": "physically_interacts_with" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -45989,33 +45129,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-positively_regulates-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-physically_interacts_with-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-positively_regulates-Gene": [ + "ChemicalSubstance-physically_interacts_with-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "CellularComponent" } ], "parameters": { - "fields": "positively_regulates" + "fields": "physically_interacts_with" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -46023,33 +45163,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-positively_regulates-Gene" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-physically_interacts_with-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-prevents-Disease": [ + "ChemicalSubstance-physically_interacts_with-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "prevents" + "fields": "physically_interacts_with" }, "path": "/query", - "predicate": "prevents", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -46057,33 +45197,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-prevents-Disease" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-physically_interacts_with-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-related_to-AnatomicalEntity": [ + "ChemicalSubstance-physically_interacts_with-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Disease" } ], "parameters": { - "fields": "related_to" + "fields": "physically_interacts_with" }, "path": "/query", - "predicate": "related_to", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -46091,33 +45231,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-related_to-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-physically_interacts_with-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-related_to-BiologicalProcess": [ + "ChemicalSubstance-physically_interacts_with-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "Gene" } ], "parameters": { - "fields": "related_to" + "fields": "physically_interacts_with" }, "path": "/query", - "predicate": "related_to", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -46125,33 +45265,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-related_to-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-physically_interacts_with-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-related_to-CellularComponent": [ + "ChemicalSubstance-physically_interacts_with-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "CellularComponent" + "semantic": "PhenotypicFeature" } ], "parameters": { - "fields": "related_to" + "fields": "physically_interacts_with" }, "path": "/query", - "predicate": "related_to", + "predicate": "physically_interacts_with", "requestBody": { "body": { "q": "{inputs[0]}", @@ -46159,33 +45299,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-related_to-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-physically_interacts_with-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-related_to-ChemicalSubstance": [ + "ChemicalSubstance-positively_regulated_by-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "AnatomicalEntity" } ], "parameters": { - "fields": "related_to" + "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "related_to", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -46193,33 +45333,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-related_to-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulated_by-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-related_to-Disease": [ + "ChemicalSubstance-positively_regulated_by-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "related_to" + "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "related_to", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -46227,33 +45367,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-related_to-Disease" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulated_by-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-related_to-Gene": [ + "ChemicalSubstance-positively_regulated_by-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "Cell" } ], "parameters": { - "fields": "related_to" + "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "related_to", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -46261,33 +45401,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-related_to-Gene" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulated_by-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-related_to-PhenotypicFeature": [ + "ChemicalSubstance-positively_regulated_by-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "CellularComponent" } ], "parameters": { - "fields": "related_to" + "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "related_to", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -46295,33 +45435,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-related_to-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulated_by-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "BiologicalProcess-treats-Disease": [ + "ChemicalSubstance-positively_regulated_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "treats" + "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "treats", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -46329,1163 +45469,1595 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/BiologicalProcess-treats-Disease" + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulated_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } - ] - }, - "x-bte-response-mapping": { - "BiologicalProcess-affected_by-AnatomicalEntity": { - "pmid": "affected_by.pmid", - "umls": "affected_by.umls" - }, - "BiologicalProcess-affected_by-BiologicalProcess": { - "pmid": "affected_by.pmid", - "umls": "affected_by.umls" - }, - "BiologicalProcess-affected_by-CellularComponent": { - "pmid": "affected_by.pmid", - "umls": "affected_by.umls" - }, - "BiologicalProcess-affected_by-ChemicalSubstance": { - "pmid": "affected_by.pmid", - "umls": "affected_by.umls" - }, - "BiologicalProcess-affected_by-Disease": { - "pmid": "affected_by.pmid", - "umls": "affected_by.umls" - }, - "BiologicalProcess-affected_by-Gene": { - "pmid": "affected_by.pmid", - "umls": "affected_by.umls" - }, - "BiologicalProcess-affected_by-PhenotypicFeature": { - "pmid": "affected_by.pmid", - "umls": "affected_by.umls" - }, - "BiologicalProcess-affects-AnatomicalEntity": { - "pmid": "affects.pmid", - "umls": "affects.umls" - }, - "BiologicalProcess-affects-BiologicalProcess": { - "pmid": "affects.pmid", - "umls": "affects.umls" - }, - "BiologicalProcess-affects-Cell": { - "pmid": "affects.pmid", - "umls": "affects.umls" - }, - "BiologicalProcess-affects-CellularComponent": { - "pmid": "affects.pmid", - "umls": "affects.umls" - }, - "BiologicalProcess-affects-ChemicalSubstance": { - "pmid": "affects.pmid", - "umls": "affects.umls" - }, - "BiologicalProcess-affects-Disease": { - "pmid": "affects.pmid", - "umls": "affects.umls" - }, - "BiologicalProcess-affects-Gene": { - "pmid": "affects.pmid", - "umls": "affects.umls" - }, - "BiologicalProcess-affects-PhenotypicFeature": { - "pmid": "affects.pmid", - "umls": "affects.umls" - }, - "BiologicalProcess-caused_by-AnatomicalEntity": { - "pmid": "caused_by.pmid", - "umls": "caused_by.umls" - }, - "BiologicalProcess-caused_by-BiologicalProcess": { - "pmid": "caused_by.pmid", - "umls": "caused_by.umls" - }, - "BiologicalProcess-caused_by-Cell": { - "pmid": "caused_by.pmid", - "umls": "caused_by.umls" - }, - "BiologicalProcess-caused_by-CellularComponent": { - "pmid": "caused_by.pmid", - "umls": "caused_by.umls" - }, - "BiologicalProcess-caused_by-ChemicalSubstance": { - "pmid": "caused_by.pmid", - "umls": "caused_by.umls" - }, - "BiologicalProcess-caused_by-Disease": { - "pmid": "caused_by.pmid", - "umls": "caused_by.umls" - }, - "BiologicalProcess-caused_by-Gene": { - "pmid": "caused_by.pmid", - "umls": "caused_by.umls" - }, - "BiologicalProcess-caused_by-PhenotypicFeature": { - "pmid": "caused_by.pmid", - "umls": "caused_by.umls" - }, - "BiologicalProcess-causes-BiologicalProcess": { - "pmid": "causes.pmid", - "umls": "causes.umls" - }, - "BiologicalProcess-causes-Disease": { - "pmid": "causes.pmid", - "umls": "causes.umls" - }, - "BiologicalProcess-disrupted_by-BiologicalProcess": { - "pmid": "disrupted_by.pmid", - "umls": "disrupted_by.umls" - }, - "BiologicalProcess-disrupted_by-Cell": { - "pmid": "disrupted_by.pmid", - "umls": "disrupted_by.umls" - }, - "BiologicalProcess-disrupted_by-CellularComponent": { - "pmid": "disrupted_by.pmid", - "umls": "disrupted_by.umls" - }, - "BiologicalProcess-disrupted_by-ChemicalSubstance": { - "pmid": "disrupted_by.pmid", - "umls": "disrupted_by.umls" - }, - "BiologicalProcess-disrupted_by-Disease": { - "pmid": "disrupted_by.pmid", - "umls": "disrupted_by.umls" - }, - "BiologicalProcess-disrupted_by-Gene": { - "pmid": "disrupted_by.pmid", - "umls": "disrupted_by.umls" - }, - "BiologicalProcess-disrupted_by-PhenotypicFeature": { - "pmid": "disrupted_by.pmid", - "umls": "disrupted_by.umls" - }, - "BiologicalProcess-disrupts-AnatomicalEntity": { - "pmid": "disrupts.pmid", - "umls": "disrupts.umls" - }, - "BiologicalProcess-disrupts-BiologicalProcess": { - "pmid": "disrupts.pmid", - "umls": "disrupts.umls" - }, - "BiologicalProcess-disrupts-Cell": { - "pmid": "disrupts.pmid", - "umls": "disrupts.umls" - }, - "BiologicalProcess-disrupts-CellularComponent": { - "pmid": "disrupts.pmid", - "umls": "disrupts.umls" - }, - "BiologicalProcess-disrupts-Disease": { - "pmid": "disrupts.pmid", - "umls": "disrupts.umls" - }, - "BiologicalProcess-disrupts-Gene": { - "pmid": "disrupts.pmid", - "umls": "disrupts.umls" - }, - "BiologicalProcess-negatively_regulated_by-BiologicalProcess": { - "pmid": "negatively_regulated_by.pmid", - "umls": "negatively_regulated_by.umls" - }, - "BiologicalProcess-negatively_regulated_by-ChemicalSubstance": { - "pmid": "negatively_regulated_by.pmid", - "umls": "negatively_regulated_by.umls" - }, - "BiologicalProcess-negatively_regulated_by-Disease": { - "pmid": "negatively_regulated_by.pmid", - "umls": "negatively_regulated_by.umls" - }, - "BiologicalProcess-negatively_regulated_by-Gene": { - "pmid": "negatively_regulated_by.pmid", - "umls": "negatively_regulated_by.umls" - }, - "BiologicalProcess-negatively_regulated_by-PhenotypicFeature": { - "pmid": "negatively_regulated_by.pmid", - "umls": "negatively_regulated_by.umls" - }, - "BiologicalProcess-negatively_regulates-BiologicalProcess": { - "pmid": "negatively_regulates.pmid", - "umls": "negatively_regulates.umls" - }, - "BiologicalProcess-negatively_regulates-ChemicalSubstance": { - "pmid": "negatively_regulates.pmid", - "umls": "negatively_regulates.umls" - }, - "BiologicalProcess-negatively_regulates-Disease": { - "pmid": "negatively_regulates.pmid", - "umls": "negatively_regulates.umls" - }, - "BiologicalProcess-negatively_regulates-Gene": { - "pmid": "negatively_regulates.pmid", - "umls": "negatively_regulates.umls" - }, - "BiologicalProcess-physically_interacts_with-BiologicalProcess": { - "pmid": "physically_interacts_with.pmid", - "umls": "physically_interacts_with.umls" - }, - "BiologicalProcess-physically_interacts_with-ChemicalSubstance": { - "pmid": "physically_interacts_with.pmid", - "umls": "physically_interacts_with.umls" - }, - "BiologicalProcess-physically_interacts_with-Disease": { - "pmid": "physically_interacts_with.pmid", - "umls": "physically_interacts_with.umls" - }, - "BiologicalProcess-physically_interacts_with-Gene": { - "pmid": "physically_interacts_with.pmid", - "umls": "physically_interacts_with.umls" - }, - "BiologicalProcess-positively_regulated_by-BiologicalProcess": { - "pmid": "positively_regulated_by.pmid", - "umls": "positively_regulated_by.umls" - }, - "BiologicalProcess-positively_regulated_by-ChemicalSubstance": { - "pmid": "positively_regulated_by.pmid", - "umls": "positively_regulated_by.umls" - }, - "BiologicalProcess-positively_regulated_by-Disease": { - "pmid": "positively_regulated_by.pmid", - "umls": "positively_regulated_by.umls" - }, - "BiologicalProcess-positively_regulated_by-Gene": { - "pmid": "positively_regulated_by.pmid", - "umls": "positively_regulated_by.umls" - }, - "BiologicalProcess-positively_regulates-BiologicalProcess": { - "pmid": "positively_regulates.pmid", - "umls": "positively_regulates.umls" - }, - "BiologicalProcess-positively_regulates-ChemicalSubstance": { - "pmid": "positively_regulates.pmid", - "umls": "positively_regulates.umls" - }, - "BiologicalProcess-positively_regulates-Gene": { - "pmid": "positively_regulates.pmid", - "umls": "positively_regulates.umls" - }, - "BiologicalProcess-prevents-Disease": { - "pmid": "prevents.pmid", - "umls": "prevents.umls" - }, - "BiologicalProcess-related_to-AnatomicalEntity": { - "pmid": "related_to.pmid", - "umls": "related_to.umls" - }, - "BiologicalProcess-related_to-BiologicalProcess": { - "pmid": "related_to.pmid", - "umls": "related_to.umls" - }, - "BiologicalProcess-related_to-CellularComponent": { - "pmid": "related_to.pmid", - "umls": "related_to.umls" - }, - "BiologicalProcess-related_to-ChemicalSubstance": { - "pmid": "related_to.pmid", - "umls": "related_to.umls" - }, - "BiologicalProcess-related_to-Disease": { - "pmid": "related_to.pmid", - "umls": "related_to.umls" - }, - "BiologicalProcess-related_to-Gene": { - "pmid": "related_to.pmid", - "umls": "related_to.umls" - }, - "BiologicalProcess-related_to-PhenotypicFeature": { - "pmid": "related_to.pmid", - "umls": "related_to.umls" - }, - "BiologicalProcess-treats-Disease": { - "pmid": "treats.pmid", - "umls": "treats.umls" - } - } - }, - "info": { - "contact": { - "email": "help@biothings.io", - "name": "Chunlei Wu", - "x-id": "https://github.com/newgene", - "x-role": "responsible developer" - }, - "description": "Documentation of the SEMMED disease query web services. Learn more about [mydisease.info](http://pending.biothings.io/semmed)", - "termsOfService": "http://biothings.ncats.io", - "title": "SEMMED Biological Process API", - "version": "1.0", - "x-translator": { - "component": "KP", - "team": [ - "Service Provider" - ] - } - }, - "paths": { - "/geneset": { - "post": { - "parameters": [ - { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" + ], + "ChemicalSubstance-positively_regulated_by-Disease": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "Disease" + } + ], + "parameters": { + "fields": "positively_regulated_by" }, - { - "$ref": "#/components/parameters/fields", - "name": "fields" + "path": "/query", + "predicate": "entity_positively_regulated_by_entity", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } }, - { - "$ref": "#/components/parameters/email", - "name": "email" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulated_by-Disease" }, - { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "requestBody": { - "content": { - "application/x-www-form-urlencoded": { - "schema": { - "properties": { - "ids": { - "description": "multiple disease IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", - "type": "string" - } - }, - "required": [ - "ids" - ] - } + "source": "SEMMED", + "supportBatch": true + } + ], + "ChemicalSubstance-positively_regulated_by-Gene": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" } - } - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "items": { - "$ref": "#/components/schemas/Disease" - }, - "type": "array" - } - } - }, - "description": "A list of matching disease objects" + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "Gene" + } + ], + "parameters": { + "fields": "positively_regulated_by" }, - "400": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResult" - } - } - }, - "description": "A response indicating an improperly formatted query" - } - }, - "summary": "For a list of disease IDs, return the matching disease object", - "tags": [ - "gene" - ] - } - }, - "/geneset/{genesetid}": { - "get": { - "parameters": [ - { - "description": "Retrieve disease objects based on ID", - "example": "C0004096", - "in": "path", - "name": "genesetid", - "required": true, - "schema": { - "type": "string" + "path": "/query", + "predicate": "entity_positively_regulated_by_entity", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" } }, - { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulated_by-Gene" }, - { - "$ref": "#/components/parameters/callback", - "name": "callback" + "source": "SEMMED", + "supportBatch": true + } + ], + "ChemicalSubstance-positively_regulated_by-PhenotypicFeature": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "PhenotypicFeature" + } + ], + "parameters": { + "fields": "positively_regulated_by" }, - { - "$ref": "#/components/parameters/fields", - "name": "fields" + "path": "/query", + "predicate": "entity_positively_regulated_by_entity", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } }, - { - "$ref": "#/components/parameters/email", - "name": "email" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulated_by-PhenotypicFeature" }, - { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Disease" - } - } - }, - "description": "A matching disease object" + "source": "SEMMED", + "supportBatch": true + } + ], + "ChemicalSubstance-positively_regulates-AnatomicalEntity": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "AnatomicalEntity" + } + ], + "parameters": { + "fields": "positively_regulates" }, - "404": { - "description": "A response indicating an unknown disease ID" - } - }, - "summary": "Retrieve disease objects based on ID", - "tags": [ - "disease" - ] - } - }, - "/metadata": { - "get": { - "parameters": [ - { - "$ref": "#/components/parameters/callback", - "in": "query", - "name": "callback" - } - ], - "responses": { - "200": { - "description": "mydisease.info metadata object" - } - }, - "summary": "Get metadata about the data available from mydisease.info", - "tags": [ - "metadata" - ] - } - }, - "/metadata/fields": { - "get": { - "parameters": [ - { - "$ref": "#/components/parameters/search", - "name": "search" + "path": "/query", + "predicate": "entity_positively_regulates_entity", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } }, - { - "$ref": "#/components/parameters/callback", - "name": "callback" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulates-AnatomicalEntity" }, - { - "$ref": "#/components/parameters/prefix", - "name": "prefix" + "source": "SEMMED", + "supportBatch": true + } + ], + "ChemicalSubstance-positively_regulates-BiologicalProcess": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "BiologicalProcess" + } + ], + "parameters": { + "fields": "positively_regulates" }, - { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "responses": { - "200": { - "description": "mydisease.info metadata fields object" - } - }, - "summary": "Get metadata about the data fields available from a mydisease.info chem object", - "tags": [ - "metadata" - ] - } - }, - "/query": { - "get": { - "parameters": [ - { - "description": "Query string. The detailed query syntax can be found from our [docs](http://mydisease.info). Examples: \"cancer\", \"primary ciliary dyskinesia\", \"DOID:9562\"", - "example": "cancer", - "in": "query", - "name": "q", - "required": true, - "schema": { - "type": "string" + "path": "/query", + "predicate": "entity_positively_regulates_entity", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" } }, - { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulates-BiologicalProcess" }, - { - "$ref": "#/components/parameters/fields", - "name": "fields" + "source": "SEMMED", + "supportBatch": true + } + ], + "ChemicalSubstance-positively_regulates-Cell": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "Cell" + } + ], + "parameters": { + "fields": "positively_regulates" }, - { - "$ref": "#/components/parameters/facet_size", - "name": "facet_size" + "path": "/query", + "predicate": "entity_positively_regulates_entity", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } }, - { - "$ref": "#/components/parameters/sort", - "name": "sort" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulates-Cell" }, - { - "$ref": "#/components/parameters/callback", - "name": "callback" + "source": "SEMMED", + "supportBatch": true + } + ], + "ChemicalSubstance-positively_regulates-CellularComponent": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "CellularComponent" + } + ], + "parameters": { + "fields": "positively_regulates" }, - { - "$ref": "#/components/parameters/email", - "name": "email" + "path": "/query", + "predicate": "entity_positively_regulates_entity", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } }, - { - "$ref": "#/components/parameters/facets", - "name": "facets" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulates-CellularComponent" }, - { - "$ref": "#/components/parameters/size", - "name": "size" + "source": "SEMMED", + "supportBatch": true + } + ], + "ChemicalSubstance-positively_regulates-ChemicalSubstance": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "parameters": { + "fields": "positively_regulates" }, - { - "$ref": "#/components/parameters/from", - "name": "from" + "path": "/query", + "predicate": "entity_positively_regulates_entity", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } }, - { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/QueryResult" - } - } - }, - "description": "A query response with the \"hits\" property" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulates-ChemicalSubstance" }, - "400": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResult" - } - } - }, - "description": "A response indicating an improperly formatted query" - } - }, - "summary": "Make disease queries and return matching disease hits. Supports JSONP and CORS as well.", - "tags": [ - "query" - ] - }, - "post": { - "parameters": [ - { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" + "source": "SEMMED", + "supportBatch": true + } + ], + "ChemicalSubstance-positively_regulates-Disease": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "Disease" + } + ], + "parameters": { + "fields": "positively_regulates" }, - { - "$ref": "#/components/parameters/email", - "name": "email" + "path": "/query", + "predicate": "entity_positively_regulates_entity", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } }, - { - "$ref": "#/components/parameters/fields", - "name": "fields" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulates-Disease" }, - { - "$ref": "#/components/parameters/size", - "name": "size" + "source": "SEMMED", + "supportBatch": true + } + ], + "ChemicalSubstance-positively_regulates-Gene": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "Gene" + } + ], + "parameters": { + "fields": "positively_regulates" }, - { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "requestBody": { - "content": { - "application/x-www-form-urlencoded": { - "schema": { - "properties": { - "q": { - "description": "multiple 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" - } - } - } + "path": "/query", + "predicate": "entity_positively_regulates_entity", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" } - } - }, - "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" - ], - "x-bte-kgs-operations": [ - { - "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affected_by-AnatomicalEntity" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulates-Gene" }, - { - "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affected_by-ChemicalSubstance" + "source": "SEMMED", + "supportBatch": true + } + ], + "ChemicalSubstance-positively_regulates-PhenotypicFeature": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "PhenotypicFeature" + } + ], + "parameters": { + "fields": "positively_regulates" }, - { - "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affected_by-BiologicalProcess" + "path": "/query", + "predicate": "entity_positively_regulates_entity", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } }, - { - "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affected_by-Disease" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulates-PhenotypicFeature" }, - { - "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affected_by-PhenotypicFeature" + "source": "SEMMED", + "supportBatch": true + } + ], + "ChemicalSubstance-prevents-Disease": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "Disease" + } + ], + "parameters": { + "fields": "prevents" }, - { - "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affected_by-Gene" + "path": "/query", + "predicate": "prevents", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } }, - { - "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affected_by-CellularComponent" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-prevents-Disease" }, - { - "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affects-AnatomicalEntity" + "source": "SEMMED", + "supportBatch": true + } + ], + "ChemicalSubstance-produced_by-AnatomicalEntity": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "AnatomicalEntity" + } + ], + "parameters": { + "fields": "produced_by" }, - { - "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affects-Cell" + "path": "/query", + "predicate": "produced_by", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } }, - { - "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affects-ChemicalSubstance" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-produced_by-AnatomicalEntity" }, - { - "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affects-BiologicalProcess" + "source": "SEMMED", + "supportBatch": true + } + ], + "ChemicalSubstance-produced_by-BiologicalProcess": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "BiologicalProcess" + } + ], + "parameters": { + "fields": "produced_by" }, - { - "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affects-Disease" + "path": "/query", + "predicate": "produced_by", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } }, - { - "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affects-PhenotypicFeature" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-produced_by-BiologicalProcess" }, - { - "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affects-Gene" + "source": "SEMMED", + "supportBatch": true + } + ], + "ChemicalSubstance-produced_by-Cell": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "Cell" + } + ], + "parameters": { + "fields": "produced_by" }, - { - "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-affects-CellularComponent" + "path": "/query", + "predicate": "produced_by", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } }, - { - "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-caused_by-AnatomicalEntity" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-produced_by-Cell" }, - { - "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-caused_by-Cell" + "source": "SEMMED", + "supportBatch": true + } + ], + "ChemicalSubstance-produced_by-CellularComponent": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "CellularComponent" + } + ], + "parameters": { + "fields": "produced_by" }, - { - "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-caused_by-ChemicalSubstance" + "path": "/query", + "predicate": "produced_by", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } }, - { - "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-caused_by-BiologicalProcess" + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-produced_by-CellularComponent" }, - { - "$ref": "#/components/x-bte-kgs-operations/BiologicalProcess-caused_by-Disease" + "source": "SEMMED", + "supportBatch": true + } + ], + "ChemicalSubstance-produced_by-ChemicalSubstance": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "ChemicalSubstance" + } + ], + "parameters": { + "fields": "produced_by" }, - { - "$ref": 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"negatively_regulated_by.pmid", + "umls": "negatively_regulated_by.umls" + }, + "ChemicalSubstance-negatively_regulated_by-ChemicalSubstance": { + "pmid": "negatively_regulated_by.pmid", + "umls": "negatively_regulated_by.umls" + }, + "ChemicalSubstance-negatively_regulated_by-Disease": { + "pmid": "negatively_regulated_by.pmid", + "umls": "negatively_regulated_by.umls" + }, + "ChemicalSubstance-negatively_regulated_by-Gene": { + "pmid": "negatively_regulated_by.pmid", + "umls": "negatively_regulated_by.umls" + }, + "ChemicalSubstance-negatively_regulated_by-PhenotypicFeature": { + "pmid": "negatively_regulated_by.pmid", + "umls": "negatively_regulated_by.umls" + }, + "ChemicalSubstance-negatively_regulates-AnatomicalEntity": { + "pmid": "negatively_regulates.pmid", + "umls": "negatively_regulates.umls" + }, + "ChemicalSubstance-negatively_regulates-BiologicalProcess": { + "pmid": "negatively_regulates.pmid", + "umls": "negatively_regulates.umls" + }, + "ChemicalSubstance-negatively_regulates-Cell": { + "pmid": "negatively_regulates.pmid", + "umls": "negatively_regulates.umls" + }, + "ChemicalSubstance-negatively_regulates-CellularComponent": { + "pmid": "negatively_regulates.pmid", + "umls": "negatively_regulates.umls" + }, + "ChemicalSubstance-negatively_regulates-ChemicalSubstance": { + "pmid": "negatively_regulates.pmid", + "umls": "negatively_regulates.umls" + }, + "ChemicalSubstance-negatively_regulates-Disease": { + "pmid": "negatively_regulates.pmid", + "umls": "negatively_regulates.umls" + }, + "ChemicalSubstance-negatively_regulates-Gene": { + "pmid": "negatively_regulates.pmid", + "umls": "negatively_regulates.umls" + }, + "ChemicalSubstance-negatively_regulates-PhenotypicFeature": { + "pmid": "negatively_regulates.pmid", + "umls": "negatively_regulates.umls" + }, + "ChemicalSubstance-physically_interacts_with-AnatomicalEntity": { + "pmid": "physically_interacts_with.pmid", + "umls": "physically_interacts_with.umls" + }, + "ChemicalSubstance-physically_interacts_with-BiologicalProcess": { + "pmid": "physically_interacts_with.pmid", + "umls": "physically_interacts_with.umls" + }, + "ChemicalSubstance-physically_interacts_with-Cell": { + "pmid": "physically_interacts_with.pmid", + "umls": "physically_interacts_with.umls" + }, + "ChemicalSubstance-physically_interacts_with-CellularComponent": { + "pmid": "physically_interacts_with.pmid", + "umls": "physically_interacts_with.umls" + }, + "ChemicalSubstance-physically_interacts_with-ChemicalSubstance": { + "pmid": "physically_interacts_with.pmid", + "umls": "physically_interacts_with.umls" + }, + "ChemicalSubstance-physically_interacts_with-Disease": { + "pmid": "physically_interacts_with.pmid", + "umls": "physically_interacts_with.umls" + }, + "ChemicalSubstance-physically_interacts_with-Gene": { + "pmid": "physically_interacts_with.pmid", + "umls": "physically_interacts_with.umls" + }, + "ChemicalSubstance-physically_interacts_with-PhenotypicFeature": { + "pmid": "physically_interacts_with.pmid", + "umls": "physically_interacts_with.umls" + }, + "ChemicalSubstance-positively_regulated_by-AnatomicalEntity": { + "pmid": "positively_regulated_by.pmid", + "umls": "positively_regulated_by.umls" + }, + "ChemicalSubstance-positively_regulated_by-BiologicalProcess": { + "pmid": "positively_regulated_by.pmid", + "umls": "positively_regulated_by.umls" + }, + "ChemicalSubstance-positively_regulated_by-Cell": { + "pmid": "positively_regulated_by.pmid", + "umls": "positively_regulated_by.umls" + }, + "ChemicalSubstance-positively_regulated_by-CellularComponent": { + "pmid": "positively_regulated_by.pmid", + "umls": "positively_regulated_by.umls" + }, + "ChemicalSubstance-positively_regulated_by-ChemicalSubstance": { + "pmid": "positively_regulated_by.pmid", + "umls": "positively_regulated_by.umls" + }, + "ChemicalSubstance-positively_regulated_by-Disease": { + "pmid": "positively_regulated_by.pmid", + "umls": "positively_regulated_by.umls" + }, + "ChemicalSubstance-positively_regulated_by-Gene": { + "pmid": "positively_regulated_by.pmid", + "umls": "positively_regulated_by.umls" + }, + "ChemicalSubstance-positively_regulated_by-PhenotypicFeature": { + "pmid": "positively_regulated_by.pmid", + "umls": "positively_regulated_by.umls" + }, + "ChemicalSubstance-positively_regulates-AnatomicalEntity": { + "pmid": "positively_regulates.pmid", + "umls": "positively_regulates.umls" + }, + "ChemicalSubstance-positively_regulates-BiologicalProcess": { + "pmid": "positively_regulates.pmid", + "umls": "positively_regulates.umls" + }, + "ChemicalSubstance-positively_regulates-Cell": { + "pmid": "positively_regulates.pmid", + "umls": "positively_regulates.umls" + }, + "ChemicalSubstance-positively_regulates-CellularComponent": { + "pmid": "positively_regulates.pmid", + "umls": "positively_regulates.umls" + }, + "ChemicalSubstance-positively_regulates-ChemicalSubstance": { + "pmid": "positively_regulates.pmid", + "umls": "positively_regulates.umls" + }, + "ChemicalSubstance-positively_regulates-Disease": { + "pmid": "positively_regulates.pmid", + "umls": "positively_regulates.umls" + }, + "ChemicalSubstance-positively_regulates-Gene": { + "pmid": "positively_regulates.pmid", + "umls": "positively_regulates.umls" + }, + "ChemicalSubstance-positively_regulates-PhenotypicFeature": { + "pmid": "positively_regulates.pmid", + "umls": "positively_regulates.umls" + }, + "ChemicalSubstance-prevents-Disease": { + "pmid": "prevents.pmid", + "umls": "prevents.umls" + }, + "ChemicalSubstance-produced_by-AnatomicalEntity": { + "pmid": "produced_by.pmid", + "umls": "produced_by.umls" + }, + "ChemicalSubstance-produced_by-BiologicalProcess": { + "pmid": "produced_by.pmid", + "umls": "produced_by.umls" + }, + "ChemicalSubstance-produced_by-Cell": { + "pmid": "produced_by.pmid", + "umls": "produced_by.umls" + }, + "ChemicalSubstance-produced_by-CellularComponent": { + "pmid": "produced_by.pmid", + "umls": "produced_by.umls" + }, + "ChemicalSubstance-produced_by-ChemicalSubstance": { + "pmid": "produced_by.pmid", + "umls": "produced_by.umls" + }, + "ChemicalSubstance-produced_by-Disease": { + "pmid": "produced_by.pmid", + "umls": "produced_by.umls" + }, + "ChemicalSubstance-produced_by-Gene": { + "pmid": "produced_by.pmid", + "umls": "produced_by.umls" + }, + "ChemicalSubstance-produced_by-PhenotypicFeature": { + "pmid": "produced_by.pmid", + "umls": "produced_by.umls" + }, + "ChemicalSubstance-produces-AnatomicalEntity": { + "pmid": "produces.pmid", + "umls": "produces.umls" + }, + "ChemicalSubstance-produces-Cell": { + "pmid": "produces.pmid", + "umls": "produces.umls" + }, + "ChemicalSubstance-produces-ChemicalSubstance": { + "pmid": "produces.pmid", + "umls": "produces.umls" + }, + "ChemicalSubstance-produces-Gene": { + "pmid": "produces.pmid", + "umls": "produces.umls" + }, + "ChemicalSubstance-produces-PhenotypicFeature": { + "pmid": "produces.pmid", + "umls": "produces.umls" + }, + "ChemicalSubstance-related_to-AnatomicalEntity": { + "pmid": "related_to.pmid", + "umls": "related_to.umls" + }, + "ChemicalSubstance-related_to-BiologicalProcess": { + "pmid": "related_to.pmid", + "umls": "related_to.umls" + }, + "ChemicalSubstance-related_to-ChemicalSubstance": { + "pmid": "related_to.pmid", + "umls": "related_to.umls" + }, + "ChemicalSubstance-related_to-Disease": { + "pmid": "related_to.pmid", + "umls": "related_to.umls" + }, + "ChemicalSubstance-related_to-Gene": { + "pmid": "related_to.pmid", + "umls": "related_to.umls" + }, + "ChemicalSubstance-related_to-PhenotypicFeature": { + "pmid": "related_to.pmid", + "umls": "related_to.umls" + }, + "ChemicalSubstance-treats-Disease": { + "pmid": "treats.pmid", + "umls": "treats.umls" } } }, - "servers": [ - { - "description": "Production server", - "url": "https://biothings.ncats.io/semmedbp" - } - ], - "tags": [ - { - "name": "chemical" - }, - { - "name": "annotation" - }, - { - "name": "query" - }, - { - "name": "translator" - }, - { - "name": "biothings" - }, - { - "name": "semmed" - } - ] - }, - { - "_id": "dc91716f44207d2e1287c727f281d339", - "_meta": { - "date_created": "2020-12-08T17:54:41.142148+00:00", - "last_updated": "2021-03-05T08:02:06.079146+00:00", - "slug": "bte_trapi", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biothings_explorer/smartapi.yaml", - "username": "kevinxin90" - }, - "_score": 0.47008187, "info": { "contact": { - "email": "kevinxin@scripps.edu", - "name": "Jiwen Xin", - "url": "https://github.com/kevinxin90" + "email": "help@biothings.io", + "name": "Chunlei Wu", + "x-id": "https://github.com/newgene", + "x-role": "responsible developer" }, - "description": "A ReasonerStdAPI for BioThings Explorer", - "termsOfService": "https://biothings.io/about", - "title": "BioThings Explorer ReasonerStdAPI", - "version": "1.0.0", - "x-reasoner_standard_version": "1.0.0", + "description": "Documentation of the SEMMED disease query web services. Learn more about [mydisease.info](http://pending.biothings.io/semmed)", + "termsOfService": "http://biothings.ncats.io", + "title": "SEMMED Chemical API", + "version": "1.0", "x-translator": { - "component": "ARA", + "component": "KP", "team": [ - "Exploring Agent" + "Service Provider" ] } }, "paths": { - "/metakg": { - "get": { + "/chemical": { + "post": { "parameters": [ { - "description": "The subject type of the association, e.g. Gene", - "example": "Gene", - "in": "query", - "name": "subject", - "schema": { - "type": "string" - } - }, - { - "description": "The object type of the association, e.g. ChemicalSubstance", - "example": "ChemicalSubstance", - "in": "query", - "name": "object", - "schema": { - "type": "string" - } + "$ref": "#/components/parameters/dotfield", + "name": "dotfield" }, { - "description": "The predicate of the association, e.g. Gene", - "example": "physically_interacts_with", - "in": "query", - "name": "predicate", - "schema": { - "type": "string" - } + "$ref": "#/components/parameters/fields", + "name": "fields" }, { - "description": "The API providing the association, e.g. MyChem.info API", - "example": "MyChem.info API", - "in": "query", - "name": "api", - "schema": { - "type": "string" - } + "$ref": "#/components/parameters/email", + "name": "email" }, { - "description": "The data source providing the association, e.g. drugbank", - "example": "drugbank", - "in": "query", - "name": "provided_by", - "schema": { - "type": "string" - } + "$ref": "#/components/parameters/format", + "name": "format" } ], - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "description": "Array of all associations", - "items": { - "properties": { - "api": { - "description": "The api providing the association, e.g. MyChem.info", - "properties": { - "name": { - "description": "The api providing the association, e.g. MyChem.info", - "example": "MyChem.info API", - "type": "string" - }, - "smartapi": { - "description": "smartapi related data", - "properties": { - "id": { - "description": "unique smartapi id for the api", - "example": "8f08d1446e0bb9c2b323713ce83e2bd3", - "type": "string" - }, - "metadata": { - "description": "the url for smartapi specification", - "example": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/mychem.info/openapi_full.yml", - "type": "string" - }, - "ui": { - "description": "the web UI url for the API", - "example": "https://smart-api.info/ui/8f08d1446e0bb9c2b323713ce83e2bd3", - "type": "string" - } - }, - "type": "object" - } - }, - "type": "object" - }, - "object": { - "description": "The object type of the association, e.g. ChemicalSubstance", - "example": "ChemicalSubstance", - "type": "string" - }, - "predicate": { - "description": "The predicate of the association, e.g. physically_interacts_with", - "example": "physically_interacts_with", - "type": "string" - }, - "provided_by": { - "description": "The data source providing the association, e.g. ChEMBL", - "example": "ChEMBL", - "type": "string" - }, - "subject": { - "description": "The subject type of the association, e.g. Gene", - "example": "Gene", - "type": "string" - } - }, - "type": "object" - }, - "type": "array" - } - } - }, - "description": "Association information including subject, object, predicate, api, provided_by and smartapi info." - } - }, - "summary": "retrieve associations within smartapi, if no parameters provided, will return all associations", - "tags": [ - "metadata" - ] - } - }, - "/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": { - "chemical_substance": { - "chemical_substance": [ - "correlated_with" - ] - } - }, - "type": "object" - } - } - }, - "description": "Predicates by source and target" - } - }, - "summary": "Get supported relationships by source and target", - "tags": [ - "metadata", - "0.9.2" - ] - } - }, - "/v1/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": [ - "predicates", - "1.0.0" - ] - } - }, - "/v1/smartapi/{smartapi_id}/predicates": { - "get": { - "parameters": [ - { - "description": "SmartAPI ID of an API, you can get it from https://smart-api.info/registry", - "example": "978fe380a147a8641caf72320862697b", - "in": "path", - "name": "smartapi_id", - "required": true, - "schema": { - "type": "string" + "requestBody": { + "content": { + "application/x-www-form-urlencoded": { + "schema": { + "properties": { + "ids": { + "description": "multiple disease IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", + "type": "string" + } + }, + "required": [ + "ids" + ] + } } } - ], + }, "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" - ] - } + "items": { + "$ref": "#/components/schemas/Disease" }, - "type": "object" + "type": "array" } } }, - "description": "Predicates by source and target" + "description": "A list of matching disease objects" + }, + "400": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResult" + } + } + }, + "description": "A response indicating an improperly formatted query" } }, - "summary": "Get supported relationships by source and target for individual smartAPI", + "summary": "For a list of disease IDs, return the matching disease object", "tags": [ - "predicates", - "1.0.0" + "gene" ] } }, - "/v1/team/{team_name}/predicates": { + "/chemical/{chemicalid}": { "get": { "parameters": [ { - "description": "Translator Team Name, e.g. Service Provider, Multiomics Provider", - "example": "Multiomics Provider", + "description": "Retrieve disease objects based on ID", + "example": "C0004096", "in": "path", - "name": "team_name", + "name": "chemicalid", "required": true, "schema": { - "enum": [ - "Multiomics Provider", - "Text Mining Provider", - "Service Provider" - ], "type": "string" } + }, + { + "$ref": "#/components/parameters/dotfield", + "name": "dotfield" + }, + { + "$ref": "#/components/parameters/callback", + "name": "callback" + }, + { + "$ref": "#/components/parameters/fields", + "name": "fields" + }, + { + "$ref": "#/components/parameters/email", + "name": "email" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" } ], "responses": { @@ -47493,581 +47065,659 @@ "content": { "application/json": { "schema": { - "additionalProperties": { - "additionalProperties": { - "description": "Array of predicates", - "items": { - "type": "string" - }, - "type": "array" - }, - "description": "Target map", - "type": "object" - }, - "description": "Source map", - "example": { - "biolink:ChemicalSubstance": { - "biolink:Gene": [ - "biolink:directly_interacts_with", - "biolink:decreases_activity_of" - ] - } - }, - "type": "object" + "$ref": "#/components/schemas/Disease" } } }, - "description": "Predicates by source and target" + "description": "A matching disease object" + }, + "404": { + "description": "A response indicating an unknown disease ID" } }, - "summary": "Get supported relationships by source and target for a KP/ARA team", + "summary": "Retrieve disease objects based on ID", "tags": [ - "predicates", - "1.0.0" + "disease" ] } }, - "/v1/query": { - "post": { - "description": "", - "operationId": "query", - "requestBody": { - "content": { - "application/json": { - "example": { - "message": { - "query_graph": { - "edges": { - "e00": { - "object": "n01", - "subject": "n00" - } - }, - "nodes": { - "n00": { - "category": "biolink:Disease", - "id": "MONDO:0005737" - }, - "n01": { - "category": "biolink:ChemicalSubstance" - } - } - } - } - }, - "schema": { - "$ref": "#/components/schemas/Query" - } - } - }, - "description": "Query information to be submitted", - "required": true - }, + "/metadata": { + "get": { + "parameters": [ + { + "$ref": "#/components/parameters/callback", + "in": "query", + "name": "callback" + } + ], "responses": { "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Response" - } - } - }, - "description": "OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized." - }, - "400": { - "content": { - "application/json": { - "schema": { - "type": "string" - } - } - }, - "description": "Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)." - }, - "500": { - "content": { - "application/json": { - "schema": { - "type": "string" - } - } - }, - "description": "Internal server error." - }, - "501": { - "content": { - "application/json": { - "schema": { - "type": "string" - } - } - }, - "description": "Not implemented." + "description": "mydisease.info metadata object" } }, - "summary": "Query BioThings Explorer TRAPI API as ARA", + "summary": "Get metadata about the data available from mydisease.info", "tags": [ - "query", - "1.0.0" - ], - "x-swagger-router-controller": "swagger_server.controllers.query_controller" + "metadata" + ] } }, - "/v1/smartapi/{smartapi_id}/query": { - "post": { - "description": "", - "operationId": "querySmartAPI", + "/metadata/fields": { + "get": { "parameters": [ { - "description": "SmartAPI ID of an API, you can get it from https://smart-api.info/registry", - "example": "978fe380a147a8641caf72320862697b", - "in": "path", - "name": "smartapi_id", - "required": true, - "schema": { - "type": "string" - } + "$ref": "#/components/parameters/search", + "name": "search" + }, + { + "$ref": "#/components/parameters/callback", + "name": "callback" + }, + { + "$ref": "#/components/parameters/prefix", + "name": "prefix" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" } ], - "requestBody": { - "content": { - "application/json": { - "example": { - "message": { - "query_graph": { - "edges": { - "e00": { - "object": "n01", - "subject": "n00" - } - }, - "nodes": { - "n00": { - "category": "biolink:Gene", - "id": "NCBIGENE:1017" - }, - "n01": { - "category": "biolink:ChemicalSubstance" - } - } - } - } - }, - "schema": { - "$ref": "#/components/schemas/Query" - } - } - }, - "description": "Query information to be submitted", - "required": true - }, "responses": { "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Response" - } - } - }, - "description": "OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized." - }, - "400": { - "content": { - "application/json": { - "schema": { - "type": "string" - } - } - }, - "description": "Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)." - }, - "500": { - "content": { - "application/json": { - "schema": { - "type": "string" - } - } - }, - "description": "Internal server error." - }, - "501": { - "content": { - "application/json": { - "schema": { - "type": "string" - } - } - }, - "description": "Not implemented." + "description": "mydisease.info metadata fields object" } }, - "summary": "Query individual SmartAPI as TRAPI service using SmartAPI ID", + "summary": "Get metadata about the data fields available from a mydisease.info chem object", "tags": [ - "query", - "1.0.0" - ], - "x-swagger-router-controller": "swagger_server.controllers.query_controller" + "metadata" + ] } }, - "/v1/team/{team_name}/query": { - "post": { - "description": "", - "operationId": "queryTeam", + "/query": { + "get": { "parameters": [ { - "description": "Translator Team Name, e.g. Service Provider, Multiomics Provider", - "example": "Text Mining Provider", - "in": "path", - "name": "team_name", + "description": "Query string. The detailed query syntax can be found from our [docs](http://mydisease.info). Examples: \"cancer\", \"primary ciliary dyskinesia\", \"DOID:9562\"", + "example": "cancer", + "in": "query", + "name": "q", "required": true, "schema": { - "enum": [ - "Multiomics Provider", - "Text Mining Provider", - "Service Provider" - ], "type": "string" } + }, + { + "$ref": "#/components/parameters/dotfield", + "name": "dotfield" + }, + { + "$ref": "#/components/parameters/fields", + "name": "fields" + }, + { + "$ref": "#/components/parameters/facet_size", + "name": "facet_size" + }, + { + "$ref": "#/components/parameters/sort", + "name": "sort" + }, + { + "$ref": "#/components/parameters/callback", + "name": "callback" + }, + { + "$ref": "#/components/parameters/email", + "name": "email" + }, + { + "$ref": "#/components/parameters/facets", + "name": "facets" + }, + { + "$ref": "#/components/parameters/size", + "name": "size" + }, + { + "$ref": "#/components/parameters/from", + "name": "from" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" } ], - "requestBody": { - "content": { - "application/json": { - "example": { - "message": { - "query_graph": { - "edges": { - "e00": { - "object": "n01", - "subject": "n00" - } - }, - "nodes": { - "n00": { - "category": "biolink:Gene", - "id": "NCBIGENE:1017" - }, - "n01": { - "category": "biolink:ChemicalSubstance" - } - } - } - } - }, - "schema": { - "$ref": "#/components/schemas/Query" - } - } - }, - "description": "Query information to be submitted", - "required": true - }, "responses": { "200": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Response" + "$ref": "#/components/schemas/QueryResult" } } }, - "description": "OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized." + "description": "A query response with the \"hits\" property" }, "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 individual Translator team as individual TRAPI service using team name", - "tags": [ - "query", - "1.0.0" - ], - "x-swagger-router-controller": "swagger_server.controllers.query_controller" - } - }, - "/query/": { - "post": { - "requestBody": { - "content": { - "application/json": { - "example": { - "message": { - "query_graph": { - "edges": [ - { - "id": "e00", - "source_id": "n00", - "target_id": "n01" - }, - { - "id": "e01", - "source_id": "n01", - "target_id": "n02" - } - ], - "nodes": [ - { - "curie": "MONDO:0005737", - "id": "n00", - "type": "disease" - }, - { - "id": "n01", - "set": true, - "type": "gene" - }, - { - "id": "n02", - "type": "chemical_substance" - } - ] - } - } - }, - "schema": { - "$ref": "#/components/schemas/Query" - } - } - }, - "description": "A message with question graph.", - "required": true - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Message" + "$ref": "#/components/schemas/ErrorResult" } } }, - "description": "A message with knowledge graph and answers." + "description": "A response indicating an improperly formatted query" } }, - "summary": "Get answers to a question", + "summary": "Make disease queries and return matching disease hits. Supports JSONP and CORS as well.", "tags": [ - "0.9.2", "query" ] - } - }, - "/smartapi/{smartapi_id}/query/": { + }, "post": { "parameters": [ { - "description": "SmartAPI ID of an API, you can get it from https://smart-api.info/registry", - "example": "978fe380a147a8641caf72320862697b", - "in": "path", - "name": "smartapi_id", - "required": true, - "schema": { - "type": "string" - } + "$ref": "#/components/parameters/dotfield", + "name": "dotfield" + }, + { + "$ref": "#/components/parameters/email", + "name": "email" + }, + { + "$ref": "#/components/parameters/fields", + "name": "fields" + }, + { + "$ref": "#/components/parameters/size", + "name": "size" + }, + { + "$ref": "#/components/parameters/format", + "name": "format" } ], "requestBody": { "content": { - "application/json": { - "example": { - "message": { - "query_graph": { - "edges": [ - { - "id": "e00", - "source_id": "n00", - "target_id": "n01" - } - ], - "nodes": [ - { - "curie": "NCBIGENE:1017", - "id": "n00", - "type": "gene" - }, - { - "id": "n01", - "type": "chemical_substance" - } - ] + "application/x-www-form-urlencoded": { + "schema": { + "properties": { + "q": { + "description": "multiple 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" } } - }, - "schema": { - "$ref": "#/components/schemas/Query" } } - }, - "description": "A message with question graph.", - "required": true + } }, "responses": { "200": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Message" + "$ref": "#/components/schemas/QueryPOSTResult" } } }, - "description": "A message with knowledge graph and answers." + "description": "Query response objects with the \"hits\" property" + }, + "400": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResult" + } + } + }, + "description": "A response indicating an improperly formatted query" } }, - "summary": "Get answers to a question using a specific API", + "summary": "Make batch disease queries and return matching disease hits", "tags": [ - "0.9.2", "query" + ], + "x-bte-kgs-operations": [ + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affected_by-ChemicalSubstance" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affected_by-Disease" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affected_by-BiologicalProcess" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affected_by-Gene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affects-AnatomicalEntity" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affects-Cell" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affects-ChemicalSubstance" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affects-BiologicalProcess" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affects-Disease" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affects-PhenotypicFeature" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affects-Gene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affects-CellularComponent" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-causes-Disease" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-causes-BiologicalProcess" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-coexists_with-AnatomicalEntity" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-coexists_with-Cell" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-coexists_with-ChemicalSubstance" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-coexists_with-BiologicalProcess" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-coexists_with-Disease" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-coexists_with-PhenotypicFeature" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-coexists_with-Gene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-coexists_with-CellularComponent" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-disrupted_by-ChemicalSubstance" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-disrupted_by-Gene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-disrupts-AnatomicalEntity" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-disrupts-Cell" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-disrupts-ChemicalSubstance" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-disrupts-BiologicalProcess" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-disrupts-Disease" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-disrupts-PhenotypicFeature" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-disrupts-Gene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-disrupts-CellularComponent" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulated_by-AnatomicalEntity" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulated_by-Cell" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulated_by-ChemicalSubstance" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulated_by-BiologicalProcess" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulated_by-Disease" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulated_by-PhenotypicFeature" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulated_by-Gene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulated_by-CellularComponent" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulates-AnatomicalEntity" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulates-Cell" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulates-ChemicalSubstance" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulates-BiologicalProcess" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulates-Disease" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulates-PhenotypicFeature" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulates-Gene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulates-CellularComponent" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-physically_interacts_with-AnatomicalEntity" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-physically_interacts_with-Cell" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-physically_interacts_with-ChemicalSubstance" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-physically_interacts_with-BiologicalProcess" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-physically_interacts_with-Disease" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-physically_interacts_with-PhenotypicFeature" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-physically_interacts_with-Gene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-physically_interacts_with-CellularComponent" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulated_by-AnatomicalEntity" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulated_by-Cell" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulated_by-ChemicalSubstance" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulated_by-BiologicalProcess" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulated_by-Disease" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulated_by-PhenotypicFeature" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulated_by-Gene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulated_by-CellularComponent" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulates-AnatomicalEntity" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulates-Cell" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulates-ChemicalSubstance" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulates-BiologicalProcess" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulates-Disease" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulates-PhenotypicFeature" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulates-Gene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulates-CellularComponent" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-prevents-Disease" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produced_by-AnatomicalEntity" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produced_by-Cell" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produced_by-ChemicalSubstance" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produced_by-BiologicalProcess" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produced_by-Disease" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produced_by-PhenotypicFeature" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produced_by-Gene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produced_by-CellularComponent" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produces-AnatomicalEntity" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produces-Cell" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produces-ChemicalSubstance" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produces-PhenotypicFeature" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produces-Gene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-related_to-AnatomicalEntity" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-related_to-ChemicalSubstance" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-related_to-BiologicalProcess" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-related_to-Disease" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-related_to-PhenotypicFeature" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-related_to-Gene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-treats-Disease" + } ] } + } + }, + "servers": [ + { + "description": "Production server", + "url": "https://biothings.ncats.io/semmedchemical" + } + ], + "tags": [ + { + "name": "chemical" }, - "/source/{source_name}/query/": { - "post": { - "parameters": [ - { - "description": "The name of the data source", - "example": "drugbank", - "in": "path", - "name": "source_name", - "required": true, - "schema": { - "type": "string" + { + "name": "annotation" + }, + { + "name": "query" + }, + { + "name": "translator" + }, + { + "name": "biothings" + }, + { + "name": "semmed" + } + ] + }, + { + "_id": "ed0ee52921c7cbce24033ffd1369922e", + "_meta": { + "date_created": "2020-12-07T23:03:08.522992+00:00", + "last_updated": "2021-03-29T07:04:44.533773+00:00", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/semmed/semmed_disease.yaml", + "username": "kevinxin90" + }, + "_score": 0.4848808, + "components": { + "x-bte-kgs-operations": { + "Disease-affected_by-AnatomicalEntity": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "Disease" } - } - ], - "requestBody": { - "content": { - "application/json": { - "example": { - "message": { - "query_graph": { - "edges": [ - { - "id": "e00", - "source_id": "n00", - "target_id": "n01" - } - ], - "nodes": [ - { - "curie": "NCBIGENE:1017", - "id": "n00", - "type": "gene" - }, - { - "id": "n01", - "type": "chemical_substance" - } - ] - } - } - }, - "schema": { - "$ref": "#/components/schemas/Query" - } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "AnatomicalEntity" + } + ], + "parameters": { + "fields": "affected_by" + }, + "path": "/query", + "predicate": "affected_by", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/Disease-affected_by-AnatomicalEntity" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "Disease-affected_by-BiologicalProcess": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "Disease" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "BiologicalProcess" + } + ], + "parameters": { + "fields": "affected_by" + }, + "path": "/query", + "predicate": "affected_by", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/Disease-affected_by-BiologicalProcess" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "Disease-affected_by-Cell": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "Disease" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "Cell" } + ], + "parameters": { + "fields": "affected_by" }, - "description": "A message with question graph.", - "required": true - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Message" - } - } - }, - "description": "A message with knowledge graph and answers." - } - }, - "summary": "Get answers to a question using a specific data source.", - "tags": [ - "0.9.2", - "query" - ] - } - } - }, - "servers": [ - { - "url": "https://api.bte.ncats.io" - } - ], - "tags": [ - { - "name": "1.0.0" - }, - { - "name": "0.9.2" - }, - { - "name": "translator" - }, - { - "name": "biothings" - }, - { - "name": "metadata" - }, - { - "name": "query" - } - ] - }, - { - "_id": "7c07eca4ef5ceb532d06c0180e86aedd", - "_meta": { - "date_created": "2020-12-07T22:59:11.235751+00:00", - "last_updated": "2021-03-05T08:01:56.315342+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/semmed/semmed_chemical.yaml", - "username": "kevinxin90" - }, - "_score": 0.47008187, - "components": { - "x-bte-kgs-operations": { - "ChemicalSubstance-affected_by-BiologicalProcess": [ + "path": "/query", + "predicate": "affected_by", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/Disease-affected_by-Cell" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "Disease-affected_by-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "CellularComponent" } ], "parameters": { @@ -48082,19 +47732,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affected_by-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/Disease-affected_by-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-affected_by-ChemicalSubstance": [ + "Disease-affected_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48116,19 +47766,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affected_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/Disease-affected_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-affected_by-Disease": [ + "Disease-affected_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48150,19 +47800,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affected_by-Disease" + "$ref": "#/components/x-bte-response-mapping/Disease-affected_by-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-affected_by-Gene": [ + "Disease-affected_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48184,19 +47834,53 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affected_by-Gene" + "$ref": "#/components/x-bte-response-mapping/Disease-affected_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-affects-AnatomicalEntity": [ + "Disease-affected_by-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "PhenotypicFeature" + } + ], + "parameters": { + "fields": "affected_by" + }, + "path": "/query", + "predicate": "affected_by", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/Disease-affected_by-PhenotypicFeature" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "Disease-affects-AnatomicalEntity": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "Disease" } ], "method": "post", @@ -48218,19 +47902,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affects-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/Disease-affects-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-affects-BiologicalProcess": [ + "Disease-affects-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48252,19 +47936,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affects-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/Disease-affects-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-affects-Cell": [ + "Disease-affects-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48286,19 +47970,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affects-Cell" + "$ref": "#/components/x-bte-response-mapping/Disease-affects-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-affects-CellularComponent": [ + "Disease-affects-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48320,19 +48004,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affects-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/Disease-affects-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-affects-ChemicalSubstance": [ + "Disease-affects-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48354,19 +48038,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affects-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/Disease-affects-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-affects-Disease": [ + "Disease-affects-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48388,19 +48072,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affects-Disease" + "$ref": "#/components/x-bte-response-mapping/Disease-affects-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-affects-Gene": [ + "Disease-affects-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48422,19 +48106,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affects-Gene" + "$ref": "#/components/x-bte-response-mapping/Disease-affects-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-affects-PhenotypicFeature": [ + "Disease-affects-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48456,21 +48140,293 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-affects-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/Disease-affects-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-causes-BiologicalProcess": [ + "Disease-caused_by-AnatomicalEntity": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "Disease" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "AnatomicalEntity" + } + ], + "parameters": { + "fields": "caused_by" + }, + "path": "/query", + "predicate": "caused_by", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/Disease-caused_by-AnatomicalEntity" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "Disease-caused_by-BiologicalProcess": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "Disease" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "BiologicalProcess" + } + ], + "parameters": { + "fields": "caused_by" + }, + "path": "/query", + "predicate": "caused_by", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/Disease-caused_by-BiologicalProcess" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "Disease-caused_by-Cell": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "Disease" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "Cell" + } + ], + "parameters": { + "fields": "caused_by" + }, + "path": "/query", + "predicate": "caused_by", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/Disease-caused_by-Cell" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "Disease-caused_by-CellularComponent": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "Disease" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "CellularComponent" + } + ], + "parameters": { + "fields": "caused_by" + }, + "path": "/query", + "predicate": "caused_by", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/Disease-caused_by-CellularComponent" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "Disease-caused_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ + { + "id": "UMLS", + "semantic": "Disease" + } + ], + "method": "post", + "outputs": [ { "id": "UMLS", "semantic": "ChemicalSubstance" } ], + "parameters": { + "fields": "caused_by" + }, + "path": "/query", + "predicate": "caused_by", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/Disease-caused_by-ChemicalSubstance" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "Disease-caused_by-Disease": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "Disease" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "Disease" + } + ], + "parameters": { + "fields": "caused_by" + }, + "path": "/query", + "predicate": "caused_by", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/Disease-caused_by-Disease" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "Disease-caused_by-Gene": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "Disease" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "Gene" + } + ], + "parameters": { + "fields": "caused_by" + }, + "path": "/query", + "predicate": "caused_by", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/Disease-caused_by-Gene" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "Disease-caused_by-PhenotypicFeature": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "Disease" + } + ], + "method": "post", + "outputs": [ + { + "id": "UMLS", + "semantic": "PhenotypicFeature" + } + ], + "parameters": { + "fields": "caused_by" + }, + "path": "/query", + "predicate": "caused_by", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "umls" + } + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/Disease-caused_by-PhenotypicFeature" + }, + "source": "SEMMED", + "supportBatch": true + } + ], + "Disease-causes-BiologicalProcess": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "UMLS", + "semantic": "Disease" + } + ], "method": "post", "outputs": [ { @@ -48490,19 +48446,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-causes-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/Disease-causes-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-causes-Disease": [ + "Disease-causes-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48524,19 +48480,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-causes-Disease" + "$ref": "#/components/x-bte-response-mapping/Disease-causes-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-coexists_with-AnatomicalEntity": [ + "Disease-coexists_with-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48558,19 +48514,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-coexists_with-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/Disease-coexists_with-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-coexists_with-BiologicalProcess": [ + "Disease-coexists_with-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48592,19 +48548,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-coexists_with-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/Disease-coexists_with-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-coexists_with-Cell": [ + "Disease-coexists_with-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48626,19 +48582,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-coexists_with-Cell" + "$ref": "#/components/x-bte-response-mapping/Disease-coexists_with-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-coexists_with-CellularComponent": [ + "Disease-coexists_with-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48660,19 +48616,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-coexists_with-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/Disease-coexists_with-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-coexists_with-ChemicalSubstance": [ + "Disease-coexists_with-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48694,19 +48650,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-coexists_with-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/Disease-coexists_with-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-coexists_with-Disease": [ + "Disease-coexists_with-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48728,19 +48684,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-coexists_with-Disease" + "$ref": "#/components/x-bte-response-mapping/Disease-coexists_with-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-coexists_with-Gene": [ + "Disease-coexists_with-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48762,19 +48718,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-coexists_with-Gene" + "$ref": "#/components/x-bte-response-mapping/Disease-coexists_with-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-coexists_with-PhenotypicFeature": [ + "Disease-coexists_with-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48796,19 +48752,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-coexists_with-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/Disease-coexists_with-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-disrupted_by-ChemicalSubstance": [ + "Disease-derives_from-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48819,10 +48775,10 @@ } ], "parameters": { - "fields": "disrupted_by" + "fields": "derives_from" }, "path": "/query", - "predicate": "disrupted_by", + "predicate": "derives_from", "requestBody": { "body": { "q": "{inputs[0]}", @@ -48830,19 +48786,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-disrupted_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/Disease-derives_from-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-disrupted_by-Gene": [ + "Disease-derives_from-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48853,10 +48809,10 @@ } ], "parameters": { - "fields": "disrupted_by" + "fields": "derives_from" }, "path": "/query", - "predicate": "disrupted_by", + "predicate": "derives_from", "requestBody": { "body": { "q": "{inputs[0]}", @@ -48864,67 +48820,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-disrupted_by-Gene" + "$ref": "#/components/x-bte-response-mapping/Disease-derives_from-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-disrupts-AnatomicalEntity": [ + "Disease-derives_info-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ - { - "id": "UMLS", - "semantic": "AnatomicalEntity" - } - ], - "parameters": { - "fields": "disrupts" - }, - "path": "/query", - "predicate": "disrupts", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-disrupts-AnatomicalEntity" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "ChemicalSubstance-disrupts-BiologicalProcess": [ - { - "inputSeparator": ",", - "inputs": [ { "id": "UMLS", "semantic": "ChemicalSubstance" } ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "BiologicalProcess" - } - ], "parameters": { - "fields": "disrupts" + "fields": "derives_info" }, "path": "/query", - "predicate": "disrupts", + "predicate": "derives_info", "requestBody": { "body": { "q": "{inputs[0]}", @@ -48932,33 +48854,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-disrupts-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/Disease-derives_info-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-disrupts-Cell": [ + "Disease-disrupted_by-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Cell" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "disrupts" + "fields": "disrupted_by" }, "path": "/query", - "predicate": "disrupts", + "predicate": "disrupted_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -48966,19 +48888,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-disrupts-Cell" + "$ref": "#/components/x-bte-response-mapping/Disease-disrupted_by-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-disrupts-CellularComponent": [ + "Disease-disrupted_by-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -48989,10 +48911,10 @@ } ], "parameters": { - "fields": "disrupts" + "fields": "disrupted_by" }, "path": "/query", - "predicate": "disrupts", + "predicate": "disrupted_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -49000,19 +48922,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-disrupts-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/Disease-disrupted_by-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-disrupts-ChemicalSubstance": [ + "Disease-disrupted_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -49023,10 +48945,10 @@ } ], "parameters": { - "fields": "disrupts" + "fields": "disrupted_by" }, "path": "/query", - "predicate": "disrupts", + "predicate": "disrupted_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -49034,19 +48956,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-disrupts-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/Disease-disrupted_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-disrupts-Disease": [ + "Disease-disrupted_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -49057,10 +48979,10 @@ } ], "parameters": { - "fields": "disrupts" + "fields": "disrupted_by" }, "path": "/query", - "predicate": "disrupts", + "predicate": "disrupted_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -49068,19 +48990,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-disrupts-Disease" + "$ref": "#/components/x-bte-response-mapping/Disease-disrupted_by-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-disrupts-Gene": [ + "Disease-disrupted_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -49091,10 +49013,10 @@ } ], "parameters": { - "fields": "disrupts" + "fields": "disrupted_by" }, "path": "/query", - "predicate": "disrupts", + "predicate": "disrupted_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -49102,19 +49024,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-disrupts-Gene" + "$ref": "#/components/x-bte-response-mapping/Disease-disrupted_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-disrupts-PhenotypicFeature": [ + "Disease-disrupted_by-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -49125,10 +49047,10 @@ } ], "parameters": { - "fields": "disrupts" + "fields": "disrupted_by" }, "path": "/query", - "predicate": "disrupts", + "predicate": "disrupted_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -49136,19 +49058,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-disrupts-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/Disease-disrupted_by-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-negatively_regulated_by-AnatomicalEntity": [ + "Disease-disrupts-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -49159,10 +49081,10 @@ } ], "parameters": { - "fields": "negatively_regulated_by" + "fields": "disrupts" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", @@ -49170,19 +49092,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulated_by-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/Disease-disrupts-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-negatively_regulated_by-BiologicalProcess": [ + "Disease-disrupts-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -49193,10 +49115,10 @@ } ], "parameters": { - "fields": "negatively_regulated_by" + "fields": "disrupts" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", @@ -49204,19 +49126,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulated_by-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/Disease-disrupts-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-negatively_regulated_by-Cell": [ + "Disease-disrupts-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -49227,10 +49149,10 @@ } ], "parameters": { - "fields": "negatively_regulated_by" + "fields": "disrupts" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", @@ -49238,19 +49160,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulated_by-Cell" + "$ref": "#/components/x-bte-response-mapping/Disease-disrupts-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-negatively_regulated_by-CellularComponent": [ + "Disease-disrupts-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -49261,44 +49183,10 @@ } ], "parameters": { - "fields": "negatively_regulated_by" - }, - "path": "/query", - "predicate": "negatively_regulated_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulated_by-CellularComponent" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "ChemicalSubstance-negatively_regulated_by-ChemicalSubstance": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "ChemicalSubstance" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "ChemicalSubstance" - } - ], - "parameters": { - "fields": "negatively_regulated_by" + "fields": "disrupts" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", @@ -49306,19 +49194,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulated_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/Disease-disrupts-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-negatively_regulated_by-Disease": [ + "Disease-disrupts-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -49329,10 +49217,10 @@ } ], "parameters": { - "fields": "negatively_regulated_by" + "fields": "disrupts" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", @@ -49340,19 +49228,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulated_by-Disease" + "$ref": "#/components/x-bte-response-mapping/Disease-disrupts-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-negatively_regulated_by-Gene": [ + "Disease-disrupts-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -49363,10 +49251,10 @@ } ], "parameters": { - "fields": "negatively_regulated_by" + "fields": "disrupts" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", @@ -49374,19 +49262,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulated_by-Gene" + "$ref": "#/components/x-bte-response-mapping/Disease-disrupts-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-negatively_regulated_by-PhenotypicFeature": [ + "Disease-disrupts-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -49397,10 +49285,10 @@ } ], "parameters": { - "fields": "negatively_regulated_by" + "fields": "disrupts" }, "path": "/query", - "predicate": "negatively_regulated_by", + "predicate": "disrupts", "requestBody": { "body": { "q": "{inputs[0]}", @@ -49408,33 +49296,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulated_by-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/Disease-disrupts-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-negatively_regulates-AnatomicalEntity": [ + "Disease-negatively_regulated_by-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "negatively_regulates" + "fields": "negatively_regulated_by" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -49442,33 +49330,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulates-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/Disease-negatively_regulated_by-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-negatively_regulates-BiologicalProcess": [ + "Disease-negatively_regulated_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "negatively_regulates" + "fields": "negatively_regulated_by" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -49476,33 +49364,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulates-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/Disease-negatively_regulated_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-negatively_regulates-Cell": [ + "Disease-negatively_regulated_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Cell" + "semantic": "Disease" } ], "parameters": { - "fields": "negatively_regulates" + "fields": "negatively_regulated_by" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -49510,33 +49398,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulates-Cell" + "$ref": "#/components/x-bte-response-mapping/Disease-negatively_regulated_by-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-negatively_regulates-CellularComponent": [ + "Disease-negatively_regulated_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "CellularComponent" + "semantic": "Gene" } ], "parameters": { - "fields": "negatively_regulates" + "fields": "negatively_regulated_by" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -49544,33 +49432,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulates-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/Disease-negatively_regulated_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-negatively_regulates-ChemicalSubstance": [ + "Disease-negatively_regulated_by-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "PhenotypicFeature" } ], "parameters": { - "fields": "negatively_regulates" + "fields": "negatively_regulated_by" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "entity_negatively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -49578,33 +49466,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulates-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/Disease-negatively_regulated_by-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-negatively_regulates-Disease": [ + "Disease-negatively_regulates-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Disease" + "semantic": "BiologicalProcess" } ], "parameters": { "fields": "negatively_regulates" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -49612,33 +49500,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulates-Disease" + "$ref": "#/components/x-bte-response-mapping/Disease-negatively_regulates-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-negatively_regulates-Gene": [ + "Disease-negatively_regulates-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "ChemicalSubstance" } ], "parameters": { "fields": "negatively_regulates" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -49646,33 +49534,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulates-Gene" + "$ref": "#/components/x-bte-response-mapping/Disease-negatively_regulates-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-negatively_regulates-PhenotypicFeature": [ + "Disease-negatively_regulates-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "Disease" } ], "parameters": { "fields": "negatively_regulates" }, "path": "/query", - "predicate": "negatively_regulates", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -49680,33 +49568,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-negatively_regulates-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/Disease-negatively_regulates-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-physically_interacts_with-AnatomicalEntity": [ + "Disease-negatively_regulates-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Gene" } ], "parameters": { - "fields": "physically_interacts_with" + "fields": "negatively_regulates" }, "path": "/query", - "predicate": "physically_interacts_with", + "predicate": "entity_negatively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -49714,19 +49602,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-physically_interacts_with-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/Disease-negatively_regulates-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-physically_interacts_with-BiologicalProcess": [ + "Disease-physically_interacts_with-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -49748,53 +49636,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-physically_interacts_with-BiologicalProcess" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "ChemicalSubstance-physically_interacts_with-Cell": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "ChemicalSubstance" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "Cell" - } - ], - "parameters": { - "fields": "physically_interacts_with" - }, - "path": "/query", - "predicate": "physically_interacts_with", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-physically_interacts_with-Cell" + "$ref": "#/components/x-bte-response-mapping/Disease-physically_interacts_with-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-physically_interacts_with-CellularComponent": [ + "Disease-physically_interacts_with-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -49816,19 +49670,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-physically_interacts_with-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/Disease-physically_interacts_with-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-physically_interacts_with-ChemicalSubstance": [ + "Disease-physically_interacts_with-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -49850,19 +49704,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-physically_interacts_with-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/Disease-physically_interacts_with-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-physically_interacts_with-Disease": [ + "Disease-physically_interacts_with-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -49884,19 +49738,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-physically_interacts_with-Disease" + "$ref": "#/components/x-bte-response-mapping/Disease-physically_interacts_with-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-physically_interacts_with-Gene": [ + "Disease-physically_interacts_with-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -49918,19 +49772,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-physically_interacts_with-Gene" + "$ref": "#/components/x-bte-response-mapping/Disease-physically_interacts_with-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-physically_interacts_with-PhenotypicFeature": [ + "Disease-physically_interacts_with-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -49952,67 +49806,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-physically_interacts_with-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/Disease-physically_interacts_with-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-positively_regulated_by-AnatomicalEntity": [ + "Disease-positively_regulated_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ - { - "id": "UMLS", - "semantic": "AnatomicalEntity" - } - ], - "parameters": { - "fields": "positively_regulated_by" - }, - "path": "/query", - "predicate": "positively_regulated_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulated_by-AnatomicalEntity" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "ChemicalSubstance-positively_regulated_by-BiologicalProcess": [ - { - "inputSeparator": ",", - "inputs": [ { "id": "UMLS", "semantic": "ChemicalSubstance" } ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "BiologicalProcess" - } - ], "parameters": { "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50020,33 +49840,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulated_by-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/Disease-positively_regulated_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-positively_regulated_by-Cell": [ + "Disease-positively_regulated_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Cell" + "semantic": "Disease" } ], "parameters": { "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50054,33 +49874,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulated_by-Cell" + "$ref": "#/components/x-bte-response-mapping/Disease-positively_regulated_by-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-positively_regulated_by-CellularComponent": [ + "Disease-positively_regulated_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "CellularComponent" + "semantic": "Gene" } ], "parameters": { "fields": "positively_regulated_by" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "entity_positively_regulated_by_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50088,33 +49908,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulated_by-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/Disease-positively_regulated_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-positively_regulated_by-ChemicalSubstance": [ + "Disease-positively_regulates-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "positively_regulated_by" + "fields": "positively_regulates" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "entity_positively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50122,101 +49942,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulated_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/Disease-positively_regulates-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-positively_regulated_by-Disease": [ + "Disease-positively_regulates-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ - { - "id": "UMLS", - "semantic": "ChemicalSubstance" - } - ], - "method": "post", - "outputs": [ { "id": "UMLS", "semantic": "Disease" } ], - "parameters": { - "fields": "positively_regulated_by" - }, - "path": "/query", - "predicate": "positively_regulated_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulated_by-Disease" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "ChemicalSubstance-positively_regulated_by-Gene": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "ChemicalSubstance" - } - ], "method": "post", "outputs": [ - { - "id": "UMLS", - "semantic": "Gene" - } - ], - "parameters": { - "fields": "positively_regulated_by" - }, - "path": "/query", - "predicate": "positively_regulated_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulated_by-Gene" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "ChemicalSubstance-positively_regulated_by-PhenotypicFeature": [ - { - "inputSeparator": ",", - "inputs": [ { "id": "UMLS", "semantic": "ChemicalSubstance" } ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "PhenotypicFeature" - } - ], "parameters": { - "fields": "positively_regulated_by" + "fields": "positively_regulates" }, "path": "/query", - "predicate": "positively_regulated_by", + "predicate": "entity_positively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50224,33 +49976,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulated_by-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/Disease-positively_regulates-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-positively_regulates-AnatomicalEntity": [ + "Disease-positively_regulates-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Disease" } ], "parameters": { "fields": "positively_regulates" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "entity_positively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50258,33 +50010,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulates-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/Disease-positively_regulates-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-positively_regulates-BiologicalProcess": [ + "Disease-positively_regulates-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "Gene" } ], "parameters": { "fields": "positively_regulates" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "entity_positively_regulates_entity", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50292,33 +50044,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulates-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/Disease-positively_regulates-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-positively_regulates-Cell": [ + "Disease-prevented_by-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Cell" + "semantic": "AnatomicalEntity" } ], "parameters": { - "fields": "positively_regulates" + "fields": "prevented_by" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "prevented_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50326,33 +50078,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulates-Cell" + "$ref": "#/components/x-bte-response-mapping/Disease-prevented_by-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-positively_regulates-CellularComponent": [ + "Disease-prevented_by-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "CellularComponent" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "positively_regulates" + "fields": "prevented_by" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "prevented_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50360,19 +50112,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulates-CellularComponent" + "$ref": "#/components/x-bte-response-mapping/Disease-prevented_by-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-positively_regulates-ChemicalSubstance": [ + "Disease-prevented_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -50383,10 +50135,10 @@ } ], "parameters": { - "fields": "positively_regulates" + "fields": "prevented_by" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "prevented_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50394,19 +50146,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulates-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/Disease-prevented_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-positively_regulates-Disease": [ + "Disease-prevented_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -50417,10 +50169,10 @@ } ], "parameters": { - "fields": "positively_regulates" + "fields": "prevented_by" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "prevented_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50428,19 +50180,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulates-Disease" + "$ref": "#/components/x-bte-response-mapping/Disease-prevented_by-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-positively_regulates-Gene": [ + "Disease-prevented_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -50451,10 +50203,10 @@ } ], "parameters": { - "fields": "positively_regulates" + "fields": "prevented_by" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "prevented_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50462,19 +50214,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulates-Gene" + "$ref": "#/components/x-bte-response-mapping/Disease-prevented_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-positively_regulates-PhenotypicFeature": [ + "Disease-prevented_by-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -50485,10 +50237,10 @@ } ], "parameters": { - "fields": "positively_regulates" + "fields": "prevented_by" }, "path": "/query", - "predicate": "positively_regulates", + "predicate": "prevented_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50496,19 +50248,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-positively_regulates-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/Disease-prevented_by-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-prevents-Disease": [ + "Disease-prevents-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -50530,19 +50282,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-prevents-Disease" + "$ref": "#/components/x-bte-response-mapping/Disease-prevents-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-produced_by-AnatomicalEntity": [ + "Disease-related_to-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -50553,10 +50305,10 @@ } ], "parameters": { - "fields": "produced_by" + "fields": "related_to" }, "path": "/query", - "predicate": "produced_by", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50564,19 +50316,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-produced_by-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/Disease-related_to-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-produced_by-BiologicalProcess": [ + "Disease-related_to-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -50587,10 +50339,10 @@ } ], "parameters": { - "fields": "produced_by" + "fields": "related_to" }, "path": "/query", - "predicate": "produced_by", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50598,19 +50350,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-produced_by-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/Disease-related_to-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-produced_by-Cell": [ + "Disease-related_to-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -50621,10 +50373,10 @@ } ], "parameters": { - "fields": "produced_by" + "fields": "related_to" }, "path": "/query", - "predicate": "produced_by", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50632,19 +50384,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-produced_by-Cell" + "$ref": "#/components/x-bte-response-mapping/Disease-related_to-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-produced_by-CellularComponent": [ + "Disease-related_to-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -50655,44 +50407,10 @@ } ], "parameters": { - "fields": "produced_by" - }, - "path": "/query", - "predicate": "produced_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-produced_by-CellularComponent" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "ChemicalSubstance-produced_by-ChemicalSubstance": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "ChemicalSubstance" - } - ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "ChemicalSubstance" - } - ], - "parameters": { - "fields": "produced_by" + "fields": "related_to" }, "path": "/query", - "predicate": "produced_by", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50700,101 +50418,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-produced_by-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/Disease-related_to-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-produced_by-Disease": [ + "Disease-related_to-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ - { - "id": "UMLS", - "semantic": "ChemicalSubstance" - } - ], - "method": "post", - "outputs": [ { "id": "UMLS", "semantic": "Disease" } ], - "parameters": { - "fields": "produced_by" - }, - "path": "/query", - "predicate": "produced_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-produced_by-Disease" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "ChemicalSubstance-produced_by-Gene": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "UMLS", - "semantic": "ChemicalSubstance" - } - ], "method": "post", "outputs": [ - { - "id": "UMLS", - "semantic": "Gene" - } - ], - "parameters": { - "fields": "produced_by" - }, - "path": "/query", - "predicate": "produced_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "umls" - } - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-produced_by-Gene" - }, - "source": "SEMMED", - "supportBatch": true - } - ], - "ChemicalSubstance-produced_by-PhenotypicFeature": [ - { - "inputSeparator": ",", - "inputs": [ { "id": "UMLS", "semantic": "ChemicalSubstance" } ], - "method": "post", - "outputs": [ - { - "id": "UMLS", - "semantic": "PhenotypicFeature" - } - ], "parameters": { - "fields": "produced_by" + "fields": "related_to" }, "path": "/query", - "predicate": "produced_by", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50802,33 +50452,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-produced_by-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/Disease-related_to-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-produces-AnatomicalEntity": [ + "Disease-related_to-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Disease" } ], "parameters": { - "fields": "produces" + "fields": "related_to" }, "path": "/query", - "predicate": "produces", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50836,33 +50486,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-produces-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/Disease-related_to-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-produces-Cell": [ + "Disease-related_to-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Cell" + "semantic": "Gene" } ], "parameters": { - "fields": "produces" + "fields": "related_to" }, "path": "/query", - "predicate": "produces", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50870,33 +50520,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-produces-Cell" + "$ref": "#/components/x-bte-response-mapping/Disease-related_to-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-produces-ChemicalSubstance": [ + "Disease-related_to-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "PhenotypicFeature" } ], "parameters": { - "fields": "produces" + "fields": "related_to" }, "path": "/query", - "predicate": "produces", + "predicate": "related_to", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50904,33 +50554,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-produces-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/Disease-related_to-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-produces-Gene": [ + "Disease-treated_by-AnatomicalEntity": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "Gene" + "semantic": "AnatomicalEntity" } ], "parameters": { - "fields": "produces" + "fields": "treated_by" }, "path": "/query", - "predicate": "produces", + "predicate": "treated_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50938,33 +50588,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-produces-Gene" + "$ref": "#/components/x-bte-response-mapping/Disease-treated_by-AnatomicalEntity" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-produces-PhenotypicFeature": [ + "Disease-treated_by-BiologicalProcess": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "PhenotypicFeature" + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "produces" + "fields": "treated_by" }, "path": "/query", - "predicate": "produces", + "predicate": "treated_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -50972,33 +50622,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-produces-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/Disease-treated_by-BiologicalProcess" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-related_to-AnatomicalEntity": [ + "Disease-treated_by-Cell": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "AnatomicalEntity" + "semantic": "Cell" } ], "parameters": { - "fields": "related_to" + "fields": "treated_by" }, "path": "/query", - "predicate": "related_to", + "predicate": "treated_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -51006,33 +50656,33 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-related_to-AnatomicalEntity" + "$ref": "#/components/x-bte-response-mapping/Disease-treated_by-Cell" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-related_to-BiologicalProcess": [ + "Disease-treated_by-CellularComponent": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", "outputs": [ { "id": "UMLS", - "semantic": "BiologicalProcess" + "semantic": "CellularComponent" } ], "parameters": { - "fields": "related_to" + "fields": "treated_by" }, "path": "/query", - "predicate": "related_to", + "predicate": "treated_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -51040,19 +50690,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-related_to-BiologicalProcess" + "$ref": "#/components/x-bte-response-mapping/Disease-treated_by-CellularComponent" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-related_to-ChemicalSubstance": [ + "Disease-treated_by-ChemicalSubstance": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -51063,10 +50713,10 @@ } ], "parameters": { - "fields": "related_to" + "fields": "treated_by" }, "path": "/query", - "predicate": "related_to", + "predicate": "treated_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -51074,19 +50724,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-related_to-ChemicalSubstance" + "$ref": "#/components/x-bte-response-mapping/Disease-treated_by-ChemicalSubstance" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-related_to-Disease": [ + "Disease-treated_by-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -51097,10 +50747,10 @@ } ], "parameters": { - "fields": "related_to" + "fields": "treated_by" }, "path": "/query", - "predicate": "related_to", + "predicate": "treated_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -51108,19 +50758,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-related_to-Disease" + "$ref": "#/components/x-bte-response-mapping/Disease-treated_by-Disease" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-related_to-Gene": [ + "Disease-treated_by-Gene": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -51131,10 +50781,10 @@ } ], "parameters": { - "fields": "related_to" + "fields": "treated_by" }, "path": "/query", - "predicate": "related_to", + "predicate": "treated_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -51142,19 +50792,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-related_to-Gene" + "$ref": "#/components/x-bte-response-mapping/Disease-treated_by-Gene" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-related_to-PhenotypicFeature": [ + "Disease-treated_by-PhenotypicFeature": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -51165,10 +50815,10 @@ } ], "parameters": { - "fields": "related_to" + "fields": "treated_by" }, "path": "/query", - "predicate": "related_to", + "predicate": "treated_by", "requestBody": { "body": { "q": "{inputs[0]}", @@ -51176,19 +50826,19 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-related_to-PhenotypicFeature" + "$ref": "#/components/x-bte-response-mapping/Disease-treated_by-PhenotypicFeature" }, "source": "SEMMED", "supportBatch": true } ], - "ChemicalSubstance-treats-Disease": [ + "Disease-treats-Disease": [ { "inputSeparator": ",", "inputs": [ { "id": "UMLS", - "semantic": "ChemicalSubstance" + "semantic": "Disease" } ], "method": "post", @@ -51210,7 +50860,7 @@ } }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/ChemicalSubstance-treats-Disease" + "$ref": "#/components/x-bte-response-mapping/Disease-treats-Disease" }, "source": "SEMMED", "supportBatch": true @@ -51218,375 +50868,387 @@ ] }, "x-bte-response-mapping": { - "ChemicalSubstance-affected_by-BiologicalProcess": { + "Disease-affected_by-AnatomicalEntity": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "ChemicalSubstance-affected_by-ChemicalSubstance": { + "Disease-affected_by-BiologicalProcess": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "ChemicalSubstance-affected_by-Disease": { + "Disease-affected_by-Cell": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "ChemicalSubstance-affected_by-Gene": { + "Disease-affected_by-CellularComponent": { "pmid": "affected_by.pmid", "umls": "affected_by.umls" }, - "ChemicalSubstance-affects-AnatomicalEntity": { + "Disease-affected_by-ChemicalSubstance": { + "pmid": "affected_by.pmid", + "umls": "affected_by.umls" + }, + "Disease-affected_by-Disease": { + "pmid": "affected_by.pmid", + "umls": "affected_by.umls" + }, + "Disease-affected_by-Gene": { + "pmid": "affected_by.pmid", + "umls": "affected_by.umls" + }, + "Disease-affected_by-PhenotypicFeature": { + "pmid": "affected_by.pmid", + "umls": "affected_by.umls" + }, + "Disease-affects-AnatomicalEntity": { "pmid": "affects.pmid", "umls": "affects.umls" }, - "ChemicalSubstance-affects-BiologicalProcess": { + "Disease-affects-BiologicalProcess": { "pmid": "affects.pmid", "umls": "affects.umls" }, - "ChemicalSubstance-affects-Cell": { + "Disease-affects-Cell": { "pmid": "affects.pmid", "umls": "affects.umls" }, - "ChemicalSubstance-affects-CellularComponent": { + "Disease-affects-CellularComponent": { "pmid": "affects.pmid", "umls": "affects.umls" }, - "ChemicalSubstance-affects-ChemicalSubstance": { + "Disease-affects-ChemicalSubstance": { "pmid": "affects.pmid", "umls": "affects.umls" }, - "ChemicalSubstance-affects-Disease": { + "Disease-affects-Disease": { "pmid": "affects.pmid", "umls": "affects.umls" }, - "ChemicalSubstance-affects-Gene": { + "Disease-affects-Gene": { "pmid": "affects.pmid", "umls": "affects.umls" }, - "ChemicalSubstance-affects-PhenotypicFeature": { + "Disease-affects-PhenotypicFeature": { "pmid": "affects.pmid", "umls": "affects.umls" }, - "ChemicalSubstance-causes-BiologicalProcess": { + "Disease-caused_by-AnatomicalEntity": { + "pmid": "caused_by.pmid", + "umls": "caused_by.umls" + }, + "Disease-caused_by-BiologicalProcess": { + "pmid": "caused_by.pmid", + "umls": "caused_by.umls" + }, + "Disease-caused_by-Cell": { + "pmid": "caused_by.pmid", + "umls": "caused_by.umls" + }, + "Disease-caused_by-CellularComponent": { + "pmid": "caused_by.pmid", + "umls": "caused_by.umls" + }, + "Disease-caused_by-ChemicalSubstance": { + "pmid": "caused_by.pmid", + "umls": "caused_by.umls" + }, + "Disease-caused_by-Disease": { + "pmid": "caused_by.pmid", + "umls": "caused_by.umls" + }, + "Disease-caused_by-Gene": { + "pmid": "caused_by.pmid", + "umls": "caused_by.umls" + }, + "Disease-caused_by-PhenotypicFeature": { + "pmid": "caused_by.pmid", + "umls": "caused_by.umls" + }, + "Disease-causes-BiologicalProcess": { "pmid": "causes.pmid", "umls": "causes.umls" }, - "ChemicalSubstance-causes-Disease": { + "Disease-causes-Disease": { "pmid": "causes.pmid", "umls": "causes.umls" }, - "ChemicalSubstance-coexists_with-AnatomicalEntity": { + "Disease-coexists_with-AnatomicalEntity": { "pmid": "coexists_with.pmid", "umls": "coexists_with.umls" }, - "ChemicalSubstance-coexists_with-BiologicalProcess": { + "Disease-coexists_with-BiologicalProcess": { "pmid": "coexists_with.pmid", "umls": "coexists_with.umls" }, - "ChemicalSubstance-coexists_with-Cell": { + "Disease-coexists_with-Cell": { "pmid": "coexists_with.pmid", "umls": "coexists_with.umls" }, - "ChemicalSubstance-coexists_with-CellularComponent": { + "Disease-coexists_with-CellularComponent": { "pmid": "coexists_with.pmid", "umls": "coexists_with.umls" }, - "ChemicalSubstance-coexists_with-ChemicalSubstance": { + "Disease-coexists_with-ChemicalSubstance": { "pmid": "coexists_with.pmid", "umls": "coexists_with.umls" }, - "ChemicalSubstance-coexists_with-Disease": { + "Disease-coexists_with-Disease": { "pmid": "coexists_with.pmid", "umls": "coexists_with.umls" }, - "ChemicalSubstance-coexists_with-Gene": { + "Disease-coexists_with-Gene": { "pmid": "coexists_with.pmid", "umls": "coexists_with.umls" }, - "ChemicalSubstance-coexists_with-PhenotypicFeature": { + "Disease-coexists_with-PhenotypicFeature": { "pmid": "coexists_with.pmid", "umls": "coexists_with.umls" }, - "ChemicalSubstance-disrupted_by-ChemicalSubstance": { + "Disease-derives_from-ChemicalSubstance": { + "pmid": "derives_from.pmid", + "umls": "derives_from.umls" + }, + "Disease-derives_from-Gene": { + "pmid": "derives_from.pmid", + "umls": "derives_from.umls" + }, + "Disease-derives_info-ChemicalSubstance": { + "pmid": "derives_info.pmid", + "umls": "derives_info.umls" + }, + "Disease-disrupted_by-BiologicalProcess": { "pmid": "disrupted_by.pmid", "umls": "disrupted_by.umls" }, - "ChemicalSubstance-disrupted_by-Gene": { + "Disease-disrupted_by-CellularComponent": { "pmid": "disrupted_by.pmid", "umls": "disrupted_by.umls" }, - "ChemicalSubstance-disrupts-AnatomicalEntity": { - "pmid": "disrupts.pmid", - "umls": "disrupts.umls" + "Disease-disrupted_by-ChemicalSubstance": { + "pmid": "disrupted_by.pmid", + "umls": "disrupted_by.umls" }, - "ChemicalSubstance-disrupts-BiologicalProcess": { + "Disease-disrupted_by-Disease": { + "pmid": "disrupted_by.pmid", + "umls": "disrupted_by.umls" + }, + "Disease-disrupted_by-Gene": { + "pmid": "disrupted_by.pmid", + "umls": "disrupted_by.umls" + }, + "Disease-disrupted_by-PhenotypicFeature": { + "pmid": "disrupted_by.pmid", + "umls": "disrupted_by.umls" + }, + "Disease-disrupts-AnatomicalEntity": { "pmid": "disrupts.pmid", "umls": "disrupts.umls" }, - "ChemicalSubstance-disrupts-Cell": { + "Disease-disrupts-BiologicalProcess": { "pmid": "disrupts.pmid", "umls": "disrupts.umls" }, - "ChemicalSubstance-disrupts-CellularComponent": { + "Disease-disrupts-Cell": { "pmid": "disrupts.pmid", "umls": "disrupts.umls" }, - "ChemicalSubstance-disrupts-ChemicalSubstance": { + "Disease-disrupts-CellularComponent": { "pmid": "disrupts.pmid", "umls": "disrupts.umls" }, - "ChemicalSubstance-disrupts-Disease": { + "Disease-disrupts-Disease": { "pmid": "disrupts.pmid", "umls": "disrupts.umls" }, - "ChemicalSubstance-disrupts-Gene": { + "Disease-disrupts-Gene": { "pmid": "disrupts.pmid", "umls": "disrupts.umls" }, - "ChemicalSubstance-disrupts-PhenotypicFeature": { + "Disease-disrupts-PhenotypicFeature": { "pmid": "disrupts.pmid", "umls": "disrupts.umls" }, - "ChemicalSubstance-negatively_regulated_by-AnatomicalEntity": { - "pmid": "negatively_regulated_by.pmid", - "umls": "negatively_regulated_by.umls" - }, - "ChemicalSubstance-negatively_regulated_by-BiologicalProcess": { - "pmid": "negatively_regulated_by.pmid", - "umls": "negatively_regulated_by.umls" - }, - "ChemicalSubstance-negatively_regulated_by-Cell": { - "pmid": "negatively_regulated_by.pmid", - "umls": "negatively_regulated_by.umls" - }, - "ChemicalSubstance-negatively_regulated_by-CellularComponent": { + "Disease-negatively_regulated_by-BiologicalProcess": { "pmid": "negatively_regulated_by.pmid", "umls": "negatively_regulated_by.umls" }, - "ChemicalSubstance-negatively_regulated_by-ChemicalSubstance": { + "Disease-negatively_regulated_by-ChemicalSubstance": { "pmid": "negatively_regulated_by.pmid", "umls": "negatively_regulated_by.umls" }, - "ChemicalSubstance-negatively_regulated_by-Disease": { + "Disease-negatively_regulated_by-Disease": { "pmid": "negatively_regulated_by.pmid", "umls": "negatively_regulated_by.umls" }, - "ChemicalSubstance-negatively_regulated_by-Gene": { + "Disease-negatively_regulated_by-Gene": { "pmid": "negatively_regulated_by.pmid", "umls": "negatively_regulated_by.umls" }, - "ChemicalSubstance-negatively_regulated_by-PhenotypicFeature": { + "Disease-negatively_regulated_by-PhenotypicFeature": { "pmid": "negatively_regulated_by.pmid", "umls": "negatively_regulated_by.umls" }, - "ChemicalSubstance-negatively_regulates-AnatomicalEntity": { - "pmid": "negatively_regulates.pmid", - "umls": "negatively_regulates.umls" - }, - "ChemicalSubstance-negatively_regulates-BiologicalProcess": { - "pmid": "negatively_regulates.pmid", - "umls": "negatively_regulates.umls" - }, - "ChemicalSubstance-negatively_regulates-Cell": { - "pmid": "negatively_regulates.pmid", - "umls": "negatively_regulates.umls" - }, - "ChemicalSubstance-negatively_regulates-CellularComponent": { - "pmid": "negatively_regulates.pmid", - "umls": "negatively_regulates.umls" - }, - "ChemicalSubstance-negatively_regulates-ChemicalSubstance": { + "Disease-negatively_regulates-BiologicalProcess": { "pmid": "negatively_regulates.pmid", "umls": "negatively_regulates.umls" }, - "ChemicalSubstance-negatively_regulates-Disease": { + "Disease-negatively_regulates-ChemicalSubstance": { "pmid": "negatively_regulates.pmid", "umls": "negatively_regulates.umls" }, - "ChemicalSubstance-negatively_regulates-Gene": { + "Disease-negatively_regulates-Disease": { "pmid": "negatively_regulates.pmid", "umls": "negatively_regulates.umls" }, - "ChemicalSubstance-negatively_regulates-PhenotypicFeature": { + "Disease-negatively_regulates-Gene": { "pmid": "negatively_regulates.pmid", "umls": "negatively_regulates.umls" }, - "ChemicalSubstance-physically_interacts_with-AnatomicalEntity": { - "pmid": "physically_interacts_with.pmid", - "umls": "physically_interacts_with.umls" - }, - "ChemicalSubstance-physically_interacts_with-BiologicalProcess": { - "pmid": "physically_interacts_with.pmid", - "umls": "physically_interacts_with.umls" - }, - "ChemicalSubstance-physically_interacts_with-Cell": { + "Disease-physically_interacts_with-BiologicalProcess": { "pmid": "physically_interacts_with.pmid", "umls": "physically_interacts_with.umls" }, - "ChemicalSubstance-physically_interacts_with-CellularComponent": { + "Disease-physically_interacts_with-CellularComponent": { "pmid": "physically_interacts_with.pmid", "umls": "physically_interacts_with.umls" }, - "ChemicalSubstance-physically_interacts_with-ChemicalSubstance": { + "Disease-physically_interacts_with-ChemicalSubstance": { "pmid": "physically_interacts_with.pmid", "umls": "physically_interacts_with.umls" }, - "ChemicalSubstance-physically_interacts_with-Disease": { + "Disease-physically_interacts_with-Disease": { "pmid": "physically_interacts_with.pmid", "umls": "physically_interacts_with.umls" }, - "ChemicalSubstance-physically_interacts_with-Gene": { + "Disease-physically_interacts_with-Gene": { "pmid": "physically_interacts_with.pmid", "umls": "physically_interacts_with.umls" }, - "ChemicalSubstance-physically_interacts_with-PhenotypicFeature": { + "Disease-physically_interacts_with-PhenotypicFeature": { "pmid": "physically_interacts_with.pmid", "umls": "physically_interacts_with.umls" }, - "ChemicalSubstance-positively_regulated_by-AnatomicalEntity": { - "pmid": "positively_regulated_by.pmid", - "umls": "positively_regulated_by.umls" - }, - "ChemicalSubstance-positively_regulated_by-BiologicalProcess": { - "pmid": "positively_regulated_by.pmid", - "umls": "positively_regulated_by.umls" - }, - "ChemicalSubstance-positively_regulated_by-Cell": { - "pmid": "positively_regulated_by.pmid", - "umls": "positively_regulated_by.umls" - }, - "ChemicalSubstance-positively_regulated_by-CellularComponent": { - "pmid": "positively_regulated_by.pmid", - "umls": "positively_regulated_by.umls" - }, - "ChemicalSubstance-positively_regulated_by-ChemicalSubstance": { - "pmid": "positively_regulated_by.pmid", - "umls": "positively_regulated_by.umls" - }, - "ChemicalSubstance-positively_regulated_by-Disease": { + "Disease-positively_regulated_by-ChemicalSubstance": { "pmid": "positively_regulated_by.pmid", "umls": "positively_regulated_by.umls" }, - "ChemicalSubstance-positively_regulated_by-Gene": { + "Disease-positively_regulated_by-Disease": { "pmid": "positively_regulated_by.pmid", "umls": "positively_regulated_by.umls" }, - "ChemicalSubstance-positively_regulated_by-PhenotypicFeature": { + "Disease-positively_regulated_by-Gene": { "pmid": "positively_regulated_by.pmid", "umls": "positively_regulated_by.umls" }, - "ChemicalSubstance-positively_regulates-AnatomicalEntity": { - "pmid": "positively_regulates.pmid", - "umls": "positively_regulates.umls" - }, - "ChemicalSubstance-positively_regulates-BiologicalProcess": { - "pmid": "positively_regulates.pmid", - "umls": "positively_regulates.umls" - }, - "ChemicalSubstance-positively_regulates-Cell": { - "pmid": "positively_regulates.pmid", - "umls": "positively_regulates.umls" - }, - "ChemicalSubstance-positively_regulates-CellularComponent": { - "pmid": "positively_regulates.pmid", - "umls": "positively_regulates.umls" - }, - "ChemicalSubstance-positively_regulates-ChemicalSubstance": { + "Disease-positively_regulates-BiologicalProcess": { "pmid": "positively_regulates.pmid", "umls": "positively_regulates.umls" }, - "ChemicalSubstance-positively_regulates-Disease": { + "Disease-positively_regulates-ChemicalSubstance": { "pmid": "positively_regulates.pmid", "umls": "positively_regulates.umls" }, - "ChemicalSubstance-positively_regulates-Gene": { + "Disease-positively_regulates-Disease": { "pmid": "positively_regulates.pmid", "umls": "positively_regulates.umls" }, - "ChemicalSubstance-positively_regulates-PhenotypicFeature": { + "Disease-positively_regulates-Gene": { "pmid": "positively_regulates.pmid", "umls": "positively_regulates.umls" }, - "ChemicalSubstance-prevents-Disease": { - "pmid": "prevents.pmid", - "umls": "prevents.umls" - }, - "ChemicalSubstance-produced_by-AnatomicalEntity": { - "pmid": "produced_by.pmid", - "umls": "produced_by.umls" - }, - "ChemicalSubstance-produced_by-BiologicalProcess": { - "pmid": "produced_by.pmid", - "umls": "produced_by.umls" - }, - "ChemicalSubstance-produced_by-Cell": { - "pmid": "produced_by.pmid", - "umls": "produced_by.umls" - }, - "ChemicalSubstance-produced_by-CellularComponent": { - "pmid": "produced_by.pmid", - "umls": "produced_by.umls" - }, - "ChemicalSubstance-produced_by-ChemicalSubstance": { - "pmid": "produced_by.pmid", - "umls": "produced_by.umls" + "Disease-prevented_by-AnatomicalEntity": { + "pmid": "prevented_by.pmid", + "umls": "prevented_by.umls" }, - "ChemicalSubstance-produced_by-Disease": { - "pmid": "produced_by.pmid", - "umls": "produced_by.umls" + "Disease-prevented_by-BiologicalProcess": { + "pmid": "prevented_by.pmid", + "umls": "prevented_by.umls" }, - "ChemicalSubstance-produced_by-Gene": { - "pmid": "produced_by.pmid", - "umls": "produced_by.umls" + "Disease-prevented_by-ChemicalSubstance": { + "pmid": "prevented_by.pmid", + "umls": "prevented_by.umls" }, - "ChemicalSubstance-produced_by-PhenotypicFeature": { - "pmid": "produced_by.pmid", - "umls": "produced_by.umls" + "Disease-prevented_by-Disease": { + "pmid": "prevented_by.pmid", + "umls": "prevented_by.umls" }, - "ChemicalSubstance-produces-AnatomicalEntity": { - "pmid": "produces.pmid", - "umls": "produces.umls" + "Disease-prevented_by-Gene": { + "pmid": "prevented_by.pmid", + "umls": "prevented_by.umls" }, - "ChemicalSubstance-produces-Cell": { - "pmid": "produces.pmid", - "umls": "produces.umls" + "Disease-prevented_by-PhenotypicFeature": { + "pmid": "prevented_by.pmid", + "umls": "prevented_by.umls" }, - "ChemicalSubstance-produces-ChemicalSubstance": { - "pmid": "produces.pmid", - "umls": "produces.umls" + "Disease-prevents-Disease": { + "pmid": "prevents.pmid", + "umls": "prevents.umls" }, - "ChemicalSubstance-produces-Gene": { - "pmid": "produces.pmid", - "umls": "produces.umls" + "Disease-related_to-AnatomicalEntity": { + "pmid": "related_to.pmid", + "umls": "related_to.umls" }, - "ChemicalSubstance-produces-PhenotypicFeature": { - "pmid": "produces.pmid", - "umls": "produces.umls" + "Disease-related_to-BiologicalProcess": { + "pmid": "related_to.pmid", + "umls": "related_to.umls" }, - "ChemicalSubstance-related_to-AnatomicalEntity": { + "Disease-related_to-Cell": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "ChemicalSubstance-related_to-BiologicalProcess": { + "Disease-related_to-CellularComponent": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "ChemicalSubstance-related_to-ChemicalSubstance": { + "Disease-related_to-ChemicalSubstance": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "ChemicalSubstance-related_to-Disease": { + "Disease-related_to-Disease": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "ChemicalSubstance-related_to-Gene": { + "Disease-related_to-Gene": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "ChemicalSubstance-related_to-PhenotypicFeature": { + "Disease-related_to-PhenotypicFeature": { "pmid": "related_to.pmid", "umls": "related_to.umls" }, - "ChemicalSubstance-treats-Disease": { + "Disease-treated_by-AnatomicalEntity": { + "pmid": "treated_by.pmid", + "umls": "treated_by.umls" + }, + "Disease-treated_by-BiologicalProcess": { + "pmid": "treated_by.pmid", + "umls": "treated_by.umls" + }, + "Disease-treated_by-Cell": { + "pmid": "treated_by.pmid", + "umls": "treated_by.umls" + }, + "Disease-treated_by-CellularComponent": { + "pmid": "treated_by.pmid", + "umls": "treated_by.umls" + }, + "Disease-treated_by-ChemicalSubstance": { + "pmid": "treated_by.pmid", + "umls": "treated_by.umls" + }, + "Disease-treated_by-Disease": { + "pmid": "treated_by.pmid", + "umls": "treated_by.umls" + }, + "Disease-treated_by-Gene": { + "pmid": "treated_by.pmid", + "umls": "treated_by.umls" + }, + "Disease-treated_by-PhenotypicFeature": { + "pmid": "treated_by.pmid", + "umls": "treated_by.umls" + }, + "Disease-treats-Disease": { "pmid": "treats.pmid", "umls": "treats.umls" } @@ -51599,9 +51261,9 @@ "x-id": "https://github.com/newgene", "x-role": "responsible developer" }, - "description": "Documentation of the SEMMED disease query web services. Learn more about [mydisease.info](http://pending.biothings.io/semmed)", + "description": "Documentation of the SEMMED disease query web services. Learn more about [semmed disease](http://pending.biothings.io/semmed)", "termsOfService": "http://biothings.ncats.io", - "title": "SEMMED Chemical API", + "title": "SEMMED Disease API", "version": "1.0", "x-translator": { "component": "KP", @@ -51611,7 +51273,7 @@ } }, "paths": { - "/chemical": { + "/disease": { "post": { "parameters": [ { @@ -51679,14 +51341,14 @@ ] } }, - "/chemical/{chemicalid}": { + "/disease/{diseaseid}": { "get": { "parameters": [ { "description": "Retrieve disease objects based on ID", "example": "C0004096", "in": "path", - "name": "chemicalid", + "name": "diseaseid", "required": true, "schema": { "type": "string" @@ -51935,283 +51597,292 @@ ], "x-bte-kgs-operations": [ { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affected_by-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/Disease-affected_by-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affected_by-Disease" + "$ref": "#/components/x-bte-kgs-operations/Disease-affected_by-Cell" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affected_by-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/Disease-affected_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affected_by-Gene" + "$ref": "#/components/x-bte-kgs-operations/Disease-affected_by-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affects-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/Disease-affected_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affects-Cell" + "$ref": "#/components/x-bte-kgs-operations/Disease-affected_by-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affects-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/Disease-affected_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affects-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/Disease-affected_by-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affects-Disease" + "$ref": "#/components/x-bte-kgs-operations/Disease-affects-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affects-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/Disease-affects-Cell" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affects-Gene" + "$ref": "#/components/x-bte-kgs-operations/Disease-affects-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-affects-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/Disease-affects-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-causes-Disease" + "$ref": "#/components/x-bte-kgs-operations/Disease-affects-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-causes-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/Disease-affects-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-coexists_with-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/Disease-affects-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-coexists_with-Cell" + "$ref": "#/components/x-bte-kgs-operations/Disease-affects-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-coexists_with-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/Disease-caused_by-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-coexists_with-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/Disease-caused_by-Cell" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-coexists_with-Disease" + "$ref": "#/components/x-bte-kgs-operations/Disease-caused_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-coexists_with-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/Disease-caused_by-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-coexists_with-Gene" + "$ref": "#/components/x-bte-kgs-operations/Disease-caused_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-coexists_with-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/Disease-caused_by-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-disrupted_by-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/Disease-caused_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-disrupted_by-Gene" + "$ref": "#/components/x-bte-kgs-operations/Disease-caused_by-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-disrupts-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/Disease-causes-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-disrupts-Cell" + "$ref": "#/components/x-bte-kgs-operations/Disease-causes-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-disrupts-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/Disease-coexists_with-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-disrupts-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/Disease-coexists_with-Cell" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-disrupts-Disease" + "$ref": "#/components/x-bte-kgs-operations/Disease-coexists_with-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-disrupts-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/Disease-coexists_with-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-disrupts-Gene" + "$ref": "#/components/x-bte-kgs-operations/Disease-coexists_with-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-disrupts-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/Disease-coexists_with-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulated_by-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/Disease-coexists_with-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulated_by-Cell" + "$ref": "#/components/x-bte-kgs-operations/Disease-coexists_with-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulated_by-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/Disease-derives_from-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulated_by-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/Disease-derives_from-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulated_by-Disease" + "$ref": "#/components/x-bte-kgs-operations/Disease-derives_info-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulated_by-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/Disease-disrupted_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulated_by-Gene" + "$ref": "#/components/x-bte-kgs-operations/Disease-disrupted_by-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulated_by-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/Disease-disrupted_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulates-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/Disease-disrupted_by-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulates-Cell" + "$ref": "#/components/x-bte-kgs-operations/Disease-disrupted_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulates-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/Disease-disrupted_by-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulates-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/Disease-disrupts-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulates-Disease" + "$ref": "#/components/x-bte-kgs-operations/Disease-disrupts-Cell" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulates-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/Disease-disrupts-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulates-Gene" + "$ref": "#/components/x-bte-kgs-operations/Disease-disrupts-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-negatively_regulates-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/Disease-disrupts-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-physically_interacts_with-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/Disease-disrupts-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-physically_interacts_with-Cell" + "$ref": "#/components/x-bte-kgs-operations/Disease-disrupts-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-physically_interacts_with-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/Disease-negatively_regulated_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-physically_interacts_with-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/Disease-negatively_regulated_by-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-physically_interacts_with-Disease" + "$ref": "#/components/x-bte-kgs-operations/Disease-negatively_regulated_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-physically_interacts_with-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/Disease-negatively_regulated_by-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-physically_interacts_with-Gene" + "$ref": "#/components/x-bte-kgs-operations/Disease-negatively_regulated_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-physically_interacts_with-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/Disease-negatively_regulates-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulated_by-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/Disease-negatively_regulates-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulated_by-Cell" + "$ref": "#/components/x-bte-kgs-operations/Disease-negatively_regulates-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulated_by-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/Disease-negatively_regulates-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulated_by-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/Disease-physically_interacts_with-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulated_by-Disease" + "$ref": "#/components/x-bte-kgs-operations/Disease-physically_interacts_with-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulated_by-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/Disease-physically_interacts_with-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulated_by-Gene" + "$ref": "#/components/x-bte-kgs-operations/Disease-physically_interacts_with-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulated_by-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/Disease-physically_interacts_with-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulates-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/Disease-physically_interacts_with-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulates-Cell" + "$ref": "#/components/x-bte-kgs-operations/Disease-positively_regulated_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulates-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/Disease-positively_regulated_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulates-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/Disease-positively_regulated_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulates-Disease" + "$ref": "#/components/x-bte-kgs-operations/Disease-positively_regulates-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulates-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/Disease-positively_regulates-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulates-Gene" + "$ref": "#/components/x-bte-kgs-operations/Disease-positively_regulates-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-positively_regulates-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/Disease-positively_regulates-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-prevents-Disease" + "$ref": "#/components/x-bte-kgs-operations/Disease-prevented_by-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produced_by-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/Disease-prevented_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produced_by-Cell" + "$ref": "#/components/x-bte-kgs-operations/Disease-prevented_by-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produced_by-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/Disease-prevented_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produced_by-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/Disease-prevented_by-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produced_by-Disease" + "$ref": "#/components/x-bte-kgs-operations/Disease-prevented_by-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produced_by-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/Disease-prevents-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produced_by-Gene" + "$ref": "#/components/x-bte-kgs-operations/Disease-related_to-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produced_by-CellularComponent" + "$ref": "#/components/x-bte-kgs-operations/Disease-related_to-Cell" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produces-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/Disease-related_to-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produces-Cell" + "$ref": "#/components/x-bte-kgs-operations/Disease-related_to-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produces-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/Disease-related_to-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produces-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/Disease-related_to-PhenotypicFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-produces-Gene" + "$ref": "#/components/x-bte-kgs-operations/Disease-related_to-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-related_to-AnatomicalEntity" + "$ref": "#/components/x-bte-kgs-operations/Disease-related_to-CellularComponent" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-related_to-ChemicalSubstance" + "$ref": "#/components/x-bte-kgs-operations/Disease-treated_by-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-related_to-BiologicalProcess" + "$ref": "#/components/x-bte-kgs-operations/Disease-treated_by-Cell" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-related_to-Disease" + "$ref": "#/components/x-bte-kgs-operations/Disease-treated_by-ChemicalSubstance" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-related_to-PhenotypicFeature" + "$ref": "#/components/x-bte-kgs-operations/Disease-treated_by-BiologicalProcess" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-related_to-Gene" + "$ref": "#/components/x-bte-kgs-operations/Disease-treated_by-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/ChemicalSubstance-treats-Disease" + "$ref": "#/components/x-bte-kgs-operations/Disease-treated_by-PhenotypicFeature" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Disease-treated_by-Gene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Disease-treated_by-CellularComponent" + }, + { + "$ref": "#/components/x-bte-kgs-operations/Disease-treats-Disease" } ] } @@ -52220,7 +51891,7 @@ "servers": [ { "description": "Production server", - "url": "https://biothings.ncats.io/semmedchemical" + "url": "https://biothings.ncats.io/semmed" } ], "tags": [ @@ -52245,91 +51916,162 @@ ] }, { - "_id": "a7f784626a426d054885a5f33f17d3f8", + "_id": "34bad236d77bea0a0ee6c6cba5be54a6", "_meta": { - "date_created": "2020-12-07T23:02:08.115894+00:00", - "last_updated": "2021-03-05T08:02:36.474514+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/DISEASES/smartapi.yaml", + "date_created": "2020-12-07T23:05:11.871445+00:00", + "last_updated": "2021-03-29T07:02:11.855327+00:00", + "slug": "go_ma", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/go_mf/smartapi.yaml", "username": "kevinxin90" }, - "_score": 0.47008187, + "_score": 0.45173043, "components": { "x-bte-kgs-operations": { - "disease-gene": [ + "has_part": [ { "inputSeparator": ",", "inputs": [ { - "id": "DOID", - "semantic": "Disease" + "id": "GO", + "semantic": "MolecularActivity" } ], "outputs": [ { - "id": "SYMBOL", - "semantic": "Gene" + "id": "GO", + "semantic": "MolecularActivity" } ], "parameters": { - "fields": "DISEASES.associatedWith" + "fields": "_id" }, - "predicate": "related_to", + "predicate": "has_part", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "DISEASES.doid" + "scopes": "part_of.go" }, "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/disease-gene" + "$ref": "#/components/x-bte-response-mapping/has_part" }, - "source": "DISEASES", + "source": "Gene Ontology", "supportBatch": true } ], - "gene-disease": [ + "has_subclass": [ { "inputSeparator": ",", "inputs": [ { - "id": "SYMBOL", - "semantic": "Gene" + "id": "GO", + "semantic": "MolecularActivity" } ], "outputs": [ { - "id": "DOID", - "semantic": "Disease" + "id": "GO", + "semantic": "MolecularActivity" } ], "parameters": { - "fields": "DISEASES.doid", - "size": "250" + "fields": "children" }, - "predicate": "related_to", + "predicate": "has_subclass", "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "DISEASES.associatedWith.symbol" + "scopes": "_id" }, "header": "application/x-www-form-urlencoded" }, "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/gene-disease" + "$ref": "#/components/x-bte-response-mapping/has_subclass" }, - "source": "DISEASES", + "source": "Gene Ontology", + "supportBatch": true + } + ], + "part_of": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "GO", + "semantic": "MolecularActivity" + } + ], + "outputs": [ + { + "id": "GO", + "semantic": "MolecularActivity" + } + ], + "parameters": { + "fields": "part_of.go" + }, + "predicate": "part_of", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "_id" + }, + "header": "application/x-www-form-urlencoded" + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/part_of" + }, + "source": "Gene Ontology", + "supportBatch": true + } + ], + "subclass_of": [ + { + "inputSeparator": ",", + "inputs": [ + { + "id": "GO", + "semantic": "MolecularActivity" + } + ], + "outputs": [ + { + "id": "GO", + "semantic": "MolecularActivity" + } + ], + "parameters": { + "fields": "parents" + }, + "predicate": "subclass_of", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "_id" + }, + "header": "application/x-www-form-urlencoded" + }, + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/subclass_of" + }, + "source": "Gene Ontology", "supportBatch": true } ] }, "x-bte-response-mapping": { - "disease-gene": { - "SYMBOL": "DISEASES.associatedWith.symbol", - "category": "DISEASES.associatedWith.category" + "has_part": { + "GO": "_id" }, - "gene-disease": { - "DOID": "DISEASES.doid" + "has_subclass": { + "GO": "children" + }, + "part_of": { + "GO": "part_of.go" + }, + "subclass_of": { + "GO": "parents" } } }, @@ -52340,9 +52082,9 @@ "x-id": "https://github.com/kevinxin90", "x-role": "responsible developer" }, - "description": "Documentation of the DISEASES query web services.", + "description": "Documentation of the Gene Ontology Molecular Activity query web services.", "termsOfService": "https://biothings.io/about", - "title": "DISEASES API", + "title": "Gene Ontology Molecular Activity API", "version": "1.0", "x-translator": { "component": "KP", @@ -52352,7 +52094,7 @@ } }, "paths": { - "/disease": { + "/geneset": { "post": { "parameters": [ { @@ -52378,7 +52120,7 @@ "schema": { "properties": { "ids": { - "description": "multiple MONDO Disease IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", + "description": "multiple GO geneset IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", "type": "string" } }, @@ -52395,13 +52137,13 @@ "application/json": { "schema": { "items": { - "$ref": "#/components/schemas/Disease" + "$ref": "#/components/schemas/Geneset" }, "type": "array" } } }, - "description": "A list of matching disease objects" + "description": "A list of matching geneset objects" }, "400": { "content": { @@ -52414,20 +52156,20 @@ "description": "A response indicating an improperly formatted query" } }, - "summary": "For a list of disease IDs, return the matching disease object", + "summary": "For a list of geneset IDs, return the matching geneset object", "tags": [ - "disease" + "geneset" ] } }, - "/disease/{diseaseid}": { + "/geneset/{genesetid}": { "get": { "parameters": [ { - "description": "Retrieve disease objects based on MONDO disease ID Supports JSONP and CORS as well.", - "example": "MONDO:0016537", + "description": "Retrieve geneset objects based on GO geneset ID. Supports JSONP and CORS as well.", + "example": "GO:0018672", "in": "path", - "name": "diseaseid", + "name": "genesetid", "required": true, "schema": { "type": "string" @@ -52459,19 +52201,19 @@ "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Disease" + "$ref": "#/components/schemas/Geneset" } } }, - "description": "A matching disease object" + "description": "A matching geneset object" }, "404": { - "description": "A response indicating an unknown disease ID" + "description": "A response indicating an unknown geneset ID" } }, - "summary": "Retrieve disease objects based on ID", + "summary": "Retrieve geneset objects based on ID", "tags": [ - "disease" + "geneset" ] } }, @@ -52520,7 +52262,7 @@ "description": "DISEASES metadata fields object" } }, - "summary": "Get metadata about the data fields available from a DISEASES disease object", + "summary": "Get metadata about the data fields available object", "tags": [ "metadata" ] @@ -52531,7 +52273,7 @@ "parameters": [ { "description": "Query string.", - "example": "DISEASES.doid:\"DOID:0110389\"", + "example": "parents:\"GO:0016705\"", "in": "query", "name": "q", "required": true, @@ -52602,7 +52344,7 @@ "description": "A response indicating an improperly formatted query" } }, - "summary": "Make queries and return matching disease hits. Supports JSONP and CORS as well.", + "summary": "Make queries and return matching geneset hits. Supports JSONP and CORS as well.", "tags": [ "query" ] @@ -52657,10 +52399,7 @@ } } }, - "description": "Query response objects with the \"hits\" property", - "x-bte-response-mapping": { - "$ref": "#/components/x-bte-response-mapping/query-post" - } + "description": "Query response objects with the \"hits\" property" }, "400": { "content": { @@ -52673,16 +52412,22 @@ "description": "A response indicating an improperly formatted query" } }, - "summary": "Make batch disease queries and return matching disease hits", + "summary": "Make batch geneset queries and return matching geneset hits", "tags": [ "query" ], "x-bte-kgs-operations": [ { - "$ref": "#/components/x-bte-kgs-operations/disease-gene" + "$ref": "#/components/x-bte-kgs-operations/has_subclass" }, { - "$ref": "#/components/x-bte-kgs-operations/gene-disease" + "$ref": "#/components/x-bte-kgs-operations/subclass_of" + }, + { + "$ref": "#/components/x-bte-kgs-operations/part_of" + }, + { + "$ref": "#/components/x-bte-kgs-operations/has_part" } ] } @@ -52691,22 +52436,22 @@ "servers": [ { "description": "Encrypted Production server", - "url": "https://biothings.ncats.io/DISEASES" + "url": "https://biothings.ncats.io/go_mf" }, { "description": "Production server", - "url": "http://biothings.ncats.io/DISEASES" + "url": "http://biothings.ncats.io/go_mf" } ], "tags": [ { - "name": "gene" + "name": "ontology" }, { - "name": "disease" + "name": "molecular activity" }, { - "name": "annotation" + "name": "geneset" }, { "name": "query" @@ -52720,925 +52465,881 @@ ] }, { - "_id": "edeb26858bd27d0322af93e7a9e08761", + "_id": "dc91716f44207d2e1287c727f281d339", "_meta": { - "date_created": "2020-12-07T23:07:08.266867+00:00", - "last_updated": "2021-03-05T08:02:26.275973+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/pfocr/smartapi.yaml", + "date_created": "2021-03-11T18:52:08.763346+00:00", + "last_updated": "2021-03-29T07:02:18.499585+00:00", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biothings_explorer/smartapi.yaml", "username": "kevinxin90" }, - "_score": 0.47008187, - "components": { - "x-bte-kgs-operations": { - "associatedWith": { - "inputSeparator": ",", - "inputs": [ - { - "id": "pathwayFigureID", - "semantic": "Pathway" - } - ], - "outputs": [ - { - "id": "entrez", - "semantic": "Gene" - } - ], - "parameters": { - "dotfield": false, - "fields": "associatedWith" - }, - "requestBody": { - "body": { - "q": "{input1}", - "scopes": "_id" - }, - "header": "application/x-www-form-urlencoded" - }, - "supportBatch": true - } - }, - "x-bte-response-mapping": { - "query-post": { - "@context": "http://schema.org", - "@type": "Pathway", - "bts:associatedWith": { - "$input": "bts:pathwayFigureID", - "$source": "PFOCR", - "@type": "Gene", - "bts:entrez": "associatedWith.genes", - "bts:pmc": "associatedWith.pmc" - }, - "bts:pathwayFigureID": "_id" - } - } - }, + "_score": 0.45173043, "info": { "contact": { - "email": "help@biothings.io", - "name": "JIWEN XIN", - "x-id": "https://github.com/kevinxin90", - "x-role": "responsible developer" + "email": "kevinxin@scripps.edu", + "name": "Jiwen Xin", + "url": "https://github.com/kevinxin90" }, - "description": "Documentation of the pfocr query web services.", + "description": "A ReasonerStdAPI for BioThings Explorer", "termsOfService": "https://biothings.io/about", - "title": "pfocr API", - "version": "1.0", + "title": "BioThings Explorer ReasonerStdAPI", + "version": "1.0.0", "x-translator": { - "component": "KP", + "component": "ARA", "team": [ - "Service Provider" + "Exploring Agent" ] + }, + "x-trapi": { + "version": "1.0.0" } }, "paths": { - "/geneset": { - "post": { + "/metakg": { + "get": { "parameters": [ { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" + "description": "The subject type of the association, e.g. Gene", + "example": "Gene", + "in": "query", + "name": "subject", + "schema": { + "type": "string" + } }, { - "$ref": "#/components/parameters/fields", - "name": "fields" + "description": "The object type of the association, e.g. ChemicalSubstance", + "example": "ChemicalSubstance", + "in": "query", + "name": "object", + "schema": { + "type": "string" + } }, { - "$ref": "#/components/parameters/email", - "name": "email" + "description": "The predicate of the association, e.g. Gene", + "example": "physically_interacts_with", + "in": "query", + "name": "predicate", + "schema": { + "type": "string" + } }, { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "requestBody": { - "content": { - "application/x-www-form-urlencoded": { - "schema": { - "properties": { - "ids": { - "description": "multiple geneset IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", - "type": "string" - } - }, - "required": [ - "ids" - ] - } + "description": "The API providing the association, e.g. MyChem.info API", + "example": "MyChem.info API", + "in": "query", + "name": "api", + "schema": { + "type": "string" + } + }, + { + "description": "The data source providing the association, e.g. drugbank", + "example": "drugbank", + "in": "query", + "name": "provided_by", + "schema": { + "type": "string" } } - }, + ], "responses": { "200": { "content": { "application/json": { "schema": { + "description": "Array of all associations", "items": { - "$ref": "#/components/schemas/Geneset" + "properties": { + "api": { + "description": "The api providing the association, e.g. MyChem.info", + "properties": { + "name": { + "description": "The api providing the association, e.g. MyChem.info", + "example": "MyChem.info API", + "type": "string" + }, + "smartapi": { + "description": "smartapi related data", + "properties": { + "id": { + "description": "unique smartapi id for the api", + "example": "8f08d1446e0bb9c2b323713ce83e2bd3", + "type": "string" + }, + "metadata": { + "description": "the url for smartapi specification", + "example": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/mychem.info/openapi_full.yml", + "type": "string" + }, + "ui": { + "description": "the web UI url for the API", + "example": "https://smart-api.info/ui/8f08d1446e0bb9c2b323713ce83e2bd3", + "type": "string" + } + }, + "type": "object" + } + }, + "type": "object" + }, + "object": { + "description": "The object type of the association, e.g. ChemicalSubstance", + "example": "ChemicalSubstance", + "type": "string" + }, + "predicate": { + "description": "The predicate of the association, e.g. physically_interacts_with", + "example": "physically_interacts_with", + "type": "string" + }, + "provided_by": { + "description": "The data source providing the association, e.g. ChEMBL", + "example": "ChEMBL", + "type": "string" + }, + "subject": { + "description": "The subject type of the association, e.g. Gene", + "example": "Gene", + "type": "string" + } + }, + "type": "object" }, "type": "array" } } }, - "description": "A list of matching geneset objects" - }, - "400": { + "description": "Association information including subject, object, predicate, api, provided_by and smartapi info." + } + }, + "summary": "retrieve associations within smartapi, if no parameters provided, will return all associations", + "tags": [ + "metadata" + ] + } + }, + "/predicates": { + "get": { + "responses": { + "200": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/ErrorResult" + "additionalProperties": { + "additionalProperties": { + "description": "Array of predicates", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": "Target map", + "type": "object" + }, + "description": "Source map", + "example": { + "chemical_substance": { + "chemical_substance": [ + "correlated_with" + ] + } + }, + "type": "object" } } }, - "description": "A response indicating an improperly formatted query" + "description": "Predicates by source and target" } }, - "summary": "For a list of geneset IDs, return the matching geneset object", + "summary": "Get supported relationships by source and target", "tags": [ - "geneset" + "metadata", + "0.9.2" ] } }, - "/geneset/{genesetid}": { + "/v1/predicates": { "get": { - "parameters": [ - { - "description": "Retrieve geneset objects based on geneset ID Supports JSONP and CORS as well.", - "example": "PMC2673547__nihms99366f8.jpg", - "in": "path", - "name": "genesetid", - "required": true, - "schema": { - "type": "string" - } - }, - { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" - }, - { - "$ref": "#/components/parameters/callback", - "name": "callback" - }, - { - "$ref": "#/components/parameters/fields", - "name": "fields" - }, - { - "$ref": "#/components/parameters/email", - "name": "email" - }, - { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], "responses": { "200": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/geneset" + "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": "A matching geneset object" - }, - "404": { - "description": "A response indicating an unknown geneset ID" + "description": "Predicates by source and target" } }, - "summary": "Retrieve geneset objects based on ID", + "summary": "Get supported relationships by source and target", "tags": [ - "geneset" + "predicates", + "1.0.0" ] } }, - "/metadata": { + "/v1/smartapi/{smartapi_id}/predicates": { "get": { "parameters": [ { - "$ref": "#/components/parameters/callback", - "in": "query", - "name": "callback" + "description": "SmartAPI ID of an API, you can get it from https://smart-api.info/registry", + "example": "978fe380a147a8641caf72320862697b", + "in": "path", + "name": "smartapi_id", + "required": true, + "schema": { + "type": "string" + } } ], "responses": { "200": { - "description": "pfocr metadata object" + "content": { + "application/json": { + "schema": { + "additionalProperties": { + "additionalProperties": { + "description": "Array of predicates", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": "Target map", + "type": "object" + }, + "description": "Source map", + "example": { + "biolink:ChemicalSubstance": { + "biolink:Gene": [ + "biolink:directly_interacts_with", + "biolink:decreases_activity_of" + ] + } + }, + "type": "object" + } + } + }, + "description": "Predicates by source and target" } }, - "summary": "Get metadata about the data available from pfocr", + "summary": "Get supported relationships by source and target for individual smartAPI", "tags": [ - "metadata" + "predicates", + "1.0.0" ] } }, - "/metadata/fields": { + "/v1/team/{team_name}/predicates": { "get": { "parameters": [ { - "$ref": "#/components/parameters/search", - "name": "search" - }, - { - "$ref": "#/components/parameters/callback", - "name": "callback" - }, - { - "$ref": "#/components/parameters/prefix", - "name": "prefix" - }, - { - "$ref": "#/components/parameters/format", - "name": "format" + "description": "Translator Team Name, e.g. Service Provider, Multiomics Provider", + "example": "Multiomics Provider", + "in": "path", + "name": "team_name", + "required": true, + "schema": { + "enum": [ + "Multiomics Provider", + "Text Mining Provider", + "Service Provider" + ], + "type": "string" + } } ], "responses": { "200": { - "description": "pfocr metadata fields object" + "content": { + "application/json": { + "schema": { + "additionalProperties": { + "additionalProperties": { + "description": "Array of predicates", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": "Target map", + "type": "object" + }, + "description": "Source map", + "example": { + "biolink:ChemicalSubstance": { + "biolink:Gene": [ + "biolink:directly_interacts_with", + "biolink:decreases_activity_of" + ] + } + }, + "type": "object" + } + } + }, + "description": "Predicates by source and target" } }, - "summary": "Get metadata about the data fields available from a pfocr geneset object", + "summary": "Get supported relationships by source and target for a KP/ARA team", "tags": [ - "metadata" + "predicates", + "1.0.0" ] } }, - "/query": { - "get": { - "parameters": [ - { - "description": "Query string.", - "example": "associatedWith.genes:1378", - "in": "query", - "name": "q", - "required": true, - "schema": { - "type": "string" - } - }, - { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" - }, - { - "$ref": "#/components/parameters/fields", - "name": "fields" - }, - { - "$ref": "#/components/parameters/facet_size", - "name": "facet_size" - }, - { - "$ref": "#/components/parameters/sort", - "name": "sort" - }, - { - "$ref": "#/components/parameters/callback", - "name": "callback" - }, - { - "$ref": "#/components/parameters/email", - "name": "email" - }, - { - "$ref": "#/components/parameters/facets", - "name": "facets" - }, - { - "$ref": "#/components/parameters/size", - "name": "size" - }, - { - "$ref": "#/components/parameters/from", - "name": "from" + "/v1/query": { + "post": { + "description": "", + "operationId": "query", + "requestBody": { + "content": { + "application/json": { + "example": { + "message": { + "query_graph": { + "edges": { + "e00": { + "object": "n01", + "subject": "n00" + } + }, + "nodes": { + "n00": { + "category": "biolink:Disease", + "id": "MONDO:0005737" + }, + "n01": { + "category": "biolink:ChemicalSubstance" + } + } + } + } + }, + "schema": { + "$ref": "#/components/schemas/Query" + } + } }, - { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], + "description": "Query information to be submitted", + "required": true + }, "responses": { "200": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/QueryResult" + "$ref": "#/components/schemas/Response" } } }, - "description": "A query response with the \"hits\" property" + "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": { - "$ref": "#/components/schemas/ErrorResult" + "type": "string" } } }, - "description": "A response indicating an improperly formatted query" + "description": "Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)." + }, + "500": { + "content": { + "application/json": { + "schema": { + "type": "string" + } + } + }, + "description": "Internal server error." + }, + "501": { + "content": { + "application/json": { + "schema": { + "type": "string" + } + } + }, + "description": "Not implemented." } }, - "summary": "Make queries and return matching geneset hits. Supports JSONP and CORS as well.", + "summary": "Query BioThings Explorer TRAPI API as ARA", "tags": [ - "query" - ] - }, + "query", + "1.0.0" + ], + "x-swagger-router-controller": "swagger_server.controllers.query_controller" + } + }, + "/v1/smartapi/{smartapi_id}/query": { "post": { + "description": "", + "operationId": "querySmartAPI", "parameters": [ { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" - }, - { - "$ref": "#/components/parameters/email", - "name": "email" - }, - { - "$ref": "#/components/parameters/fields", - "name": "fields" - }, - { - "$ref": "#/components/parameters/size", - "name": "size" - }, - { - "$ref": "#/components/parameters/format", - "name": "format" + "description": "SmartAPI ID of an API, you can get it from https://smart-api.info/registry", + "example": "978fe380a147a8641caf72320862697b", + "in": "path", + "name": "smartapi_id", + "required": true, + "schema": { + "type": "string" + } } ], "requestBody": { "content": { - "application/x-www-form-urlencoded": { - "schema": { - "properties": { - "q": { - "description": "multiple 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" + "application/json": { + "example": { + "message": { + "query_graph": { + "edges": { + "e00": { + "object": "n01", + "subject": "n00" + } + }, + "nodes": { + "n00": { + "category": "biolink:Gene", + "id": "NCBIGENE:1017" + }, + "n01": { + "category": "biolink:ChemicalSubstance" + } + } } } + }, + "schema": { + "$ref": "#/components/schemas/Query" } } - } + }, + "description": "Query information to be submitted", + "required": true }, "responses": { "200": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/QueryPOSTResult" + "$ref": "#/components/schemas/Response" } } }, - "description": "Query response objects with the \"hits\" property", - "x-bte-response-mapping": { - "$ref": "#/components/x-bte-response-mapping/query-post" - } + "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": { - "$ref": "#/components/schemas/ErrorResult" + "type": "string" } } }, - "description": "A response indicating an improperly formatted query" - } - }, - "summary": "Make batch geneset queries and return matching geneset hits", - "tags": [ - "query" - ], - "x-bte-kgs-operations": { - "associatedWith": { - "$ref": "#/components/x-bte-kgs-operations/associatedWith" - } - } - } - } - }, - "servers": [ - { - "description": "Encrypted Production server", - "url": "https://pending.biothings.io/pfocr" - }, - { - "description": "Production server", - "url": "http://pending.biothings.io/pfocr" - } - ], - "tags": [ - { - "name": "geneset" - }, - { - "name": "gene" - }, - { - "name": "annotation" - }, - { - "name": "query" - }, - { - "name": "translator" - }, - { - "name": "biothings" - } - ] - }, - { - "_id": "1f47552dabd67351d4c625adb0a10d00", - "_meta": { - "date_created": "2020-12-07T23:04:37.029674+00:00", - "last_updated": "2021-03-05T08:03:39.260037+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/EBIgene2phenotype/smartapi.yaml", - "username": "kevinxin90" - }, - "_score": 0.47008187, - "components": { - "x-bte-kgs-operations": { - "gene_related_to_phenotype": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "HGNC", - "semantic": "Gene" - } - ], - "outputs": [ - { - "id": "HP", - "semantic": "PhenotypicFeature" - } - ], - "parameters": { - "fields": "gene2phenotype" + "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)." }, - "predicate": "related_to", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "_id" + "500": { + "content": { + "application/json": { + "schema": { + "type": "string" + } + } }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/gene_related_to_phenotype" - }, - "source": "EBI", - "supportBatch": true - } - ], - "phenotype_related_to_gene": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "HP", - "semantic": "PhenotypicFeature" - } - ], - "outputs": [ - { - "id": "HGNC", - "semantic": "Gene" - } - ], - "parameters": { - "fields": "_id", - "size": "350" + "description": "Internal server error." }, - "predicate": "related_to", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "gene2phenotype.phenotypes" + "501": { + "content": { + "application/json": { + "schema": { + "type": "string" + } + } }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/phenotype_related_to_gene" - }, - "source": "EBI", - "supportBatch": true - } - ] - }, - "x-bte-response-mapping": { - "gene_related_to_phenotype": { - "HP": "gene2phenotype.phenotypes", - "probability": "gene2phenotype.DDD_category", - "pubmed": "gene2phenotype.pmids" - }, - "phenotype_related_to_gene": { - "HGNC": "_id" + "description": "Not implemented." + } + }, + "summary": "Query individual SmartAPI as TRAPI service using SmartAPI ID", + "tags": [ + "query", + "1.0.0" + ], + "x-swagger-router-controller": "swagger_server.controllers.query_controller" } - } - }, - "info": { - "contact": { - "email": "help@biothings.io", - "name": "JIWEN XIN", - "x-id": "https://github.com/kevinxin90", - "x-role": "responsible developer" }, - "description": "Documentation of the EBIgene2phenotype query web services.", - "termsOfService": "https://biothings.io/about", - "title": "EBIgene2phenotype API", - "version": "1.0", - "x-translator": { - "component": "KP", - "team": [ - "Service Provider" - ] - } - }, - "paths": { - "/gene": { + "/v1/team/{team_name}/query": { "post": { + "description": "", + "operationId": "queryTeam", "parameters": [ { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" - }, - { - "$ref": "#/components/parameters/fields", - "name": "fields" - }, - { - "$ref": "#/components/parameters/email", - "name": "email" - }, - { - "$ref": "#/components/parameters/format", - "name": "format" + "description": "Translator Team Name, e.g. Service Provider, Multiomics Provider", + "example": "Text Mining Provider", + "in": "path", + "name": "team_name", + "required": true, + "schema": { + "enum": [ + "Multiomics Provider", + "Text Mining Provider", + "Service Provider" + ], + "type": "string" + } } ], "requestBody": { "content": { - "application/x-www-form-urlencoded": { - "schema": { - "properties": { - "ids": { - "description": "multiple HGNC Gene IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", - "type": "string" + "application/json": { + "example": { + "message": { + "query_graph": { + "edges": { + "e00": { + "object": "n01", + "subject": "n00" + } + }, + "nodes": { + "n00": { + "category": "biolink:Gene", + "id": "NCBIGENE:1017" + }, + "n01": { + "category": "biolink:ChemicalSubstance" + } + } } - }, - "required": [ - "ids" - ] + } + }, + "schema": { + "$ref": "#/components/schemas/Query" } } - } + }, + "description": "Query information to be submitted", + "required": true }, "responses": { "200": { "content": { "application/json": { "schema": { - "items": { - "$ref": "#/components/schemas/Gene" - }, - "type": "array" + "$ref": "#/components/schemas/Response" } } }, - "description": "A list of matching gene objects" + "description": "OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized." }, "400": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/ErrorResult" + "type": "string" } } }, - "description": "A response indicating an improperly formatted query" - } - }, - "summary": "For a list of chemical IDs, return the matching gene object", - "tags": [ - "gene" - ] - } - }, - "/gene/{geneid}": { - "get": { - "parameters": [ - { - "description": "Retrieve gene objects based on HGNC Gene ID Supports JSONP and CORS as well.", - "example": 851, - "in": "path", - "name": "geneid", - "required": true, - "schema": { - "type": "string" - } - }, - { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" - }, - { - "$ref": "#/components/parameters/callback", - "name": "callback" - }, - { - "$ref": "#/components/parameters/fields", - "name": "fields" - }, - { - "$ref": "#/components/parameters/email", - "name": "email" + "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)." }, - { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "responses": { - "200": { + "500": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Gene" + "type": "string" } } }, - "description": "A matching gene object" + "description": "Internal server error." }, - "404": { - "description": "A response indicating an unknown gene ID" + "501": { + "content": { + "application/json": { + "schema": { + "type": "string" + } + } + }, + "description": "Not implemented." } }, - "summary": "Retrieve gene objects based on ID", + "summary": "Query individual Translator team as individual TRAPI service using team name", "tags": [ - "gene" - ] - } - }, - "/metadata": { - "get": { - "parameters": [ - { - "$ref": "#/components/parameters/callback", - "in": "query", - "name": "callback" - } + "query", + "1.0.0" ], - "responses": { - "200": { - "description": "EBIgene2phenotype metadata object" - } - }, - "summary": "Get metadata about the data available from EBIgene2phenotype", - "tags": [ - "metadata" - ] + "x-swagger-router-controller": "swagger_server.controllers.query_controller" } }, - "/metadata/fields": { - "get": { - "parameters": [ - { - "$ref": "#/components/parameters/search", - "name": "search" - }, - { - "$ref": "#/components/parameters/callback", - "name": "callback" - }, - { - "$ref": "#/components/parameters/prefix", - "name": "prefix" + "/query/": { + "post": { + "requestBody": { + "content": { + "application/json": { + "example": { + "message": { + "query_graph": { + "edges": [ + { + "id": "e00", + "source_id": "n00", + "target_id": "n01" + }, + { + "id": "e01", + "source_id": "n01", + "target_id": "n02" + } + ], + "nodes": [ + { + "curie": "MONDO:0005737", + "id": "n00", + "type": "disease" + }, + { + "id": "n01", + "set": true, + "type": "gene" + }, + { + "id": "n02", + "type": "chemical_substance" + } + ] + } + } + }, + "schema": { + "$ref": "#/components/schemas/Query" + } + } }, - { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], + "description": "A message with question graph.", + "required": true + }, "responses": { "200": { - "description": "EBIgene2phenotype metadata fields object" + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Message" + } + } + }, + "description": "A message with knowledge graph and answers." } }, - "summary": "Get metadata about the data fields available from a EBIgene2phenotype gene object", + "summary": "Get answers to a question", "tags": [ - "metadata" + "0.9.2", + "query" ] } }, - "/query": { - "get": { + "/smartapi/{smartapi_id}/query/": { + "post": { "parameters": [ { - "description": "Query string.", - "example": "gene2phenotype.mutation_consequence:\"loss of function\"", - "in": "query", - "name": "q", + "description": "SmartAPI ID of an API, you can get it from https://smart-api.info/registry", + "example": "978fe380a147a8641caf72320862697b", + "in": "path", + "name": "smartapi_id", "required": true, "schema": { "type": "string" } - }, - { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" - }, - { - "$ref": "#/components/parameters/fields", - "name": "fields" - }, - { - "$ref": "#/components/parameters/facet_size", - "name": "facet_size" - }, - { - "$ref": "#/components/parameters/sort", - "name": "sort" - }, - { - "$ref": "#/components/parameters/callback", - "name": "callback" - }, - { - "$ref": "#/components/parameters/email", - "name": "email" - }, - { - "$ref": "#/components/parameters/facets", - "name": "facets" - }, - { - "$ref": "#/components/parameters/size", - "name": "size" - }, - { - "$ref": "#/components/parameters/from", - "name": "from" - }, - { - "$ref": "#/components/parameters/format", - "name": "format" } ], - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/QueryResult" + "requestBody": { + "content": { + "application/json": { + "example": { + "message": { + "query_graph": { + "edges": [ + { + "id": "e00", + "source_id": "n00", + "target_id": "n01" + } + ], + "nodes": [ + { + "curie": "NCBIGENE:1017", + "id": "n00", + "type": "gene" + }, + { + "id": "n01", + "type": "chemical_substance" + } + ] + } } + }, + "schema": { + "$ref": "#/components/schemas/Query" } - }, - "description": "A query response with the \"hits\" property" + } }, - "400": { + "description": "A message with question graph.", + "required": true + }, + "responses": { + "200": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/ErrorResult" + "$ref": "#/components/schemas/Message" } } }, - "description": "A response indicating an improperly formatted query" + "description": "A message with knowledge graph and answers." } }, - "summary": "Make queries and return matching gene hits. Supports JSONP and CORS as well.", + "summary": "Get answers to a question using a specific API", "tags": [ + "0.9.2", "query" ] - }, + } + }, + "/source/{source_name}/query/": { "post": { "parameters": [ { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" - }, - { - "$ref": "#/components/parameters/email", - "name": "email" - }, - { - "$ref": "#/components/parameters/fields", - "name": "fields" - }, - { - "$ref": "#/components/parameters/size", - "name": "size" - }, - { - "$ref": "#/components/parameters/format", - "name": "format" + "description": "The name of the data source", + "example": "drugbank", + "in": "path", + "name": "source_name", + "required": true, + "schema": { + "type": "string" + } } ], "requestBody": { "content": { - "application/x-www-form-urlencoded": { - "schema": { - "properties": { - "q": { - "description": "multiple 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" + "application/json": { + "example": { + "message": { + "query_graph": { + "edges": [ + { + "id": "e00", + "source_id": "n00", + "target_id": "n01" + } + ], + "nodes": [ + { + "curie": "NCBIGENE:1017", + "id": "n00", + "type": "gene" + }, + { + "id": "n01", + "type": "chemical_substance" + } + ] } } + }, + "schema": { + "$ref": "#/components/schemas/Query" } } - } + }, + "description": "A message with question graph.", + "required": true }, "responses": { "200": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/QueryPOSTResult" - } - } - }, - "description": "Query response objects with the \"hits\" property" - }, - "400": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResult" + "$ref": "#/components/schemas/Message" } } }, - "description": "A response indicating an improperly formatted query" + "description": "A message with knowledge graph and answers." } }, - "summary": "Make batch gene queries and return matching gene hits", + "summary": "Get answers to a question using a specific data source.", "tags": [ + "0.9.2", "query" - ], - "x-bte-kgs-operations": [ - { - "$ref": "#/components/x-bte-kgs-operations/gene_related_to_phenotype" - }, - { - "$ref": "#/components/x-bte-kgs-operations/phenotype_related_to_gene" - } ] } } }, "servers": [ { - "description": "Encrypted Production server", - "url": "https://biothings.ncats.io/ebigene2phenotype" - }, - { - "description": "Production server", - "url": "http://biothings.ncats.io/ebigene2phenotype" + "url": "https://api.bte.ncats.io" } ], "tags": [ { - "name": "gene" + "name": "1.0.0" }, { - "name": "phenotype" + "name": "0.9.2" }, { - "name": "annotation" + "name": "translator" }, { - "name": "query" + "name": "trapi" }, { - "name": "translator" + "name": "biothings" }, { - "name": "biothings" + "name": "metadata" + }, + { + "name": "query" } ] }, { - "_id": "cc857d5b7c8b7609b5bbb38ff990bfff", + "_id": "f339b28426e7bf72028f60feefcd7465", "_meta": { - "date_created": "2020-12-07T23:07:17.431637+00:00", - "last_updated": "2021-03-05T08:01:22.183205+00:00", - "slug": "go_bp", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/go_bp/smartapi.yaml", + "date_created": "2020-12-07T23:01:11.475174+00:00", + "last_updated": "2021-03-29T07:02:39.969707+00:00", + "slug": "go_cc", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/go_cc/smartapi.yaml", "username": "kevinxin90" }, - "_score": 0.43758613, + "_score": 0.45173043, "components": { "x-bte-kgs-operations": { "has_part": [ @@ -53647,13 +53348,13 @@ "inputs": [ { "id": "GO", - "semantic": "BiologicalProcess" + "semantic": "CellularComponent" } ], "outputs": [ { "id": "GO", - "semantic": "BiologicalProcess" + "semantic": "CellularComponent" } ], "parameters": { @@ -53680,13 +53381,13 @@ "inputs": [ { "id": "GO", - "semantic": "BiologicalProcess" + "semantic": "CellularComponent" } ], "outputs": [ { "id": "GO", - "semantic": "BiologicalProcess" + "semantic": "CellularComponent" } ], "parameters": { @@ -53707,85 +53408,19 @@ "supportBatch": true } ], - "negatively_regulated_by": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "GO", - "semantic": "BiologicalProcess" - } - ], - "outputs": [ - { - "id": "GO", - "semantic": "BiologicalProcess" - } - ], - "parameters": { - "fields": "_id" - }, - "predicate": "negatively_regulated_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "negatively_regulates.go" - }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/negatively_regulated_by" - }, - "source": "Gene Ontology", - "supportBatch": true - } - ], - "negatively_regulates": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "GO", - "semantic": "BiologicalProcess" - } - ], - "outputs": [ - { - "id": "GO", - "semantic": "BiologicalProcess" - } - ], - "parameters": { - "fields": "negatively_regulates.go" - }, - "predicate": "negatively_regulates", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "_id" - }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/negatively_regulates" - }, - "source": "Gene Ontology", - "supportBatch": true - } - ], "part_of": [ { "inputSeparator": ",", "inputs": [ { "id": "GO", - "semantic": "BiologicalProcess" + "semantic": "CellularComponent" } ], "outputs": [ { "id": "GO", - "semantic": "BiologicalProcess" + "semantic": "CellularComponent" } ], "parameters": { @@ -53806,151 +53441,19 @@ "supportBatch": true } ], - "positively_regulated_by": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "GO", - "semantic": "BiologicalProcess" - } - ], - "outputs": [ - { - "id": "GO", - "semantic": "BiologicalProcess" - } - ], - "parameters": { - "fields": "_id" - }, - "predicate": "positively_regulated_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "positively_regulates.go" - }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/positively_regulated_by" - }, - "source": "Gene Ontology", - "supportBatch": true - } - ], - "positively_regulates": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "GO", - "semantic": "BiologicalProcess" - } - ], - "outputs": [ - { - "id": "GO", - "semantic": "BiologicalProcess" - } - ], - "parameters": { - "fields": "positively_regulates.go" - }, - "predicate": "positively_regulates", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "_id" - }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/positively_regulates" - }, - "source": "Gene Ontology", - "supportBatch": true - } - ], - "regulated_by": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "GO", - "semantic": "BiologicalProcess" - } - ], - "outputs": [ - { - "id": "GO", - "semantic": "BiologicalProcess" - } - ], - "parameters": { - "fields": "_id" - }, - "predicate": "regulated_by", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "regulates.go" - }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/regulated_by" - }, - "source": "Gene Ontology", - "supportBatch": true - } - ], - "regulates": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "GO", - "semantic": "BiologicalProcess" - } - ], - "outputs": [ - { - "id": "GO", - "semantic": "BiologicalProcess" - } - ], - "parameters": { - "fields": "regulates.go" - }, - "predicate": "regulates", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "_id" - }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/regulates" - }, - "source": "Gene Ontology", - "supportBatch": true - } - ], "subclass_of": [ { "inputSeparator": ",", "inputs": [ { "id": "GO", - "semantic": "BiologicalProcess" + "semantic": "CellularComponent" } ], "outputs": [ { "id": "GO", - "semantic": "BiologicalProcess" + "semantic": "CellularComponent" } ], "parameters": { @@ -53979,27 +53482,9 @@ "has_subclass": { "GO": "children" }, - "negatively_regulated_by": { - "GO": "_id" - }, - "negatively_regulates": { - "GO": "negatively_regulates.go" - }, "part_of": { "GO": "part_of.go" }, - "positively_regulated_by": { - "GO": "_id" - }, - "positively_regulates": { - "GO": "positively_regulates.go" - }, - "regulated_by": { - "GO": "_id" - }, - "regulates": { - "GO": "regulates.go" - }, "subclass_of": { "GO": "parents" } @@ -54012,9 +53497,9 @@ "x-id": "https://github.com/kevinxin90", "x-role": "responsible developer" }, - "description": "Documentation of the Gene Ontology Biological Process query web services.", + "description": "Documentation of the Gene Ontology Cellular Component query web services.", "termsOfService": "https://biothings.io/about", - "title": "Gene Ontology Biological Process API", + "title": "Gene Ontology Cellular Component API", "version": "1.0", "x-translator": { "component": "KP", @@ -54097,7 +53582,7 @@ "parameters": [ { "description": "Retrieve geneset objects based on GO geneset ID. Supports JSONP and CORS as well.", - "example": "GO:0042121", + "example": "GO:0098791", "in": "path", "name": "genesetid", "required": true, @@ -54203,7 +53688,7 @@ "parameters": [ { "description": "Query string.", - "example": "parents:\"GO:0071704\"", + "example": "parents:\"GO:0098791\"", "in": "query", "name": "q", "required": true, @@ -54353,29 +53838,11 @@ { "$ref": "#/components/x-bte-kgs-operations/subclass_of" }, - { - "$ref": "#/components/x-bte-kgs-operations/positively_regulates" - }, - { - "$ref": "#/components/x-bte-kgs-operations/negatively_regulates" - }, - { - "$ref": "#/components/x-bte-kgs-operations/positively_regulated_by" - }, - { - "$ref": "#/components/x-bte-kgs-operations/negatively_regulated_by" - }, - { - "$ref": "#/components/x-bte-kgs-operations/has_part" - }, { "$ref": "#/components/x-bte-kgs-operations/part_of" }, { - "$ref": "#/components/x-bte-kgs-operations/regulates" - }, - { - "$ref": "#/components/x-bte-kgs-operations/regulated_by" + "$ref": "#/components/x-bte-kgs-operations/has_part" } ] } @@ -54384,11 +53851,11 @@ "servers": [ { "description": "Encrypted Production server", - "url": "https://biothings.ncats.io/go_bp" + "url": "https://biothings.ncats.io/go_cc" }, { "description": "Production server", - "url": "http://biothings.ncats.io/go_bp" + "url": "http://biothings.ncats.io/go_cc" } ], "tags": [ @@ -54396,7 +53863,7 @@ "name": "ontology" }, { - "name": "biological process" + "name": "cellular component" }, { "name": "geneset" @@ -54413,409 +53880,378 @@ ] }, { - "_id": "5076f09382b38d56a77e376416b634ca", + "_id": "cc857d5b7c8b7609b5bbb38ff990bfff", "_meta": { - "date_created": "2020-12-11T01:19:27.868824+00:00", - "last_updated": "2021-03-05T08:01:44.637923+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/clinical_risk_factor/smartapi.yml", + "date_created": "2020-12-07T23:07:17.431637+00:00", + "last_updated": "2021-03-29T07:04:53.083275+00:00", + "slug": "go_bp", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/go_bp/smartapi.yaml", "username": "kevinxin90" }, - "_score": 0.43758613, + "_score": 0.45173043, "components": { "x-bte-kgs-operations": { - "attribute-disease": [ + "has_part": [ { + "inputSeparator": ",", "inputs": [ { - "id": "NCIT", - "semantic": "Attribute" + "id": "GO", + "semantic": "BiologicalProcess" } ], "outputs": [ { - "id": "MONDO", - "semantic": "DiseaseOrPhenotypicFeature" + "id": "GO", + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "association,object.MONDO", - "q": "subject.id:\"{inputs[0]}\"", - "size": "1000" - }, - "predicate": "affects_risk_for", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/disease" + "fields": "_id" }, - "source": "Multiomics Provider", - "supportBatch": false - } - ], - "attribute-disease1": [ - { - "inputs": [ - { - "id": "NCIT", - "semantic": "Attribute" - } - ], - "outputs": [ - { - "id": "DOID", - "semantic": "DiseaseOrPhenotypicFeature" - } - ], - "parameters": { - "fields": "association,object.DOID", - "q": "subject.id:\"{inputs[0]}\"", - "size": "1000" + "predicate": "has_part", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "part_of.go" + }, + "header": "application/x-www-form-urlencoded" }, - "predicate": "affects_risk_for", "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/disease-doid" + "$ref": "#/components/x-bte-response-mapping/has_part" }, - "source": "Multiomics Provider", - "supportBatch": false + "source": "Gene Ontology", + "supportBatch": true } ], - "disease-disease1": [ + "has_subclass": [ { + "inputSeparator": ",", "inputs": [ { - "id": "NCIT", - "semantic": "DiseaseOrPhenotypicFeature" + "id": "GO", + "semantic": "BiologicalProcess" } ], "outputs": [ { - "id": "MONDO", - "semantic": "DiseaseOrPhenotypicFeature" + "id": "GO", + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "association,object.MONDO", - "q": "subject.id:\"{inputs[0]}\"", - "size": "1000" - }, - "predicate": "affects_risk_for", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/disease" + "fields": "children" }, - "source": "Multiomics Provider", - "supportBatch": false - } - ], - "disease-disease2": [ - { - "inputs": [ - { - "id": "MONDO", - "semantic": "DiseaseOrPhenotypicFeature" - } - ], - "outputs": [ - { - "id": "MONDO", - "semantic": "DiseaseOrPhenotypicFeature" - } - ], - "parameters": { - "fields": "association,object.MONDO", - "q": "subject.id:\"{inputs[0]}\"", - "size": "1000" + "predicate": "has_subclass", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "_id" + }, + "header": "application/x-www-form-urlencoded" }, - "predicate": "affects_risk_for", "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/disease" + "$ref": "#/components/x-bte-response-mapping/has_subclass" }, - "source": "Multiomics Provider", - "supportBatch": false + "source": "Gene Ontology", + "supportBatch": true } ], - "disease-disease3": [ + "negatively_regulated_by": [ { + "inputSeparator": ",", "inputs": [ { - "id": "NCIT", - "semantic": "DiseaseOrPhenotypicFeature" + "id": "GO", + "semantic": "BiologicalProcess" } ], "outputs": [ { - "id": "DOID", - "semantic": "DiseaseOrPhenotypicFeature" + "id": "GO", + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "association,object.DOID", - "q": "subject.id:\"{inputs[0]}\"", - "size": "1000" - }, - "predicate": "affects_risk_for", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/disease-doid" + "fields": "_id" }, - "source": "Multiomics Provider", - "supportBatch": false - } - ], - "disease-disease4": [ - { - "inputs": [ - { - "id": "MONDO", - "semantic": "DiseaseOrPhenotypicFeature" - } - ], - "outputs": [ - { - "id": "DOID", - "semantic": "DiseaseOrPhenotypicFeature" - } - ], - "parameters": { - "fields": "association,object.DOID", - "q": "subject.id:\"{inputs[0]}\"", - "size": "1000" + "predicate": "process_negatively_regulated_by_process", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "negatively_regulates.go" + }, + "header": "application/x-www-form-urlencoded" }, - "predicate": "affects_risk_for", "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/disease-doid" + "$ref": "#/components/x-bte-response-mapping/negatively_regulated_by" }, - "source": "Multiomics Provider", - "supportBatch": false + "source": "Gene Ontology", + "supportBatch": true } ], - "drug_exposure-disease1": [ + "negatively_regulates": [ { + "inputSeparator": ",", "inputs": [ { - "id": "NCIT", - "semantic": "DrugExposure" + "id": "GO", + "semantic": "BiologicalProcess" } ], "outputs": [ { - "id": "MONDO", - "semantic": "DiseaseOrPhenotypicFeature" + "id": "GO", + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "association,object.MONDO", - "q": "subject.id:\"{inputs[0]}\"", - "size": "1000" - }, - "predicate": "affects_risk_for", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/disease" + "fields": "negatively_regulates.go" }, - "source": "Multiomics Provider", - "supportBatch": false - } - ], - "drug_exposure-disease2": [ - { - "inputs": [ - { - "id": "CHEBI", - "semantic": "DrugExposure" - } - ], - "outputs": [ - { - "id": "MONDO", - "semantic": "DiseaseOrPhenotypicFeature" - } - ], - "parameters": { - "fields": "association,object.MONDO", - "q": "subject.id:\"{inputs[0]}\"", - "size": "1000" + "predicate": "process_negatively_regulates_process", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "_id" + }, + "header": "application/x-www-form-urlencoded" }, - "predicate": "affects_risk_for", "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/disease" + "$ref": "#/components/x-bte-response-mapping/negatively_regulates" }, - "source": "Multiomics Provider", - "supportBatch": false + "source": "Gene Ontology", + "supportBatch": true } ], - "drug_exposure-disease3": [ + "part_of": [ { + "inputSeparator": ",", "inputs": [ { - "id": "NCIT", - "semantic": "DrugExposure" + "id": "GO", + "semantic": "BiologicalProcess" } ], "outputs": [ { - "id": "DOID", - "semantic": "DiseaseOrPhenotypicFeature" + "id": "GO", + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "association,object.DOID", - "q": "subject.id:\"{inputs[0]}\"", - "size": "1000" + "fields": "part_of.go" + }, + "predicate": "part_of", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "_id" + }, + "header": "application/x-www-form-urlencoded" }, - "predicate": "affects_risk_for", "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/disease-doid" + "$ref": "#/components/x-bte-response-mapping/part_of" }, - "source": "Multiomics Provider", - "supportBatch": false + "source": "Gene Ontology", + "supportBatch": true } ], - "drug_exposure-disease4": [ + "positively_regulated_by": [ { + "inputSeparator": ",", "inputs": [ { - "id": "CHEBI", - "semantic": "DrugExposure" + "id": "GO", + "semantic": "BiologicalProcess" } ], "outputs": [ { - "id": "DOID", - "semantic": "DiseaseOrPhenotypicFeature" + "id": "GO", + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "association,object.DOID", - "q": "subject.id:\"{inputs[0]}\"", - "size": "1000" + "fields": "_id" + }, + "predicate": "process_positively_regulated_by_process", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "positively_regulates.go" + }, + "header": "application/x-www-form-urlencoded" }, - "predicate": "affects_risk_for", "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/disease-doid" + "$ref": "#/components/x-bte-response-mapping/positively_regulated_by" }, - "source": "Multiomics Provider", - "supportBatch": false + "source": "Gene Ontology", + "supportBatch": true } ], - "observation-disease": [ + "positively_regulates": [ { + "inputSeparator": ",", "inputs": [ { - "id": "NCIT", - "semantic": "Observation" + "id": "GO", + "semantic": "BiologicalProcess" } ], "outputs": [ { - "id": "MONDO", - "semantic": "DiseaseOrPhenotypicFeature" + "id": "GO", + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "association,object.MONDO", - "q": "subject.id:\"{inputs[0]}\"", - "size": "1000" + "fields": "positively_regulates.go" + }, + "predicate": "process_positively_regulates_process", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "_id" + }, + "header": "application/x-www-form-urlencoded" }, - "predicate": "affects_risk_for", "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/disease" + "$ref": "#/components/x-bte-response-mapping/positively_regulates" }, - "source": "Multiomics Provider", - "supportBatch": false + "source": "Gene Ontology", + "supportBatch": true } ], - "observation-disease1": [ + "regulated_by": [ { + "inputSeparator": ",", "inputs": [ { - "id": "NCIT", - "semantic": "Observation" + "id": "GO", + "semantic": "BiologicalProcess" } ], "outputs": [ { - "id": "DOID", - "semantic": "DiseaseOrPhenotypicFeature" + "id": "GO", + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "association,object.DOID", - "q": "subject.id:\"{inputs[0]}\"", - "size": "1000" + "fields": "_id" + }, + "predicate": "regulated_by", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "regulates.go" + }, + "header": "application/x-www-form-urlencoded" }, - "predicate": "affects_risk_for", "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/disease-doid" + "$ref": "#/components/x-bte-response-mapping/regulated_by" }, - "source": "Multiomics Provider", - "supportBatch": false + "source": "Gene Ontology", + "supportBatch": true } ], - "symptom-disease": [ + "regulates": [ { + "inputSeparator": ",", "inputs": [ { - "id": "NCIT", - "semantic": "Symptom" + "id": "GO", + "semantic": "BiologicalProcess" } ], "outputs": [ { - "id": "MONDO", - "semantic": "DiseaseOrPhenotypicFeature" + "id": "GO", + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "association,object.MONDO", - "q": "subject.id:\"{inputs[0]}\"", - "size": "1000" + "fields": "regulates.go" + }, + "predicate": "regulates", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "_id" + }, + "header": "application/x-www-form-urlencoded" }, - "predicate": "affects_risk_for", "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/disease" + "$ref": "#/components/x-bte-response-mapping/regulates" }, - "source": "Multiomics Provider", - "supportBatch": false + "source": "Gene Ontology", + "supportBatch": true } ], - "symptom-disease1": [ + "subclass_of": [ { + "inputSeparator": ",", "inputs": [ { - "id": "NCIT", - "semantic": "Symptom" + "id": "GO", + "semantic": "BiologicalProcess" } ], "outputs": [ { - "id": "DOID", - "semantic": "DiseaseOrPhenotypicFeature" + "id": "GO", + "semantic": "BiologicalProcess" } ], "parameters": { - "fields": "association,object.DOID", - "q": "subject.id:\"{inputs[0]}\"", - "size": "1000" + "fields": "parents" + }, + "predicate": "subclass_of", + "requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "_id" + }, + "header": "application/x-www-form-urlencoded" }, - "predicate": "affects_risk_for", "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/disease-doid" + "$ref": "#/components/x-bte-response-mapping/subclass_of" }, - "source": "Multiomics Provider", - "supportBatch": false + "source": "Gene Ontology", + "supportBatch": true } ] }, "x-bte-response-mapping": { - "disease": { - "MONDO": "hits.object.MONDO", - "has_auc_roc": "hits.association.has_auc_roc", - "has_feature_importance": "hits.association.has_feature_importance", - "relation": "hits.association.relation", - "uses_classifier": "hits.associatioin.uses_classifier" - }, - "disease-doid": { - "DOID": "hits.object.DOID", - "has_auc_roc": "hits.association.has_auc_roc", - "has_feature_importance": "hits.association.has_feature_importance", - "relation": "hits.association.relation", - "uses_classifier": "hits.associatioin.uses_classifier" + "has_part": { + "GO": "_id" + }, + "has_subclass": { + "GO": "children" + }, + "negatively_regulated_by": { + "GO": "_id" + }, + "negatively_regulates": { + "GO": "negatively_regulates.go" + }, + "part_of": { + "GO": "part_of.go" + }, + "positively_regulated_by": { + "GO": "_id" + }, + "positively_regulates": { + "GO": "positively_regulates.go" + }, + "regulated_by": { + "GO": "_id" + }, + "regulates": { + "GO": "regulates.go" + }, + "subclass_of": { + "GO": "parents" } } }, @@ -54826,20 +54262,19 @@ "x-id": "https://github.com/kevinxin90", "x-role": "responsible developer" }, - "description": "Documentation of the Clinical Risk KP query web services.", + "description": "Documentation of the Gene Ontology Biological Process query web services.", "termsOfService": "https://biothings.io/about", - "title": "Clinical Risk KP API", + "title": "Gene Ontology Biological Process API", "version": "1.0", "x-translator": { "component": "KP", "team": [ - "Multiomics Provider", "Service Provider" ] } }, "paths": { - "/association": { + "/geneset": { "post": { "parameters": [ { @@ -54865,7 +54300,7 @@ "schema": { "properties": { "ids": { - "description": "multiple association IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", + "description": "multiple GO geneset IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", "type": "string" } }, @@ -54882,13 +54317,13 @@ "application/json": { "schema": { "items": { - "$ref": "#/components/schemas/Association" + "$ref": "#/components/schemas/Geneset" }, "type": "array" } } }, - "description": "A list of matching association objects" + "description": "A list of matching geneset objects" }, "400": { "content": { @@ -54901,20 +54336,20 @@ "description": "A response indicating an improperly formatted query" } }, - "summary": "For a list of association IDs, return the matching disease object", + "summary": "For a list of geneset IDs, return the matching geneset object", "tags": [ - "association" + "geneset" ] } }, - "/association/{associationid}": { + "/geneset/{genesetid}": { "get": { "parameters": [ { - "description": "Retrieve association objects based on Association ID Supports JSONP and CORS as well.", - "example": "NCIT:C25150-Age-diabetes mellitus (disease)-Gradient Boosting-34.87", + "description": "Retrieve geneset objects based on GO geneset ID. Supports JSONP and CORS as well.", + "example": "GO:0042121", "in": "path", - "name": "associationid", + "name": "genesetid", "required": true, "schema": { "type": "string" @@ -54946,19 +54381,19 @@ "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Association" + "$ref": "#/components/schemas/Geneset" } } }, - "description": "A matching association object" + "description": "A matching geneset object" }, "404": { - "description": "A response indicating an unknown association ID" + "description": "A response indicating an unknown geneset ID" } }, - "summary": "Retrieve association objects based on ID", + "summary": "Retrieve geneset objects based on ID", "tags": [ - "association" + "geneset" ] } }, @@ -54973,10 +54408,10 @@ ], "responses": { "200": { - "description": "KP metadata object" + "description": "DISEASES metadata object" } }, - "summary": "Get metadata about the data available from the API", + "summary": "Get metadata about the data available from DISEASES", "tags": [ "metadata" ] @@ -55004,10 +54439,10 @@ ], "responses": { "200": { - "description": "metadata fields object" + "description": "DISEASES metadata fields object" } }, - "summary": "Get metadata about the data fields available", + "summary": "Get metadata about the data fields available object", "tags": [ "metadata" ] @@ -55018,7 +54453,7 @@ "parameters": [ { "description": "Query string.", - "example": "subject.id:NCIT\\:C28421", + "example": "parents:\"GO:0071704\"", "in": "query", "name": "q", "required": true, @@ -55059,83 +54494,39 @@ "name": "size" }, { - "$ref": "#/components/parameters/from", - "name": "from" - }, - { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/QueryResult" - } - } - }, - "description": "A query response with the \"hits\" property" - }, - "400": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResult" - } - } - }, - "description": "A response indicating an improperly formatted query" - } - }, - "summary": "Make queries and return matching association hits. Supports JSONP and CORS as well.", - "tags": [ - "query" - ], - "x-bte-kgs-operations": [ - { - "$ref": "#/components/x-bte-kgs-operations/attribute-disease" - }, - { - "$ref": "#/components/x-bte-kgs-operations/drug_exposure-disease1" - }, - { - "$ref": "#/components/x-bte-kgs-operations/drug_exposure-disease2" - }, - { - "$ref": "#/components/x-bte-kgs-operations/observation-disease" - }, - { - "$ref": "#/components/x-bte-kgs-operations/symptom-disease" - }, - { - "$ref": "#/components/x-bte-kgs-operations/disease-disease1" - }, - { - "$ref": "#/components/x-bte-kgs-operations/disease-disease2" - }, - { - "$ref": "#/components/x-bte-kgs-operations/attribute-disease1" - }, - { - "$ref": "#/components/x-bte-kgs-operations/drug_exposure-disease3" - }, - { - "$ref": "#/components/x-bte-kgs-operations/drug_exposure-disease4" - }, - { - "$ref": "#/components/x-bte-kgs-operations/observation-disease1" - }, - { - "$ref": "#/components/x-bte-kgs-operations/symptom-disease1" + "$ref": "#/components/parameters/from", + "name": "from" }, { - "$ref": "#/components/x-bte-kgs-operations/disease-disease3" + "$ref": "#/components/parameters/format", + "name": "format" + } + ], + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/QueryResult" + } + } + }, + "description": "A query response with the \"hits\" property" }, - { - "$ref": "#/components/x-bte-kgs-operations/disease-disease4" + "400": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResult" + } + } + }, + "description": "A response indicating an improperly formatted query" } + }, + "summary": "Make queries and return matching geneset hits. Supports JSONP and CORS as well.", + "tags": [ + "query" ] }, "post": { @@ -55201,9 +54592,41 @@ "description": "A response indicating an improperly formatted query" } }, - "summary": "Make batch disease queries and return matching disease hits", + "summary": "Make batch geneset queries and return matching geneset hits", "tags": [ "query" + ], + "x-bte-kgs-operations": [ + { + "$ref": "#/components/x-bte-kgs-operations/has_subclass" + }, + { + "$ref": "#/components/x-bte-kgs-operations/subclass_of" + }, + { + "$ref": "#/components/x-bte-kgs-operations/positively_regulates" + }, + { + "$ref": "#/components/x-bte-kgs-operations/negatively_regulates" + }, + { + "$ref": "#/components/x-bte-kgs-operations/positively_regulated_by" + }, + { + "$ref": "#/components/x-bte-kgs-operations/negatively_regulated_by" + }, + { + "$ref": "#/components/x-bte-kgs-operations/has_part" + }, + { + "$ref": "#/components/x-bte-kgs-operations/part_of" + }, + { + "$ref": "#/components/x-bte-kgs-operations/regulates" + }, + { + "$ref": "#/components/x-bte-kgs-operations/regulated_by" + } ] } } @@ -55211,22 +54634,22 @@ "servers": [ { "description": "Encrypted Production server", - "url": "https://biothings.ncats.io/clinical_risk_kp" + "url": "https://biothings.ncats.io/go_bp" }, { "description": "Production server", - "url": "http://biothings.ncats.io/clinical_risk_kp" + "url": "http://biothings.ncats.io/go_bp" } ], "tags": [ { - "name": "disease" + "name": "ontology" }, { - "name": "association" + "name": "biological process" }, { - "name": "annotation" + "name": "geneset" }, { "name": "query" @@ -55236,169 +54659,364 @@ }, { "name": "biothings" - }, - { - "name": "biothings_graph" } ] }, { - "_id": "34bad236d77bea0a0ee6c6cba5be54a6", + "_id": "978fe380a147a8641caf72320862697b", "_meta": { - "date_created": "2020-12-07T23:05:11.871445+00:00", - "last_updated": "2021-03-05T08:01:54.277457+00:00", - "slug": "go_ma", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/go_mf/smartapi.yaml", + "date_created": "2021-01-14T20:06:05.747171+00:00", + "last_updated": "2021-03-29T07:01:45.083236+00:00", + "slug": "text-mining-target-assoc", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/text_mining/smartapi.yaml", "username": "kevinxin90" }, - "_score": 0.43758613, + "_score": 0.4228227, "components": { "x-bte-kgs-operations": { - "has_part": [ + "chemical-gene-negative": [ { - "inputSeparator": ",", "inputs": [ { - "id": "GO", - "semantic": "MolecularActivity" + "id": "CHEBI", + "semantic": "ChemicalSubstance" } ], "outputs": [ { - "id": "GO", - "semantic": "MolecularActivity" + "id": "PR", + "semantic": "Gene" } ], "parameters": { - "fields": "_id" + "fields": "object.PR,association.evidence", + "q": "subject.CHEBI:\"{inputs[0]}\" AND association.edge_label:negatively_regulates_entity_to_entity", + "size": 1000 }, - "predicate": "has_part", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "part_of.go" - }, - "header": "application/x-www-form-urlencoded" + "predicate": "entity_negatively_regulates_entity", + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/chemical-gene" + }, + "source": "Text Mining KP", + "supportBatch": false + } + ], + "chemical-gene-positive": [ + { + "inputs": [ + { + "id": "CHEBI", + "semantic": "ChemicalSubstance" + } + ], + "outputs": [ + { + "id": "PR", + "semantic": "Gene" + } + ], + "parameters": { + "fields": "object.PR,association.evidence", + "q": "subject.CHEBI:\"{inputs[0]}\" AND association.edge_label:positively_regulates_entity_to_entity", + "size": 1000 }, + "predicate": "entity_positively_regulates_entity", "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/has_part" + "$ref": "#/components/x-bte-response-mapping/chemical-gene" }, - "source": "Gene Ontology", - "supportBatch": true + "source": "Text Mining KP", + "supportBatch": false } ], - "has_subclass": [ + "chemical-geneorgeneproduct-negative": [ { - "inputSeparator": ",", "inputs": [ { - "id": "GO", - "semantic": "MolecularActivity" + "id": "CHEBI", + "semantic": "ChemicalSubstance" } ], "outputs": [ { - "id": "GO", - "semantic": "MolecularActivity" + "id": "PR", + "semantic": "GeneOrGeneProduct" } ], "parameters": { - "fields": "children" + "fields": "object.PR,association.evidence", + "q": "subject.CHEBI:\"{inputs[0]}\" AND association.edge_label:negatively_regulates_entity_to_entity", + "size": 1000 }, - "predicate": "has_subclass", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "_id" - }, - "header": "application/x-www-form-urlencoded" + "predicate": "entity_negatively_regulates_entity", + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/chemical-gene" + }, + "source": "Text Mining KP", + "supportBatch": false + } + ], + "chemical-geneorgeneproduct-positive": [ + { + "inputs": [ + { + "id": "CHEBI", + "semantic": "ChemicalSubstance" + } + ], + "outputs": [ + { + "id": "PR", + "semantic": "GeneOrGeneProduct" + } + ], + "parameters": { + "fields": "object.PR,association.evidence", + "q": "subject.CHEBI:\"{inputs[0]}\" AND association.edge_label:positively_regulates_entity_to_entity", + "size": 1000 }, + "predicate": "entity_positively_regulates_entity", "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/has_subclass" + "$ref": "#/components/x-bte-response-mapping/chemical-gene" }, - "source": "Gene Ontology", - "supportBatch": true + "source": "Text Mining KP", + "supportBatch": false } ], - "part_of": [ + "chemical-protein-negative": [ { - "inputSeparator": ",", "inputs": [ { - "id": "GO", - "semantic": "MolecularActivity" + "id": "CHEBI", + "semantic": "ChemicalSubstance" } ], "outputs": [ { - "id": "GO", - "semantic": "MolecularActivity" + "id": "PR", + "semantic": "Protein" } ], "parameters": { - "fields": "part_of.go" + "fields": "object.PR,association.evidence", + "q": "subject.CHEBI:\"{inputs[0]}\" AND association.edge_label:negatively_regulates_entity_to_entity", + "size": 1000 }, - "predicate": "part_of", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "_id" - }, - "header": "application/x-www-form-urlencoded" + "predicate": "entity_negatively_regulates_entity", + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/chemical-gene" + }, + "source": "Text Mining KP", + "supportBatch": false + } + ], + "chemical-protein-positive": [ + { + "inputs": [ + { + "id": "CHEBI", + "semantic": "ChemicalSubstance" + } + ], + "outputs": [ + { + "id": "PR", + "semantic": "Protein" + } + ], + "parameters": { + "fields": "object.PR,association.evidence", + "q": "subject.CHEBI:\"{inputs[0]}\" AND association.edge_label:positively_regulates_entity_to_entity", + "size": 1000 }, + "predicate": "entity_positively_regulates_entity", "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/part_of" + "$ref": "#/components/x-bte-response-mapping/chemical-gene" }, - "source": "Gene Ontology", - "supportBatch": true + "source": "Text Mining KP", + "supportBatch": false } ], - "subclass_of": [ + "gene-chemical-negative": [ { - "inputSeparator": ",", "inputs": [ { - "id": "GO", - "semantic": "MolecularActivity" + "id": "PR", + "semantic": "Gene" } ], "outputs": [ { - "id": "GO", - "semantic": "MolecularActivity" + "id": "CHEBI", + "semantic": "ChemicalSubstance" } ], "parameters": { - "fields": "parents" + "fields": "subject.CHEBI,association.evidence", + "q": "object.PR:\"{inputs[0]}\" AND association.edge_label:negatively_regulates_entity_to_entity", + "size": 1000 }, - "predicate": "subclass_of", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "_id" - }, - "header": "application/x-www-form-urlencoded" + "predicate": "entity_negatively_regulated_by_entity", + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/gene-chemical" + }, + "source": "Text Mining KP", + "supportBatch": false + } + ], + "gene-chemical-positive": [ + { + "inputs": [ + { + "id": "PR", + "semantic": "Gene" + } + ], + "outputs": [ + { + "id": "CHEBI", + "semantic": "ChemicalSubstance" + } + ], + "parameters": { + "fields": "subject.CHEBI,association.evidence", + "q": "object.PR:\"{inputs[0]}\" AND association.edge_label:positively_regulates_entity_to_entity", + "size": 1000 }, + "predicate": "entity_positively_regulated_by_entity", "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/subclass_of" + "$ref": "#/components/x-bte-response-mapping/gene-chemical" }, - "source": "Gene Ontology", - "supportBatch": true + "source": "Text Mining KP", + "supportBatch": false + } + ], + "geneorgeneproduct-chemical-negative": [ + { + "inputs": [ + { + "id": "PR", + "semantic": "GeneOrGeneProduct" + } + ], + "outputs": [ + { + "id": "CHEBI", + "semantic": "ChemicalSubstance" + } + ], + "parameters": { + "fields": "subject.CHEBI,association.evidence", + "q": "object.PR:\"{inputs[0]}\" AND association.edge_label:negatively_regulates_entity_to_entity", + "size": 1000 + }, + "predicate": "entity_negatively_regulated_by_entity", + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/gene-chemical" + }, + "source": "Text Mining KP", + "supportBatch": false + } + ], + "geneorgeneproduct-chemical-positive": [ + { + "inputs": [ + { + "id": "PR", + "semantic": "GeneOrGeneProduct" + } + ], + "outputs": [ + { + "id": "CHEBI", + "semantic": "ChemicalSubstance" + } + ], + "parameters": { + "fields": "subject.CHEBI,association.evidence", + "q": "object.PR:\"{inputs[0]}\" AND association.edge_label:positively_regulates_entity_to_entity", + "size": 1000 + }, + "predicate": "entity_positively_regulated_by_entity", + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/gene-chemical" + }, + "source": "Text Mining KP", + "supportBatch": false + } + ], + "protein-chemical-negative": [ + { + "inputs": [ + { + "id": "PR", + "semantic": "Protein" + } + ], + "outputs": [ + { + "id": "CHEBI", + "semantic": "ChemicalSubstance" + } + ], + "parameters": { + "fields": "subject.CHEBI,association.evidence", + "q": "object.PR:\"{inputs[0]}\" AND association.edge_label:negatively_regulates_entity_to_entity", + "size": 1000 + }, + "predicate": "entity_negatively_regulated_by_entity", + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/gene-chemical" + }, + "source": "Text Mining KP", + "supportBatch": false + } + ], + "protein-chemical-positive": [ + { + "inputs": [ + { + "id": "PR", + "semantic": "Protein" + } + ], + "outputs": [ + { + "id": "CHEBI", + "semantic": "ChemicalSubstance" + } + ], + "parameters": { + "fields": "subject.CHEBI,association.evidence", + "q": "object.PR:\"{inputs[0]}\" AND association.edge_label:positively_regulates_entity_to_entity", + "size": 1000 + }, + "predicate": "entity_positively_regulated_by_entity", + "response_mapping": { + "$ref": "#/components/x-bte-response-mapping/gene-chemical" + }, + "source": "Text Mining KP", + "supportBatch": false } ] }, "x-bte-response-mapping": { - "has_part": { - "GO": "_id" - }, - "has_subclass": { - "GO": "children" - }, - "part_of": { - "GO": "part_of.go" + "chemical-gene": { + "PR": "hits.object.PR", + "object_spans": "hits.association.evidence.object_spans", + "pubmed": "hits.association.evidence.publications", + "relation_spans": "hits.association.evidence.relation_spans", + "score": "hits.association.evidence.score", + "sentence": "hits.association.evidence.sentence", + "subject_spans": "hits.association.evidence.subject_spans" }, - "subclass_of": { - "GO": "parents" + "gene-chemical": { + "CHEBI": "hits.subject.CHEBI", + "object_spans": "hits.association.evidence.object_spans", + "pubmed": "hits.association.evidence.publications", + "relation_spans": "hits.association.evidence.relation_spans", + "score": "hits.association.evidence.score", + "sentence": "hits.association.evidence.sentence", + "subject_spans": "hits.association.evidence.subject_spans" } } }, @@ -55409,19 +55027,20 @@ "x-id": "https://github.com/kevinxin90", "x-role": "responsible developer" }, - "description": "Documentation of the Gene Ontology Molecular Activity query web services.", + "description": "Documentation of the Text Mining Targeted Association query web services.", "termsOfService": "https://biothings.io/about", - "title": "Gene Ontology Molecular Activity API", + "title": "Text Mining Targeted Association API", "version": "1.0", "x-translator": { "component": "KP", "team": [ + "Text Mining Provider", "Service Provider" ] } }, "paths": { - "/geneset": { + "/association": { "post": { "parameters": [ { @@ -55447,7 +55066,7 @@ "schema": { "properties": { "ids": { - "description": "multiple GO geneset IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", + "description": "multiple association IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", "type": "string" } }, @@ -55464,13 +55083,13 @@ "application/json": { "schema": { "items": { - "$ref": "#/components/schemas/Geneset" + "$ref": "#/components/schemas/Association" }, "type": "array" } } }, - "description": "A list of matching geneset objects" + "description": "A list of matching association objects" }, "400": { "content": { @@ -55483,20 +55102,20 @@ "description": "A response indicating an improperly formatted query" } }, - "summary": "For a list of geneset IDs, return the matching geneset object", + "summary": "For a list of association IDs, return the matching disease object", "tags": [ - "geneset" + "association" ] } }, - "/geneset/{genesetid}": { + "/association/{associationid}": { "get": { "parameters": [ { - "description": "Retrieve geneset objects based on GO geneset ID. Supports JSONP and CORS as well.", - "example": "GO:0018672", + "description": "Retrieve association objects based on Association ID Supports JSONP and CORS as well.", + "example": "275bfadd2b4c60c3", "in": "path", - "name": "genesetid", + "name": "associationid", "required": true, "schema": { "type": "string" @@ -55528,19 +55147,19 @@ "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Geneset" + "$ref": "#/components/schemas/Association" } } }, - "description": "A matching geneset object" + "description": "A matching association object" }, "404": { - "description": "A response indicating an unknown geneset ID" + "description": "A response indicating an unknown association ID" } }, - "summary": "Retrieve geneset objects based on ID", + "summary": "Retrieve association objects based on ID", "tags": [ - "geneset" + "association" ] } }, @@ -55555,10 +55174,10 @@ ], "responses": { "200": { - "description": "DISEASES metadata object" + "description": "KP metadata object" } }, - "summary": "Get metadata about the data available from DISEASES", + "summary": "Get metadata about the data available from the API", "tags": [ "metadata" ] @@ -55586,10 +55205,10 @@ ], "responses": { "200": { - "description": "DISEASES metadata fields object" + "description": "metadata fields object" } }, - "summary": "Get metadata about the data fields available object", + "summary": "Get metadata about the data fields available", "tags": [ "metadata" ] @@ -55600,7 +55219,7 @@ "parameters": [ { "description": "Query string.", - "example": "parents:\"GO:0016705\"", + "example": "object.id:CHEMBL.COMPOUND\\:CHEMBL26", "in": "query", "name": "q", "required": true, @@ -55671,9 +55290,47 @@ "description": "A response indicating an improperly formatted query" } }, - "summary": "Make queries and return matching geneset hits. Supports JSONP and CORS as well.", + "summary": "Make queries and return matching association hits. Supports JSONP and CORS as well.", "tags": [ "query" + ], + "x-bte-kgs-operations": [ + { + "$ref": "#/components/x-bte-kgs-operations/chemical-gene-positive" + }, + { + "$ref": "#/components/x-bte-kgs-operations/chemical-gene-negative" + }, + { + "$ref": "#/components/x-bte-kgs-operations/gene-chemical-positive" + }, + { + "$ref": "#/components/x-bte-kgs-operations/gene-chemical-negative" + }, + { + "$ref": "#/components/x-bte-kgs-operations/chemical-protein-positive" + }, + { + "$ref": "#/components/x-bte-kgs-operations/chemical-protein-negative" + }, + { + "$ref": "#/components/x-bte-kgs-operations/protein-chemical-positive" + }, + { + "$ref": "#/components/x-bte-kgs-operations/protein-chemical-negative" + }, + { + "$ref": "#/components/x-bte-kgs-operations/chemical-geneorgeneproduct-positive" + }, + { + "$ref": "#/components/x-bte-kgs-operations/chemical-geneorgeneproduct-negative" + }, + { + "$ref": "#/components/x-bte-kgs-operations/geneorgeneproduct-chemical-positive" + }, + { + "$ref": "#/components/x-bte-kgs-operations/geneorgeneproduct-chemical-negative" + } ] }, "post": { @@ -55739,23 +55396,9 @@ "description": "A response indicating an improperly formatted query" } }, - "summary": "Make batch geneset queries and return matching geneset hits", + "summary": "Make batch disease queries and return matching disease hits", "tags": [ "query" - ], - "x-bte-kgs-operations": [ - { - "$ref": "#/components/x-bte-kgs-operations/has_subclass" - }, - { - "$ref": "#/components/x-bte-kgs-operations/subclass_of" - }, - { - "$ref": "#/components/x-bte-kgs-operations/part_of" - }, - { - "$ref": "#/components/x-bte-kgs-operations/has_part" - } ] } } @@ -55763,22 +55406,25 @@ "servers": [ { "description": "Encrypted Production server", - "url": "https://biothings.ncats.io/go_mf" + "url": "https://biothings.ncats.io/text_mining_targeted_association" }, { "description": "Production server", - "url": "http://biothings.ncats.io/go_mf" + "url": "http://biothings.ncats.io/text_mining_targeted_association" } ], "tags": [ { - "name": "ontology" + "name": "gene" }, { - "name": "molecular activity" + "name": "chemical" }, { - "name": "geneset" + "name": "association" + }, + { + "name": "annotation" }, { "name": "query" @@ -55788,166 +55434,89 @@ }, { "name": "biothings" + }, + { + "name": "biothings_graph" } ] }, { - "_id": "f339b28426e7bf72028f60feefcd7465", + "_id": "5219cefb9d2b8d5df08c3a956fdd20f3", "_meta": { - "date_created": "2020-12-07T23:01:11.475174+00:00", - "last_updated": "2021-03-05T08:02:08.654947+00:00", - "slug": "go_cc", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/go_cc/smartapi.yaml", + "date_created": "2021-02-11T00:04:22.638313+00:00", + "last_updated": "2021-03-29T07:02:14.358916+00:00", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/tcga_mut_freq/smartapi.yaml", "username": "kevinxin90" }, - "_score": 0.43758613, + "_score": 0.4228227, "components": { "x-bte-kgs-operations": { - "has_part": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "GO", - "semantic": "CellularComponent" - } - ], - "outputs": [ - { - "id": "GO", - "semantic": "CellularComponent" - } - ], - "parameters": { - "fields": "_id" - }, - "predicate": "has_part", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "part_of.go" - }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/has_part" - }, - "source": "Gene Ontology", - "supportBatch": true - } - ], - "has_subclass": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "GO", - "semantic": "CellularComponent" - } - ], - "outputs": [ - { - "id": "GO", - "semantic": "CellularComponent" - } - ], - "parameters": { - "fields": "children" - }, - "predicate": "has_subclass", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "_id" - }, - "header": "application/x-www-form-urlencoded" - }, - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/has_subclass" - }, - "source": "Gene Ontology", - "supportBatch": true - } - ], - "part_of": [ + "disease-gene": [ { - "inputSeparator": ",", "inputs": [ { - "id": "GO", - "semantic": "CellularComponent" + "id": "MONDO", + "semantic": "Disease" } ], "outputs": [ { - "id": "GO", - "semantic": "CellularComponent" + "id": "SYMBOL", + "semantic": "Gene" } ], "parameters": { - "fields": "part_of.go" - }, - "predicate": "part_of", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "_id" - }, - "header": "application/x-www-form-urlencoded" + "fields": "association.freq_by_sample,subject.SYMBOL", + "q": "object.id:\"{inputs[0]}\" AND association.freq_by_sample:>0.1", + "size": "1000", + "sort": "-association.freq_by_sample" }, + "predicate": "gene_has_variant_that_contributes_to_disease_association", "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/part_of" + "$ref": "#/components/x-bte-response-mapping/disease-gene" }, - "source": "Gene Ontology", - "supportBatch": true + "source": "Multiomics Provider", + "supportBatch": false } ], - "subclass_of": [ + "gene-disease": [ { "inputSeparator": ",", "inputs": [ { - "id": "GO", - "semantic": "CellularComponent" + "id": "SYMBOL", + "semantic": "Gene" } ], "outputs": [ { - "id": "GO", - "semantic": "CellularComponent" + "id": "MONDO", + "semantic": "Disease" } ], "parameters": { - "fields": "parents" - }, - "predicate": "subclass_of", - "requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "_id" - }, - "header": "application/x-www-form-urlencoded" + "fields": "association.freq_by_sample,object.MONDO", + "q": "subject.SYMBOL:{inputs[0]} AND association.freq_by_sample:>0.1", + "size": "1000", + "sort": "-association.freq_by_sample" }, + "predicate": "gene_has_variant_that_contributes_to_disease_association", "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/subclass_of" + "$ref": "#/components/x-bte-response-mapping/gene-disease" }, - "source": "Gene Ontology", + "source": "Multiomics Provider", "supportBatch": true } ] }, "x-bte-response-mapping": { - "has_part": { - "GO": "_id" - }, - "has_subclass": { - "GO": "children" - }, - "part_of": { - "GO": "part_of.go" + "disease-gene": { + "SYMBOL": "hits.subject.SYMBOL", + "frequency": "hits.association.freq_by_sample" }, - "subclass_of": { - "GO": "parents" + "gene-disease": { + "MONDO": "hits.object.MONDO", + "frequency": "hits.association.freq_by_sample" } } }, @@ -55958,19 +55527,20 @@ "x-id": "https://github.com/kevinxin90", "x-role": "responsible developer" }, - "description": "Documentation of the Gene Ontology Cellular Component query web services.", + "description": "Documentation of the TCGA Mutation Frequency KP query web services.", "termsOfService": "https://biothings.io/about", - "title": "Gene Ontology Cellular Component API", + "title": "TCGA Mutation Frequency KP API", "version": "1.0", "x-translator": { "component": "KP", "team": [ + "Multiomics Provider", "Service Provider" ] } }, "paths": { - "/geneset": { + "/association": { "post": { "parameters": [ { @@ -55996,7 +55566,7 @@ "schema": { "properties": { "ids": { - "description": "multiple GO geneset IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", + "description": "multiple association IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", "type": "string" } }, @@ -56013,13 +55583,13 @@ "application/json": { "schema": { "items": { - "$ref": "#/components/schemas/Geneset" + "$ref": "#/components/schemas/Association" }, "type": "array" } } }, - "description": "A list of matching geneset objects" + "description": "A list of matching association objects" }, "400": { "content": { @@ -56032,20 +55602,20 @@ "description": "A response indicating an improperly formatted query" } }, - "summary": "For a list of geneset IDs, return the matching geneset object", + "summary": "For a list of association IDs, return the matching disease object", "tags": [ - "geneset" + "association" ] } }, - "/geneset/{genesetid}": { + "/association/{associationid}": { "get": { "parameters": [ { - "description": "Retrieve geneset objects based on GO geneset ID. Supports JSONP and CORS as well.", - "example": "GO:0098791", + "description": "Retrieve association objects based on Association ID Supports JSONP and CORS as well.", + "example": "NRAS-TCGA-LUAD", "in": "path", - "name": "genesetid", + "name": "associationid", "required": true, "schema": { "type": "string" @@ -56077,19 +55647,19 @@ "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Geneset" + "$ref": "#/components/schemas/Association" } } }, - "description": "A matching geneset object" + "description": "A matching association object" }, "404": { - "description": "A response indicating an unknown geneset ID" + "description": "A response indicating an unknown association ID" } }, - "summary": "Retrieve geneset objects based on ID", + "summary": "Retrieve association objects based on ID", "tags": [ - "geneset" + "association" ] } }, @@ -56104,10 +55674,10 @@ ], "responses": { "200": { - "description": "DISEASES metadata object" + "description": "KP metadata object" } }, - "summary": "Get metadata about the data available from DISEASES", + "summary": "Get metadata about the data available from the API", "tags": [ "metadata" ] @@ -56135,10 +55705,10 @@ ], "responses": { "200": { - "description": "DISEASES metadata fields object" + "description": "metadata fields object" } }, - "summary": "Get metadata about the data fields available object", + "summary": "Get metadata about the data fields available", "tags": [ "metadata" ] @@ -56149,7 +55719,7 @@ "parameters": [ { "description": "Query string.", - "example": "parents:\"GO:0098791\"", + "example": "object.MONDO:\"MONDO:0005061\"", "in": "query", "name": "q", "required": true, @@ -56220,9 +55790,17 @@ "description": "A response indicating an improperly formatted query" } }, - "summary": "Make queries and return matching geneset hits. Supports JSONP and CORS as well.", + "summary": "Make queries and return matching association hits. Supports JSONP and CORS as well.", "tags": [ "query" + ], + "x-bte-kgs-operations": [ + { + "$ref": "#/components/x-bte-kgs-operations/disease-gene" + }, + { + "$ref": "#/components/x-bte-kgs-operations/gene-disease" + } ] }, "post": { @@ -56288,23 +55866,9 @@ "description": "A response indicating an improperly formatted query" } }, - "summary": "Make batch geneset queries and return matching geneset hits", + "summary": "Make batch disease queries and return matching disease hits", "tags": [ "query" - ], - "x-bte-kgs-operations": [ - { - "$ref": "#/components/x-bte-kgs-operations/has_subclass" - }, - { - "$ref": "#/components/x-bte-kgs-operations/subclass_of" - }, - { - "$ref": "#/components/x-bte-kgs-operations/part_of" - }, - { - "$ref": "#/components/x-bte-kgs-operations/has_part" - } ] } } @@ -56312,22 +55876,25 @@ "servers": [ { "description": "Encrypted Production server", - "url": "https://biothings.ncats.io/go_cc" + "url": "https://biothings.ncats.io/tcga_mut_freq_kp" }, { "description": "Production server", - "url": "http://biothings.ncats.io/go_cc" + "url": "http://biothings.ncats.io/tcga_mut_freq_kp" } ], "tags": [ { - "name": "ontology" + "name": "gene" }, { - "name": "cellular component" + "name": "disease" }, { - "name": "geneset" + "name": "association" + }, + { + "name": "annotation" }, { "name": "query" @@ -56337,6 +55904,9 @@ }, { "name": "biothings" + }, + { + "name": "biothings_graph" } ] }, @@ -56344,11 +55914,11 @@ "_id": "e3edd325c76f2992a111b43a907a4870", "_meta": { "date_created": "2021-01-27T00:01:56.625919+00:00", - "last_updated": "2021-03-05T08:02:03.325212+00:00", + "last_updated": "2021-03-29T07:01:50.894930+00:00", "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/dgidb/openapi.yml", "username": "newgene" }, - "_score": 0.4092927, + "_score": 0.4228227, "components": { "x-bte-kgs-operations": { "chemical-gene": [ @@ -56826,11 +56396,11 @@ "_id": "5be0f321a829792e934545998b9c6afe", "_meta": { "date_created": "2021-01-12T23:30:46.860511+00:00", - "last_updated": "2021-03-05T08:02:05.363977+00:00", + "last_updated": "2021-03-29T07:02:21.480221+00:00", "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/text_mining/cooccurrence.yaml", "username": "kevinxin90" }, - "_score": 0.4092927, + "_score": 0.4228227, "components": { "x-bte-kgs-operations": { "AnatomicalEntity-AnatomicalEntity": [ @@ -65683,948 +65253,170 @@ { "$ref": "#/components/x-bte-kgs-operations/SequenceFeature-Protein" }, - { - "$ref": "#/components/x-bte-kgs-operations/SequenceFeature-Protein-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/SequenceFeature-SequenceFeature" - }, - { - "$ref": "#/components/x-bte-kgs-operations/SequenceFeature-SequenceFeature-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/SequenceFeature-AnatomicalEntity" - }, - { - "$ref": "#/components/x-bte-kgs-operations/SequenceFeature-AnatomicalEntity-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/SequenceFeature-OrganismTaxon" - }, - { - "$ref": "#/components/x-bte-kgs-operations/SequenceFeature-OrganismTaxon-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-ChemicalSubstance" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-ChemicalSubstance-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-Cell" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-Cell-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-BiologicalProcess" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-BiologicalProcess-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-CellularComponent" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-CellularComponent-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-MolecularActivity" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-MolecularActivity-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-PhenotypicFeature" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-PhenotypicFeature-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-Disease" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-Disease-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-Gene" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-Gene-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-Protein" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-Protein-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-SequenceFeature" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-SequenceFeature-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-AnatomicalEntity" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-AnatomicalEntity-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-OrganismTaxon" - }, - { - "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-OrganismTaxon-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-ChemicalSubstance" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-ChemicalSubstance-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-Cell" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-Cell-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-BiologicalProcess" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-BiologicalProcess-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-CellularComponent" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-CellularComponent-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-MolecularActivity" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-MolecularActivity-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-PhenotypicFeature" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-PhenotypicFeature-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-Disease" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-Disease-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-Gene" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-Gene-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-Protein" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-Protein-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-SequenceFeature" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-SequenceFeature-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-AnatomicalEntity" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-AnatomicalEntity-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-OrganismTaxon" - }, - { - "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-OrganismTaxon-reverse" - } - ] - }, - "post": { - "parameters": [ - { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" - }, - { - "$ref": "#/components/parameters/email", - "name": "email" - }, - { - "$ref": "#/components/parameters/fields", - "name": "fields" - }, - { - "$ref": "#/components/parameters/size", - "name": "size" - }, - { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "requestBody": { - "content": { - "application/x-www-form-urlencoded": { - "schema": { - "properties": { - "q": { - "description": "multiple query terms separated by comma (also \"+\" or whitespace). Does not support wildcard queries", - "type": "string" - }, - "scopes": { - "description": "a comma-separated list of fields as the search \"scopes\" (fields to search through for query term). The available \"fields\" that can be passed to the \"scopes\" parameter are listed in the **/metadata/fields** endpoint.string Default: \"scopes=_id\".", - "type": "string" - } - } - } - } - } - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/QueryPOSTResult" - } - } - }, - "description": "Query response objects with the \"hits\" property" - }, - "400": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResult" - } - } - }, - "description": "A response indicating an improperly formatted query" - } - }, - "summary": "Make batch disease queries and return matching disease hits", - "tags": [ - "query" - ] - } - } - }, - "servers": [ - { - "description": "Encrypted Production server", - "url": "https://biothings.ncats.io/text_mining_co_occurrence_kp" - }, - { - "description": "Production server", - "url": "http://biothings.ncats.io/text_mining_co_occurrence_kp/" - } - ], - "tags": [ - { - "name": "gene" - }, - { - "name": "chemical" - }, - { - "name": "association" - }, - { - "name": "annotation" - }, - { - "name": "query" - }, - { - "name": "translator" - }, - { - "name": "biothings" - }, - { - "name": "biothings_graph" - } - ] - }, - { - "_id": "978fe380a147a8641caf72320862697b", - "_meta": { - "date_created": "2021-01-14T20:06:05.747171+00:00", - "last_updated": "2021-03-05T08:01:54.708546+00:00", - "slug": "text-mining-target-assoc", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/text_mining/smartapi.yaml", - "username": "kevinxin90" - }, - "_score": 0.4092927, - "components": { - "x-bte-kgs-operations": { - "chemical-gene-negative": [ - { - "inputs": [ - { - "id": "CHEBI", - "semantic": "ChemicalSubstance" - } - ], - "outputs": [ - { - "id": "PR", - "semantic": "Gene" - } - ], - "parameters": { - "fields": "object.PR,association.evidence", - "q": "subject.CHEBI:\"{inputs[0]}\" AND association.edge_label:negatively_regulates_entity_to_entity", - "size": 1000 - }, - "predicate": "negatively_regulates", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/chemical-gene" - }, - "source": "Text Mining KP", - "supportBatch": false - } - ], - "chemical-gene-positive": [ - { - "inputs": [ - { - "id": "CHEBI", - "semantic": "ChemicalSubstance" - } - ], - "outputs": [ - { - "id": "PR", - "semantic": "Gene" - } - ], - "parameters": { - "fields": "object.PR,association.evidence", - "q": "subject.CHEBI:\"{inputs[0]}\" AND association.edge_label:positively_regulates_entity_to_entity", - "size": 1000 - }, - "predicate": "positively_regulates", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/chemical-gene" - }, - "source": "Text Mining KP", - "supportBatch": false - } - ], - "chemical-geneorgeneproduct-negative": [ - { - "inputs": [ - { - "id": "CHEBI", - "semantic": "ChemicalSubstance" - } - ], - "outputs": [ - { - "id": "PR", - "semantic": "GeneOrGeneProduct" - } - ], - "parameters": { - "fields": "object.PR,association.evidence", - "q": "subject.CHEBI:\"{inputs[0]}\" AND association.edge_label:negatively_regulates_entity_to_entity", - "size": 1000 - }, - "predicate": "negatively_regulates", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/chemical-gene" - }, - "source": "Text Mining KP", - "supportBatch": false - } - ], - "chemical-geneorgeneproduct-positive": [ - { - "inputs": [ - { - "id": "CHEBI", - "semantic": "ChemicalSubstance" - } - ], - "outputs": [ - { - "id": "PR", - "semantic": "GeneOrGeneProduct" - } - ], - "parameters": { - "fields": "object.PR,association.evidence", - "q": "subject.CHEBI:\"{inputs[0]}\" AND association.edge_label:positively_regulates_entity_to_entity", - "size": 1000 - }, - "predicate": "positively_regulates", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/chemical-gene" - }, - "source": "Text Mining KP", - "supportBatch": false - } - ], - "chemical-protein-negative": [ - { - "inputs": [ - { - "id": "CHEBI", - "semantic": "ChemicalSubstance" - } - ], - "outputs": [ - { - "id": "PR", - "semantic": "Protein" - } - ], - "parameters": { - "fields": "object.PR,association.evidence", - "q": "subject.CHEBI:\"{inputs[0]}\" AND association.edge_label:negatively_regulates_entity_to_entity", - "size": 1000 + { + "$ref": "#/components/x-bte-kgs-operations/SequenceFeature-Protein-reverse" }, - "predicate": "negatively_regulates", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/chemical-gene" + { + "$ref": "#/components/x-bte-kgs-operations/SequenceFeature-SequenceFeature" }, - "source": "Text Mining KP", - "supportBatch": false - } - ], - "chemical-protein-positive": [ - { - "inputs": [ - { - "id": "CHEBI", - "semantic": "ChemicalSubstance" - } - ], - "outputs": [ - { - "id": "PR", - "semantic": "Protein" - } - ], - "parameters": { - "fields": "object.PR,association.evidence", - "q": "subject.CHEBI:\"{inputs[0]}\" AND association.edge_label:positively_regulates_entity_to_entity", - "size": 1000 + { + "$ref": "#/components/x-bte-kgs-operations/SequenceFeature-SequenceFeature-reverse" }, - "predicate": "positively_regulates", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/chemical-gene" + { + "$ref": "#/components/x-bte-kgs-operations/SequenceFeature-AnatomicalEntity" }, - "source": "Text Mining KP", - "supportBatch": false - } - ], - "gene-chemical-negative": [ - { - "inputs": [ - { - "id": "PR", - "semantic": "Gene" - } - ], - "outputs": [ - { - "id": "CHEBI", - "semantic": "ChemicalSubstance" - } - ], - "parameters": { - "fields": "subject.CHEBI,association.evidence", - "q": "object.PR:\"{inputs[0]}\" AND association.edge_label:negatively_regulates_entity_to_entity", - "size": 1000 + { + "$ref": "#/components/x-bte-kgs-operations/SequenceFeature-AnatomicalEntity-reverse" }, - "predicate": "negatively_regulated_by", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/gene-chemical" + { + "$ref": "#/components/x-bte-kgs-operations/SequenceFeature-OrganismTaxon" }, - "source": "Text Mining KP", - "supportBatch": false - } - ], - "gene-chemical-positive": [ - { - "inputs": [ - { - "id": "PR", - "semantic": "Gene" - } - ], - "outputs": [ - { - "id": "CHEBI", - "semantic": "ChemicalSubstance" - } - ], - "parameters": { - "fields": "subject.CHEBI,association.evidence", - "q": "object.PR:\"{inputs[0]}\" AND association.edge_label:positively_regulates_entity_to_entity", - "size": 1000 + { + "$ref": "#/components/x-bte-kgs-operations/SequenceFeature-OrganismTaxon-reverse" }, - "predicate": "positively_regulated_by", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/gene-chemical" + { + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-ChemicalSubstance" }, - "source": "Text Mining KP", - "supportBatch": false - } - ], - "geneorgeneproduct-chemical-negative": [ - { - "inputs": [ - { - "id": "PR", - "semantic": "GeneOrGeneProduct" - } - ], - "outputs": [ - { - "id": "CHEBI", - "semantic": "ChemicalSubstance" - } - ], - "parameters": { - "fields": "subject.CHEBI,association.evidence", - "q": "object.PR:\"{inputs[0]}\" AND association.edge_label:negatively_regulates_entity_to_entity", - "size": 1000 + { + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-ChemicalSubstance-reverse" }, - "predicate": "negatively_regulated_by", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/gene-chemical" + { + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-Cell" }, - "source": "Text Mining KP", - "supportBatch": false - } - ], - "geneorgeneproduct-chemical-positive": [ - { - "inputs": [ - { - "id": "PR", - "semantic": "GeneOrGeneProduct" - } - ], - "outputs": [ - { - "id": "CHEBI", - "semantic": "ChemicalSubstance" - } - ], - "parameters": { - "fields": "subject.CHEBI,association.evidence", - "q": "object.PR:\"{inputs[0]}\" AND association.edge_label:positively_regulates_entity_to_entity", - "size": 1000 + { + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-Cell-reverse" }, - "predicate": "positively_regulated_by", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/gene-chemical" + { + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-BiologicalProcess" }, - "source": "Text Mining KP", - "supportBatch": false - } - ], - "protein-chemical-negative": [ - { - "inputs": [ - { - "id": "PR", - "semantic": "Protein" - } - ], - "outputs": [ - { - "id": "CHEBI", - "semantic": "ChemicalSubstance" - } - ], - "parameters": { - "fields": "subject.CHEBI,association.evidence", - "q": "object.PR:\"{inputs[0]}\" AND association.edge_label:negatively_regulates_entity_to_entity", - "size": 1000 + { + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-BiologicalProcess-reverse" }, - "predicate": "negatively_regulated_by", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/gene-chemical" + { + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-CellularComponent" }, - "source": "Text Mining KP", - "supportBatch": false - } - ], - "protein-chemical-positive": [ - { - "inputs": [ - { - "id": "PR", - "semantic": "Protein" - } - ], - "outputs": [ - { - "id": "CHEBI", - "semantic": "ChemicalSubstance" - } - ], - "parameters": { - "fields": "subject.CHEBI,association.evidence", - "q": "object.PR:\"{inputs[0]}\" AND association.edge_label:positively_regulates_entity_to_entity", - "size": 1000 + { + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-CellularComponent-reverse" }, - "predicate": "positively_regulated_by", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/gene-chemical" + { + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-MolecularActivity" }, - "source": "Text Mining KP", - "supportBatch": false - } - ] - }, - "x-bte-response-mapping": { - "chemical-gene": { - "PR": "hits.object.PR", - "object_spans": "hits.association.evidence.object_spans", - "pubmed": "hits.association.evidence.publications", - "relation_spans": "hits.association.evidence.relation_spans", - "score": "hits.association.evidence.score", - "sentence": "hits.association.evidence.sentence", - "subject_spans": "hits.association.evidence.subject_spans" - }, - "gene-chemical": { - "CHEBI": "hits.subject.CHEBI", - "object_spans": "hits.association.evidence.object_spans", - "pubmed": "hits.association.evidence.publications", - "relation_spans": "hits.association.evidence.relation_spans", - "score": "hits.association.evidence.score", - "sentence": "hits.association.evidence.sentence", - "subject_spans": "hits.association.evidence.subject_spans" - } - } - }, - "info": { - "contact": { - "email": "help@biothings.io", - "name": "JIWEN XIN", - "x-id": "https://github.com/kevinxin90", - "x-role": "responsible developer" - }, - "description": "Documentation of the Text Mining Targeted Association query web services.", - "termsOfService": "https://biothings.io/about", - "title": "Text Mining Targeted Association API", - "version": "1.0", - "x-translator": { - "component": "KP", - "team": [ - "Text Mining Provider", - "Service Provider" - ] - } - }, - "paths": { - "/association": { - "post": { - "parameters": [ { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-MolecularActivity-reverse" }, { - "$ref": "#/components/parameters/fields", - "name": "fields" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-PhenotypicFeature" }, { - "$ref": "#/components/parameters/email", - "name": "email" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-PhenotypicFeature-reverse" }, { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "requestBody": { - "content": { - "application/x-www-form-urlencoded": { - "schema": { - "properties": { - "ids": { - "description": "multiple association IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", - "type": "string" - } - }, - "required": [ - "ids" - ] - } - } - } - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "items": { - "$ref": "#/components/schemas/Association" - }, - "type": "array" - } - } - }, - "description": "A list of matching association objects" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-Disease" }, - "400": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResult" - } - } - }, - "description": "A response indicating an improperly formatted query" - } - }, - "summary": "For a list of association IDs, return the matching disease object", - "tags": [ - "association" - ] - } - }, - "/association/{associationid}": { - "get": { - "parameters": [ { - "description": "Retrieve association objects based on Association ID Supports JSONP and CORS as well.", - "example": "275bfadd2b4c60c3", - "in": "path", - "name": "associationid", - "required": true, - "schema": { - "type": "string" - } + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-Disease-reverse" }, { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-Gene" }, { - "$ref": "#/components/parameters/callback", - "name": "callback" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-Gene-reverse" }, { - "$ref": "#/components/parameters/fields", - "name": "fields" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-Protein" }, { - "$ref": "#/components/parameters/email", - "name": "email" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-Protein-reverse" }, { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Association" - } - } - }, - "description": "A matching association object" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-SequenceFeature" }, - "404": { - "description": "A response indicating an unknown association ID" - } - }, - "summary": "Retrieve association objects based on ID", - "tags": [ - "association" - ] - } - }, - "/metadata": { - "get": { - "parameters": [ { - "$ref": "#/components/parameters/callback", - "in": "query", - "name": "callback" - } - ], - "responses": { - "200": { - "description": "KP metadata object" - } - }, - "summary": "Get metadata about the data available from the API", - "tags": [ - "metadata" - ] - } - }, - "/metadata/fields": { - "get": { - "parameters": [ + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-SequenceFeature-reverse" + }, { - "$ref": "#/components/parameters/search", - "name": "search" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-AnatomicalEntity" }, { - "$ref": "#/components/parameters/callback", - "name": "callback" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-AnatomicalEntity-reverse" }, { - "$ref": "#/components/parameters/prefix", - "name": "prefix" + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-OrganismTaxon" }, { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "responses": { - "200": { - "description": "metadata fields object" - } - }, - "summary": "Get metadata about the data fields available", - "tags": [ - "metadata" - ] - } - }, - "/query": { - "get": { - "parameters": [ + "$ref": "#/components/x-bte-kgs-operations/AnatomicalEntity-OrganismTaxon-reverse" + }, { - "description": "Query string.", - "example": "object.id:CHEMBL.COMPOUND\\:CHEMBL26", - "in": "query", - "name": "q", - "required": true, - "schema": { - "type": "string" - } + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-ChemicalSubstance" }, { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-ChemicalSubstance-reverse" }, { - "$ref": "#/components/parameters/fields", - "name": "fields" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-Cell" }, { - "$ref": "#/components/parameters/facet_size", - "name": "facet_size" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-Cell-reverse" }, { - "$ref": "#/components/parameters/sort", - "name": "sort" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-BiologicalProcess" }, { - "$ref": "#/components/parameters/callback", - "name": "callback" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-BiologicalProcess-reverse" }, { - "$ref": "#/components/parameters/email", - "name": "email" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-CellularComponent" }, { - "$ref": "#/components/parameters/facets", - "name": "facets" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-CellularComponent-reverse" }, { - "$ref": "#/components/parameters/size", - "name": "size" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-MolecularActivity" }, { - "$ref": "#/components/parameters/from", - "name": "from" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-MolecularActivity-reverse" }, { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/QueryResult" - } - } - }, - "description": "A query response with the \"hits\" property" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-PhenotypicFeature" }, - "400": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResult" - } - } - }, - "description": "A response indicating an improperly formatted query" - } - }, - "summary": "Make queries and return matching association hits. Supports JSONP and CORS as well.", - "tags": [ - "query" - ], - "x-bte-kgs-operations": [ { - "$ref": "#/components/x-bte-kgs-operations/chemical-gene-positive" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-PhenotypicFeature-reverse" }, { - "$ref": "#/components/x-bte-kgs-operations/chemical-gene-negative" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-Disease" }, { - "$ref": "#/components/x-bte-kgs-operations/gene-chemical-positive" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-Disease-reverse" }, { - "$ref": "#/components/x-bte-kgs-operations/gene-chemical-negative" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-Gene" }, { - "$ref": "#/components/x-bte-kgs-operations/chemical-protein-positive" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-Gene-reverse" }, { - "$ref": "#/components/x-bte-kgs-operations/chemical-protein-negative" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-Protein" }, { - "$ref": "#/components/x-bte-kgs-operations/protein-chemical-positive" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-Protein-reverse" }, { - "$ref": "#/components/x-bte-kgs-operations/protein-chemical-negative" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-SequenceFeature" }, { - "$ref": "#/components/x-bte-kgs-operations/chemical-geneorgeneproduct-positive" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-SequenceFeature-reverse" }, { - "$ref": "#/components/x-bte-kgs-operations/chemical-geneorgeneproduct-negative" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-AnatomicalEntity" }, { - "$ref": "#/components/x-bte-kgs-operations/geneorgeneproduct-chemical-positive" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-AnatomicalEntity-reverse" }, { - "$ref": "#/components/x-bte-kgs-operations/geneorgeneproduct-chemical-negative" + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-OrganismTaxon" + }, + { + "$ref": "#/components/x-bte-kgs-operations/OrganismTaxon-OrganismTaxon-reverse" } ] }, @@ -66701,11 +65493,11 @@ "servers": [ { "description": "Encrypted Production server", - "url": "https://biothings.ncats.io/text_mining_targeted_association" + "url": "https://biothings.ncats.io/text_mining_co_occurrence_kp" }, { "description": "Production server", - "url": "http://biothings.ncats.io/text_mining_targeted_association" + "url": "http://biothings.ncats.io/text_mining_co_occurrence_kp/" } ], "tags": [ @@ -66739,11 +65531,11 @@ "_id": "4974ebbf2c1ae31a25a7a7b2d9e4b0d4", "_meta": { "date_created": "2021-02-02T17:28:59.950975+00:00", - "last_updated": "2021-03-05T08:02:23.372768+00:00", + "last_updated": "2021-03-29T07:03:20.621663+00:00", "url": "https://storage.googleapis.com/multiomics_provider_kp_data/multiomics_wellness.yaml", "username": "rtroper" }, - "_score": 0.4092927, + "_score": 0.4228227, "components": { "x-bte-kgs-operations": { "ChemicalSubstance-ChemicalSubstance": [ @@ -70988,516 +69780,46 @@ "$ref": "#/components/x-bte-kgs-operations/Protein2-ChemicalSubstance-reverse" }, { - "$ref": "#/components/x-bte-kgs-operations/Protein2-ChemicalSubstance1" - }, - { - "$ref": "#/components/x-bte-kgs-operations/Protein2-ChemicalSubstance1-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/Protein2-ChemicalSubstance2" - }, - { - "$ref": "#/components/x-bte-kgs-operations/Protein2-ChemicalSubstance2-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/Protein2-ChemicalSubstance3" - }, - { - "$ref": "#/components/x-bte-kgs-operations/Protein2-ChemicalSubstance3-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/Protein2-ChemicalSubstance4" - }, - { - "$ref": "#/components/x-bte-kgs-operations/Protein2-ChemicalSubstance4-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/Protein2-Protein" - }, - { - "$ref": "#/components/x-bte-kgs-operations/Protein2-Protein-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/Protein2-Protein1" - }, - { - "$ref": "#/components/x-bte-kgs-operations/Protein2-Protein1-reverse" - }, - { - "$ref": "#/components/x-bte-kgs-operations/Protein2-Protein2" - }, - { - "$ref": "#/components/x-bte-kgs-operations/Protein2-Protein2-reverse" - } - ] - }, - "post": { - "parameters": [ - { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" - }, - { - "$ref": "#/components/parameters/email", - "name": "email" - }, - { - "$ref": "#/components/parameters/fields", - "name": "fields" - }, - { - "$ref": "#/components/parameters/size", - "name": "size" - }, - { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "requestBody": { - "content": { - "application/x-www-form-urlencoded": { - "schema": { - "properties": { - "q": { - "description": "multiple query terms separated by comma (also \"+\" or whitespace). Does not support wildcard queries", - "type": "string" - }, - "scopes": { - "description": "a comma-separated list of fields as the search \"scopes\" (fields to search through for query term). The available \"fields\" that can be passed to the \"scopes\" parameter are listed in the **/metadata/fields** endpoint.string Default: \"scopes=_id\".", - "type": "string" - } - } - } - } - } - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/QueryPOSTResult" - } - } - }, - "description": "Query response objects with the \"hits\" property" - }, - "400": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResult" - } - } - }, - "description": "A response indicating an improperly formatted query" - } - }, - "summary": "Make batch disease queries and return matching disease hits", - "tags": [ - "query" - ] - } - } - }, - "servers": [ - { - "description": "Encrypted Production server", - "url": "https://biothings.ncats.io/multiomics_wellness_kp" - }, - { - "description": "Production server", - "url": "http://biothings.ncats.io/multiomics_wellness_kp" - } - ], - "tags": [ - { - "name": "protein" - }, - { - "name": "chemical_substance" - }, - { - "name": "association" - }, - { - "name": "annotation" - }, - { - "name": "query" - }, - { - "name": "translator" - }, - { - "name": "biothings" - }, - { - "name": "biothings_graph" - } - ] - }, - { - "_id": "5219cefb9d2b8d5df08c3a956fdd20f3", - "_meta": { - "date_created": "2021-02-11T00:04:22.638313+00:00", - "last_updated": "2021-03-05T08:04:46.465179+00:00", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/tcga_mut_freq/smartapi.yaml", - "username": "kevinxin90" - }, - "_score": 0.4092927, - "components": { - "x-bte-kgs-operations": { - "disease-gene": [ - { - "inputs": [ - { - "id": "MONDO", - "semantic": "Disease" - } - ], - "outputs": [ - { - "id": "SYMBOL", - "semantic": "Gene" - } - ], - "parameters": { - "fields": "association.freq_by_sample,subject.SYMBOL", - "q": "object.id:\"{inputs[0]}\" AND association.freq_by_sample:>0.1", - "size": "1000", - "sort": "-association.freq_by_sample" - }, - "predicate": "gene_has_variant_that_contributes_to_disease_association", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/disease-gene" - }, - "source": "Multiomics Provider", - "supportBatch": false - } - ], - "gene-disease": [ - { - "inputSeparator": ",", - "inputs": [ - { - "id": "SYMBOL", - "semantic": "Gene" - } - ], - "outputs": [ - { - "id": "MONDO", - "semantic": "Disease" - } - ], - "parameters": { - "fields": "association.freq_by_sample,object.MONDO", - "q": "subject.SYMBOL:{inputs[0]} AND association.freq_by_sample:>0.1", - "size": "1000", - "sort": "-association.freq_by_sample" - }, - "predicate": "gene_has_variant_that_contributes_to_disease_association", - "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/gene-disease" - }, - "source": "Multiomics Provider", - "supportBatch": true - } - ] - }, - "x-bte-response-mapping": { - "disease-gene": { - "SYMBOL": "hits.subject.SYMBOL", - "frequency": "hits.association.freq_by_sample" - }, - "gene-disease": { - "MONDO": "hits.object.MONDO", - "frequency": "hits.association.freq_by_sample" - } - } - }, - "info": { - "contact": { - "email": "help@biothings.io", - "name": "JIWEN XIN", - "x-id": "https://github.com/kevinxin90", - "x-role": "responsible developer" - }, - "description": "Documentation of the TCGA Mutation Frequency KP query web services.", - "termsOfService": "https://biothings.io/about", - "title": "TCGA Mutation Frequency KP API", - "version": "1.0", - "x-translator": { - "component": "KP", - "team": [ - "Multiomics Provider", - "Service Provider" - ] - } - }, - "paths": { - "/association": { - "post": { - "parameters": [ - { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" - }, - { - "$ref": "#/components/parameters/fields", - "name": "fields" - }, - { - "$ref": "#/components/parameters/email", - "name": "email" - }, - { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "requestBody": { - "content": { - "application/x-www-form-urlencoded": { - "schema": { - "properties": { - "ids": { - "description": "multiple association IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.", - "type": "string" - } - }, - "required": [ - "ids" - ] - } - } - } - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "items": { - "$ref": "#/components/schemas/Association" - }, - "type": "array" - } - } - }, - "description": "A list of matching association objects" - }, - "400": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResult" - } - } - }, - "description": "A response indicating an improperly formatted query" - } - }, - "summary": "For a list of association IDs, return the matching disease object", - "tags": [ - "association" - ] - } - }, - "/association/{associationid}": { - "get": { - "parameters": [ - { - "description": "Retrieve association objects based on Association ID Supports JSONP and CORS as well.", - "example": "NRAS-TCGA-LUAD", - "in": "path", - "name": "associationid", - "required": true, - "schema": { - "type": "string" - } - }, - { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" - }, - { - "$ref": "#/components/parameters/callback", - "name": "callback" - }, - { - "$ref": "#/components/parameters/fields", - "name": "fields" - }, - { - "$ref": "#/components/parameters/email", - "name": "email" - }, - { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Association" - } - } - }, - "description": "A matching association object" - }, - "404": { - "description": "A response indicating an unknown association ID" - } - }, - "summary": "Retrieve association objects based on ID", - "tags": [ - "association" - ] - } - }, - "/metadata": { - "get": { - "parameters": [ - { - "$ref": "#/components/parameters/callback", - "in": "query", - "name": "callback" - } - ], - "responses": { - "200": { - "description": "KP metadata object" - } - }, - "summary": "Get metadata about the data available from the API", - "tags": [ - "metadata" - ] - } - }, - "/metadata/fields": { - "get": { - "parameters": [ - { - "$ref": "#/components/parameters/search", - "name": "search" - }, - { - "$ref": "#/components/parameters/callback", - "name": "callback" - }, - { - "$ref": "#/components/parameters/prefix", - "name": "prefix" + "$ref": "#/components/x-bte-kgs-operations/Protein2-ChemicalSubstance1" }, { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "responses": { - "200": { - "description": "metadata fields object" - } - }, - "summary": "Get metadata about the data fields available", - "tags": [ - "metadata" - ] - } - }, - "/query": { - "get": { - "parameters": [ - { - "description": "Query string.", - "example": "object.MONDO:\"MONDO:0005061\"", - "in": "query", - "name": "q", - "required": true, - "schema": { - "type": "string" - } + "$ref": "#/components/x-bte-kgs-operations/Protein2-ChemicalSubstance1-reverse" }, { - "$ref": "#/components/parameters/dotfield", - "name": "dotfield" + "$ref": "#/components/x-bte-kgs-operations/Protein2-ChemicalSubstance2" }, { - "$ref": "#/components/parameters/fields", - "name": "fields" + "$ref": "#/components/x-bte-kgs-operations/Protein2-ChemicalSubstance2-reverse" }, { - "$ref": "#/components/parameters/facet_size", - "name": "facet_size" + "$ref": "#/components/x-bte-kgs-operations/Protein2-ChemicalSubstance3" }, { - "$ref": "#/components/parameters/sort", - "name": "sort" + "$ref": "#/components/x-bte-kgs-operations/Protein2-ChemicalSubstance3-reverse" }, { - "$ref": "#/components/parameters/callback", - "name": "callback" + "$ref": "#/components/x-bte-kgs-operations/Protein2-ChemicalSubstance4" }, { - "$ref": "#/components/parameters/email", - "name": "email" + "$ref": "#/components/x-bte-kgs-operations/Protein2-ChemicalSubstance4-reverse" }, { - "$ref": "#/components/parameters/facets", - "name": "facets" + "$ref": "#/components/x-bte-kgs-operations/Protein2-Protein" }, { - "$ref": "#/components/parameters/size", - "name": "size" + "$ref": "#/components/x-bte-kgs-operations/Protein2-Protein-reverse" }, { - "$ref": "#/components/parameters/from", - "name": "from" + "$ref": "#/components/x-bte-kgs-operations/Protein2-Protein1" }, { - "$ref": "#/components/parameters/format", - "name": "format" - } - ], - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/QueryResult" - } - } - }, - "description": "A query response with the \"hits\" property" + "$ref": "#/components/x-bte-kgs-operations/Protein2-Protein1-reverse" }, - "400": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResult" - } - } - }, - "description": "A response indicating an improperly formatted query" - } - }, - "summary": "Make queries and return matching association hits. Supports JSONP and CORS as well.", - "tags": [ - "query" - ], - "x-bte-kgs-operations": [ { - "$ref": "#/components/x-bte-kgs-operations/disease-gene" + "$ref": "#/components/x-bte-kgs-operations/Protein2-Protein2" }, { - "$ref": "#/components/x-bte-kgs-operations/gene-disease" + "$ref": "#/components/x-bte-kgs-operations/Protein2-Protein2-reverse" } ] }, @@ -71574,19 +69896,19 @@ "servers": [ { "description": "Encrypted Production server", - "url": "https://biothings.ncats.io/tcga_mut_freq_kp" + "url": "https://biothings.ncats.io/multiomics_wellness_kp" }, { "description": "Production server", - "url": "http://biothings.ncats.io/tcga_mut_freq_kp" + "url": "http://biothings.ncats.io/multiomics_wellness_kp" } ], "tags": [ { - "name": "gene" + "name": "protein" }, { - "name": "disease" + "name": "chemical_substance" }, { "name": "association" @@ -71608,428 +69930,15 @@ } ] }, - { - "_id": "fd006b0be2774dde2dca18dd9d1005cd", - "_meta": { - "date_created": "2021-02-11T00:00:33.392925+00:00", - "last_updated": "2021-03-05T08:01:03.926933+00:00", - "url": "https://arax.ncats.io/api/arax/v1.0/openapi.json", - "username": "edeutsch" - }, - "_score": 0.38443583, - "info": { - "contact": { - "email": "edeutsch@systemsbiology.org" - }, - "description": "TRAPI 1.0 endpoint for the NCATS Biomedical Translator Reasoner called ARAX", - "license": { - "name": "Apache 2.0", - "url": "http://www.apache.org/licenses/LICENSE-2.0.html" - }, - "termsOfService": "https://github.com/RTXteam/RTX/blob/master/LICENSE", - "title": "ARAX Translator Reasoner", - "version": "1.0.0", - "x-translator": { - "component": "ARA", - "team": "Expander Agent" - } - }, - "paths": { - "/PubmedMeshNgd/{term1}/{term2}": { - "get": { - "operationId": "pubmed_mesh_ngd", - "parameters": [ - { - "description": "First of two terms. Order not important.", - "explode": false, - "in": "path", - "name": "term1", - "required": true, - "schema": { - "type": "string" - }, - "style": "simple" - }, - { - "description": "Second of two terms. Order not important.", - "explode": false, - "in": "path", - "name": "term2", - "required": true, - "schema": { - "type": "string" - }, - "style": "simple" - } - ], - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/MeshNgdResponse" - } - } - }, - "description": "successful operation" - }, - "400": { - "description": "Invalid terms" - } - }, - "summary": "Query to get the Normalized Google Distance between two MeSH terms based on co-occurrence in all PubMed article annotations", - "tags": [ - "PubmedMeshNgd" - ], - "x-openapi-router-controller": "openapi_server.controllers.pubmed_mesh_ngd_controller" - } - }, - "/entity": { - "get": { - "operationId": "get_entity", - "parameters": [ - { - "description": "A string to search by (name, abbreviation, CURIE, etc.). The parameter may be repeated for multiple search strings.", - "explode": true, - "in": "query", - "name": "q", - "required": true, - "schema": { - "example": [ - "MESH:D014867", - "NCIT:C34373" - ], - "items": { - "type": "string" - }, - "type": "array" - }, - "style": "form" - } - ], - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "type": "object" - } - } - }, - "description": "successful operation" - }, - "404": { - "description": "Entity not found" - } - }, - "summary": "Obtain CURIE and synonym information about a search term", - "tags": [ - "entity" - ], - "x-openapi-router-controller": "openapi_server.controllers.entity_controller" - } - }, - "/exampleQuestions": { - "get": { - "operationId": "example_questions", - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "items": { - "type": "object" - }, - "type": "array" - } - } - }, - "description": "successful operation" - } - }, - "summary": "Request a list of example questions that ARAX can answer", - "tags": [ - "exampleQuestions" - ], - "x-openapi-router-controller": "openapi_server.controllers.example_questions_controller" - } - }, - "/predicates": { - "get": { - "operationId": "predicates", - "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" - ], - "x-openapi-router-controller": "openapi_server.controllers.predicates_controller" - } - }, - "/query": { - "post": { - "operationId": "query", - "parameters": [ - { - "description": "Set to true in order to bypass any possible cached response and try to answer the query over again\n", - "explode": true, - "in": "query", - "name": "bypass_cache", - "required": false, - "schema": { - "default": false, - "type": "boolean" - }, - "style": "form" - } - ], - "requestBody": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Query" - } - } - }, - "description": "Query information to be submitted", - "required": true - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Response" - } - } - }, - "description": "OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized." - }, - "400": { - "content": { - "application/json": { - "schema": { - "type": "string" - } - } - }, - "description": "Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)." - }, - "500": { - "content": { - "application/json": { - "schema": { - "type": "string" - } - } - }, - "description": "Internal server error." - }, - "501": { - "content": { - "application/json": { - "schema": { - "type": "string" - } - } - }, - "description": "Not implemented." - } - }, - "summary": "Query reasoner via one of several inputs", - "tags": [ - "query" - ], - "x-openapi-router-controller": "openapi_server.controllers.query_controller" - } - }, - "/response/{response_id}": { - "get": { - "operationId": "get_response", - "parameters": [ - { - "description": "Integer identifier of the response to return", - "explode": false, - "in": "path", - "name": "response_id", - "required": true, - "schema": { - "type": "string" - }, - "style": "simple" - } - ], - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Response" - } - } - }, - "description": "successful operation" - }, - "404": { - "description": "response_id not found" - } - }, - "summary": "Request a previously stored response from the server", - "tags": [ - "response" - ], - "x-openapi-router-controller": "openapi_server.controllers.response_controller" - } - }, - "/translate": { - "post": { - "operationId": "translate", - "requestBody": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Question" - } - } - }, - "description": "Question information to be translated", - "required": true - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "items": { - "$ref": "#/components/schemas/Query" - }, - "type": "array" - } - } - }, - "description": "successful operation" - }, - "400": { - "description": "Invalid status value" - } - }, - "summary": "Translate natural language question into a standardized query", - "tags": [ - "translate" - ], - "x-openapi-router-controller": "openapi_server.controllers.translate_controller" - } - } - }, - "servers": [ - { - "url": "https://arax.ncats.io/api/arax/v1.0" - } - ], - "tags": [ - { - "description": "Get supported relationships by source and target", - "externalDocs": { - "description": "Documentation for the reasoner predicates function", - "url": "http://arax.ncats.io/overview.html#predicates" - }, - "name": "predicates" - }, - { - "description": "Query reasoner using a predefined question type", - "externalDocs": { - "description": "Documentation for the reasoner query function", - "url": "http://arax.ncats.io/overview.html#query" - }, - "name": "query" - }, - { - "name": "translator" - }, - { - "name": "reasoner" - }, - { - "description": "Request a previously stored response from the server", - "externalDocs": { - "description": "Documentation for the reasoner response function", - "url": "https://arax.ncats.io/overview.html#response" - }, - "name": "response" - }, - { - "description": "Translate natural language question into a standardized query", - "externalDocs": { - "description": "Documentation for the reasoner translate function", - "url": "https://arax.ncats.io/overview.html#translate" - }, - "name": "translate" - }, - { - "description": "Return identifier and type of some entity in the knowledge graph", - "externalDocs": { - "description": "Documentation for the reasoner entity function", - "url": "https://arax.ncats.io/overview.html#entity" - }, - "name": "entity" - }, - { - "description": "Return a list of example questions that the reasoner can answer", - "externalDocs": { - "description": "Documentation for the reasoner exampleQuestions function", - "url": "https://arax.ncats.io/overview.html#exampleQuestions" - }, - "name": "exampleQuestions" - }, - { - "description": "Query to get the Normalized Google Distance between two MeSH terms based on co-occurance in all PubMed article annotations", - "externalDocs": { - "description": "Documentation for the reasoner PubmedMeshNgd function", - "url": "https://arax.ncats.io/overview.html#PubmedMeshNgd" - }, - "name": "PubmedMeshNgd" - } - ] - }, { "_id": "adf20dd6ff23dfe18e8e012bde686e31", "_meta": { "date_created": "2020-12-07T23:04:56.997349+00:00", - "last_updated": "2021-03-05T08:01:55.255825+00:00", + "last_updated": "2021-03-29T07:00:47.151423+00:00", "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/drug_response_kp/smartapi.yaml", "username": "kevinxin90" }, - "_score": 0.38443583, + "_score": 0.39739227, "components": { "x-bte-kgs-operations": { "chemical-gene": [ @@ -72497,15 +70406,428 @@ } ] }, + { + "_id": "fd006b0be2774dde2dca18dd9d1005cd", + "_meta": { + "date_created": "2021-02-11T00:00:33.392925+00:00", + "last_updated": "2021-03-08T08:01:15.410744+00:00", + "url": "https://arax.ncats.io/api/arax/v1.0/openapi.json", + "username": "edeutsch" + }, + "_score": 0.39739227, + "info": { + "contact": { + "email": "edeutsch@systemsbiology.org" + }, + "description": "TRAPI 1.0 endpoint for the NCATS Biomedical Translator Reasoner called ARAX", + "license": { + "name": "Apache 2.0", + "url": "http://www.apache.org/licenses/LICENSE-2.0.html" + }, + "termsOfService": "https://github.com/RTXteam/RTX/blob/master/LICENSE", + "title": "ARAX Translator Reasoner", + "version": "1.0.0", + "x-translator": { + "component": "ARA", + "team": "Expander Agent" + } + }, + "paths": { + "/PubmedMeshNgd/{term1}/{term2}": { + "get": { + "operationId": "pubmed_mesh_ngd", + "parameters": [ + { + "description": "First of two terms. Order not important.", + "explode": false, + "in": "path", + "name": "term1", + "required": true, + "schema": { + "type": "string" + }, + "style": "simple" + }, + { + "description": "Second of two terms. Order not important.", + "explode": false, + "in": "path", + "name": "term2", + "required": true, + "schema": { + "type": "string" + }, + "style": "simple" + } + ], + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/MeshNgdResponse" + } + } + }, + "description": "successful operation" + }, + "400": { + "description": "Invalid terms" + } + }, + "summary": "Query to get the Normalized Google Distance between two MeSH terms based on co-occurrence in all PubMed article annotations", + "tags": [ + "PubmedMeshNgd" + ], + "x-openapi-router-controller": "openapi_server.controllers.pubmed_mesh_ngd_controller" + } + }, + "/entity": { + "get": { + "operationId": "get_entity", + "parameters": [ + { + "description": "A string to search by (name, abbreviation, CURIE, etc.). The parameter may be repeated for multiple search strings.", + "explode": true, + "in": "query", + "name": "q", + "required": true, + "schema": { + "example": [ + "MESH:D014867", + "NCIT:C34373" + ], + "items": { + "type": "string" + }, + "type": "array" + }, + "style": "form" + } + ], + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "type": "object" + } + } + }, + "description": "successful operation" + }, + "404": { + "description": "Entity not found" + } + }, + "summary": "Obtain CURIE and synonym information about a search term", + "tags": [ + "entity" + ], + "x-openapi-router-controller": "openapi_server.controllers.entity_controller" + } + }, + "/exampleQuestions": { + "get": { + "operationId": "example_questions", + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "items": { + "type": "object" + }, + "type": "array" + } + } + }, + "description": "successful operation" + } + }, + "summary": "Request a list of example questions that ARAX can answer", + "tags": [ + "exampleQuestions" + ], + "x-openapi-router-controller": "openapi_server.controllers.example_questions_controller" + } + }, + "/predicates": { + "get": { + "operationId": "predicates", + "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" + ], + "x-openapi-router-controller": "openapi_server.controllers.predicates_controller" + } + }, + "/query": { + "post": { + "operationId": "query", + "parameters": [ + { + "description": "Set to true in order to bypass any possible cached response and try to answer the query over again\n", + "explode": true, + "in": "query", + "name": "bypass_cache", + "required": false, + "schema": { + "default": false, + "type": "boolean" + }, + "style": "form" + } + ], + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Query" + } + } + }, + "description": "Query information to be submitted", + "required": true + }, + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Response" + } + } + }, + "description": "OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized." + }, + "400": { + "content": { + "application/json": { + "schema": { + "type": "string" + } + } + }, + "description": "Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)." + }, + "500": { + "content": { + "application/json": { + "schema": { + "type": "string" + } + } + }, + "description": "Internal server error." + }, + "501": { + "content": { + "application/json": { + "schema": { + "type": "string" + } + } + }, + "description": "Not implemented." + } + }, + "summary": "Query reasoner via one of several inputs", + "tags": [ + "query" + ], + "x-openapi-router-controller": "openapi_server.controllers.query_controller" + } + }, + "/response/{response_id}": { + "get": { + "operationId": "get_response", + "parameters": [ + { + "description": "Integer identifier of the response to return", + "explode": false, + "in": "path", + "name": "response_id", + "required": true, + "schema": { + "type": "string" + }, + "style": "simple" + } + ], + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Response" + } + } + }, + "description": "successful operation" + }, + "404": { + "description": "response_id not found" + } + }, + "summary": "Request a previously stored response from the server", + "tags": [ + "response" + ], + "x-openapi-router-controller": "openapi_server.controllers.response_controller" + } + }, + "/translate": { + "post": { + "operationId": "translate", + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Question" + } + } + }, + "description": "Question information to be translated", + "required": true + }, + "responses": { + "200": { + "content": { + "application/json": { + "schema": { + "items": { + "$ref": "#/components/schemas/Query" + }, + "type": "array" + } + } + }, + "description": "successful operation" + }, + "400": { + "description": "Invalid status value" + } + }, + "summary": "Translate natural language question into a standardized query", + "tags": [ + "translate" + ], + "x-openapi-router-controller": "openapi_server.controllers.translate_controller" + } + } + }, + "servers": [ + { + "url": "https://arax.ncats.io/api/arax/v1.0" + } + ], + "tags": [ + { + "description": "Get supported relationships by source and target", + "externalDocs": { + "description": "Documentation for the reasoner predicates function", + "url": "http://arax.ncats.io/overview.html#predicates" + }, + "name": "predicates" + }, + { + "description": "Query reasoner using a predefined question type", + "externalDocs": { + "description": "Documentation for the reasoner query function", + "url": "http://arax.ncats.io/overview.html#query" + }, + "name": "query" + }, + { + "name": "translator" + }, + { + "name": "reasoner" + }, + { + "description": "Request a previously stored response from the server", + "externalDocs": { + "description": "Documentation for the reasoner response function", + "url": "https://arax.ncats.io/overview.html#response" + }, + "name": "response" + }, + { + "description": "Translate natural language question into a standardized query", + "externalDocs": { + "description": "Documentation for the reasoner translate function", + "url": "https://arax.ncats.io/overview.html#translate" + }, + "name": "translate" + }, + { + "description": "Return identifier and type of some entity in the knowledge graph", + "externalDocs": { + "description": "Documentation for the reasoner entity function", + "url": "https://arax.ncats.io/overview.html#entity" + }, + "name": "entity" + }, + { + "description": "Return a list of example questions that the reasoner can answer", + "externalDocs": { + "description": "Documentation for the reasoner exampleQuestions function", + "url": "https://arax.ncats.io/overview.html#exampleQuestions" + }, + "name": "exampleQuestions" + }, + { + "description": "Query to get the Normalized Google Distance between two MeSH terms based on co-occurance in all PubMed article annotations", + "externalDocs": { + "description": "Documentation for the reasoner PubmedMeshNgd function", + "url": "https://arax.ncats.io/overview.html#PubmedMeshNgd" + }, + "name": "PubmedMeshNgd" + } + ] + }, { "_id": "d22b657426375a5295e7da8a303b9893", "_meta": { "date_created": "2021-01-27T00:02:35.434735+00:00", - "last_updated": "2021-03-05T08:04:45.776814+00:00", + "last_updated": "2021-03-29T07:03:07.405162+00:00", "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biolink/openapi.yml", "username": "newgene" }, - "_score": 0.38443583, + "_score": 0.39739227, "components": { "x-bte-kgs-operations": { "anatomy-gene": [ @@ -73734,11 +72056,11 @@ "_id": "9ee398a738916a98b612068cc022454f", "_meta": { "date_created": "2020-12-11T23:57:12.070157+00:00", - "last_updated": "2021-03-05T08:02:27.010215+00:00", + "last_updated": "2021-03-29T07:03:32.923006+00:00", "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/LINCS/smartapi.yml", "username": "kevinxin90" }, - "_score": 0.36242527, + "_score": 0.37484735, "components": { "x-bte-kgs-operations": { "drug-indication": [ @@ -74208,15 +72530,15 @@ ] }, { - "_id": "fc8245e92c970298449294fc04211869", + "_id": "70117385218edc9bc01633829011dfcf", "_meta": { - "date_created": "2021-02-04T00:00:10.655676+00:00", - "last_updated": "2021-03-05T08:00:52.153666+00:00", - "slug": "cohdcovid", - "url": "https://raw.githubusercontent.com/WengLab-InformaticsResearch/cohd_api/cohd_covid/cohd/cohd_oas3.yaml", + "date_created": "2021-02-03T00:00:11.872122+00:00", + "last_updated": "2021-03-29T07:00:54.956711+00:00", + "slug": "cohd", + "url": "https://raw.githubusercontent.com/WengLab-InformaticsResearch/cohd_api/master/cohd/cohd_oas3.yaml", "username": "CaseyTa" }, - "_score": 0.3427986, + "_score": 0.3547231, "components": { "x-bte-kgs-response-mappings": { "chi_square": { @@ -74247,13 +72569,13 @@ "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", + "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.io/terms/", - "title": "Columbia Open Health Data (COHD) for COVID-19 Research", + "termsOfService": "http://cohd.nsides.io/terms/", + "title": "Columbia Open Health Data (COHD)", "version": "3.0.0", "x-accessRestriction": "none", "x-implementationLanguage": "Python", @@ -74262,6 +72584,9 @@ "team": [ "Clinical Data Provider" ] + }, + "x-trapi": { + "version": "1.0.0" } }, "paths": { @@ -74279,7 +72604,7 @@ "items": { "properties": { "dataset_description": { - "example": "Hospitalized patients with a COVID-19 condition and/or positive lab test (non-hierarchical)", + "example": "5-year non-hierarchical dataset: Includes clinical data from 2013-2017", "type": "string" }, "dataset_id": { @@ -74287,7 +72612,7 @@ "type": "integer" }, "dataset_name": { - "example": "COVID Cohort (non-hierarchical)", + "example": "5-year non-hierarchical", "type": "string" } }, @@ -74434,13 +72759,13 @@ ] } }, - "/metadata/visitCount": { + "/metadata/patientCount": { "get": { - "description": "Returns the number of visits in the dataset.", - "operationId": "visitCount", + "description": "Returns the number of patients in the dataset.", + "operationId": "patientCount", "parameters": [ { - "description": "The dataset_id of the dataset to query.", + "description": "The dataset_id of the dataset to query. Default dataset is the 5-year dataset.", "example": 1, "in": "query", "name": "dataset_id", @@ -74477,13 +72802,13 @@ } } }, - "description": "An array of visit counts." + "description": "An array of patient counts." }, "default": { "description": "Unexpected error" } }, - "summary": "The number of visits in the dataset", + "summary": "The number of patients in the dataset", "tags": [ "Metadata" ] @@ -75485,7 +73810,7 @@ "type": "integer" }, "concept_frequency": { - "example": 5.585247351056813e-06, + "example": 0.000005585247351056813, "type": "integer" }, "concept_id_1": { @@ -76045,7 +74370,7 @@ }, "/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", + "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": [ { @@ -76509,6 +74834,368 @@ ] } }, + "/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": { @@ -76546,7 +75233,7 @@ "summary": "Get supported relationships by source and target", "tags": [ "translator", - "reasoner" + "trapi" ] } }, @@ -76557,7 +75244,7 @@ "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}", + "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": { "$ref": "#/components/schemas/Query" } @@ -76611,7 +75298,7 @@ "summary": "Query COHD following NCATS Translator Reasoner Standard API", "tags": [ "translator", - "reasoner" + "trapi" ], "x-bte-kgs-operations": [ { @@ -76693,7 +75380,7 @@ "requestBody": { "content": { "application/json": { - "example": "{\n \"max_results\": 50,\n \"message\": {\n \"query_graph\": {\n \"nodes\": [\n {\n \"id\": \"n00\",\n \"curie\": \"MONDO:0021113\",\n \"type\": \"biolink:Disease\"\n },\n {\n \"id\": \"n01\",\n \"type\": \"biolink:Procedure\"\n }\n ],\n \"edges\": [\n {\n \"id\": \"e00\",\n \"type\": \"biolink:correlated_with\",\n \"source_id\": \"n00\",\n \"target_id\": \"n01\"\n }\n ]\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\n \"dataset_id\": 3,\n \"confidence_interval\": 0.99,\n \"min_cooccurrence\": 50,\n \"threshold\": 0.5,\n \"local_oxo\": true,\n \"ontology_targets\": {\n \"biolink:Disease\": [\"ICD9\", \"SNOMEDCT\", \"DOID\"],\n \"biolink:Drug\": [\"RxNorm\"],\n \"biolink:Procedure\": [\"ICD10PCS\", \"SNOMEDCT\"],\n \"_DEFAULT\": []\n },\n \"biolink_only\": true\n }\n}", + "example": "{\n \"max_results\": 50,\n \"message\": {\n \"query_graph\": {\n \"nodes\": [\n {\n \"id\": \"n00\",\n \"curie\": \"DOID:9053\",\n \"type\": \"biolink:Disease\"\n },\n {\n \"id\": \"n01\",\n \"type\": \"biolink:Procedure\"\n }\n ],\n \"edges\": [\n {\n \"id\": \"e00\",\n \"type\": \"biolink:correlated_with\",\n \"source_id\": \"n00\",\n \"target_id\": \"n01\"\n }\n ]\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\n \"dataset_id\": 3,\n \"confidence_interval\": 0.99,\n \"min_cooccurrence\": 50,\n \"threshold\": 0.5,\n \"local_oxo\": true,\n \"ontology_targets\": {\n \"biolink:Disease\": [\"ICD9\", \"SNOMEDCT\", \"DOID\"],\n \"biolink:Drug\": [\"RxNorm\"],\n \"biolink:Procedure\": [\"ICD10PCS\", \"SNOMEDCT\"],\n \"_DEFAULT\": []\n },\n \"biolink_only\": true\n }\n}", "schema": { "$ref": "#/components/schemas/Query" } @@ -76720,7 +75407,7 @@ "summary": "Query COHD following NCATS Translator Reasoner Standard API version 0.9.3", "tags": [ "translator", - "reasoner" + "trapi" ], "x-bte-kgs-operations": [ { @@ -76926,7 +75613,10 @@ }, "servers": [ { - "url": "http://covid.cohd.io/api/" + "url": "http://tr-kp-clinical.ncats.io/api/" + }, + { + "url": "http://cohd.io/api/" } ], "tags": [ @@ -76956,20 +75646,20 @@ }, { "description": "Implements the NCATS Translator Reasoner API standards", - "name": "reasoner" + "name": "trapi" } ] }, { - "_id": "70117385218edc9bc01633829011dfcf", + "_id": "fc8245e92c970298449294fc04211869", "_meta": { - "date_created": "2021-02-03T00:00:11.872122+00:00", - "last_updated": "2021-03-05T08:00:50.895429+00:00", - "slug": "cohd", - "url": "https://raw.githubusercontent.com/WengLab-InformaticsResearch/cohd_api/master/cohd/cohd_oas3.yaml", + "date_created": "2021-02-04T00:00:10.655676+00:00", + "last_updated": "2021-03-29T07:01:01.427095+00:00", + "slug": "cohdcovid", + "url": "https://raw.githubusercontent.com/WengLab-InformaticsResearch/cohd_api/cohd_covid/cohd/cohd_oas3.yaml", "username": "CaseyTa" }, - "_score": 0.3427986, + "_score": 0.3547231, "components": { "x-bte-kgs-response-mappings": { "chi_square": { @@ -77000,13 +75690,13 @@ "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", + "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.nsides.io/terms/", - "title": "Columbia Open Health Data (COHD)", + "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", @@ -77015,6 +75705,9 @@ "team": [ "Clinical Data Provider" ] + }, + "x-trapi": { + "version": "1.0.0" } }, "paths": { @@ -77032,7 +75725,7 @@ "items": { "properties": { "dataset_description": { - "example": "5-year non-hierarchical dataset: Includes clinical data from 2013-2017", + "example": "Hospitalized patients with a COVID-19 condition and/or positive lab test (non-hierarchical)", "type": "string" }, "dataset_id": { @@ -77040,7 +75733,7 @@ "type": "integer" }, "dataset_name": { - "example": "5-year non-hierarchical", + "example": "COVID Cohort (non-hierarchical)", "type": "string" } }, @@ -77187,13 +75880,13 @@ ] } }, - "/metadata/patientCount": { + "/metadata/visitCount": { "get": { - "description": "Returns the number of patients in the dataset.", - "operationId": "patientCount", + "description": "Returns the number of visits in the dataset.", + "operationId": "visitCount", "parameters": [ { - "description": "The dataset_id of the dataset to query. Default dataset is the 5-year dataset.", + "description": "The dataset_id of the dataset to query.", "example": 1, "in": "query", "name": "dataset_id", @@ -77230,13 +75923,13 @@ } } }, - "description": "An array of patient counts." + "description": "An array of visit counts." }, "default": { "description": "Unexpected error" } }, - "summary": "The number of patients in the dataset", + "summary": "The number of visits in the dataset", "tags": [ "Metadata" ] @@ -78238,7 +76931,7 @@ "type": "integer" }, "concept_frequency": { - "example": 5.585247351056813e-06, + "example": 0.000005585247351056813, "type": "integer" }, "concept_id_1": { @@ -78798,7 +77491,7 @@ }, "/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", + "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": [ { @@ -79262,368 +77955,6 @@ ] } }, - "/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": { @@ -79661,7 +77992,7 @@ "summary": "Get supported relationships by source and target", "tags": [ "translator", - "reasoner" + "trapi" ] } }, @@ -79672,7 +78003,7 @@ "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}", + "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": { "$ref": "#/components/schemas/Query" } @@ -79726,7 +78057,7 @@ "summary": "Query COHD following NCATS Translator Reasoner Standard API", "tags": [ "translator", - "reasoner" + "trapi" ], "x-bte-kgs-operations": [ { @@ -79808,7 +78139,7 @@ "requestBody": { "content": { "application/json": { - "example": "{\n \"max_results\": 50,\n \"message\": {\n \"query_graph\": {\n \"nodes\": [\n {\n \"id\": \"n00\",\n \"curie\": \"DOID:9053\",\n \"type\": \"biolink:Disease\"\n },\n {\n \"id\": \"n01\",\n \"type\": \"biolink:Procedure\"\n }\n ],\n \"edges\": [\n {\n \"id\": \"e00\",\n \"type\": \"biolink:correlated_with\",\n \"source_id\": \"n00\",\n \"target_id\": \"n01\"\n }\n ]\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\n \"dataset_id\": 3,\n \"confidence_interval\": 0.99,\n \"min_cooccurrence\": 50,\n \"threshold\": 0.5,\n \"local_oxo\": true,\n \"ontology_targets\": {\n \"biolink:Disease\": [\"ICD9\", \"SNOMEDCT\", \"DOID\"],\n \"biolink:Drug\": [\"RxNorm\"],\n \"biolink:Procedure\": [\"ICD10PCS\", \"SNOMEDCT\"],\n \"_DEFAULT\": []\n },\n \"biolink_only\": true\n }\n}", + "example": "{\n \"max_results\": 50,\n \"message\": {\n \"query_graph\": {\n \"nodes\": [\n {\n \"id\": \"n00\",\n \"curie\": \"MONDO:0021113\",\n \"type\": \"biolink:Disease\"\n },\n {\n \"id\": \"n01\",\n \"type\": \"biolink:Procedure\"\n }\n ],\n \"edges\": [\n {\n \"id\": \"e00\",\n \"type\": \"biolink:correlated_with\",\n \"source_id\": \"n00\",\n \"target_id\": \"n01\"\n }\n ]\n }\n },\n \"query_options\": {\n \"method\": \"obsExpRatio\",\n \"dataset_id\": 3,\n \"confidence_interval\": 0.99,\n \"min_cooccurrence\": 50,\n \"threshold\": 0.5,\n \"local_oxo\": true,\n \"ontology_targets\": {\n \"biolink:Disease\": [\"ICD9\", \"SNOMEDCT\", \"DOID\"],\n \"biolink:Drug\": [\"RxNorm\"],\n \"biolink:Procedure\": [\"ICD10PCS\", \"SNOMEDCT\"],\n \"_DEFAULT\": []\n },\n \"biolink_only\": true\n }\n}", "schema": { "$ref": "#/components/schemas/Query" } @@ -79835,7 +78166,7 @@ "summary": "Query COHD following NCATS Translator Reasoner Standard API version 0.9.3", "tags": [ "translator", - "reasoner" + "trapi" ], "x-bte-kgs-operations": [ { @@ -80041,10 +78372,7 @@ }, "servers": [ { - "url": "http://tr-kp-clinical.ncats.io/api/" - }, - { - "url": "http://cohd.io/api/" + "url": "http://covid.cohd.io/api/" } ], "tags": [ @@ -80074,7 +78402,7 @@ }, { "description": "Implements the NCATS Translator Reasoner API standards", - "name": "reasoner" + "name": "trapi" } ] }, @@ -80082,11 +78410,11 @@ "_id": "1bef5ecbb0b9aee90023ce9faa2c8974", "_meta": { "date_created": "2021-02-05T00:07:47.751386+00:00", - "last_updated": "2021-03-05T08:02:25.604478+00:00", + "last_updated": "2021-03-29T07:03:31.245961+00:00", "url": "https://storage.googleapis.com/multiomics_provider_kp_data/clinical_risk_kp.yaml", "username": "rtroper" }, - "_score": 0.3427986, + "_score": 0.3547231, "components": { "x-bte-kgs-operations": { "ChemicalSubstance-ChemicalSubstance-associated_with_decreased_risk_for": [ @@ -89693,475 +88021,6 @@ "name": "biothings_graph" } ] - }, - { - "_id": "14cfbb82d72211adde316005a84d6e66", - "_meta": { - "date_created": "2017-10-25T14:22:41.463970+00:00", - "last_updated": "2021-02-17T07:41:48.209784+00:00", - "url": "http://biggim.ncats.io/api/metadata/openapiv3", - "username": "JohnCEarls" - }, - "_score": 0.32518846, - "info": { - "contact": { - "email": "john.c.earls@gmail.com", - "name": "John C. Earls" - }, - "description": "Big GIM (Gene Interaction Miner) is a Translator Knowledge Source that contains function interaction data for all pairs of genes. Functional interaction data are available from four different sources: 1) tissue-specific gene expression correlations from healthy tissue samples (GTEx), 2) tissue-specific gene expression correlations from cancer samples (TCGA), 3) tissue-specific probabilities of function interaction (GIANT), and 4) direct interactions (BioGRID). The data is stored as a Google BigQuery table enabling fast access.", - "title": "Big GIM(Gene Interaction Miner)", - "version": "1.0" - }, - "paths": { - "/metadata/study": { - "get": { - "operationId": "get_metadata_studies", - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Study" - } - } - }, - "description": "Success" - } - }, - "summary": "Return all available studies", - "tags": [ - "metadata" - ] - } - }, - "/interactions/query/status/{request_id}": { - "get": { - "operationId": "get_interactions_status", - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Query_request_status" - } - } - }, - "description": "OK" - }, - "404": { - "description": "Request id not found" - } - }, - "summary": "Gets the status of a query request", - "tags": [ - "interactions" - ] - }, - "parameters": [ - { - "description": "The request id for a query", - "in": "path", - "name": "request_id", - "required": true, - "schema": { - "type": "string" - } - } - ] - }, - "/metadata/openapiv3": { - "get": { - "operationId": "get_open_api_spec", - "responses": { - "200": { - "description": "Success" - } - }, - "summary": "Return the OpenAPI v3 spec for this API", - "tags": [ - "metadata" - ] - } - }, - "/metadata/table/{table_name}": { - "get": { - "operationId": "get_metadata_table_resource", - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Table" - } - } - }, - "description": "Success" - }, - "404": { - "description": "Table not found" - } - }, - "summary": "Retrieve metadata about a table", - "tags": [ - "metadata" - ] - }, - "parameters": [ - { - "description": "the name of a biqquery table", - "in": "path", - "name": "table_name", - "required": true, - "schema": { - "type": "string" - } - } - ] - }, - "/metadata/table": { - "get": { - "operationId": "get_metadata_table_resources", - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Table" - } - } - }, - "description": "Success" - } - }, - "summary": "Retrieve list of available tables", - "tags": [ - "metadata" - ] - } - }, - "/metadata/study/{study_name}": { - "get": { - "operationId": "get_metadata_study", - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Study" - } - } - }, - "description": "Success" - }, - "404": { - "description": "Study not found" - } - }, - "summary": "Return a single study and associated substudies", - "tags": [ - "metadata" - ] - }, - "parameters": [ - { - "description": "the name of a Big GIM study", - "in": "path", - "name": "study_name", - "required": true, - "schema": { - "type": "string" - } - } - ] - }, - "/metadata/tissue/{tissue_name}": { - "get": { - "operationId": "get_tissue", - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/TissueSubstudies" - } - } - }, - "description": "Success" - }, - "404": { - "description": "Tissue not found" - } - }, - "summary": "Return a list of substudies and columns associated with a tissue", - "tags": [ - "metadata" - ] - }, - "parameters": [ - { - "description": "the name of tissue", - "in": "path", - "name": "tissue_name", - "required": true, - "schema": { - "type": "string" - } - } - ] - }, - "/metadata/swagger": { - "get": { - "operationId": "get_swagger_spec", - "responses": { - "200": { - "description": "Success" - } - }, - "summary": "Return the swagger v2 spec for this API", - "tags": [ - "metadata" - ] - } - }, - "/metadata/tissue": { - "get": { - "operationId": "get_tissue", - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Tissues" - } - } - }, - "description": "Success" - } - }, - "summary": "Return a list of available tissues", - "tags": [ - "metadata" - ] - } - }, - "/metadata/table/{table_name}/column/{column_name}": { - "get": { - "operationId": "get_metadata_column_resource", - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Column" - } - } - }, - "description": "Success" - }, - "404": { - "description": "Column not found" - } - }, - "summary": "Retrieve metadata about a tables column", - "tags": [ - "metadata" - ] - }, - "parameters": [ - { - "description": "the name of a biqquery table", - "in": "path", - "name": "table_name", - "required": true, - "schema": { - "type": "string" - } - }, - { - "description": "the name of a column in this biqquery table", - "in": "path", - "name": "column_name", - "required": true, - "schema": { - "type": "string" - } - } - ] - }, - "/interactions/query": { - "get": { - "operationId": "get_interactions_query", - "parameters": [ - { - "description": "\nThe type of join made on restrictions. Either `intersect` or `union`\n\n**Default**: intersect\n\n**Example**: intersect\n", - "in": "query", - "name": "restriction_join", - "schema": { - "type": "string" - } - }, - { - "description": "\nThe maximum number of rows to return.\n\n\n**Default**: 10000\n", - "in": "query", - "name": "limit", - "schema": { - "type": "string" - } - }, - { - "description": "\nA list of pairs of values `column name,value` with which to restrict the results of the query to rows where the value of the column is greater than the given value.\n\n**Default**: No restrictions\n\n**Example**: TCGA_GBM_Correlation,.2, GTEx_Brain_Correlation,.2\n", - "in": "query", - "name": "restriction_gt", - "schema": { - "type": "string" - } - }, - { - "description": "\nA list of pairs of values `column name,value` with which to restrict the results of the query to rows where the value of the column is less than the given value.\n\n**Default**: No restrictions\n\n**Example**:TCGA_GBM_Pvalue,1.3, GTEx_Brain_Pvalue,1.3\n", - "in": "query", - "name": "restriction_lt", - "schema": { - "type": "string" - } - }, - { - "description": "\nThe table to select from.\n\nAvailable tables are provided by `/api/metadata/tables`.\n\n**Default**: BigGIM_70_v1\n", - "in": "query", - "name": "table", - "schema": { - "type": "string" - } - }, - { - "description": "Entrez gene ids to select.\n\nIf not given, the query selects any gene related to a gene in ids 1.\nIf given, the query only selects relations that contain a gene in ids1 and a gene in ids2.\n\n**Default**: all genes.\n\n**Example**:\"5111,6996,57697,6815,889,7112,2176,1019,5888,5706\"\n", - "in": "query", - "name": "ids2", - "schema": { - "type": "string" - } - }, - { - "description": "\nA list of pairs of values `column name,value` with which to restrict the results of the query to rows where the value of the column is True or False.\n\n**Default**: No restrictions\n\n**Example**: BioGRID_Interaction,True\n", - "in": "query", - "name": "restriction_bool", - "schema": { - "type": "string" - } - }, - { - "description": "A comma delimited list of column names to return.\n\nGene ids are always returned and do not need to be specified. If a column is not present, then an error is returned.\n\nAvailable columns are provided by `/api/metadata/tables/{table_name}/columns`.\n\n**Default**: all columns.\n\n**Example**: TCGA_GBM_Correlation,TCGA_GBM_Pvalue,GTEx_Brain_Correlation,GTEx_Brain_Pvalue\n", - "in": "query", - "name": "columns", - "schema": { - "type": "string" - } - }, - { - "description": "A comma delimited list of Entrez gene ids to select.\n \n**Default**: all genes.\n\n**Example**:\"5111,6996,57697,6815,889,7112,2176,1019,5888,5706\"\n", - "in": "query", - "name": "ids1", - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/The_query_response" - } - } - }, - "description": "Success" - }, - "400": { - "description": "Bad query request." - } - }, - "summary": "Submit a new query request", - "tags": [ - "interactions" - ] - }, - "post": { - "operationId": "post_interactions_query", - "requestBody": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Query_request" - } - } - }, - "required": true - }, - "responses": { - "200": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/The_query_response" - } - } - }, - "description": "Success" - }, - "400": { - "description": "Bad query request." - } - }, - "summary": "Submit a new query request", - "tags": [ - "interactions" - ] - } - } - }, - "servers": [ - { - "url": "http://biggim.ncats.io/api" - } - ], - "tags": [ - { - "name": "translator" - }, - { - "name": "ISB" - }, - { - "name": "gene" - }, - { - "name": "similarity" - }, - { - "name": "tissue" - }, - { - "name": "TCGA" - }, - { - "name": "GIANT" - }, - { - "name": "BioGrid" - }, - { - "name": "GTEx" - }, - { - "name": "BigQuery" - }, - { - "name": "network" - }, - { - "name": "DeepTranslate" - } - ] } ] } \ No newline at end of file From 02afc54bb71492cba9c0a311aef27a416798a8fa Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 30 Mar 2021 18:02:32 -0700 Subject: [PATCH 24/68] feat: :sparkles: support constructing TRAPI based bte edge --- src/qedge2bteedge.js | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/src/qedge2bteedge.js b/src/qedge2bteedge.js index 17c133ab..b26d7c9a 100644 --- a/src/qedge2bteedge.js +++ b/src/qedge2bteedge.js @@ -1,5 +1,6 @@ const _ = require('lodash'); const LogEntry = require('./log_entry'); +const config = require("./config"); const ID_WITH_PREFIXES = ['MONDO', 'DOID', 'UBERON', 'EFO', 'HP', 'CHEBI', 'CL', 'MGI', 'NCIT']; const debug = require('debug')('biothings-explorer-trapi:qedge2btedge'); @@ -40,6 +41,7 @@ module.exports = class QEdge2BTEEdgeHandler { input_type: qEdge.getSubject().getCategories(), output_type: qEdge.getObject().getCategories(), predicate: qEdge.getPredicate(), + api_name: config.API_LIST }; debug(`Filter criteria is: ${JSON.stringify(filterCriteria)}`); let smartapi_edges = kg.filter(filterCriteria); @@ -57,10 +59,8 @@ module.exports = class QEdge2BTEEdgeHandler { new LogEntry( 'DEBUG', null, - `BTE found ${ - smartapi_edges.length - } smartapi edges corresponding to ${qEdge.getID()}. These smartaip edges comes from ${ - new Set(this._findAPIsFromSmartAPIEdges(smartapi_edges)).size + `BTE found ${smartapi_edges.length + } smartapi edges corresponding to ${qEdge.getID()}. These smartaip edges comes from ${new Set(this._findAPIsFromSmartAPIEdges(smartapi_edges)).size } unique APIs. They are ${Array.from(new Set(this._findAPIsFromSmartAPIEdges(smartapi_edges))).join(',')}`, ).getLog(), ); @@ -123,7 +123,13 @@ module.exports = class QEdge2BTEEdgeHandler { debug(`Input id: ${inputID}`); for (const curie in resolvedIDs) { resolvedIDs[curie].map((entity) => { - if (entity.semanticType === inputType && inputID in entity.dbIDs) { + if (smartAPIEdge.tags.includes("bte-trapi")) { + if (entity.semanticType === inputType) { + input_resolved_identifiers[curie] = [entity]; + inputs.push(entity.primaryID); + id_mapping[entity.primaryID] = curie; + } + } else if (entity.semanticType === inputType && inputID in entity.dbIDs) { entity.dbIDs[inputID].map((id) => { if (ID_WITH_PREFIXES.includes(inputID) || id.includes(':')) { id_mapping[id] = curie; From 138d45dd8502f3abccd36df0bc8ee8adfe132bdc Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 30 Mar 2021 18:02:40 -0700 Subject: [PATCH 25/68] test: :white_check_mark: add integrity test --- __test__/integration/integrity.test.js | 36 ++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 __test__/integration/integrity.test.js diff --git a/__test__/integration/integrity.test.js b/__test__/integration/integrity.test.js new file mode 100644 index 00000000..40826de9 --- /dev/null +++ b/__test__/integration/integrity.test.js @@ -0,0 +1,36 @@ +const TRAPIQueryHandler = require("../../src/index"); +const fs = require("fs"); +var path = require('path'); + +describe("Testing TRAPIQueryHandler Module", () => { + const example_foler = path.resolve(__dirname, '../data'); + + test("When looking for chemicals affected by Phenotype Increased Urinary Glycerol, Glycerol should pop up", async () => { + const queryHandler = new TRAPIQueryHandler.TRAPIQueryHandler(); + const query = JSON.parse(fs.readFileSync(path.join(example_foler, 'increased_urinary_glycerol_affects_glycerol.json'))); + queryHandler.setQueryGraph(query.message.query_graph); + await queryHandler.query(); + const res = queryHandler.getResponse(); + expect(res.message.knowledge_graph.nodes).toHaveProperty('CHEBI:17754'); + }) + + test("When looking for genes related to Disease DYSKINESIA, FAMILIAL, WITH FACIAL MYOKYMIA, ACDY5 should pop up", async () => { + const queryHandler = new TRAPIQueryHandler.TRAPIQueryHandler(); + const query = JSON.parse(fs.readFileSync(path.join(example_foler, 'FDFM_caused_by_ACDY5.json'))); + queryHandler.setQueryGraph(query.message.query_graph); + await queryHandler.query(); + const res = queryHandler.getResponse(); + expect(res.message.knowledge_graph.nodes).toHaveProperty('NCBIGENE:111'); + }) + + test("When looking for chemicals targeting IL1 Signaling patway, curcumin should pop up", async () => { + const queryHandler = new TRAPIQueryHandler.TRAPIQueryHandler(); + const query = JSON.parse(fs.readFileSync(path.join(example_foler, 'chemicals_targeting_IL1_Signaling_Pathway.json'))); + queryHandler.setQueryGraph(query.message.query_graph); + await queryHandler.query(); + const res = queryHandler.getResponse(); + expect(res.message.knowledge_graph.nodes).toHaveProperty('CHEBI:3962'); + }) + + +}) \ No newline at end of file From 18d96dc968ec6c814235197fb1638a032d057736 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 30 Mar 2021 18:02:55 -0700 Subject: [PATCH 26/68] build: :arrow_up: upgrade dependency --- package-lock.json | 20 ++++++++++---------- package.json | 4 ++-- 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/package-lock.json b/package-lock.json index 6783d75c..7821c2d0 100644 --- a/package-lock.json +++ b/package-lock.json @@ -427,9 +427,9 @@ "dev": true }, "@biothings-explorer/api-response-transform": { - "version": "1.10.0", - "resolved": "https://registry.npmjs.org/@biothings-explorer/api-response-transform/-/api-response-transform-1.10.0.tgz", - "integrity": "sha512-xeKI66ArD/unJOxvU+shUt1X0kPnGCyk4MIUc35smUFMK+b9MDOrkuKbR9YK7yoEIe7XMzKMhekVfESF+zUB9w==", + "version": "1.10.1", + "resolved": "https://registry.npmjs.org/@biothings-explorer/api-response-transform/-/api-response-transform-1.10.1.tgz", + "integrity": "sha512-9/mPSkjf8TscSHdqrDsz1Ov112j/CHYdUdndxTqRTKKrDObOCJlSt6krU8S8G7vmgrc8BAJh3PnH+eLlj0At4Q==", "requires": { "@biothings-explorer/json-transformer": "^1.0.2", "@commitlint/cli": "^11.0.0", @@ -450,11 +450,11 @@ } }, "@biothings-explorer/call-apis": { - "version": "1.17.0", - "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.17.0.tgz", - "integrity": "sha512-OuKnC6RN6TpqYHiTAZdys9n4CqdRQduUuTqUc0GQAJBTZLG/yS3waAX2RZi68VYFECVBpTJpTLmS2gEoF5bZRw==", + "version": "1.17.1", + "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.17.1.tgz", + "integrity": "sha512-mfrYTnDPobRV97saGOGfnNLgXJNQm4AUtoLpeC4RAji/bOvMtSmtdUUnyQt/SbwKdJXWY0Y5RfQQCKbNmjwhgg==", "requires": { - "@biothings-explorer/api-response-transform": "^1.10.0", + "@biothings-explorer/api-response-transform": "^1.10.1", "axios": "^0.21.1", "biomedical_id_resolver": "^3.5.0", "debug": "^4.3.1", @@ -472,9 +472,9 @@ } }, "@biothings-explorer/smartapi-kg": { - "version": "3.3.0", - "resolved": "https://registry.npmjs.org/@biothings-explorer/smartapi-kg/-/smartapi-kg-3.3.0.tgz", - "integrity": "sha512-pCoq3w/U6M7mi9ppL+d00IFz01USTg4QJyTuJ/oegbE7uqUd2DcoTeOo9SEIMk9MZPfPlbLvRJ+ZosW4qh6dGA==", + "version": "3.4.0", + "resolved": "https://registry.npmjs.org/@biothings-explorer/smartapi-kg/-/smartapi-kg-3.4.0.tgz", + "integrity": "sha512-Cx7YbnCJEowo9HI+j2Rjb6vEZboa4Ja5FOtmW7BEiaAajQsJJSAdKEH1+5HiOtTyKk1zionI86QAc8jat2Q1FQ==", "requires": { "@babel/runtime": "^7.13.10", "@commitlint/cli": "^11.0.0", diff --git a/package.json b/package.json index bcd5ef3e..6bc600d6 100644 --- a/package.json +++ b/package.json @@ -50,8 +50,8 @@ "typescript": "^4.2.3" }, "dependencies": { - "@biothings-explorer/call-apis": "^1.17.0", - "@biothings-explorer/smartapi-kg": "^3.3.0", + "@biothings-explorer/call-apis": "^1.17.1", + "@biothings-explorer/smartapi-kg": "^3.4.0", "biolink-model": "^0.3.0", "biomedical_id_resolver": "^3.5.0", "debug": "^4.3.1", From 1b351ff0c2eed6bd99e94074ddd796b31532d646 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 30 Mar 2021 18:03:13 -0700 Subject: [PATCH 27/68] chore(release): 1.4.0 --- CHANGELOG.md | 10 ++++++++++ package-lock.json | 2 +- package.json | 2 +- 3 files changed, 12 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 007ef502..710a6430 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,16 @@ 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. +## [1.4.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.3.1...v1.4.0) (2021-03-31) + + +### Features + +* :sparkles: include TRAPI APIs when constructing meta-kg ([07688cb](https://github.com/kevinxin90/bte_trapi_query_graph_handler/commit/07688cb93ebe13be61dd041d2c155a478dac5d5b)) +* :sparkles: restrict to a list of APIs to use in BTE ([defdd65](https://github.com/kevinxin90/bte_trapi_query_graph_handler/commit/defdd656f30a04af85e37ef525d05ec247cc659b)) +* :sparkles: support constructing TRAPI based bte edge ([02afc54](https://github.com/kevinxin90/bte_trapi_query_graph_handler/commit/02afc54bb71492cba9c0a311aef27a416798a8fa)) +* :sparkles: support trapi quer ([1658ad2](https://github.com/kevinxin90/bte_trapi_query_graph_handler/commit/1658ad2f77cbb8c41dba72c871bca595a4495d2f)) + ### [1.3.1](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.3.0...v1.3.1) (2021-03-29) ## [1.3.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.2.2...v1.3.0) (2021-03-29) diff --git a/package-lock.json b/package-lock.json index 7821c2d0..8a7b1963 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.3.1", + "version": "1.4.0", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index 6bc600d6..d62dddfe 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.3.1", + "version": "1.4.0", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { From ac413e6185cff37ed80eb76a5de1ae7cc1352d12 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 1 Apr 2021 11:03:20 -0700 Subject: [PATCH 28/68] fix: :bug: should check for predidcatesPath param instead of smartapiPath --- src/index.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/index.js b/src/index.js index be27829f..d1c2f4a6 100644 --- a/src/index.js +++ b/src/index.js @@ -20,7 +20,7 @@ exports.TRAPIQueryHandler = class TRAPIQueryHandler { this.resolveOutputIDs = typeof this.options.enableIDResolution === 'undefined' ? true : this.options.enableIDResolution; this.path = smartAPIPath || path.resolve(__dirname, './smartapi_specs.json'); - this.predicatePath = smartAPIPath || path.resolve(__dirname, './predicates.json'); + this.predicatePath = predicatesPath || path.resolve(__dirname, './predicates.json'); } _loadMetaKG() { From 5213e18deba51e45c6169397ed2d7d3b808aecc0 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 1 Apr 2021 11:03:38 -0700 Subject: [PATCH 29/68] style: :art: style code --- src/config.js | 92 +++++++++++++++++++++++++-------------------------- 1 file changed, 46 insertions(+), 46 deletions(-) diff --git a/src/config.js b/src/config.js index 7a9a997e..e1842439 100644 --- a/src/config.js +++ b/src/config.js @@ -1,47 +1,47 @@ exports.API_LIST = [ - 'QuickGO API', - 'Ontology Lookup Service API', - 'CTD API', - 'OpenTarget API', - 'LitVar API', - 'Human Phenotype Ontology API', - 'UBERON Ontology API', - 'MyDisease.info API', - 'MyVariant.info API', - 'MyGene.info API', - 'SEMMED Disease API', - 'MyChem.info API', - 'SEMMED Anatomy API', - 'SEMMED Gene API', - 'SEMMED Phenotype API', - 'MGIgene2phenotype API', - 'SEMMED Biological Process API', - 'SEMMED Chemical API', - 'DISEASES API', - 'EBIgene2phenotype API', - 'Gene Ontology Biological Process 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 Targeted Association API', - 'Multiomics Wellness KP API', - 'BioLink API', - 'LINCS Data Portal API', - 'Automat IntAct', - 'Automat Cord19 Scibite', - 'Automat Gtopdb', - 'Automat KEGG', - 'Automat Cord19 Scigraph', - 'Automat Uberongraph', - 'Automat Human GOA', - 'Automat HGNC', - 'Automat CTD', - 'Automat HMDB', - 'Automat Hetio', - 'Automat Panther', - 'Automat Pharos', - 'Automat Chembio', - 'Automat Foodb' -] \ No newline at end of file + 'QuickGO API', + 'Ontology Lookup Service API', + 'CTD API', + 'OpenTarget API', + 'LitVar API', + 'Human Phenotype Ontology API', + 'UBERON Ontology API', + 'MyDisease.info API', + 'MyVariant.info API', + 'MyGene.info API', + 'SEMMED Disease API', + 'MyChem.info API', + 'SEMMED Anatomy API', + 'SEMMED Gene API', + 'SEMMED Phenotype API', + 'MGIgene2phenotype API', + 'SEMMED Biological Process API', + 'SEMMED Chemical API', + 'DISEASES API', + 'EBIgene2phenotype API', + 'Gene Ontology Biological Process 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 Targeted Association API', + 'Multiomics Wellness KP API', + 'BioLink API', + 'LINCS Data Portal API', + 'Automat IntAct', + 'Automat Cord19 Scibite', + 'Automat Gtopdb', + 'Automat KEGG', + 'Automat Cord19 Scigraph', + 'Automat Uberongraph', + 'Automat Human GOA', + 'Automat HGNC', + 'Automat CTD', + 'Automat HMDB', + 'Automat Hetio', + 'Automat Panther', + 'Automat Pharos', + 'Automat Chembio', + 'Automat Foodb', +]; From f378602921458578e7262a16269a450275acf434 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 1 Apr 2021 11:03:54 -0700 Subject: [PATCH 30/68] style: :art: style code --- src/qedge2bteedge.js | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/src/qedge2bteedge.js b/src/qedge2bteedge.js index b26d7c9a..6def9e37 100644 --- a/src/qedge2bteedge.js +++ b/src/qedge2bteedge.js @@ -1,6 +1,6 @@ const _ = require('lodash'); const LogEntry = require('./log_entry'); -const config = require("./config"); +const config = require('./config'); const ID_WITH_PREFIXES = ['MONDO', 'DOID', 'UBERON', 'EFO', 'HP', 'CHEBI', 'CL', 'MGI', 'NCIT']; const debug = require('debug')('biothings-explorer-trapi:qedge2btedge'); @@ -41,7 +41,7 @@ module.exports = class QEdge2BTEEdgeHandler { input_type: qEdge.getSubject().getCategories(), output_type: qEdge.getObject().getCategories(), predicate: qEdge.getPredicate(), - api_name: config.API_LIST + api_name: config.API_LIST, }; debug(`Filter criteria is: ${JSON.stringify(filterCriteria)}`); let smartapi_edges = kg.filter(filterCriteria); @@ -59,8 +59,10 @@ module.exports = class QEdge2BTEEdgeHandler { new LogEntry( 'DEBUG', null, - `BTE found ${smartapi_edges.length - } smartapi edges corresponding to ${qEdge.getID()}. These smartaip edges comes from ${new Set(this._findAPIsFromSmartAPIEdges(smartapi_edges)).size + `BTE found ${ + smartapi_edges.length + } smartapi edges corresponding to ${qEdge.getID()}. These smartaip edges comes from ${ + new Set(this._findAPIsFromSmartAPIEdges(smartapi_edges)).size } unique APIs. They are ${Array.from(new Set(this._findAPIsFromSmartAPIEdges(smartapi_edges))).join(',')}`, ).getLog(), ); @@ -123,7 +125,7 @@ module.exports = class QEdge2BTEEdgeHandler { debug(`Input id: ${inputID}`); for (const curie in resolvedIDs) { resolvedIDs[curie].map((entity) => { - if (smartAPIEdge.tags.includes("bte-trapi")) { + if (smartAPIEdge.tags.includes('bte-trapi')) { if (entity.semanticType === inputType) { input_resolved_identifiers[curie] = [entity]; inputs.push(entity.primaryID); From 9b58f625d28efc031d5c34dd4272d3c3dfdac58b Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 1 Apr 2021 11:04:09 -0700 Subject: [PATCH 31/68] build: :arrow_up: upgrade smartapi-kg dependency --- package-lock.json | 6 +++--- package.json | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/package-lock.json b/package-lock.json index 8a7b1963..a7b5026e 100644 --- a/package-lock.json +++ b/package-lock.json @@ -472,9 +472,9 @@ } }, "@biothings-explorer/smartapi-kg": { - "version": "3.4.0", - "resolved": "https://registry.npmjs.org/@biothings-explorer/smartapi-kg/-/smartapi-kg-3.4.0.tgz", - "integrity": "sha512-Cx7YbnCJEowo9HI+j2Rjb6vEZboa4Ja5FOtmW7BEiaAajQsJJSAdKEH1+5HiOtTyKk1zionI86QAc8jat2Q1FQ==", + "version": "3.5.0", + "resolved": "https://registry.npmjs.org/@biothings-explorer/smartapi-kg/-/smartapi-kg-3.5.0.tgz", + "integrity": "sha512-zrVPQ1IS5UDkfbR4Mq4eAzJizAa9fC2oTx5TjGE9mWCM/cYwLn7Vd18ce8Y7WJmJxijypZxZ7hFPCn9vs7sUmQ==", "requires": { "@babel/runtime": "^7.13.10", "@commitlint/cli": "^11.0.0", diff --git a/package.json b/package.json index d62dddfe..b2bd470f 100644 --- a/package.json +++ b/package.json @@ -51,7 +51,7 @@ }, "dependencies": { "@biothings-explorer/call-apis": "^1.17.1", - "@biothings-explorer/smartapi-kg": "^3.4.0", + "@biothings-explorer/smartapi-kg": "^3.5.0", "biolink-model": "^0.3.0", "biomedical_id_resolver": "^3.5.0", "debug": "^4.3.1", From c83b3db4b6b33c72df1bffe885116b6d5ca2e19d Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 1 Apr 2021 11:04:25 -0700 Subject: [PATCH 32/68] style: :art: style coee --- src/graph/knowledge_graph.js | 200 +++++++++++++++++------------------ 1 file changed, 100 insertions(+), 100 deletions(-) diff --git a/src/graph/knowledge_graph.js b/src/graph/knowledge_graph.js index 845281e1..98f43047 100644 --- a/src/graph/knowledge_graph.js +++ b/src/graph/knowledge_graph.js @@ -3,112 +3,112 @@ const debug = require('debug')('biothings-explorer-trapi:KnowledgeGraph'); const helper = new GraphHelper(); module.exports = class KnowledgeGraph { - constructor() { - this.nodes = {}; - this.edges = {}; - this.kg = { - nodes: this.nodes, - edges: this.edges, - }; - } + constructor() { + this.nodes = {}; + this.edges = {}; + this.kg = { + nodes: this.nodes, + edges: this.edges, + }; + } - getNodes() { - return this.nodes; - } + getNodes() { + return this.nodes; + } - getEdges() { - return this.edges; - } + getEdges() { + return this.edges; + } - _createNode(kgNode) { - const res = { - category: 'biolink:' + kgNode._semanticType, - name: kgNode._label, - attributes: [ - { - name: 'equivalent_identifiers', - value: kgNode._curies, - type: 'biolink:id', - }, - { - name: 'num_source_nodes', - value: kgNode._sourceNodes.size, - type: 'bts:num_source_nodes', - }, - { - name: 'num_target_nodes', - value: kgNode._targetNodes.size, - type: 'bts:num_target_nodes', - }, - { - name: 'source_qg_nodes', - value: Array.from(kgNode._sourceQGNodes), - type: 'bts:source_qg_nodes', - }, - { - name: 'target_qg_nodes', - value: Array.from(kgNode._targetQGNodes), - type: 'bts:target_qg_nodes', - }, - ], - }; - for (const key in kgNode._nodeAttributes) { - res.attributes.push({ - name: key, - value: kgNode._nodeAttributes[key], - type: 'bts:' + key, - }); - } - return res; + _createNode(kgNode) { + const res = { + category: 'biolink:' + kgNode._semanticType, + name: kgNode._label, + attributes: [ + { + name: 'equivalent_identifiers', + value: kgNode._curies, + type: 'biolink:id', + }, + { + name: 'num_source_nodes', + value: kgNode._sourceNodes.size, + type: 'bts:num_source_nodes', + }, + { + name: 'num_target_nodes', + value: kgNode._targetNodes.size, + type: 'bts:num_target_nodes', + }, + { + name: 'source_qg_nodes', + value: Array.from(kgNode._sourceQGNodes), + type: 'bts:source_qg_nodes', + }, + { + name: 'target_qg_nodes', + value: Array.from(kgNode._targetQGNodes), + type: 'bts:target_qg_nodes', + }, + ], + }; + for (const key in kgNode._nodeAttributes) { + res.attributes.push({ + name: key, + value: kgNode._nodeAttributes[key], + type: 'bts:' + key, + }); } + return res; + } - _createAttributes(kgEdge) { - const attributes = [ - { - name: 'provided_by', - value: Array.from(kgEdge.sources), - type: 'biolink:provided_by', - }, - { - name: 'api', - value: Array.from(kgEdge.apis), - type: 'bts:api', - }, - { - name: 'publications', - value: Array.from(kgEdge.publications), - type: 'biolink:publication', - }, - ]; - for (const key in kgEdge.attributes) { - attributes.push({ - name: key, - value: kgEdge.attributes[key], - type: 'bts:' + key, - }); - } - return attributes; + _createAttributes(kgEdge) { + const attributes = [ + { + name: 'provided_by', + value: Array.from(kgEdge.sources), + type: 'biolink:provided_by', + }, + { + name: 'api', + value: Array.from(kgEdge.apis), + type: 'bts:api', + }, + { + name: 'publications', + value: Array.from(kgEdge.publications), + type: 'biolink:publication', + }, + ]; + for (const key in kgEdge.attributes) { + attributes.push({ + name: key, + value: kgEdge.attributes[key], + type: 'bts:' + key, + }); } + return attributes; + } - _createEdge(kgEdge) { - return { - predicate: kgEdge.predicate, - subject: kgEdge.subject, - object: kgEdge.object, - attributes: this._createAttributes(kgEdge), - }; - } + _createEdge(kgEdge) { + return { + predicate: kgEdge.predicate, + subject: kgEdge.subject, + object: kgEdge.object, + attributes: this._createAttributes(kgEdge), + }; + } - update(bteGraph) { - Object.keys(bteGraph.nodes).map((node) => { - this.nodes[bteGraph.nodes[node]._primaryID] = this._createNode(bteGraph.nodes[node]); - }); - Object.keys(bteGraph.edges).map((edge) => { - this.edges[edge] = this._createEdge(bteGraph.edges[edge]); - }); - this.kg = { - nodes: this.nodes, - edges: this.edges, - }; - } + update(bteGraph) { + Object.keys(bteGraph.nodes).map((node) => { + this.nodes[bteGraph.nodes[node]._primaryID] = this._createNode(bteGraph.nodes[node]); + }); + Object.keys(bteGraph.edges).map((edge) => { + this.edges[edge] = this._createEdge(bteGraph.edges[edge]); + }); + this.kg = { + nodes: this.nodes, + edges: this.edges, + }; + } }; From 89e2b2dde7e7b896304af3d41de1f257d8bb5169 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 1 Apr 2021 11:04:36 -0700 Subject: [PATCH 33/68] chore(release): 1.5.0 --- 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 710a6430..df98b5be 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. +## [1.5.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.4.0...v1.5.0) (2021-04-01) + + +### Bug Fixes + +* :bug: should check for predidcatesPath param instead of smartapiPath ([ac413e6](https://github.com/kevinxin90/bte_trapi_query_graph_handler/commit/ac413e6185cff37ed80eb76a5de1ae7cc1352d12)) + ## [1.4.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.3.1...v1.4.0) (2021-03-31) diff --git a/package-lock.json b/package-lock.json index a7b5026e..74d3cefe 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.4.0", + "version": "1.5.0", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index b2bd470f..916d9687 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.4.0", + "version": "1.5.0", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { From b89c288e0b6f72523d2f6e1c81af0468523b06d6 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 1 Apr 2021 11:13:52 -0700 Subject: [PATCH 34/68] feat: :sparkles: allow user to specify if they want to include reasoner apis --- src/index.js | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/index.js b/src/index.js index d1c2f4a6..9105c0ee 100644 --- a/src/index.js +++ b/src/index.js @@ -14,9 +14,10 @@ const Graph = require('./graph/graph'); exports.InvalidQueryGraphError = InvalidQueryGraphError; exports.TRAPIQueryHandler = class TRAPIQueryHandler { - constructor(options = {}, smartAPIPath = undefined, predicatesPath = undefined) { + constructor(options = {}, smartAPIPath = undefined, predicatesPath = undefined, includeReasoner = false) { this.logs = []; this.options = options; + this.includeReasoner = includeReasoner; this.resolveOutputIDs = typeof this.options.enableIDResolution === 'undefined' ? true : this.options.enableIDResolution; this.path = smartAPIPath || path.resolve(__dirname, './smartapi_specs.json'); @@ -27,7 +28,7 @@ exports.TRAPIQueryHandler = class TRAPIQueryHandler { const kg = new meta_kg.default(this.path, this.predicatePath); debug(`Query options are: ${JSON.stringify(this.options)}`); debug(`SmartAPI Specs read from path: ${this.path}`); - kg.constructMetaKGSync(true, this.options); + kg.constructMetaKGSync(this.includeReasoner, this.options); return kg; } From 5f62eb84827f638d6a4578fb32612380c9d78328 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 1 Apr 2021 11:20:39 -0700 Subject: [PATCH 35/68] refactor: :recycle: set default value of includeReasoner to be true --- src/index.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/index.js b/src/index.js index 9105c0ee..873115f1 100644 --- a/src/index.js +++ b/src/index.js @@ -14,7 +14,7 @@ const Graph = require('./graph/graph'); exports.InvalidQueryGraphError = InvalidQueryGraphError; exports.TRAPIQueryHandler = class TRAPIQueryHandler { - constructor(options = {}, smartAPIPath = undefined, predicatesPath = undefined, includeReasoner = false) { + constructor(options = {}, smartAPIPath = undefined, predicatesPath = undefined, includeReasoner = true) { this.logs = []; this.options = options; this.includeReasoner = includeReasoner; From 9058c5639321d0b4572949d5ec07d1fe82dcd55c Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 1 Apr 2021 11:20:55 -0700 Subject: [PATCH 36/68] test: :white_check_mark: fix broken test due to addition of includeReasoner param --- __test__/integration/integrity.test.js | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/__test__/integration/integrity.test.js b/__test__/integration/integrity.test.js index 40826de9..d1203571 100644 --- a/__test__/integration/integrity.test.js +++ b/__test__/integration/integrity.test.js @@ -6,7 +6,7 @@ describe("Testing TRAPIQueryHandler Module", () => { const example_foler = path.resolve(__dirname, '../data'); test("When looking for chemicals affected by Phenotype Increased Urinary Glycerol, Glycerol should pop up", async () => { - const queryHandler = new TRAPIQueryHandler.TRAPIQueryHandler(); + const queryHandler = new TRAPIQueryHandler.TRAPIQueryHandler({}, undefined, undefined, true); const query = JSON.parse(fs.readFileSync(path.join(example_foler, 'increased_urinary_glycerol_affects_glycerol.json'))); queryHandler.setQueryGraph(query.message.query_graph); await queryHandler.query(); @@ -15,7 +15,7 @@ describe("Testing TRAPIQueryHandler Module", () => { }) test("When looking for genes related to Disease DYSKINESIA, FAMILIAL, WITH FACIAL MYOKYMIA, ACDY5 should pop up", async () => { - const queryHandler = new TRAPIQueryHandler.TRAPIQueryHandler(); + const queryHandler = new TRAPIQueryHandler.TRAPIQueryHandler({}, undefined, undefined, true); const query = JSON.parse(fs.readFileSync(path.join(example_foler, 'FDFM_caused_by_ACDY5.json'))); queryHandler.setQueryGraph(query.message.query_graph); await queryHandler.query(); @@ -24,7 +24,7 @@ describe("Testing TRAPIQueryHandler Module", () => { }) test("When looking for chemicals targeting IL1 Signaling patway, curcumin should pop up", async () => { - const queryHandler = new TRAPIQueryHandler.TRAPIQueryHandler(); + const queryHandler = new TRAPIQueryHandler.TRAPIQueryHandler({}, undefined, undefined, true); const query = JSON.parse(fs.readFileSync(path.join(example_foler, 'chemicals_targeting_IL1_Signaling_Pathway.json'))); queryHandler.setQueryGraph(query.message.query_graph); await queryHandler.query(); From 76a5146adc993a619f9b366fca1ee0924bf7a952 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 1 Apr 2021 11:21:04 -0700 Subject: [PATCH 37/68] chore(release): 1.5.1 --- 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 df98b5be..08767af7 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. +### [1.5.1](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.5.0...v1.5.1) (2021-04-01) + + +### Features + +* :sparkles: allow user to specify if they want to include reasoner apis ([b89c288](https://github.com/kevinxin90/bte_trapi_query_graph_handler/commit/b89c288e0b6f72523d2f6e1c81af0468523b06d6)) + ## [1.5.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.4.0...v1.5.0) (2021-04-01) diff --git a/package-lock.json b/package-lock.json index 74d3cefe..0e27060e 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.5.0", + "version": "1.5.1", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index 916d9687..c2adbb86 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.5.0", + "version": "1.5.1", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { From 54de5ab29b2308e0d19fb271cf85730f7b020800 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 1 Apr 2021 17:28:43 -0700 Subject: [PATCH 38/68] refactor: :recycle: disable filter ops by preset API list --- src/qedge2bteedge.js | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/src/qedge2bteedge.js b/src/qedge2bteedge.js index 6def9e37..833e5046 100644 --- a/src/qedge2bteedge.js +++ b/src/qedge2bteedge.js @@ -40,8 +40,7 @@ module.exports = class QEdge2BTEEdgeHandler { let filterCriteria = { input_type: qEdge.getSubject().getCategories(), output_type: qEdge.getObject().getCategories(), - predicate: qEdge.getPredicate(), - api_name: config.API_LIST, + predicate: qEdge.getPredicate() }; debug(`Filter criteria is: ${JSON.stringify(filterCriteria)}`); let smartapi_edges = kg.filter(filterCriteria); @@ -59,10 +58,8 @@ module.exports = class QEdge2BTEEdgeHandler { new LogEntry( 'DEBUG', null, - `BTE found ${ - smartapi_edges.length - } smartapi edges corresponding to ${qEdge.getID()}. These smartaip edges comes from ${ - new Set(this._findAPIsFromSmartAPIEdges(smartapi_edges)).size + `BTE found ${smartapi_edges.length + } smartapi edges corresponding to ${qEdge.getID()}. These smartaip edges comes from ${new Set(this._findAPIsFromSmartAPIEdges(smartapi_edges)).size } unique APIs. They are ${Array.from(new Set(this._findAPIsFromSmartAPIEdges(smartapi_edges))).join(',')}`, ).getLog(), ); From 24d45319dbe2eb12496d129517e0c3f977d8fad2 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 1 Apr 2021 17:29:01 -0700 Subject: [PATCH 39/68] feat: support using providing a list of APIs to include --- package-lock.json | 6 +++--- package.json | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/package-lock.json b/package-lock.json index 0e27060e..8bee152b 100644 --- a/package-lock.json +++ b/package-lock.json @@ -472,9 +472,9 @@ } }, "@biothings-explorer/smartapi-kg": { - "version": "3.5.0", - "resolved": "https://registry.npmjs.org/@biothings-explorer/smartapi-kg/-/smartapi-kg-3.5.0.tgz", - "integrity": "sha512-zrVPQ1IS5UDkfbR4Mq4eAzJizAa9fC2oTx5TjGE9mWCM/cYwLn7Vd18ce8Y7WJmJxijypZxZ7hFPCn9vs7sUmQ==", + "version": "3.6.0", + "resolved": "https://registry.npmjs.org/@biothings-explorer/smartapi-kg/-/smartapi-kg-3.6.0.tgz", + "integrity": "sha512-c4SrlFPHV2/OuTE10Wmj2YSCFM4JQ+t9fLlPCYY7e+17UE0chaR+Xo8zpugSpByvBum/L/ZLiC9s8iib8JRemQ==", "requires": { "@babel/runtime": "^7.13.10", "@commitlint/cli": "^11.0.0", diff --git a/package.json b/package.json index c2adbb86..fd19d525 100644 --- a/package.json +++ b/package.json @@ -51,7 +51,7 @@ }, "dependencies": { "@biothings-explorer/call-apis": "^1.17.1", - "@biothings-explorer/smartapi-kg": "^3.5.0", + "@biothings-explorer/smartapi-kg": "^3.6.0", "biolink-model": "^0.3.0", "biomedical_id_resolver": "^3.5.0", "debug": "^4.3.1", From ad63c6f3150e98f69b0bd01881b24624c5d7b956 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 1 Apr 2021 17:29:10 -0700 Subject: [PATCH 40/68] chore(release): 1.6.0 --- 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 08767af7..1f66e9f5 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. +## [1.6.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.5.1...v1.6.0) (2021-04-02) + + +### Features + +* support using providing a list of APIs to include ([24d4531](https://github.com/kevinxin90/bte_trapi_query_graph_handler/commit/24d45319dbe2eb12496d129517e0c3f977d8fad2)) + ### [1.5.1](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.5.0...v1.5.1) (2021-04-01) diff --git a/package-lock.json b/package-lock.json index 8bee152b..0d955153 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.5.1", + "version": "1.6.0", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index fd19d525..6e9a494b 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.5.1", + "version": "1.6.0", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { From ea6298a71c86a718569b02e60f2adeabd704eb8d Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Fri, 2 Apr 2021 10:57:13 -0700 Subject: [PATCH 41/68] chore: :recycle: add debug messages --- src/graph/graph.js | 2 ++ src/index.js | 1 + src/query_results.js | 2 ++ 3 files changed, 5 insertions(+) diff --git a/src/graph/graph.js b/src/graph/graph.js index 846ad065..27448006 100644 --- a/src/graph/graph.js +++ b/src/graph/graph.js @@ -1,6 +1,7 @@ const kg_edge = require('./kg_edge'); const kg_node = require('./kg_node'); const helper = require('../helper'); +const debug = require('debug')('biothings-explorer-trapi:Graph'); module.exports = class Graph { constructor() { @@ -12,6 +13,7 @@ module.exports = class Graph { } update(queryResult) { + debug(`Updating BTE Graph now.`) const bteAttributes = ['name', 'label', 'id', 'api', 'provided_by', 'publications']; queryResult.map((record) => { const inputPrimaryID = this.helper._getInputID(record); diff --git a/src/index.js b/src/index.js index 873115f1..f0ca5949 100644 --- a/src/index.js +++ b/src/index.js @@ -106,6 +106,7 @@ exports.TRAPIQueryHandler = class TRAPIQueryHandler { if (res.length === 0) { return; } + debug('Start to notify subscribers now.') handlers[i].notify(res); debug(`Updated TRAPI knowledge graph using query results for depth ${i + 1}`); } diff --git a/src/query_results.js b/src/query_results.js index 64dcbbdc..a023e07e 100644 --- a/src/query_results.js +++ b/src/query_results.js @@ -1,5 +1,6 @@ const GraphHelper = require('./helper'); const helper = new GraphHelper(); +const debug = require('debug')('biothings-explorer-trapi:QueryResult'); module.exports = class QueryResult { constructor() { @@ -36,6 +37,7 @@ module.exports = class QueryResult { } update(queryResult) { + debug(`Updating query results now!`) queryResult.map((record) => { this.results.push({ node_bindings: this._createNodeBindings(record), From b941c63af46e4ed5dab2dba6a57e6f30db16d5fe Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Fri, 2 Apr 2021 10:57:27 -0700 Subject: [PATCH 42/68] style: :art: style code --- src/qedge2bteedge.js | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/qedge2bteedge.js b/src/qedge2bteedge.js index 833e5046..45f98231 100644 --- a/src/qedge2bteedge.js +++ b/src/qedge2bteedge.js @@ -40,7 +40,7 @@ module.exports = class QEdge2BTEEdgeHandler { let filterCriteria = { input_type: qEdge.getSubject().getCategories(), output_type: qEdge.getObject().getCategories(), - predicate: qEdge.getPredicate() + predicate: qEdge.getPredicate(), }; debug(`Filter criteria is: ${JSON.stringify(filterCriteria)}`); let smartapi_edges = kg.filter(filterCriteria); @@ -58,8 +58,10 @@ module.exports = class QEdge2BTEEdgeHandler { new LogEntry( 'DEBUG', null, - `BTE found ${smartapi_edges.length - } smartapi edges corresponding to ${qEdge.getID()}. These smartaip edges comes from ${new Set(this._findAPIsFromSmartAPIEdges(smartapi_edges)).size + `BTE found ${ + smartapi_edges.length + } smartapi edges corresponding to ${qEdge.getID()}. These smartaip edges comes from ${ + new Set(this._findAPIsFromSmartAPIEdges(smartapi_edges)).size } unique APIs. They are ${Array.from(new Set(this._findAPIsFromSmartAPIEdges(smartapi_edges))).join(',')}`, ).getLog(), ); From 437321e6f654627043a677e7d1268d169706b9b5 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Fri, 2 Apr 2021 10:57:50 -0700 Subject: [PATCH 43/68] feat: :sparkles: support limiting ops from /predicates to user specified api names --- package-lock.json | 6 +++--- package.json | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/package-lock.json b/package-lock.json index 0d955153..c86dff4d 100644 --- a/package-lock.json +++ b/package-lock.json @@ -472,9 +472,9 @@ } }, "@biothings-explorer/smartapi-kg": { - "version": "3.6.0", - "resolved": "https://registry.npmjs.org/@biothings-explorer/smartapi-kg/-/smartapi-kg-3.6.0.tgz", - "integrity": "sha512-c4SrlFPHV2/OuTE10Wmj2YSCFM4JQ+t9fLlPCYY7e+17UE0chaR+Xo8zpugSpByvBum/L/ZLiC9s8iib8JRemQ==", + "version": "3.7.0", + "resolved": "https://registry.npmjs.org/@biothings-explorer/smartapi-kg/-/smartapi-kg-3.7.0.tgz", + "integrity": "sha512-cFbyaAwvsozBcTe3fdtD6jO85B1Q3zHSLkh4ZCbE3yNgM7ocU99YAIRfR1iSDw8dremC8VnNDgkhyMf7fGdDKA==", "requires": { "@babel/runtime": "^7.13.10", "@commitlint/cli": "^11.0.0", diff --git a/package.json b/package.json index 6e9a494b..eb8dc769 100644 --- a/package.json +++ b/package.json @@ -51,7 +51,7 @@ }, "dependencies": { "@biothings-explorer/call-apis": "^1.17.1", - "@biothings-explorer/smartapi-kg": "^3.6.0", + "@biothings-explorer/smartapi-kg": "^3.7.0", "biolink-model": "^0.3.0", "biomedical_id_resolver": "^3.5.0", "debug": "^4.3.1", From ee0ffedfb8cb13e6ae5841a3f1a9d703fd88abeb Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Fri, 2 Apr 2021 10:58:02 -0700 Subject: [PATCH 44/68] chore(release): 1.7.0 --- 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 1f66e9f5..213c03db 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. +## [1.7.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.6.0...v1.7.0) (2021-04-02) + + +### Features + +* :sparkles: support limiting ops from /predicates to user specified api names ([437321e](https://github.com/kevinxin90/bte_trapi_query_graph_handler/commit/437321e6f654627043a677e7d1268d169706b9b5)) + ## [1.6.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.5.1...v1.6.0) (2021-04-02) diff --git a/package-lock.json b/package-lock.json index c86dff4d..c25de937 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.6.0", + "version": "1.7.0", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index eb8dc769..a7c77054 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.6.0", + "version": "1.7.0", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { From 4d1c3d49e61a446ff76cf7106671dbda794ea0a3 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 20 Apr 2021 08:54:19 -0700 Subject: [PATCH 45/68] feat: :sparkles: set a 3s timeout for all TRAPI APIs --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index a7c77054..ac2b5725 100644 --- a/package.json +++ b/package.json @@ -50,7 +50,7 @@ "typescript": "^4.2.3" }, "dependencies": { - "@biothings-explorer/call-apis": "^1.17.1", + "@biothings-explorer/call-apis": "^1.17.2", "@biothings-explorer/smartapi-kg": "^3.7.0", "biolink-model": "^0.3.0", "biomedical_id_resolver": "^3.5.0", From 87f412eae73ef53f2ef118badad20daef5c9c615 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 20 Apr 2021 08:54:37 -0700 Subject: [PATCH 46/68] feat: :sparkles: set a 3s timeout for all TRAPI APIs --- package-lock.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/package-lock.json b/package-lock.json index c25de937..b36e2a07 100644 --- a/package-lock.json +++ b/package-lock.json @@ -450,9 +450,9 @@ } }, "@biothings-explorer/call-apis": { - "version": "1.17.1", - "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.17.1.tgz", - "integrity": "sha512-mfrYTnDPobRV97saGOGfnNLgXJNQm4AUtoLpeC4RAji/bOvMtSmtdUUnyQt/SbwKdJXWY0Y5RfQQCKbNmjwhgg==", + "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==", "requires": { "@biothings-explorer/api-response-transform": "^1.10.1", "axios": "^0.21.1", From 0e0c28e5783ea2d46d751e4519ebb0890d349345 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 20 Apr 2021 08:54:49 -0700 Subject: [PATCH 47/68] style: :art: style code --- src/graph/graph.js | 2 +- src/index.js | 2 +- src/query_results.js | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/graph/graph.js b/src/graph/graph.js index 27448006..ea62b7bd 100644 --- a/src/graph/graph.js +++ b/src/graph/graph.js @@ -13,7 +13,7 @@ module.exports = class Graph { } update(queryResult) { - debug(`Updating BTE Graph now.`) + debug(`Updating BTE Graph now.`); const bteAttributes = ['name', 'label', 'id', 'api', 'provided_by', 'publications']; queryResult.map((record) => { const inputPrimaryID = this.helper._getInputID(record); diff --git a/src/index.js b/src/index.js index f0ca5949..29f77388 100644 --- a/src/index.js +++ b/src/index.js @@ -106,7 +106,7 @@ exports.TRAPIQueryHandler = class TRAPIQueryHandler { if (res.length === 0) { return; } - debug('Start to notify subscribers now.') + debug('Start to notify subscribers now.'); handlers[i].notify(res); debug(`Updated TRAPI knowledge graph using query results for depth ${i + 1}`); } diff --git a/src/query_results.js b/src/query_results.js index a023e07e..a5ffe94a 100644 --- a/src/query_results.js +++ b/src/query_results.js @@ -37,7 +37,7 @@ module.exports = class QueryResult { } update(queryResult) { - debug(`Updating query results now!`) + debug(`Updating query results now!`); queryResult.map((record) => { this.results.push({ node_bindings: this._createNodeBindings(record), From 238bbd511b657e732fff628861240ddd54b9930d Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 20 Apr 2021 08:56:09 -0700 Subject: [PATCH 48/68] chore(release): 1.8.0 --- CHANGELOG.md | 8 ++++++++ package-lock.json | 2 +- package.json | 2 +- 3 files changed, 10 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 213c03db..80d2cd92 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,14 @@ 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. +## [1.8.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.7.0...v1.8.0) (2021-04-20) + + +### Features + +* :sparkles: set a 3s timeout for all TRAPI APIs ([87f412e](https://github.com/kevinxin90/bte_trapi_query_graph_handler/commit/87f412eae73ef53f2ef118badad20daef5c9c615)) +* :sparkles: set a 3s timeout for all TRAPI APIs ([4d1c3d4](https://github.com/kevinxin90/bte_trapi_query_graph_handler/commit/4d1c3d49e61a446ff76cf7106671dbda794ea0a3)) + ## [1.7.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.6.0...v1.7.0) (2021-04-02) diff --git a/package-lock.json b/package-lock.json index b36e2a07..782efbfe 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.7.0", + "version": "1.8.0", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index ac2b5725..729ab19e 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.7.0", + "version": "1.8.0", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { From 011134c188ccddfff2b0c5054fc2a769d424308f Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 22 Apr 2021 20:56:59 -0700 Subject: [PATCH 49/68] feat: :sparkles: support biocarta pathway id --- package-lock.json | 70 ++++++++++++++++++++++++++++++++++++++++------- package.json | 4 +-- 2 files changed, 62 insertions(+), 12 deletions(-) diff --git a/package-lock.json b/package-lock.json index 782efbfe..5765fb2f 100644 --- a/package-lock.json +++ b/package-lock.json @@ -450,15 +450,65 @@ } }, "@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" + }, + "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==" + }, + "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" + } + }, + "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==", + "requires": { + "@commitlint/cli": "^11.0.0", + "@commitlint/config-conventional": "^11.0.0", + "axios": "^0.19.2", + "biolink-model": "^0.1.2", + "debug": "^4.3.1", + "husky": "^4.3.8", + "lodash": "^4.17.21" + }, + "dependencies": { + "axios": { + "version": "0.19.2", + "resolved": "https://registry.npmjs.org/axios/-/axios-0.19.2.tgz", + "integrity": "sha512-fjgm5MvRHLhx+osE2xoekY70AhARk3a6hkN+3Io1jc00jtquGvxYlKlsFUhmUET0V5te6CcZI7lcv2Ym61mjHA==", + "requires": { + "follow-redirects": "1.5.10" + } + } + } + }, + "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" + } + } } }, "@biothings-explorer/json-transformer": { @@ -1478,9 +1528,9 @@ } }, "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", @@ -1531,9 +1581,9 @@ } }, "js-yaml": { - "version": "4.0.0", - "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-4.0.0.tgz", - "integrity": "sha512-pqon0s+4ScYUvX30wxQi3PogGFAlUyH0awepWvwkj4jD4v+ova3RiYw8bmA6x2rDrEaj8i/oWKoRxpVNW+Re8Q==", + "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" } diff --git a/package.json b/package.json index 729ab19e..5330f612 100644 --- a/package.json +++ b/package.json @@ -50,10 +50,10 @@ "typescript": "^4.2.3" }, "dependencies": { - "@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", From dbedee77b25f5b8fce86f2ed41740c3186c0dc62 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 22 Apr 2021 20:57:10 -0700 Subject: [PATCH 50/68] chore(release): 1.9.0 --- 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 80d2cd92..6e0e3a8a 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. +## [1.9.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.8.0...v1.9.0) (2021-04-23) + + +### Features + +* :sparkles: support biocarta pathway id ([011134c](https://github.com/kevinxin90/bte_trapi_query_graph_handler/commit/011134c188ccddfff2b0c5054fc2a769d424308f)) + ## [1.8.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.7.0...v1.8.0) (2021-04-20) diff --git a/package-lock.json b/package-lock.json index 5765fb2f..d1bc5ec8 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.8.0", + "version": "1.9.0", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index 5330f612..2f5bd009 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.8.0", + "version": "1.9.0", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { From 2b89a08b33e51944174b8edd20c8c2b036f3261b Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Thu, 22 Apr 2021 21:37:51 -0700 Subject: [PATCH 51/68] chore(release): 1.10.0 --- CHANGELOG.md | 2 ++ package-lock.json | 66 ++++++----------------------------------------- package.json | 6 ++--- 3 files changed, 13 insertions(+), 61 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6e0e3a8a..70bcf286 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,8 @@ 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. +## [1.10.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.9.0...v1.10.0) (2021-04-23) + ## [1.9.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.8.0...v1.9.0) (2021-04-23) diff --git a/package-lock.json b/package-lock.json index d1bc5ec8..1fe8e08d 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.9.0", + "version": "1.10.0", "lockfileVersion": 1, "requires": true, "dependencies": { @@ -450,65 +450,15 @@ } }, "@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" - }, - "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==" - }, - "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" - } - }, - "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==", - "requires": { - "@commitlint/cli": "^11.0.0", - "@commitlint/config-conventional": "^11.0.0", - "axios": "^0.19.2", - "biolink-model": "^0.1.2", - "debug": "^4.3.1", - "husky": "^4.3.8", - "lodash": "^4.17.21" - }, - "dependencies": { - "axios": { - "version": "0.19.2", - "resolved": "https://registry.npmjs.org/axios/-/axios-0.19.2.tgz", - "integrity": "sha512-fjgm5MvRHLhx+osE2xoekY70AhARk3a6hkN+3Io1jc00jtquGvxYlKlsFUhmUET0V5te6CcZI7lcv2Ym61mjHA==", - "requires": { - "follow-redirects": "1.5.10" - } - } - } - }, - "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" - } - } } }, "@biothings-explorer/json-transformer": { @@ -1528,9 +1478,9 @@ } }, "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 2f5bd009..91f2c4ee 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.9.0", + "version": "1.10.0", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { @@ -50,10 +50,10 @@ "typescript": "^4.2.3" }, "dependencies": { - "@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", From fbe473580e5a2a2611a9b723eac661bf6e1bb60b Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 27 Apr 2021 07:42:45 -0700 Subject: [PATCH 52/68] fix: :bug: change NCBIGENE to NCBIGene, add RHEA --- package-lock.json | 78 ++++++++++++++++++++++++++++++++++++++--------- package.json | 4 +-- 2 files changed, 66 insertions(+), 16 deletions(-) diff --git a/package-lock.json b/package-lock.json index 1fe8e08d..ffaf3963 100644 --- a/package-lock.json +++ b/package-lock.json @@ -450,15 +450,65 @@ } }, "@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" + }, + "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==" + }, + "biolink-model": { + "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", + "js-yaml": "^4.0.0", + "pascal-case": "^3.1.2" + } + }, + "biomedical_id_resolver": { + "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": "^0.3.1", + "debug": "^4.3.1", + "husky": "^4.3.8", + "lodash": "^4.17.21" + }, + "dependencies": { + "axios": { + "version": "0.19.2", + "resolved": "https://registry.npmjs.org/axios/-/axios-0.19.2.tgz", + "integrity": "sha512-fjgm5MvRHLhx+osE2xoekY70AhARk3a6hkN+3Io1jc00jtquGvxYlKlsFUhmUET0V5te6CcZI7lcv2Ym61mjHA==", + "requires": { + "follow-redirects": "1.5.10" + } + } + } + }, + "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" + } + } } }, "@biothings-explorer/json-transformer": { @@ -1478,14 +1528,14 @@ } }, "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" @@ -1505,9 +1555,9 @@ } }, "biolink-model": { - "version": "0.1.2", - "resolved": "https://registry.npmjs.org/biolink-model/-/biolink-model-0.1.2.tgz", - "integrity": "sha512-SbTcAdocPz3RfucuQc5ZmCN3HMAKRxOd3LxfeqM5yMqMpkn8jlmTWwb6o1y5Zrkh6VDHvOKqR2n1txg0Ne7uQA==", + "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", @@ -1524,9 +1574,9 @@ } }, "follow-redirects": { - "version": "1.13.3", - "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.13.3.tgz", - "integrity": "sha512-DUgl6+HDzB0iEptNQEXLx/KhTmDb8tZUHSeLqpnjpknR70H0nC2t9N73BK6fN4hOvJ84pKlIQVQ4k5FFlBedKA==" + "version": "1.14.0", + "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.14.0.tgz", + "integrity": "sha512-0vRwd7RKQBTt+mgu87mtYeofLFZpTas2S9zY+jIeuLJMNvudIgF52nr19q40HOwH5RrhWIPuj9puybzSJiRrVg==" } } }, diff --git a/package.json b/package.json index 91f2c4ee..2e18df5c 100644 --- a/package.json +++ b/package.json @@ -50,10 +50,10 @@ "typescript": "^4.2.3" }, "dependencies": { - "@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", From 4a2288eedc413a2639d98400571e63c3078e0914 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 27 Apr 2021 07:42:55 -0700 Subject: [PATCH 53/68] chore(release): 1.11.0 --- 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 70bcf286..cb62eb3d 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. +## [1.11.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.10.0...v1.11.0) (2021-04-27) + + +### Bug Fixes + +* :bug: change NCBIGENE to NCBIGene, add RHEA ([fbe4735](https://github.com/kevinxin90/bte_trapi_query_graph_handler/commit/fbe473580e5a2a2611a9b723eac661bf6e1bb60b)) + ## [1.10.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.9.0...v1.10.0) (2021-04-23) ## [1.9.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.8.0...v1.9.0) (2021-04-23) diff --git a/package-lock.json b/package-lock.json index ffaf3963..3a42a1c6 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.10.0", + "version": "1.11.0", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index 2e18df5c..18e8ef37 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.10.0", + "version": "1.11.0", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { From 81d9335b2461c3bd730abb8ac4ac048f60df9183 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 27 Apr 2021 07:46:01 -0700 Subject: [PATCH 54/68] test: :white_check_mark: update test to change from NCBIGENE to NCBIGene --- __test__/integration/BatchEdgeQueryHandler.test.js | 2 +- __test__/integration/QueryGraphHandler.test.js | 2 +- __test__/integration/integrity.test.js | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/__test__/integration/BatchEdgeQueryHandler.test.js b/__test__/integration/BatchEdgeQueryHandler.test.js index 44a7df4b..71c54a00 100644 --- a/__test__/integration/BatchEdgeQueryHandler.test.js +++ b/__test__/integration/BatchEdgeQueryHandler.test.js @@ -10,7 +10,7 @@ describe("Testing BatchEdgeQueryHandler Module", () => { describe("Testing query function", () => { // test("test with one query edge", async () => { - // let gene_node1 = new QNode("n1", { category: "Gene", id: "NCBIGENE:1017" }); + // let gene_node1 = new QNode("n1", { category: "Gene", id: "NCBIGene:1017" }); // let chemical_node1 = new QNode("n3", { category: "ChemicalSubstance" }); // const edge1 = new QEdge("e01", { subject: gene_node1, object: chemical_node1 }); // const exeEdge1 = new QExeEdge(edge1, false, undefined); diff --git a/__test__/integration/QueryGraphHandler.test.js b/__test__/integration/QueryGraphHandler.test.js index 1378094c..d234619b 100644 --- a/__test__/integration/QueryGraphHandler.test.js +++ b/__test__/integration/QueryGraphHandler.test.js @@ -10,7 +10,7 @@ describe("Testing QueryGraphHandler Module", () => { }; const gene_entity_node = { category: "biolink:Gene", - id: "NCBIGENE:1017" + id: "NCBIGene:1017" }; const gene_class_node = { category: "biolink:Gene" diff --git a/__test__/integration/integrity.test.js b/__test__/integration/integrity.test.js index d1203571..392b1673 100644 --- a/__test__/integration/integrity.test.js +++ b/__test__/integration/integrity.test.js @@ -20,7 +20,7 @@ describe("Testing TRAPIQueryHandler Module", () => { queryHandler.setQueryGraph(query.message.query_graph); await queryHandler.query(); const res = queryHandler.getResponse(); - expect(res.message.knowledge_graph.nodes).toHaveProperty('NCBIGENE:111'); + expect(res.message.knowledge_graph.nodes).toHaveProperty('NCBIGene:111'); }) test("When looking for chemicals targeting IL1 Signaling patway, curcumin should pop up", async () => { From 892fac68c88a9ae8c348a0154787eabb74faef51 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 27 Apr 2021 07:46:15 -0700 Subject: [PATCH 55/68] docs: :memo: update documentation to reflect changes on NCBIGene --- README.md | 1444 ++++++++++++++++++++++++++--------------------------- 1 file changed, 722 insertions(+), 722 deletions(-) diff --git a/README.md b/README.md index bf8675f5..40848ad9 100644 --- a/README.md +++ b/README.md @@ -71,14 +71,14 @@ console.log(queryHandler.getResponse()) }, "knowledge_graph": { "nodes": { - "NCBIGENE:1017": { + "NCBIGene:1017": { "category": "biolink:Gene", "name": "CDK2", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:1017", + "NCBIGene:1017", "name:cyclin dependent kinase 2", "SYMBOL:CDK2", "UMLS:C1332733", @@ -402,9 +402,9 @@ console.log(queryHandler.getResponse()) } }, "edges": { - "NCBIGENE:1017-GO:0000082-MyGene.info API-entrez": { + "NCBIGene:1017-GO:0000082-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:0000082", "attributes": [ { @@ -436,9 +436,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1017-GO:0000086-MyGene.info API-entrez": { + "NCBIGene:1017-GO:0000086-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:0000086", "attributes": [ { @@ -470,9 +470,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1017-GO:0006260-MyGene.info API-entrez": { + "NCBIGene:1017-GO:0006260-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:0006260", "attributes": [ { @@ -504,9 +504,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1017-GO:0006281-MyGene.info API-entrez": { + "NCBIGene:1017-GO:0006281-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:0006281", "attributes": [ { @@ -531,9 +531,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1017-GO:0006468-MyGene.info API-entrez": { + "NCBIGene:1017-GO:0006468-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:0006468", "attributes": [ { @@ -565,9 +565,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1017-GO:0006977-MyGene.info API-entrez": { + "NCBIGene:1017-GO:0006977-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:0006977", "attributes": [ { @@ -592,9 +592,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1017-GO:0007099-MyGene.info API-entrez": { + "NCBIGene:1017-GO:0007099-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:0007099", "attributes": [ { @@ -626,9 +626,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1017-GO:0007165-MyGene.info API-entrez": { + "NCBIGene:1017-GO:0007165-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:0007165", "attributes": [ { @@ -660,9 +660,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1017-GO:0007265-MyGene.info API-entrez": { + "NCBIGene:1017-GO:0007265-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:0007265", "attributes": [ { @@ -694,9 +694,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1017-GO:0008284-MyGene.info API-entrez": { + "NCBIGene:1017-GO:0008284-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:0008284", "attributes": [ { @@ -728,9 +728,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1017-GO:0010389-MyGene.info API-entrez": { + "NCBIGene:1017-GO:0010389-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:0010389", "attributes": [ { @@ -762,9 +762,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1017-GO:0010468-MyGene.info API-entrez": { + "NCBIGene:1017-GO:0010468-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:0010468", "attributes": [ { @@ -796,9 +796,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1017-GO:0016572-MyGene.info API-entrez": { + "NCBIGene:1017-GO:0016572-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:0016572", "attributes": [ { @@ -830,9 +830,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1017-GO:0018105-MyGene.info API-entrez": { + "NCBIGene:1017-GO:0018105-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:0018105", "attributes": [ { @@ -864,9 +864,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1017-GO:0031145-MyGene.info API-entrez": { + "NCBIGene:1017-GO:0031145-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:0031145", "attributes": [ { @@ -891,9 +891,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1017-GO:0031571-MyGene.info API-entrez": { + "NCBIGene:1017-GO:0031571-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:0031571", "attributes": [ { @@ -925,9 +925,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1017-GO:0051298-MyGene.info API-entrez": { + "NCBIGene:1017-GO:0051298-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:0051298", "attributes": [ { @@ -959,9 +959,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1017-GO:0051301-MyGene.info API-entrez": { + "NCBIGene:1017-GO:0051301-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:0051301", "attributes": [ { @@ -986,9 +986,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1017-GO:0051321-MyGene.info API-entrez": { + "NCBIGene:1017-GO:0051321-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:0051321", "attributes": [ { @@ -1020,9 +1020,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1017-GO:0060968-MyGene.info API-entrez": { + "NCBIGene:1017-GO:0060968-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:0060968", "attributes": [ { @@ -1054,9 +1054,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1017-GO:0071732-MyGene.info API-entrez": { + "NCBIGene:1017-GO:0071732-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:0071732", "attributes": [ { @@ -1088,9 +1088,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1017-GO:1901796-MyGene.info API-entrez": { + "NCBIGene:1017-GO:1901796-MyGene.info API-entrez": { "predicate": "biolink:enables", - "subject": "NCBIGENE:1017", + "subject": "NCBIGene:1017", "object": "GO:1901796", "attributes": [ { @@ -1122,7 +1122,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1134,7 +1134,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0000082-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0000082-MyGene.info API-entrez" } ] } @@ -1143,7 +1143,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1155,7 +1155,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0000082-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0000082-MyGene.info API-entrez" } ] } @@ -1164,7 +1164,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1176,7 +1176,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0000086-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0000086-MyGene.info API-entrez" } ] } @@ -1185,7 +1185,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1197,7 +1197,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0000086-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0000086-MyGene.info API-entrez" } ] } @@ -1206,7 +1206,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1218,7 +1218,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0006260-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0006260-MyGene.info API-entrez" } ] } @@ -1227,7 +1227,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1239,7 +1239,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0006281-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0006281-MyGene.info API-entrez" } ] } @@ -1248,7 +1248,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1260,7 +1260,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0006468-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0006468-MyGene.info API-entrez" } ] } @@ -1269,7 +1269,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1281,7 +1281,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0006468-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0006468-MyGene.info API-entrez" } ] } @@ -1290,7 +1290,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1302,7 +1302,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0006468-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0006468-MyGene.info API-entrez" } ] } @@ -1311,7 +1311,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1323,7 +1323,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0006977-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0006977-MyGene.info API-entrez" } ] } @@ -1332,7 +1332,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1344,7 +1344,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0007099-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0007099-MyGene.info API-entrez" } ] } @@ -1353,7 +1353,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1365,7 +1365,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0007165-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0007165-MyGene.info API-entrez" } ] } @@ -1374,7 +1374,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1386,7 +1386,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0007265-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0007265-MyGene.info API-entrez" } ] } @@ -1395,7 +1395,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1407,7 +1407,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0008284-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0008284-MyGene.info API-entrez" } ] } @@ -1416,7 +1416,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1428,7 +1428,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0008284-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0008284-MyGene.info API-entrez" } ] } @@ -1437,7 +1437,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1449,7 +1449,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0010389-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0010389-MyGene.info API-entrez" } ] } @@ -1458,7 +1458,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1470,7 +1470,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0010468-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0010468-MyGene.info API-entrez" } ] } @@ -1479,7 +1479,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1491,7 +1491,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0016572-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0016572-MyGene.info API-entrez" } ] } @@ -1500,7 +1500,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1512,7 +1512,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0018105-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0018105-MyGene.info API-entrez" } ] } @@ -1521,7 +1521,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1533,7 +1533,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0031145-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0031145-MyGene.info API-entrez" } ] } @@ -1542,7 +1542,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1554,7 +1554,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0031571-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0031571-MyGene.info API-entrez" } ] } @@ -1563,7 +1563,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1575,7 +1575,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0051298-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0051298-MyGene.info API-entrez" } ] } @@ -1584,7 +1584,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1596,7 +1596,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0051301-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0051301-MyGene.info API-entrez" } ] } @@ -1605,7 +1605,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1617,7 +1617,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0051321-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0051321-MyGene.info API-entrez" } ] } @@ -1626,7 +1626,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1638,7 +1638,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0060968-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0060968-MyGene.info API-entrez" } ] } @@ -1647,7 +1647,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1659,7 +1659,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:0071732-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:0071732-MyGene.info API-entrez" } ] } @@ -1668,7 +1668,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n00": [ { - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" } ], "n01": [ @@ -1680,7 +1680,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e00": [ { - "id": "NCBIGENE:1017-GO:1901796-MyGene.info API-entrez" + "id": "NCBIGene:1017-GO:1901796-MyGene.info API-entrez" } ] } @@ -1856,14 +1856,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:116534309": { + "NCBIGene:116534309": { "category": "biolink:Gene", "name": "CD4", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:116534309", + "NCBIGene:116534309", "name:CD4 molecule", "SYMBOL:CD4" ], @@ -1871,14 +1871,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:539109": { + "NCBIGene:539109": { "category": "biolink:Gene", "name": "MMP11", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:539109", + "NCBIGene:539109", "name:matrix metallopeptidase 11", "SYMBOL:MMP11", "ENSEMBL:ENSBTAG00000006108" @@ -1887,14 +1887,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:102448557": { + "NCBIGene:102448557": { "category": "biolink:Gene", "name": "GTPBP1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:102448557", + "NCBIGene:102448557", "name:GTP binding protein 1", "SYMBOL:GTPBP1", "ENSEMBL:ENSPSIG00000004300" @@ -1903,14 +1903,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:103074707": { + "NCBIGene:103074707": { "category": "biolink:Gene", "name": "CCL2", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:103074707", + "NCBIGene:103074707", "name:C-C motif chemokine ligand 2", "SYMBOL:CCL2" ], @@ -1933,14 +1933,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:115865406": { + "NCBIGene:115865406": { "category": "biolink:Gene", "name": "BST2", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:115865406", + "NCBIGene:115865406", "name:bone marrow stromal cell antigen 2", "SYMBOL:BST2" ], @@ -1948,14 +1948,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:110132571": { + "NCBIGene:110132571": { "category": "biolink:Gene", "name": "IL1B", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:110132571", + "NCBIGene:110132571", "name:interleukin 1 beta", "SYMBOL:IL1B" ], @@ -1963,14 +1963,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:101571570": { + "NCBIGene:101571570": { "category": "biolink:Gene", "name": "Ifih1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:101571570", + "NCBIGene:101571570", "name:interferon induced with helicase C domain 1", "SYMBOL:Ifih1", "ENSEMBL:ENSODEG00000013586" @@ -1994,14 +1994,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:397686": { + "NCBIGene:397686": { "category": "biolink:Gene", "name": "IFNA1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:397686", + "NCBIGene:397686", "name:interferon, alpha 1", "SYMBOL:IFNA1", "ENSEMBL:ENSSSCG00000050619" @@ -2010,14 +2010,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:102892030": { + "NCBIGene:102892030": { "category": "biolink:Gene", "name": "ALB", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:102892030", + "NCBIGene:102892030", "name:albumin", "SYMBOL:ALB" ], @@ -2025,14 +2025,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:104045425": { + "NCBIGene:104045425": { "category": "biolink:Gene", "name": "HDX", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:104045425", + "NCBIGene:104045425", "name:highly divergent homeobox", "SYMBOL:HDX" ], @@ -2040,14 +2040,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:110137949": { + "NCBIGene:110137949": { "category": "biolink:Gene", "name": "CXCL10", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:110137949", + "NCBIGene:110137949", "name:C-X-C motif chemokine ligand 10", "SYMBOL:CXCL10" ], @@ -2055,14 +2055,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:105822820": { + "NCBIGene:105822820": { "category": "biolink:Gene", "name": "CXCL8", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:105822820", + "NCBIGene:105822820", "name:C-X-C motif chemokine ligand 8", "SYMBOL:CXCL8", "ENSEMBL:ENSPCOG00000024593" @@ -2071,14 +2071,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:116479423": { + "NCBIGene:116479423": { "category": "biolink:Gene", "name": "CLEC4M", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:116479423", + "NCBIGene:116479423", "name:C-type lectin domain family 4 member M", "SYMBOL:CLEC4M" ], @@ -2086,14 +2086,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:103814882": { + "NCBIGene:103814882": { "category": "biolink:Gene", "name": "F3", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:103814882", + "NCBIGene:103814882", "name:coagulation factor III, tissue factor", "SYMBOL:F3", "ENSEMBL:ENSSCAG00000012591" @@ -2102,14 +2102,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:101142722": { + "NCBIGene:101142722": { "category": "biolink:Gene", "name": "KPNA1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:101142722", + "NCBIGene:101142722", "name:karyopherin subunit alpha 1", "SYMBOL:KPNA1" ], @@ -2117,14 +2117,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:104673720": { + "NCBIGene:104673720": { "category": "biolink:Gene", "name": "CTSL", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:104673720", + "NCBIGene:104673720", "name:cathepsin L", "SYMBOL:CTSL", "ENSEMBL:ENSRROG00000038398" @@ -2133,14 +2133,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:116543050": { + "NCBIGene:116543050": { "category": "biolink:Gene", "name": "CTSB", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:116543050", + "NCBIGene:116543050", "name:cathepsin B", "SYMBOL:CTSB" ], @@ -2148,14 +2148,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:29798": { + "NCBIGene:29798": { "category": "biolink:Gene", "name": "C2orf27A", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:29798", + "NCBIGene:29798", "name:chromosome 2 open reading frame 27A", "SYMBOL:C2orf27A", "UMLS:C2681192", @@ -2166,14 +2166,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:118012204": { + "NCBIGene:118012204": { "category": "biolink:Gene", "name": "STAT1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:118012204", + "NCBIGene:118012204", "name:signal transducer and activator of transcription 1", "SYMBOL:STAT1" ], @@ -2181,14 +2181,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:103531663": { + "NCBIGene:103531663": { "category": "biolink:Gene", "name": "KPNA5", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:103531663", + "NCBIGene:103531663", "name:karyopherin subunit alpha 5", "SYMBOL:KPNA5" ], @@ -2211,14 +2211,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:104395366": { + "NCBIGene:104395366": { "category": "biolink:Gene", "name": "THBD", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:104395366", + "NCBIGene:104395366", "name:thrombomodulin", "SYMBOL:THBD" ], @@ -2226,14 +2226,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:100731608": { + "NCBIGene:100731608": { "category": "biolink:Gene", "name": "Isg15", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:100731608", + "NCBIGene:100731608", "name:ISG15 ubiquitin like modifier", "SYMBOL:Isg15" ], @@ -2241,14 +2241,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:108529797": { + "NCBIGene:108529797": { "category": "biolink:Gene", "name": "DDX58", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:108529797", + "NCBIGene:108529797", "name:DExD/H-box helicase 58", "SYMBOL:DDX58", "ENSEMBL:ENSRBIG00000040257" @@ -2257,14 +2257,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:106971145": { + "NCBIGene:106971145": { "category": "biolink:Gene", "name": "IFNB1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:106971145", + "NCBIGene:106971145", "name:interferon beta 1", "SYMBOL:IFNB1" ], @@ -2286,14 +2286,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:101443464": { + "NCBIGene:101443464": { "category": "biolink:Gene", "name": "GPT", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:101443464", + "NCBIGene:101443464", "name:glutamic--pyruvic transaminase", "SYMBOL:GPT" ], @@ -2301,14 +2301,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:102387082": { + "NCBIGene:102387082": { "category": "biolink:Gene", "name": "IRF7", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:102387082", + "NCBIGene:102387082", "name:interferon regulatory factor 7", "SYMBOL:IRF7" ], @@ -2316,14 +2316,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:109055884": { + "NCBIGene:109055884": { "category": "biolink:Gene", "name": "il6", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:109055884", + "NCBIGene:109055884", "name:interleukin 6 (interferon, beta 2)", "SYMBOL:il6", "ENSEMBL:ENSCCRG00000034667" @@ -2347,14 +2347,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:117759282": { + "NCBIGene:117759282": { "category": "biolink:Gene", "name": "ace2", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:117759282", + "NCBIGene:117759282", "name:angiotensin I converting enzyme 2", "SYMBOL:ace2" ], @@ -2362,14 +2362,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:103562469": { + "NCBIGene:103562469": { "category": "biolink:Gene", "name": "TNF", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:103562469", + "NCBIGene:103562469", "name:tumor necrosis factor", "SYMBOL:TNF" ], @@ -2377,14 +2377,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:112648300": { + "NCBIGene:112648300": { "category": "biolink:Gene", "name": "IL10", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:112648300", + "NCBIGene:112648300", "name:interleukin 10", "SYMBOL:IL10", "ENSEMBL:ENSCAFG00020012434" @@ -2393,14 +2393,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:105221759": { + "NCBIGene:105221759": { "category": "biolink:Gene", "name": "ERVW-1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:105221759", + "NCBIGene:105221759", "name:endogenous retrovirus group W member 1, envelope", "SYMBOL:ERVW-1" ], @@ -2408,14 +2408,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:118335909": { + "NCBIGene:118335909": { "category": "biolink:Gene", "name": "irf3", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:118335909", + "NCBIGene:118335909", "name:interferon regulatory factor 3", "SYMBOL:irf3" ], @@ -2423,14 +2423,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:101674197": { + "NCBIGene:101674197": { "category": "biolink:Gene", "name": "CCL5", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:101674197", + "NCBIGene:101674197", "name:C-C motif chemokine ligand 5", "SYMBOL:CCL5" ], @@ -2438,14 +2438,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:103089296": { + "NCBIGene:103089296": { "category": "biolink:Gene", "name": "CCL3", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:103089296", + "NCBIGene:103089296", "name:C-C motif chemokine ligand 3", "SYMBOL:CCL3" ], @@ -2453,14 +2453,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:100136221": { + "NCBIGene:100136221": { "category": "biolink:Gene", "name": "ccl4", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:100136221", + "NCBIGene:100136221", "name:CCL4 protein", "SYMBOL:ccl4", "ENSEMBL:ENSOMYG00000026069" @@ -2469,14 +2469,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:118023076": { + "NCBIGene:118023076": { "category": "biolink:Gene", "name": "FURIN", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:118023076", + "NCBIGene:118023076", "name:furin, paired basic amino acid cleaving enzyme", "SYMBOL:FURIN" ], @@ -2484,14 +2484,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:574217": { + "NCBIGene:574217": { "category": "biolink:Gene", "name": "CCL4L1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:574217", + "NCBIGene:574217", "name:chemokine (C-C motif) ligand 4-like 1", "SYMBOL:CCL4L1", "UniProtKB:Q8HYQ2", @@ -2527,14 +2527,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:3601": { + "NCBIGene:3601": { "category": "biolink:Gene", "name": "IL15RA", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:3601", + "NCBIGene:3601", "name:interleukin 15 receptor subunit alpha", "SYMBOL:IL15RA", "UMLS:C1416387", @@ -2547,14 +2547,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:5788": { + "NCBIGene:5788": { "category": "biolink:Gene", "name": "PTPRC", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:5788", + "NCBIGene:5788", "name:protein tyrosine phosphatase receptor type C", "SYMBOL:PTPRC", "UMLS:C1335285", @@ -2568,14 +2568,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:8030": { + "NCBIGene:8030": { "category": "biolink:Gene", "name": "CCDC6", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:8030", + "NCBIGene:8030", "name:coiled-coil domain containing 6", "SYMBOL:CCDC6", "UMLS:C1425774", @@ -2588,14 +2588,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:920": { + "NCBIGene:920": { "category": "biolink:Gene", "name": "CD4", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:920", + "NCBIGene:920", "name:CD4 molecule", "SYMBOL:CD4", "UMLS:C1332714", @@ -2608,14 +2608,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1514": { + "NCBIGene:1514": { "category": "biolink:Gene", "name": "CTSL", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:1514", + "NCBIGene:1514", "name:cathepsin L", "SYMBOL:CTSL", "UMLS:C1332807", @@ -2655,14 +2655,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:3439": { + "NCBIGene:3439": { "category": "biolink:Gene", "name": "IFNA1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:3439", + "NCBIGene:3439", "name:interferon alpha 1", "SYMBOL:IFNA1", "UMLS:C1415900", @@ -2714,14 +2714,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:3557": { + "NCBIGene:3557": { "category": "biolink:Gene", "name": "IL1RN", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:3557", + "NCBIGene:3557", "name:interleukin 1 receptor antagonist", "SYMBOL:IL1RN", "UMLS:C1416402", @@ -2747,14 +2747,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1520": { + "NCBIGene:1520": { "category": "biolink:Gene", "name": "CTSS", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:1520", + "NCBIGene:1520", "name:cathepsin S", "SYMBOL:CTSS", "UMLS:C1413821", @@ -2767,14 +2767,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:3806": { + "NCBIGene:3806": { "category": "biolink:Gene", "name": "KIR2DS1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:3806", + "NCBIGene:3806", "name:killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 1", "SYMBOL:KIR2DS1", "UMLS:C1416647", @@ -2792,14 +2792,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:3808": { + "NCBIGene:3808": { "category": "biolink:Gene", "name": "KIR2DS3", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:3808", + "NCBIGene:3808", "name:killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 3", "SYMBOL:KIR2DS3", "UMLS:C1416649", @@ -2827,14 +2827,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:558": { + "NCBIGene:558": { "category": "biolink:Gene", "name": "AXL", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:558", + "NCBIGene:558", "name:AXL receptor tyrosine kinase", "SYMBOL:AXL", "UMLS:C0812237", @@ -2977,14 +2977,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:4864": { + "NCBIGene:4864": { "category": "biolink:Gene", "name": "NPC1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:4864", + "NCBIGene:4864", "name:NPC intracellular cholesterol transporter 1", "SYMBOL:NPC1", "UMLS:C1417776", @@ -3062,14 +3062,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:324": { + "NCBIGene:324": { "category": "biolink:Gene", "name": "APC", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:324", + "NCBIGene:324", "name:APC regulator of WNT signaling pathway", "SYMBOL:APC", "UMLS:C0162832", @@ -3159,10 +3159,10 @@ console.log(queryHandler.getResponse()) } }, "edges": { - "MONDO:0005737-NCBIGENE:116534309-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:116534309-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:116534309", + "object": "NCBIGene:116534309", "attributes": [ { "name": "provided_by", @@ -3181,10 +3181,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:539109-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:539109-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:539109", + "object": "NCBIGene:539109", "attributes": [ { "name": "provided_by", @@ -3203,10 +3203,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:102448557-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:102448557-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:102448557", + "object": "NCBIGene:102448557", "attributes": [ { "name": "provided_by", @@ -3225,10 +3225,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:103074707-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:103074707-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:103074707", + "object": "NCBIGene:103074707", "attributes": [ { "name": "provided_by", @@ -3269,10 +3269,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:115865406-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:115865406-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:115865406", + "object": "NCBIGene:115865406", "attributes": [ { "name": "provided_by", @@ -3291,10 +3291,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:110132571-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:110132571-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:110132571", + "object": "NCBIGene:110132571", "attributes": [ { "name": "provided_by", @@ -3313,10 +3313,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:101571570-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:101571570-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:101571570", + "object": "NCBIGene:101571570", "attributes": [ { "name": "provided_by", @@ -3357,10 +3357,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:397686-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:397686-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:397686", + "object": "NCBIGene:397686", "attributes": [ { "name": "provided_by", @@ -3379,10 +3379,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:102892030-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:102892030-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:102892030", + "object": "NCBIGene:102892030", "attributes": [ { "name": "provided_by", @@ -3401,10 +3401,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:104045425-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:104045425-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:104045425", + "object": "NCBIGene:104045425", "attributes": [ { "name": "provided_by", @@ -3423,10 +3423,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:110137949-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:110137949-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:110137949", + "object": "NCBIGene:110137949", "attributes": [ { "name": "provided_by", @@ -3445,10 +3445,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:105822820-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:105822820-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:105822820", + "object": "NCBIGene:105822820", "attributes": [ { "name": "provided_by", @@ -3467,10 +3467,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:116479423-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:116479423-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:116479423", + "object": "NCBIGene:116479423", "attributes": [ { "name": "provided_by", @@ -3489,10 +3489,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:103814882-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:103814882-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:103814882", + "object": "NCBIGene:103814882", "attributes": [ { "name": "provided_by", @@ -3511,10 +3511,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:101142722-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:101142722-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:101142722", + "object": "NCBIGene:101142722", "attributes": [ { "name": "provided_by", @@ -3533,10 +3533,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:104673720-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:104673720-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:104673720", + "object": "NCBIGene:104673720", "attributes": [ { "name": "provided_by", @@ -3555,10 +3555,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:116543050-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:116543050-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:116543050", + "object": "NCBIGene:116543050", "attributes": [ { "name": "provided_by", @@ -3577,10 +3577,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:29798-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:29798-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:29798", + "object": "NCBIGene:29798", "attributes": [ { "name": "provided_by", @@ -3599,10 +3599,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:118012204-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:118012204-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:118012204", + "object": "NCBIGene:118012204", "attributes": [ { "name": "provided_by", @@ -3621,10 +3621,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:103531663-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:103531663-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:103531663", + "object": "NCBIGene:103531663", "attributes": [ { "name": "provided_by", @@ -3665,10 +3665,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:104395366-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:104395366-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:104395366", + "object": "NCBIGene:104395366", "attributes": [ { "name": "provided_by", @@ -3687,10 +3687,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:100731608-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:100731608-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:100731608", + "object": "NCBIGene:100731608", "attributes": [ { "name": "provided_by", @@ -3709,10 +3709,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:108529797-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:108529797-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:108529797", + "object": "NCBIGene:108529797", "attributes": [ { "name": "provided_by", @@ -3731,10 +3731,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:106971145-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:106971145-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:106971145", + "object": "NCBIGene:106971145", "attributes": [ { "name": "provided_by", @@ -3775,10 +3775,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:101443464-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:101443464-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:101443464", + "object": "NCBIGene:101443464", "attributes": [ { "name": "provided_by", @@ -3797,10 +3797,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:102387082-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:102387082-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:102387082", + "object": "NCBIGene:102387082", "attributes": [ { "name": "provided_by", @@ -3819,10 +3819,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:109055884-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:109055884-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:109055884", + "object": "NCBIGene:109055884", "attributes": [ { "name": "provided_by", @@ -3863,10 +3863,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:117759282-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:117759282-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:117759282", + "object": "NCBIGene:117759282", "attributes": [ { "name": "provided_by", @@ -3885,10 +3885,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:103562469-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:103562469-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:103562469", + "object": "NCBIGene:103562469", "attributes": [ { "name": "provided_by", @@ -3907,10 +3907,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:112648300-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:112648300-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:112648300", + "object": "NCBIGene:112648300", "attributes": [ { "name": "provided_by", @@ -3929,10 +3929,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:105221759-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:105221759-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:105221759", + "object": "NCBIGene:105221759", "attributes": [ { "name": "provided_by", @@ -3951,10 +3951,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:118335909-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:118335909-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:118335909", + "object": "NCBIGene:118335909", "attributes": [ { "name": "provided_by", @@ -3973,10 +3973,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:101674197-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:101674197-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:101674197", + "object": "NCBIGene:101674197", "attributes": [ { "name": "provided_by", @@ -3995,10 +3995,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:103089296-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:103089296-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:103089296", + "object": "NCBIGene:103089296", "attributes": [ { "name": "provided_by", @@ -4017,10 +4017,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:100136221-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:100136221-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:100136221", + "object": "NCBIGene:100136221", "attributes": [ { "name": "provided_by", @@ -4039,10 +4039,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:118023076-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:118023076-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:118023076", + "object": "NCBIGene:118023076", "attributes": [ { "name": "provided_by", @@ -4061,10 +4061,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:574217-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:574217-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:574217", + "object": "NCBIGene:574217", "attributes": [ { "name": "provided_by", @@ -4131,10 +4131,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:3601-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:3601-SEMMED Disease API-SEMMED": { "predicate": "biolink:affected_by", "subject": "MONDO:0005737", - "object": "NCBIGENE:3601", + "object": "NCBIGene:3601", "attributes": [ { "name": "provided_by", @@ -4155,10 +4155,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:5788-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:5788-SEMMED Disease API-SEMMED": { "predicate": "biolink:affected_by", "subject": "MONDO:0005737", - "object": "NCBIGENE:5788", + "object": "NCBIGene:5788", "attributes": [ { "name": "provided_by", @@ -4179,10 +4179,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:8030-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:8030-SEMMED Disease API-SEMMED": { "predicate": "biolink:affected_by", "subject": "MONDO:0005737", - "object": "NCBIGENE:8030", + "object": "NCBIGene:8030", "attributes": [ { "name": "provided_by", @@ -4203,10 +4203,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:920-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:920-SEMMED Disease API-SEMMED": { "predicate": "biolink:affected_by", "subject": "MONDO:0005737", - "object": "NCBIGENE:920", + "object": "NCBIGene:920", "attributes": [ { "name": "provided_by", @@ -4227,10 +4227,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:1514-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:1514-SEMMED Disease API-SEMMED": { "predicate": "biolink:affected_by", "subject": "MONDO:0005737", - "object": "NCBIGENE:1514", + "object": "NCBIGene:1514", "attributes": [ { "name": "provided_by", @@ -4299,10 +4299,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:3439-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:3439-SEMMED Disease API-SEMMED": { "predicate": "biolink:disrupted_by", "subject": "MONDO:0005737", - "object": "NCBIGENE:3439", + "object": "NCBIGene:3439", "attributes": [ { "name": "provided_by", @@ -4395,10 +4395,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:3557-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:3557-SEMMED Disease API-SEMMED": { "predicate": "biolink:prevented_by", "subject": "MONDO:0005737", - "object": "NCBIGENE:3557", + "object": "NCBIGene:3557", "attributes": [ { "name": "provided_by", @@ -4443,10 +4443,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:1520-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:1520-SEMMED Disease API-SEMMED": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:1520", + "object": "NCBIGene:1520", "attributes": [ { "name": "provided_by", @@ -4467,10 +4467,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:3806-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:3806-SEMMED Disease API-SEMMED": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:3806", + "object": "NCBIGene:3806", "attributes": [ { "name": "provided_by", @@ -4491,10 +4491,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:3808-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:3808-SEMMED Disease API-SEMMED": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:3808", + "object": "NCBIGene:3808", "attributes": [ { "name": "provided_by", @@ -4539,10 +4539,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:558-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:558-SEMMED Disease API-SEMMED": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:558", + "object": "NCBIGene:558", "attributes": [ { "name": "provided_by", @@ -4803,10 +4803,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:4864-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:4864-SEMMED Disease API-SEMMED": { "predicate": "biolink:treated_by", "subject": "MONDO:0005737", - "object": "NCBIGENE:4864", + "object": "NCBIGene:4864", "attributes": [ { "name": "provided_by", @@ -4947,10 +4947,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:324-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:324-SEMMED Disease API-SEMMED": { "predicate": "biolink:treated_by", "subject": "MONDO:0005737", - "object": "NCBIGENE:324", + "object": "NCBIGene:324", "attributes": [ { "name": "provided_by", @@ -5019,9 +5019,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:116534309-DRUGBANK:DB06241-MyChem.info API-drugbank": { + "NCBIGene:116534309-DRUGBANK:DB06241-MyChem.info API-drugbank": { "predicate": "biolink:physically_interacts_with", - "subject": "NCBIGENE:116534309", + "subject": "NCBIGene:116534309", "object": "DRUGBANK:DB06241", "attributes": [ { @@ -5036,9 +5036,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:116534309-DRUGBANK:DB12698-MyChem.info API-drugbank": { + "NCBIGene:116534309-DRUGBANK:DB12698-MyChem.info API-drugbank": { "predicate": "biolink:physically_interacts_with", - "subject": "NCBIGENE:116534309", + "subject": "NCBIGene:116534309", "object": "DRUGBANK:DB12698", "attributes": [ { @@ -5053,9 +5053,9 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:116534309-DRUGBANK:DB00098-MyChem.info API-drugbank": { + "NCBIGene:116534309-DRUGBANK:DB00098-MyChem.info API-drugbank": { "predicate": "biolink:physically_interacts_with", - "subject": "NCBIGENE:116534309", + "subject": "NCBIGene:116534309", "object": "DRUGBANK:DB00098", "attributes": [ { @@ -5082,14 +5082,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:116534309" + "id": "NCBIGene:116534309" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:116534309-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:116534309-DISEASES API-DISEASES" } ] } @@ -5103,14 +5103,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:539109" + "id": "NCBIGene:539109" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:539109-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:539109-DISEASES API-DISEASES" } ] } @@ -5124,14 +5124,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:102448557" + "id": "NCBIGene:102448557" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:102448557-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:102448557-DISEASES API-DISEASES" } ] } @@ -5145,14 +5145,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:103074707" + "id": "NCBIGene:103074707" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:103074707-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:103074707-DISEASES API-DISEASES" } ] } @@ -5187,14 +5187,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:115865406" + "id": "NCBIGene:115865406" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:115865406-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:115865406-DISEASES API-DISEASES" } ] } @@ -5208,14 +5208,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:110132571" + "id": "NCBIGene:110132571" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:110132571-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:110132571-DISEASES API-DISEASES" } ] } @@ -5229,14 +5229,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:101571570" + "id": "NCBIGene:101571570" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:101571570-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:101571570-DISEASES API-DISEASES" } ] } @@ -5271,14 +5271,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:397686" + "id": "NCBIGene:397686" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:397686-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:397686-DISEASES API-DISEASES" } ] } @@ -5292,14 +5292,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:102892030" + "id": "NCBIGene:102892030" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:102892030-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:102892030-DISEASES API-DISEASES" } ] } @@ -5313,14 +5313,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:104045425" + "id": "NCBIGene:104045425" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:104045425-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:104045425-DISEASES API-DISEASES" } ] } @@ -5334,14 +5334,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:110137949" + "id": "NCBIGene:110137949" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:110137949-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:110137949-DISEASES API-DISEASES" } ] } @@ -5355,14 +5355,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:105822820" + "id": "NCBIGene:105822820" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:105822820-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:105822820-DISEASES API-DISEASES" } ] } @@ -5376,14 +5376,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:116479423" + "id": "NCBIGene:116479423" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:116479423-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:116479423-DISEASES API-DISEASES" } ] } @@ -5397,14 +5397,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:103814882" + "id": "NCBIGene:103814882" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:103814882-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:103814882-DISEASES API-DISEASES" } ] } @@ -5418,14 +5418,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:101142722" + "id": "NCBIGene:101142722" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:101142722-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:101142722-DISEASES API-DISEASES" } ] } @@ -5439,14 +5439,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:104673720" + "id": "NCBIGene:104673720" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:104673720-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:104673720-DISEASES API-DISEASES" } ] } @@ -5460,14 +5460,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:116543050" + "id": "NCBIGene:116543050" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:116543050-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:116543050-DISEASES API-DISEASES" } ] } @@ -5481,14 +5481,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:29798" + "id": "NCBIGene:29798" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:29798-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:29798-DISEASES API-DISEASES" } ] } @@ -5502,14 +5502,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:118012204" + "id": "NCBIGene:118012204" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:118012204-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:118012204-DISEASES API-DISEASES" } ] } @@ -5523,14 +5523,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:103531663" + "id": "NCBIGene:103531663" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:103531663-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:103531663-DISEASES API-DISEASES" } ] } @@ -5565,14 +5565,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:104395366" + "id": "NCBIGene:104395366" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:104395366-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:104395366-DISEASES API-DISEASES" } ] } @@ -5586,14 +5586,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:100731608" + "id": "NCBIGene:100731608" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:100731608-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:100731608-DISEASES API-DISEASES" } ] } @@ -5607,14 +5607,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:108529797" + "id": "NCBIGene:108529797" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:108529797-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:108529797-DISEASES API-DISEASES" } ] } @@ -5628,14 +5628,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:106971145" + "id": "NCBIGene:106971145" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:106971145-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:106971145-DISEASES API-DISEASES" } ] } @@ -5670,14 +5670,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:101443464" + "id": "NCBIGene:101443464" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:101443464-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:101443464-DISEASES API-DISEASES" } ] } @@ -5691,14 +5691,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:102387082" + "id": "NCBIGene:102387082" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:102387082-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:102387082-DISEASES API-DISEASES" } ] } @@ -5712,14 +5712,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:109055884" + "id": "NCBIGene:109055884" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:109055884-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:109055884-DISEASES API-DISEASES" } ] } @@ -5754,14 +5754,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:117759282" + "id": "NCBIGene:117759282" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:117759282-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:117759282-DISEASES API-DISEASES" } ] } @@ -5775,14 +5775,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:103562469" + "id": "NCBIGene:103562469" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:103562469-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:103562469-DISEASES API-DISEASES" } ] } @@ -5796,14 +5796,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:112648300" + "id": "NCBIGene:112648300" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:112648300-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:112648300-DISEASES API-DISEASES" } ] } @@ -5817,14 +5817,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:105221759" + "id": "NCBIGene:105221759" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:105221759-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:105221759-DISEASES API-DISEASES" } ] } @@ -5838,14 +5838,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:118335909" + "id": "NCBIGene:118335909" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:118335909-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:118335909-DISEASES API-DISEASES" } ] } @@ -5859,14 +5859,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:101674197" + "id": "NCBIGene:101674197" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:101674197-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:101674197-DISEASES API-DISEASES" } ] } @@ -5880,14 +5880,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:103089296" + "id": "NCBIGene:103089296" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:103089296-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:103089296-DISEASES API-DISEASES" } ] } @@ -5901,14 +5901,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:100136221" + "id": "NCBIGene:100136221" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:100136221-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:100136221-DISEASES API-DISEASES" } ] } @@ -5922,14 +5922,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:118023076" + "id": "NCBIGene:118023076" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:118023076-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:118023076-DISEASES API-DISEASES" } ] } @@ -5943,14 +5943,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:574217" + "id": "NCBIGene:574217" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:574217-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:574217-DISEASES API-DISEASES" } ] } @@ -6006,14 +6006,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:3601" + "id": "NCBIGene:3601" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:3601-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:3601-SEMMED Disease API-SEMMED" } ] } @@ -6027,14 +6027,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:5788" + "id": "NCBIGene:5788" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:5788-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:5788-SEMMED Disease API-SEMMED" } ] } @@ -6048,14 +6048,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:8030" + "id": "NCBIGene:8030" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:8030-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:8030-SEMMED Disease API-SEMMED" } ] } @@ -6069,14 +6069,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:920" + "id": "NCBIGene:920" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:920-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:920-SEMMED Disease API-SEMMED" } ] } @@ -6090,14 +6090,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:1514" + "id": "NCBIGene:1514" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:1514-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:1514-SEMMED Disease API-SEMMED" } ] } @@ -6153,14 +6153,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:3439" + "id": "NCBIGene:3439" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:3439-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:3439-SEMMED Disease API-SEMMED" } ] } @@ -6237,14 +6237,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:3557" + "id": "NCBIGene:3557" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:3557-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:3557-SEMMED Disease API-SEMMED" } ] } @@ -6300,14 +6300,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:1520" + "id": "NCBIGene:1520" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:1520-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:1520-SEMMED Disease API-SEMMED" } ] } @@ -6321,14 +6321,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:3439" + "id": "NCBIGene:3439" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:3439-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:3439-SEMMED Disease API-SEMMED" } ] } @@ -6342,14 +6342,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:3557" + "id": "NCBIGene:3557" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:3557-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:3557-SEMMED Disease API-SEMMED" } ] } @@ -6363,14 +6363,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:3806" + "id": "NCBIGene:3806" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:3806-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:3806-SEMMED Disease API-SEMMED" } ] } @@ -6384,14 +6384,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:3808" + "id": "NCBIGene:3808" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:3808-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:3808-SEMMED Disease API-SEMMED" } ] } @@ -6426,14 +6426,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:558" + "id": "NCBIGene:558" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:558-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:558-SEMMED Disease API-SEMMED" } ] } @@ -6531,14 +6531,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:1514" + "id": "NCBIGene:1514" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:1514-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:1514-SEMMED Disease API-SEMMED" } ] } @@ -6678,14 +6678,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:4864" + "id": "NCBIGene:4864" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:4864-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:4864-SEMMED Disease API-SEMMED" } ] } @@ -6846,14 +6846,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:324" + "id": "NCBIGene:324" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:324-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:324-SEMMED Disease API-SEMMED" } ] } @@ -6925,7 +6925,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n1": [ { - "id": "NCBIGENE:116534309" + "id": "NCBIGene:116534309" } ], "n2": [ @@ -6937,7 +6937,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e02": [ { - "id": "NCBIGENE:116534309-DRUGBANK:DB06241-MyChem.info API-drugbank" + "id": "NCBIGene:116534309-DRUGBANK:DB06241-MyChem.info API-drugbank" } ] } @@ -6946,7 +6946,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n1": [ { - "id": "NCBIGENE:116534309" + "id": "NCBIGene:116534309" } ], "n2": [ @@ -6958,7 +6958,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e02": [ { - "id": "NCBIGENE:116534309-DRUGBANK:DB12698-MyChem.info API-drugbank" + "id": "NCBIGene:116534309-DRUGBANK:DB12698-MyChem.info API-drugbank" } ] } @@ -6967,7 +6967,7 @@ console.log(queryHandler.getResponse()) "node_bindings": { "n1": [ { - "id": "NCBIGENE:116534309" + "id": "NCBIGene:116534309" } ], "n2": [ @@ -6979,7 +6979,7 @@ console.log(queryHandler.getResponse()) "edge_bindings": { "e02": [ { - "id": "NCBIGENE:116534309-DRUGBANK:DB00098-MyChem.info API-drugbank" + "id": "NCBIGene:116534309-DRUGBANK:DB00098-MyChem.info API-drugbank" } ] } @@ -7356,7 +7356,7 @@ console.log(queryHandler.getResponse()) { "timestamp": "2021-03-15T22:54:02.102Z", "level": "DEBUG", - "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/text_mining_co_occurrence_kp/query\",\"params\":{\"fields\":\"subject,association\",\"q\":\"object.NCBIGENE:\\\"116534309\\\" AND subject.type:ChemicalSubstance\",\"size\":1000},\"method\":\"get\",\"timeout\":50000}", + "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/text_mining_co_occurrence_kp/query\",\"params\":{\"fields\":\"subject,association\",\"q\":\"object.NCBIGene:\\\"116534309\\\" AND subject.type:ChemicalSubstance\",\"size\":1000},\"method\":\"get\",\"timeout\":50000}", "code": null }, { @@ -7368,7 +7368,7 @@ console.log(queryHandler.getResponse()) { "timestamp": "2021-03-15T22:54:02.103Z", "level": "DEBUG", - "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/text_mining_co_occurrence_kp/query\",\"params\":{\"fields\":\"object,association\",\"q\":\"subject.NCBIGENE:\\\"116534309\\\" AND object.type:ChemicalSubstance\",\"size\":1000},\"method\":\"get\",\"timeout\":50000}", + "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/text_mining_co_occurrence_kp/query\",\"params\":{\"fields\":\"object,association\",\"q\":\"subject.NCBIGene:\\\"116534309\\\" AND object.type:ChemicalSubstance\",\"size\":1000},\"method\":\"get\",\"timeout\":50000}", "code": null }, { @@ -7380,7 +7380,7 @@ console.log(queryHandler.getResponse()) { "timestamp": "2021-03-15T22:54:02.104Z", "level": "DEBUG", - "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/dgidb/query\",\"params\":{\"fields\":\"object.CHEMBL_COMPOUND,association.provided_by,association.pubmed\",\"size\":1000},\"data\":\"q=116534309&scopes=subject.NCBIGENE\",\"method\":\"post\",\"timeout\":50000}", + "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/dgidb/query\",\"params\":{\"fields\":\"object.CHEMBL_COMPOUND,association.provided_by,association.pubmed\",\"size\":1000},\"data\":\"q=116534309&scopes=subject.NCBIGene\",\"method\":\"post\",\"timeout\":50000}", "code": null }, { @@ -7392,7 +7392,7 @@ console.log(queryHandler.getResponse()) { "timestamp": "2021-03-15T22:54:02.104Z", "level": "DEBUG", - "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/drug_response_kp/query\",\"params\":{\"fields\":\"association.context.disease.mondo,object.PUBCHEM,association.effect_size,association.pvalue\",\"q\":\"subject.NCBIGENE:116534309 AND association.effect_size:<0 AND association.pvalue:<0.05\",\"size\":\"1000\",\"sort\":\"association.pvalue\"},\"method\":\"get\",\"timeout\":50000}", + "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/drug_response_kp/query\",\"params\":{\"fields\":\"association.context.disease.mondo,object.PUBCHEM,association.effect_size,association.pvalue\",\"q\":\"subject.NCBIGene:116534309 AND association.effect_size:<0 AND association.pvalue:<0.05\",\"size\":\"1000\",\"sort\":\"association.pvalue\"},\"method\":\"get\",\"timeout\":50000}", "code": null }, { @@ -7545,14 +7545,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:116534309": { + "NCBIGene:116534309": { "category": "biolink:Gene", "name": "CD4", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:116534309", + "NCBIGene:116534309", "name:CD4 molecule", "SYMBOL:CD4" ], @@ -7560,14 +7560,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:539109": { + "NCBIGene:539109": { "category": "biolink:Gene", "name": "MMP11", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:539109", + "NCBIGene:539109", "name:matrix metallopeptidase 11", "SYMBOL:MMP11", "ENSEMBL:ENSBTAG00000006108" @@ -7576,14 +7576,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:102448557": { + "NCBIGene:102448557": { "category": "biolink:Gene", "name": "GTPBP1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:102448557", + "NCBIGene:102448557", "name:GTP binding protein 1", "SYMBOL:GTPBP1", "ENSEMBL:ENSPSIG00000004300" @@ -7592,14 +7592,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:103074707": { + "NCBIGene:103074707": { "category": "biolink:Gene", "name": "CCL2", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:103074707", + "NCBIGene:103074707", "name:C-C motif chemokine ligand 2", "SYMBOL:CCL2" ], @@ -7622,14 +7622,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:115865406": { + "NCBIGene:115865406": { "category": "biolink:Gene", "name": "BST2", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:115865406", + "NCBIGene:115865406", "name:bone marrow stromal cell antigen 2", "SYMBOL:BST2" ], @@ -7637,14 +7637,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:110132571": { + "NCBIGene:110132571": { "category": "biolink:Gene", "name": "IL1B", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:110132571", + "NCBIGene:110132571", "name:interleukin 1 beta", "SYMBOL:IL1B" ], @@ -7652,14 +7652,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:101571570": { + "NCBIGene:101571570": { "category": "biolink:Gene", "name": "Ifih1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:101571570", + "NCBIGene:101571570", "name:interferon induced with helicase C domain 1", "SYMBOL:Ifih1", "ENSEMBL:ENSODEG00000013586" @@ -7683,14 +7683,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:397686": { + "NCBIGene:397686": { "category": "biolink:Gene", "name": "IFNA1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:397686", + "NCBIGene:397686", "name:interferon, alpha 1", "SYMBOL:IFNA1", "ENSEMBL:ENSSSCG00000050619" @@ -7699,14 +7699,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:102892030": { + "NCBIGene:102892030": { "category": "biolink:Gene", "name": "ALB", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:102892030", + "NCBIGene:102892030", "name:albumin", "SYMBOL:ALB" ], @@ -7714,14 +7714,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:104045425": { + "NCBIGene:104045425": { "category": "biolink:Gene", "name": "HDX", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:104045425", + "NCBIGene:104045425", "name:highly divergent homeobox", "SYMBOL:HDX" ], @@ -7729,14 +7729,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:110137949": { + "NCBIGene:110137949": { "category": "biolink:Gene", "name": "CXCL10", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:110137949", + "NCBIGene:110137949", "name:C-X-C motif chemokine ligand 10", "SYMBOL:CXCL10" ], @@ -7744,14 +7744,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:105822820": { + "NCBIGene:105822820": { "category": "biolink:Gene", "name": "CXCL8", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:105822820", + "NCBIGene:105822820", "name:C-X-C motif chemokine ligand 8", "SYMBOL:CXCL8", "ENSEMBL:ENSPCOG00000024593" @@ -7760,14 +7760,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:116479423": { + "NCBIGene:116479423": { "category": "biolink:Gene", "name": "CLEC4M", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:116479423", + "NCBIGene:116479423", "name:C-type lectin domain family 4 member M", "SYMBOL:CLEC4M" ], @@ -7775,14 +7775,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:103814882": { + "NCBIGene:103814882": { "category": "biolink:Gene", "name": "F3", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:103814882", + "NCBIGene:103814882", "name:coagulation factor III, tissue factor", "SYMBOL:F3", "ENSEMBL:ENSSCAG00000012591" @@ -7791,14 +7791,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:101142722": { + "NCBIGene:101142722": { "category": "biolink:Gene", "name": "KPNA1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:101142722", + "NCBIGene:101142722", "name:karyopherin subunit alpha 1", "SYMBOL:KPNA1" ], @@ -7806,14 +7806,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:104673720": { + "NCBIGene:104673720": { "category": "biolink:Gene", "name": "CTSL", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:104673720", + "NCBIGene:104673720", "name:cathepsin L", "SYMBOL:CTSL", "ENSEMBL:ENSRROG00000038398" @@ -7822,14 +7822,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:116543050": { + "NCBIGene:116543050": { "category": "biolink:Gene", "name": "CTSB", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:116543050", + "NCBIGene:116543050", "name:cathepsin B", "SYMBOL:CTSB" ], @@ -7837,14 +7837,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:29798": { + "NCBIGene:29798": { "category": "biolink:Gene", "name": "C2orf27A", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:29798", + "NCBIGene:29798", "name:chromosome 2 open reading frame 27A", "SYMBOL:C2orf27A", "UMLS:C2681192", @@ -7855,14 +7855,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:118012204": { + "NCBIGene:118012204": { "category": "biolink:Gene", "name": "STAT1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:118012204", + "NCBIGene:118012204", "name:signal transducer and activator of transcription 1", "SYMBOL:STAT1" ], @@ -7870,14 +7870,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:101937382": { + "NCBIGene:101937382": { "category": "biolink:Gene", "name": "KPNA5", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:101937382", + "NCBIGene:101937382", "name:karyopherin subunit alpha 5", "SYMBOL:KPNA5" ], @@ -7900,14 +7900,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:104395366": { + "NCBIGene:104395366": { "category": "biolink:Gene", "name": "THBD", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:104395366", + "NCBIGene:104395366", "name:thrombomodulin", "SYMBOL:THBD" ], @@ -7915,14 +7915,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:100731608": { + "NCBIGene:100731608": { "category": "biolink:Gene", "name": "Isg15", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:100731608", + "NCBIGene:100731608", "name:ISG15 ubiquitin like modifier", "SYMBOL:Isg15" ], @@ -7930,14 +7930,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:108529797": { + "NCBIGene:108529797": { "category": "biolink:Gene", "name": "DDX58", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:108529797", + "NCBIGene:108529797", "name:DExD/H-box helicase 58", "SYMBOL:DDX58", "ENSEMBL:ENSRBIG00000040257" @@ -7946,14 +7946,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:106971145": { + "NCBIGene:106971145": { "category": "biolink:Gene", "name": "IFNB1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:106971145", + "NCBIGene:106971145", "name:interferon beta 1", "SYMBOL:IFNB1" ], @@ -7976,14 +7976,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:101443464": { + "NCBIGene:101443464": { "category": "biolink:Gene", "name": "GPT", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:101443464", + "NCBIGene:101443464", "name:glutamic--pyruvic transaminase", "SYMBOL:GPT" ], @@ -7991,14 +7991,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:102387082": { + "NCBIGene:102387082": { "category": "biolink:Gene", "name": "IRF7", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:102387082", + "NCBIGene:102387082", "name:interferon regulatory factor 7", "SYMBOL:IRF7" ], @@ -8006,14 +8006,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:109055884": { + "NCBIGene:109055884": { "category": "biolink:Gene", "name": "il6", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:109055884", + "NCBIGene:109055884", "name:interleukin 6 (interferon, beta 2)", "SYMBOL:il6", "ENSEMBL:ENSCCRG00000034667" @@ -8037,14 +8037,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:117759282": { + "NCBIGene:117759282": { "category": "biolink:Gene", "name": "ace2", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:117759282", + "NCBIGene:117759282", "name:angiotensin I converting enzyme 2", "SYMBOL:ace2" ], @@ -8052,14 +8052,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:103562469": { + "NCBIGene:103562469": { "category": "biolink:Gene", "name": "TNF", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:103562469", + "NCBIGene:103562469", "name:tumor necrosis factor", "SYMBOL:TNF" ], @@ -8067,14 +8067,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:112648300": { + "NCBIGene:112648300": { "category": "biolink:Gene", "name": "IL10", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:112648300", + "NCBIGene:112648300", "name:interleukin 10", "SYMBOL:IL10", "ENSEMBL:ENSCAFG00020012434" @@ -8083,14 +8083,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:106483620": { + "NCBIGene:106483620": { "category": "biolink:Gene", "name": "ERVW-1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:106483620", + "NCBIGene:106483620", "name:endogenous retrovirus group W member 1, envelope", "SYMBOL:ERVW-1" ], @@ -8098,14 +8098,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:118335909": { + "NCBIGene:118335909": { "category": "biolink:Gene", "name": "irf3", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:118335909", + "NCBIGene:118335909", "name:interferon regulatory factor 3", "SYMBOL:irf3" ], @@ -8113,14 +8113,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:101674197": { + "NCBIGene:101674197": { "category": "biolink:Gene", "name": "CCL5", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:101674197", + "NCBIGene:101674197", "name:C-C motif chemokine ligand 5", "SYMBOL:CCL5" ], @@ -8128,14 +8128,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:103089296": { + "NCBIGene:103089296": { "category": "biolink:Gene", "name": "CCL3", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:103089296", + "NCBIGene:103089296", "name:C-C motif chemokine ligand 3", "SYMBOL:CCL3" ], @@ -8158,14 +8158,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:101998427": { + "NCBIGene:101998427": { "category": "biolink:Gene", "name": "Furin", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:101998427", + "NCBIGene:101998427", "name:furin, paired basic amino acid cleaving enzyme", "SYMBOL:Furin", "ENSEMBL:ENSMOCG00000010449" @@ -8174,14 +8174,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:574217": { + "NCBIGene:574217": { "category": "biolink:Gene", "name": "CCL4L1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:574217", + "NCBIGene:574217", "name:chemokine (C-C motif) ligand 4-like 1", "SYMBOL:CCL4L1", "UniProtKB:Q8HYQ2", @@ -8217,14 +8217,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:3601": { + "NCBIGene:3601": { "category": "biolink:Gene", "name": "IL15RA", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:3601", + "NCBIGene:3601", "name:interleukin 15 receptor subunit alpha", "SYMBOL:IL15RA", "UMLS:C1416387", @@ -8237,14 +8237,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:5788": { + "NCBIGene:5788": { "category": "biolink:Gene", "name": "PTPRC", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:5788", + "NCBIGene:5788", "name:protein tyrosine phosphatase receptor type C", "SYMBOL:PTPRC", "UMLS:C1335285", @@ -8258,14 +8258,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:8030": { + "NCBIGene:8030": { "category": "biolink:Gene", "name": "CCDC6", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:8030", + "NCBIGene:8030", "name:coiled-coil domain containing 6", "SYMBOL:CCDC6", "UMLS:C1425774", @@ -8278,14 +8278,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:920": { + "NCBIGene:920": { "category": "biolink:Gene", "name": "CD4", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:920", + "NCBIGene:920", "name:CD4 molecule", "SYMBOL:CD4", "UMLS:C1332714", @@ -8298,14 +8298,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1514": { + "NCBIGene:1514": { "category": "biolink:Gene", "name": "CTSL", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:1514", + "NCBIGene:1514", "name:cathepsin L", "SYMBOL:CTSL", "UMLS:C1332807", @@ -8452,14 +8452,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:3439": { + "NCBIGene:3439": { "category": "biolink:Gene", "name": "IFNA1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:3439", + "NCBIGene:3439", "name:interferon alpha 1", "SYMBOL:IFNA1", "UMLS:C1415900", @@ -26702,14 +26702,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:3557": { + "NCBIGene:3557": { "category": "biolink:Gene", "name": "IL1RN", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:3557", + "NCBIGene:3557", "name:interleukin 1 receptor antagonist", "SYMBOL:IL1RN", "UMLS:C1416402", @@ -26735,14 +26735,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:1520": { + "NCBIGene:1520": { "category": "biolink:Gene", "name": "CTSS", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:1520", + "NCBIGene:1520", "name:cathepsin S", "SYMBOL:CTSS", "UMLS:C1413821", @@ -26755,14 +26755,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:3806": { + "NCBIGene:3806": { "category": "biolink:Gene", "name": "KIR2DS1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:3806", + "NCBIGene:3806", "name:killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 1", "SYMBOL:KIR2DS1", "UMLS:C1416647", @@ -26780,14 +26780,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:3808": { + "NCBIGene:3808": { "category": "biolink:Gene", "name": "KIR2DS3", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:3808", + "NCBIGene:3808", "name:killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 3", "SYMBOL:KIR2DS3", "UMLS:C1416649", @@ -26815,14 +26815,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:558": { + "NCBIGene:558": { "category": "biolink:Gene", "name": "AXL", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:558", + "NCBIGene:558", "name:AXL receptor tyrosine kinase", "SYMBOL:AXL", "UMLS:C0812237", @@ -26965,14 +26965,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:4864": { + "NCBIGene:4864": { "category": "biolink:Gene", "name": "NPC1", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:4864", + "NCBIGene:4864", "name:NPC intracellular cholesterol transporter 1", "SYMBOL:NPC1", "UMLS:C1417776", @@ -27050,14 +27050,14 @@ console.log(queryHandler.getResponse()) } ] }, - "NCBIGENE:324": { + "NCBIGene:324": { "category": "biolink:Gene", "name": "APC", "attributes": [ { "name": "equivalent_identifiers", "value": [ - "NCBIGENE:324", + "NCBIGene:324", "name:APC regulator of WNT signaling pathway", "SYMBOL:APC", "UMLS:C0162832", @@ -27766,10 +27766,10 @@ console.log(queryHandler.getResponse()) } }, "edges": { - "MONDO:0005737-NCBIGENE:116534309-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:116534309-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:116534309", + "object": "NCBIGene:116534309", "attributes": [ { "name": "provided_by", @@ -27788,10 +27788,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:539109-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:539109-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:539109", + "object": "NCBIGene:539109", "attributes": [ { "name": "provided_by", @@ -27810,10 +27810,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:102448557-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:102448557-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:102448557", + "object": "NCBIGene:102448557", "attributes": [ { "name": "provided_by", @@ -27832,10 +27832,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:103074707-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:103074707-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:103074707", + "object": "NCBIGene:103074707", "attributes": [ { "name": "provided_by", @@ -27876,10 +27876,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:115865406-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:115865406-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:115865406", + "object": "NCBIGene:115865406", "attributes": [ { "name": "provided_by", @@ -27898,10 +27898,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:110132571-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:110132571-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:110132571", + "object": "NCBIGene:110132571", "attributes": [ { "name": "provided_by", @@ -27920,10 +27920,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:101571570-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:101571570-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:101571570", + "object": "NCBIGene:101571570", "attributes": [ { "name": "provided_by", @@ -27964,10 +27964,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:397686-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:397686-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:397686", + "object": "NCBIGene:397686", "attributes": [ { "name": "provided_by", @@ -27986,10 +27986,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:102892030-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:102892030-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:102892030", + "object": "NCBIGene:102892030", "attributes": [ { "name": "provided_by", @@ -28008,10 +28008,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:104045425-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:104045425-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:104045425", + "object": "NCBIGene:104045425", "attributes": [ { "name": "provided_by", @@ -28030,10 +28030,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:110137949-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:110137949-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:110137949", + "object": "NCBIGene:110137949", "attributes": [ { "name": "provided_by", @@ -28052,10 +28052,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:105822820-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:105822820-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:105822820", + "object": "NCBIGene:105822820", "attributes": [ { "name": "provided_by", @@ -28074,10 +28074,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:116479423-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:116479423-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:116479423", + "object": "NCBIGene:116479423", "attributes": [ { "name": "provided_by", @@ -28096,10 +28096,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:103814882-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:103814882-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:103814882", + "object": "NCBIGene:103814882", "attributes": [ { "name": "provided_by", @@ -28118,10 +28118,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:101142722-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:101142722-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:101142722", + "object": "NCBIGene:101142722", "attributes": [ { "name": "provided_by", @@ -28140,10 +28140,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:104673720-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:104673720-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:104673720", + "object": "NCBIGene:104673720", "attributes": [ { "name": "provided_by", @@ -28162,10 +28162,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:116543050-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:116543050-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:116543050", + "object": "NCBIGene:116543050", "attributes": [ { "name": "provided_by", @@ -28184,10 +28184,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:29798-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:29798-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:29798", + "object": "NCBIGene:29798", "attributes": [ { "name": "provided_by", @@ -28206,10 +28206,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:118012204-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:118012204-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:118012204", + "object": "NCBIGene:118012204", "attributes": [ { "name": "provided_by", @@ -28228,10 +28228,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:101937382-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:101937382-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:101937382", + "object": "NCBIGene:101937382", "attributes": [ { "name": "provided_by", @@ -28272,10 +28272,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:104395366-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:104395366-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:104395366", + "object": "NCBIGene:104395366", "attributes": [ { "name": "provided_by", @@ -28294,10 +28294,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:100731608-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:100731608-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:100731608", + "object": "NCBIGene:100731608", "attributes": [ { "name": "provided_by", @@ -28316,10 +28316,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:108529797-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:108529797-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:108529797", + "object": "NCBIGene:108529797", "attributes": [ { "name": "provided_by", @@ -28338,10 +28338,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:106971145-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:106971145-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:106971145", + "object": "NCBIGene:106971145", "attributes": [ { "name": "provided_by", @@ -28382,10 +28382,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:101443464-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:101443464-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:101443464", + "object": "NCBIGene:101443464", "attributes": [ { "name": "provided_by", @@ -28404,10 +28404,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:102387082-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:102387082-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:102387082", + "object": "NCBIGene:102387082", "attributes": [ { "name": "provided_by", @@ -28426,10 +28426,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:109055884-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:109055884-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:109055884", + "object": "NCBIGene:109055884", "attributes": [ { "name": "provided_by", @@ -28470,10 +28470,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:117759282-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:117759282-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:117759282", + "object": "NCBIGene:117759282", "attributes": [ { "name": "provided_by", @@ -28492,10 +28492,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:103562469-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:103562469-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:103562469", + "object": "NCBIGene:103562469", "attributes": [ { "name": "provided_by", @@ -28514,10 +28514,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:112648300-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:112648300-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:112648300", + "object": "NCBIGene:112648300", "attributes": [ { "name": "provided_by", @@ -28536,10 +28536,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:106483620-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:106483620-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:106483620", + "object": "NCBIGene:106483620", "attributes": [ { "name": "provided_by", @@ -28558,10 +28558,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:118335909-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:118335909-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:118335909", + "object": "NCBIGene:118335909", "attributes": [ { "name": "provided_by", @@ -28580,10 +28580,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:101674197-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:101674197-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:101674197", + "object": "NCBIGene:101674197", "attributes": [ { "name": "provided_by", @@ -28602,10 +28602,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:103089296-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:103089296-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:103089296", + "object": "NCBIGene:103089296", "attributes": [ { "name": "provided_by", @@ -28646,10 +28646,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:101998427-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:101998427-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:101998427", + "object": "NCBIGene:101998427", "attributes": [ { "name": "provided_by", @@ -28668,10 +28668,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:574217-DISEASES API-DISEASES": { + "MONDO:0005737-NCBIGene:574217-DISEASES API-DISEASES": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:574217", + "object": "NCBIGene:574217", "attributes": [ { "name": "provided_by", @@ -28738,10 +28738,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:3601-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:3601-SEMMED Disease API-SEMMED": { "predicate": "biolink:affected_by", "subject": "MONDO:0005737", - "object": "NCBIGENE:3601", + "object": "NCBIGene:3601", "attributes": [ { "name": "provided_by", @@ -28762,10 +28762,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:5788-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:5788-SEMMED Disease API-SEMMED": { "predicate": "biolink:affected_by", "subject": "MONDO:0005737", - "object": "NCBIGENE:5788", + "object": "NCBIGene:5788", "attributes": [ { "name": "provided_by", @@ -28786,10 +28786,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:8030-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:8030-SEMMED Disease API-SEMMED": { "predicate": "biolink:affected_by", "subject": "MONDO:0005737", - "object": "NCBIGENE:8030", + "object": "NCBIGene:8030", "attributes": [ { "name": "provided_by", @@ -28810,10 +28810,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:920-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:920-SEMMED Disease API-SEMMED": { "predicate": "biolink:affected_by", "subject": "MONDO:0005737", - "object": "NCBIGENE:920", + "object": "NCBIGene:920", "attributes": [ { "name": "provided_by", @@ -28834,10 +28834,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:1514-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:1514-SEMMED Disease API-SEMMED": { "predicate": "biolink:affected_by", "subject": "MONDO:0005737", - "object": "NCBIGENE:1514", + "object": "NCBIGene:1514", "attributes": [ { "name": "provided_by", @@ -29082,10 +29082,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:3439-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:3439-SEMMED Disease API-SEMMED": { "predicate": "biolink:disrupted_by", "subject": "MONDO:0005737", - "object": "NCBIGENE:3439", + "object": "NCBIGene:3439", "attributes": [ { "name": "provided_by", @@ -56194,10 +56194,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:3557-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:3557-SEMMED Disease API-SEMMED": { "predicate": "biolink:prevented_by", "subject": "MONDO:0005737", - "object": "NCBIGENE:3557", + "object": "NCBIGene:3557", "attributes": [ { "name": "provided_by", @@ -56242,10 +56242,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:1520-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:1520-SEMMED Disease API-SEMMED": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:1520", + "object": "NCBIGene:1520", "attributes": [ { "name": "provided_by", @@ -56266,10 +56266,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:3806-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:3806-SEMMED Disease API-SEMMED": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:3806", + "object": "NCBIGene:3806", "attributes": [ { "name": "provided_by", @@ -56290,10 +56290,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:3808-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:3808-SEMMED Disease API-SEMMED": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:3808", + "object": "NCBIGene:3808", "attributes": [ { "name": "provided_by", @@ -56338,10 +56338,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:558-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:558-SEMMED Disease API-SEMMED": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "NCBIGENE:558", + "object": "NCBIGene:558", "attributes": [ { "name": "provided_by", @@ -56602,10 +56602,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:4864-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:4864-SEMMED Disease API-SEMMED": { "predicate": "biolink:treated_by", "subject": "MONDO:0005737", - "object": "NCBIGENE:4864", + "object": "NCBIGene:4864", "attributes": [ { "name": "provided_by", @@ -56746,10 +56746,10 @@ console.log(queryHandler.getResponse()) } ] }, - "MONDO:0005737-NCBIGENE:324-SEMMED Disease API-SEMMED": { + "MONDO:0005737-NCBIGene:324-SEMMED Disease API-SEMMED": { "predicate": "biolink:treated_by", "subject": "MONDO:0005737", - "object": "NCBIGENE:324", + "object": "NCBIGene:324", "attributes": [ { "name": "provided_by", @@ -57868,14 +57868,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:116534309" + "id": "NCBIGene:116534309" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:116534309-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:116534309-DISEASES API-DISEASES" } ] } @@ -57889,14 +57889,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:539109" + "id": "NCBIGene:539109" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:539109-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:539109-DISEASES API-DISEASES" } ] } @@ -57910,14 +57910,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:102448557" + "id": "NCBIGene:102448557" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:102448557-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:102448557-DISEASES API-DISEASES" } ] } @@ -57931,14 +57931,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:103074707" + "id": "NCBIGene:103074707" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:103074707-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:103074707-DISEASES API-DISEASES" } ] } @@ -57973,14 +57973,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:115865406" + "id": "NCBIGene:115865406" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:115865406-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:115865406-DISEASES API-DISEASES" } ] } @@ -57994,14 +57994,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:110132571" + "id": "NCBIGene:110132571" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:110132571-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:110132571-DISEASES API-DISEASES" } ] } @@ -58015,14 +58015,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:101571570" + "id": "NCBIGene:101571570" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:101571570-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:101571570-DISEASES API-DISEASES" } ] } @@ -58057,14 +58057,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:397686" + "id": "NCBIGene:397686" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:397686-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:397686-DISEASES API-DISEASES" } ] } @@ -58078,14 +58078,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:102892030" + "id": "NCBIGene:102892030" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:102892030-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:102892030-DISEASES API-DISEASES" } ] } @@ -58099,14 +58099,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:104045425" + "id": "NCBIGene:104045425" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:104045425-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:104045425-DISEASES API-DISEASES" } ] } @@ -58120,14 +58120,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:110137949" + "id": "NCBIGene:110137949" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:110137949-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:110137949-DISEASES API-DISEASES" } ] } @@ -58141,14 +58141,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:105822820" + "id": "NCBIGene:105822820" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:105822820-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:105822820-DISEASES API-DISEASES" } ] } @@ -58162,14 +58162,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:116479423" + "id": "NCBIGene:116479423" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:116479423-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:116479423-DISEASES API-DISEASES" } ] } @@ -58183,14 +58183,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:103814882" + "id": "NCBIGene:103814882" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:103814882-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:103814882-DISEASES API-DISEASES" } ] } @@ -58204,14 +58204,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:101142722" + "id": "NCBIGene:101142722" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:101142722-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:101142722-DISEASES API-DISEASES" } ] } @@ -58225,14 +58225,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:104673720" + "id": "NCBIGene:104673720" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:104673720-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:104673720-DISEASES API-DISEASES" } ] } @@ -58246,14 +58246,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:116543050" + "id": "NCBIGene:116543050" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:116543050-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:116543050-DISEASES API-DISEASES" } ] } @@ -58267,14 +58267,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:29798" + "id": "NCBIGene:29798" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:29798-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:29798-DISEASES API-DISEASES" } ] } @@ -58288,14 +58288,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:118012204" + "id": "NCBIGene:118012204" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:118012204-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:118012204-DISEASES API-DISEASES" } ] } @@ -58309,14 +58309,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:101937382" + "id": "NCBIGene:101937382" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:101937382-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:101937382-DISEASES API-DISEASES" } ] } @@ -58351,14 +58351,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:104395366" + "id": "NCBIGene:104395366" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:104395366-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:104395366-DISEASES API-DISEASES" } ] } @@ -58372,14 +58372,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:100731608" + "id": "NCBIGene:100731608" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:100731608-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:100731608-DISEASES API-DISEASES" } ] } @@ -58393,14 +58393,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:108529797" + "id": "NCBIGene:108529797" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:108529797-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:108529797-DISEASES API-DISEASES" } ] } @@ -58414,14 +58414,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:106971145" + "id": "NCBIGene:106971145" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:106971145-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:106971145-DISEASES API-DISEASES" } ] } @@ -58456,14 +58456,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:101443464" + "id": "NCBIGene:101443464" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:101443464-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:101443464-DISEASES API-DISEASES" } ] } @@ -58477,14 +58477,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:102387082" + "id": "NCBIGene:102387082" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:102387082-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:102387082-DISEASES API-DISEASES" } ] } @@ -58498,14 +58498,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:109055884" + "id": "NCBIGene:109055884" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:109055884-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:109055884-DISEASES API-DISEASES" } ] } @@ -58540,14 +58540,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:117759282" + "id": "NCBIGene:117759282" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:117759282-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:117759282-DISEASES API-DISEASES" } ] } @@ -58561,14 +58561,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:103562469" + "id": "NCBIGene:103562469" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:103562469-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:103562469-DISEASES API-DISEASES" } ] } @@ -58582,14 +58582,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:112648300" + "id": "NCBIGene:112648300" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:112648300-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:112648300-DISEASES API-DISEASES" } ] } @@ -58603,14 +58603,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:106483620" + "id": "NCBIGene:106483620" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:106483620-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:106483620-DISEASES API-DISEASES" } ] } @@ -58624,14 +58624,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:118335909" + "id": "NCBIGene:118335909" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:118335909-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:118335909-DISEASES API-DISEASES" } ] } @@ -58645,14 +58645,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:101674197" + "id": "NCBIGene:101674197" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:101674197-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:101674197-DISEASES API-DISEASES" } ] } @@ -58666,14 +58666,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:103089296" + "id": "NCBIGene:103089296" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:103089296-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:103089296-DISEASES API-DISEASES" } ] } @@ -58708,14 +58708,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:101998427" + "id": "NCBIGene:101998427" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:101998427-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:101998427-DISEASES API-DISEASES" } ] } @@ -58729,14 +58729,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:574217" + "id": "NCBIGene:574217" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:574217-DISEASES API-DISEASES" + "id": "MONDO:0005737-NCBIGene:574217-DISEASES API-DISEASES" } ] } @@ -58792,14 +58792,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:3601" + "id": "NCBIGene:3601" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:3601-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:3601-SEMMED Disease API-SEMMED" } ] } @@ -58813,14 +58813,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:5788" + "id": "NCBIGene:5788" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:5788-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:5788-SEMMED Disease API-SEMMED" } ] } @@ -58834,14 +58834,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:8030" + "id": "NCBIGene:8030" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:8030-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:8030-SEMMED Disease API-SEMMED" } ] } @@ -58855,14 +58855,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:920" + "id": "NCBIGene:920" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:920-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:920-SEMMED Disease API-SEMMED" } ] } @@ -58876,14 +58876,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:1514" + "id": "NCBIGene:1514" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:1514-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:1514-SEMMED Disease API-SEMMED" } ] } @@ -59065,14 +59065,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:3439" + "id": "NCBIGene:3439" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:3439-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:3439-SEMMED Disease API-SEMMED" } ] } @@ -85000,14 +85000,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:3557" + "id": "NCBIGene:3557" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:3557-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:3557-SEMMED Disease API-SEMMED" } ] } @@ -85063,14 +85063,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:1520" + "id": "NCBIGene:1520" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:1520-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:1520-SEMMED Disease API-SEMMED" } ] } @@ -85084,14 +85084,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:3439" + "id": "NCBIGene:3439" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:3439-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:3439-SEMMED Disease API-SEMMED" } ] } @@ -85105,14 +85105,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:3557" + "id": "NCBIGene:3557" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:3557-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:3557-SEMMED Disease API-SEMMED" } ] } @@ -85126,14 +85126,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:3806" + "id": "NCBIGene:3806" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:3806-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:3806-SEMMED Disease API-SEMMED" } ] } @@ -85147,14 +85147,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:3808" + "id": "NCBIGene:3808" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:3808-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:3808-SEMMED Disease API-SEMMED" } ] } @@ -85189,14 +85189,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:558" + "id": "NCBIGene:558" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:558-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:558-SEMMED Disease API-SEMMED" } ] } @@ -85294,14 +85294,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:1514" + "id": "NCBIGene:1514" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:1514-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:1514-SEMMED Disease API-SEMMED" } ] } @@ -85441,14 +85441,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:4864" + "id": "NCBIGene:4864" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:4864-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:4864-SEMMED Disease API-SEMMED" } ] } @@ -85609,14 +85609,14 @@ console.log(queryHandler.getResponse()) ], "n1": [ { - "id": "NCBIGENE:324" + "id": "NCBIGene:324" } ] }, "edge_bindings": { "e01": [ { - "id": "MONDO:0005737-NCBIGENE:324-SEMMED Disease API-SEMMED" + "id": "MONDO:0005737-NCBIGene:324-SEMMED Disease API-SEMMED" } ] } From 86b58dc499d2f57481e1e6326d408956eefc1430 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 27 Apr 2021 07:46:25 -0700 Subject: [PATCH 56/68] chore(release): 1.12.0 --- CHANGELOG.md | 2 ++ package-lock.json | 2 +- package.json | 2 +- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index cb62eb3d..d476159e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,8 @@ 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. +## [1.12.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.11.0...v1.12.0) (2021-04-27) + ## [1.11.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.10.0...v1.11.0) (2021-04-27) diff --git a/package-lock.json b/package-lock.json index 3a42a1c6..fb5ea2e9 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.11.0", + "version": "1.12.0", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index 18e8ef37..e2f6f710 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.11.0", + "version": "1.12.0", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { From cf647e402f9dbe83605a6836cd279dfbfd555b27 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 27 Apr 2021 07:49:26 -0700 Subject: [PATCH 57/68] refactor: :recycle: update local smartapi specs --- src/smartapi_specs.json | 278 ++++++++++++++++++++-------------------- 1 file changed, 139 insertions(+), 139 deletions(-) diff --git a/src/smartapi_specs.json b/src/smartapi_specs.json index f1685366..48ef9ab7 100644 --- a/src/smartapi_specs.json +++ b/src/smartapi_specs.json @@ -26331,7 +26331,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -26490,7 +26490,7 @@ "inputSeparator": ",", "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -26746,7 +26746,7 @@ "pubmed": "ctd.chemical_related_to_disease.pubmed" }, "disease-gene": { - "NCBIGENE": "disgenet.genes_related_to_disease.gene_id", + "NCBIGene": "disgenet.genes_related_to_disease.gene_id", "pubmed": "disgenet.genes_related_to_disease.pubmed" }, "disease-phenotype": { @@ -27223,7 +27223,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -27258,7 +27258,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -27327,7 +27327,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -27363,7 +27363,7 @@ "method": "post", "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -27397,7 +27397,7 @@ "method": "post", "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -27431,7 +27431,7 @@ "method": "post", "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -27465,7 +27465,7 @@ "method": "post", "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -27528,7 +27528,7 @@ "inputSeparator": ",", "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -27562,7 +27562,7 @@ "inputSeparator": ",", "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -27629,7 +27629,7 @@ "inputSeparator": ",", "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -27663,7 +27663,7 @@ "inputSeparator": ",", "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -27697,7 +27697,7 @@ "inputSeparator": ",", "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -27730,7 +27730,7 @@ "inputSeparator": ",", "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -27763,7 +27763,7 @@ "inputSeparator": ",", "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -27796,7 +27796,7 @@ "inputSeparator": ",", "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -27856,7 +27856,7 @@ "ENSEMBL": "ensembl.transcript" }, "entrezgene": { - "NCBIGENE": "entrezgene" + "NCBIGene": "entrezgene" }, "keggPathway": { "KEGG": "pathway.kegg.id", @@ -28403,7 +28403,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -28436,7 +28436,7 @@ "name": "clinvar.rcv.conditions.name" }, "variant-gene": { - "NCBIGENE": "dbsnp.gene.geneid" + "NCBIGene": "dbsnp.gene.geneid" }, "variant_affect_drug_response": { "clinical_significance": "civic.evidence_items.clinical_significance", @@ -52928,7 +52928,7 @@ "nodes": { "n00": { "category": "biolink:Gene", - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" }, "n01": { "category": "biolink:ChemicalSubstance" @@ -53031,7 +53031,7 @@ "nodes": { "n00": { "category": "biolink:Gene", - "id": "NCBIGENE:1017" + "id": "NCBIGene:1017" }, "n01": { "category": "biolink:ChemicalSubstance" @@ -53193,7 +53193,7 @@ ], "nodes": [ { - "curie": "NCBIGENE:1017", + "curie": "NCBIGene:1017", "id": "n00", "type": "gene" }, @@ -53261,7 +53261,7 @@ ], "nodes": [ { - "curie": "NCBIGENE:1017", + "curie": "NCBIGene:1017", "id": "n00", "type": "gene" }, @@ -55932,12 +55932,12 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], "parameters": { - "fields": "subject.NCBIGENE,association.provided_by,association.pubmed", + "fields": "subject.NCBIGene,association.provided_by,association.pubmed", "size": 1000 }, "predicate": "physically_interacts_with", @@ -55960,7 +55960,7 @@ "inputSeparator": ",", "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -55978,7 +55978,7 @@ "requestBody": { "body": { "q": "{inputs[0]}", - "scopes": "subject.NCBIGENE" + "scopes": "subject.NCBIGene" }, "header": "application/x-www-form-urlencoded" }, @@ -55992,7 +55992,7 @@ }, "x-bte-response-mapping": { "chemical-gene": { - "NCBIGENE": "subject.NCBIGENE", + "NCBIGene": "subject.NCBIGene", "pubmed": "association.pubmed", "source": "association.provided_by" }, @@ -56737,7 +56737,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -56764,7 +56764,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -57385,7 +57385,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -57412,7 +57412,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -58033,7 +58033,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -58060,7 +58060,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -58681,7 +58681,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -58708,7 +58708,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -59329,7 +59329,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -59356,7 +59356,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -59977,7 +59977,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60004,7 +60004,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60295,7 +60295,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60307,7 +60307,7 @@ ], "parameters": { "fields": "object,association", - "q": "subject.NCBIGENE:\"{inputs[0]}\" AND object.type:AnatomicalEntity", + "q": "subject.NCBIGene:\"{inputs[0]}\" AND object.type:AnatomicalEntity", "size": 1000 }, "predicate": "related_to", @@ -60322,7 +60322,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60334,7 +60334,7 @@ ], "parameters": { "fields": "subject,association", - "q": "object.NCBIGENE:\"{inputs[0]}\" AND subject.type:AnatomicalEntity", + "q": "object.NCBIGene:\"{inputs[0]}\" AND subject.type:AnatomicalEntity", "size": 1000 }, "predicate": "related_to", @@ -60349,7 +60349,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60361,7 +60361,7 @@ ], "parameters": { "fields": "object,association", - "q": "subject.NCBIGENE:\"{inputs[0]}\" AND object.type:BiologicalProcess", + "q": "subject.NCBIGene:\"{inputs[0]}\" AND object.type:BiologicalProcess", "size": 1000 }, "predicate": "related_to", @@ -60376,7 +60376,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60388,7 +60388,7 @@ ], "parameters": { "fields": "subject,association", - "q": "object.NCBIGENE:\"{inputs[0]}\" AND subject.type:BiologicalProcess", + "q": "object.NCBIGene:\"{inputs[0]}\" AND subject.type:BiologicalProcess", "size": 1000 }, "predicate": "related_to", @@ -60403,7 +60403,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60415,7 +60415,7 @@ ], "parameters": { "fields": "object,association", - "q": "subject.NCBIGENE:\"{inputs[0]}\" AND object.type:Cell", + "q": "subject.NCBIGene:\"{inputs[0]}\" AND object.type:Cell", "size": 1000 }, "predicate": "related_to", @@ -60430,7 +60430,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60442,7 +60442,7 @@ ], "parameters": { "fields": "subject,association", - "q": "object.NCBIGENE:\"{inputs[0]}\" AND subject.type:Cell", + "q": "object.NCBIGene:\"{inputs[0]}\" AND subject.type:Cell", "size": 1000 }, "predicate": "related_to", @@ -60457,7 +60457,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60469,7 +60469,7 @@ ], "parameters": { "fields": "object,association", - "q": "subject.NCBIGENE:\"{inputs[0]}\" AND object.type:CellularComponent", + "q": "subject.NCBIGene:\"{inputs[0]}\" AND object.type:CellularComponent", "size": 1000 }, "predicate": "related_to", @@ -60484,7 +60484,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60496,7 +60496,7 @@ ], "parameters": { "fields": "subject,association", - "q": "object.NCBIGENE:\"{inputs[0]}\" AND subject.type:CellularComponent", + "q": "object.NCBIGene:\"{inputs[0]}\" AND subject.type:CellularComponent", "size": 1000 }, "predicate": "related_to", @@ -60511,7 +60511,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60523,7 +60523,7 @@ ], "parameters": { "fields": "object,association", - "q": "subject.NCBIGENE:\"{inputs[0]}\" AND object.type:ChemicalSubstance", + "q": "subject.NCBIGene:\"{inputs[0]}\" AND object.type:ChemicalSubstance", "size": 1000 }, "predicate": "related_to", @@ -60538,7 +60538,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60550,7 +60550,7 @@ ], "parameters": { "fields": "subject,association", - "q": "object.NCBIGENE:\"{inputs[0]}\" AND subject.type:ChemicalSubstance", + "q": "object.NCBIGene:\"{inputs[0]}\" AND subject.type:ChemicalSubstance", "size": 1000 }, "predicate": "related_to", @@ -60565,7 +60565,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60577,7 +60577,7 @@ ], "parameters": { "fields": "object,association", - "q": "subject.NCBIGENE:\"{inputs[0]}\" AND object.type:Disease", + "q": "subject.NCBIGene:\"{inputs[0]}\" AND object.type:Disease", "size": 1000 }, "predicate": "related_to", @@ -60592,7 +60592,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60604,7 +60604,7 @@ ], "parameters": { "fields": "subject,association", - "q": "object.NCBIGENE:\"{inputs[0]}\" AND subject.type:Disease", + "q": "object.NCBIGene:\"{inputs[0]}\" AND subject.type:Disease", "size": 1000 }, "predicate": "related_to", @@ -60619,19 +60619,19 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], "parameters": { "fields": "object,association", - "q": "subject.NCBIGENE:\"{inputs[0]}\" AND object.type:Gene", + "q": "subject.NCBIGene:\"{inputs[0]}\" AND object.type:Gene", "size": 1000 }, "predicate": "related_to", @@ -60646,19 +60646,19 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], "parameters": { "fields": "subject,association", - "q": "object.NCBIGENE:\"{inputs[0]}\" AND subject.type:Gene", + "q": "object.NCBIGene:\"{inputs[0]}\" AND subject.type:Gene", "size": 1000 }, "predicate": "related_to", @@ -60673,7 +60673,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60685,7 +60685,7 @@ ], "parameters": { "fields": "object,association", - "q": "subject.NCBIGENE:\"{inputs[0]}\" AND object.type:MolecularActivity", + "q": "subject.NCBIGene:\"{inputs[0]}\" AND object.type:MolecularActivity", "size": 1000 }, "predicate": "related_to", @@ -60700,7 +60700,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60712,7 +60712,7 @@ ], "parameters": { "fields": "subject,association", - "q": "object.NCBIGENE:\"{inputs[0]}\" AND subject.type:MolecularActivity", + "q": "object.NCBIGene:\"{inputs[0]}\" AND subject.type:MolecularActivity", "size": 1000 }, "predicate": "related_to", @@ -60727,7 +60727,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60739,7 +60739,7 @@ ], "parameters": { "fields": "object,association", - "q": "subject.NCBIGENE:\"{inputs[0]}\" AND object.type:OrganismTaxon", + "q": "subject.NCBIGene:\"{inputs[0]}\" AND object.type:OrganismTaxon", "size": 1000 }, "predicate": "related_to", @@ -60754,7 +60754,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60766,7 +60766,7 @@ ], "parameters": { "fields": "subject,association", - "q": "object.NCBIGENE:\"{inputs[0]}\" AND subject.type:OrganismTaxon", + "q": "object.NCBIGene:\"{inputs[0]}\" AND subject.type:OrganismTaxon", "size": 1000 }, "predicate": "related_to", @@ -60781,7 +60781,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60793,7 +60793,7 @@ ], "parameters": { "fields": "object,association", - "q": "subject.NCBIGENE:\"{inputs[0]}\" AND object.type:PhenotypicFeature", + "q": "subject.NCBIGene:\"{inputs[0]}\" AND object.type:PhenotypicFeature", "size": 1000 }, "predicate": "related_to", @@ -60808,7 +60808,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60820,7 +60820,7 @@ ], "parameters": { "fields": "subject,association", - "q": "object.NCBIGENE:\"{inputs[0]}\" AND subject.type:PhenotypicFeature", + "q": "object.NCBIGene:\"{inputs[0]}\" AND subject.type:PhenotypicFeature", "size": 1000 }, "predicate": "related_to", @@ -60835,7 +60835,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60847,7 +60847,7 @@ ], "parameters": { "fields": "object,association", - "q": "subject.NCBIGENE:\"{inputs[0]}\" AND object.type:Protein", + "q": "subject.NCBIGene:\"{inputs[0]}\" AND object.type:Protein", "size": 1000 }, "predicate": "related_to", @@ -60862,7 +60862,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60874,7 +60874,7 @@ ], "parameters": { "fields": "subject,association", - "q": "object.NCBIGENE:\"{inputs[0]}\" AND subject.type:Protein", + "q": "object.NCBIGene:\"{inputs[0]}\" AND subject.type:Protein", "size": 1000 }, "predicate": "related_to", @@ -60889,7 +60889,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60901,7 +60901,7 @@ ], "parameters": { "fields": "object,association", - "q": "subject.NCBIGENE:\"{inputs[0]}\" AND object.type:SequenceFeature", + "q": "subject.NCBIGene:\"{inputs[0]}\" AND object.type:SequenceFeature", "size": 1000 }, "predicate": "related_to", @@ -60916,7 +60916,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -60928,7 +60928,7 @@ ], "parameters": { "fields": "subject,association", - "q": "object.NCBIGENE:\"{inputs[0]}\" AND subject.type:SequenceFeature", + "q": "object.NCBIGene:\"{inputs[0]}\" AND subject.type:SequenceFeature", "size": 1000 }, "predicate": "related_to", @@ -61273,7 +61273,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -61300,7 +61300,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -61921,7 +61921,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -61948,7 +61948,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -62569,7 +62569,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -62596,7 +62596,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -63217,7 +63217,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -63244,7 +63244,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -63865,7 +63865,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -63892,7 +63892,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -64230,11 +64230,11 @@ "ngd": "hits.association.ngd" }, "Gene": { - "NCBIGENE": "hits.object.NCBIGENE", + "NCBIGene": "hits.object.NCBIGene", "ngd": "hits.association.ngd" }, "Gene-reverse": { - "NCBIGENE": "hits.subject.NCBIGENE", + "NCBIGene": "hits.subject.NCBIGene", "ngd": "hits.association.ngd" }, "MolecularActivity": { @@ -69951,12 +69951,12 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], "parameters": { - "fields": "association.context.disease.mondo,subject.NCBIGENE,association.effect_size,association.pvalue", + "fields": "association.context.disease.mondo,subject.NCBIGene,association.effect_size,association.pvalue", "q": "object.PUBCHEM:{inputs[0]} AND association.effect_size:<0 AND association.pvalue:<0.05", "size": "1000", "sort": "association.pvalue" @@ -69973,7 +69973,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -69985,7 +69985,7 @@ ], "parameters": { "fields": "association.context.disease.mondo,object.PUBCHEM,association.effect_size,association.pvalue", - "q": "subject.NCBIGENE:{inputs[0]} AND association.effect_size:<0 AND association.pvalue:<0.05", + "q": "subject.NCBIGene:{inputs[0]} AND association.effect_size:<0 AND association.pvalue:<0.05", "size": "1000", "sort": "association.pvalue" }, @@ -70000,7 +70000,7 @@ }, "x-bte-response-mapping": { "chemical-gene": { - "NCBIGENE": "hits.subject.NCBIGENE", + "NCBIGene": "hits.subject.NCBIGene", "disease_context": "hits.association.context.disease.mondo", "effect_size": "hits.association.effect_size", "pvalue": "hits.association.pvalue" @@ -70212,7 +70212,7 @@ "parameters": [ { "description": "Query string.", - "example": "subject.NCBIGENE:51742", + "example": "subject.NCBIGene:51742", "in": "query", "name": "q", "required": true, @@ -70865,7 +70865,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -70877,7 +70877,7 @@ }, "predicate": "related_to", "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/anatomy-gene-ncbigene" + "$ref": "#/components/x-bte-response-mapping/anatomy-gene-NCBIGene" }, "supportBatch": false } @@ -70917,7 +70917,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -70929,7 +70929,7 @@ }, "predicate": "related_to", "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/disease-gene-ncbigene" + "$ref": "#/components/x-bte-response-mapping/disease-gene-NCBIGene" }, "supportBatch": false } @@ -70992,7 +70992,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -71004,7 +71004,7 @@ ], "parameters": { "direct": true, - "gene_id": "NCBIGENE:{inputs[0]}", + "gene_id": "NCBIGene:{inputs[0]}", "rows": 200, "unselect_evidence": true }, @@ -71019,7 +71019,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -71031,7 +71031,7 @@ ], "parameters": { "direct": true, - "gene_id": "NCBIGENE:{inputs[0]}", + "gene_id": "NCBIGene:{inputs[0]}", "rows": 200, "unselect_evidence": true }, @@ -71046,7 +71046,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -71058,7 +71058,7 @@ ], "parameters": { "direct": true, - "gene_id": "NCBIGENE:{inputs[0]}", + "gene_id": "NCBIGene:{inputs[0]}", "rows": 200, "unselect_evidence": true }, @@ -71071,7 +71071,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -71083,13 +71083,13 @@ ], "parameters": { "direct": true, - "gene_id": "NCBIGENE:{inputs[0]}", + "gene_id": "NCBIGene:{inputs[0]}", "rows": 200, "unselect_evidence": true }, "predicate": "related_to", "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/gene-interaction-ncbigene" + "$ref": "#/components/x-bte-response-mapping/gene-interaction-NCBIGene" }, "supportBatch": false } @@ -71098,7 +71098,7 @@ { "inputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -71110,7 +71110,7 @@ ], "parameters": { "direct": true, - "gene_id": "NCBIGENE:{inputs[0]}", + "gene_id": "NCBIGene:{inputs[0]}", "rows": 200, "unselect_evidence": true }, @@ -71237,7 +71237,7 @@ ], "outputs": [ { - "id": "NCBIGENE", + "id": "NCBIGene", "semantic": "Gene" } ], @@ -71249,7 +71249,7 @@ }, "predicate": "related_to", "response_mapping": { - "$ref": "#/components/x-bte-response-mapping/phenotype-gene-ncbigene" + "$ref": "#/components/x-bte-response-mapping/phenotype-gene-NCBIGene" }, "supportBatch": false } @@ -71316,8 +71316,8 @@ "relation": "associations.relation.label", "source": "associations.provided_by" }, - "anatomy-gene-ncbigene": { - "NCBIGENE": "associations.object.NCBIGENE", + "anatomy-gene-NCBIGene": { + "NCBIGene": "associations.object.NCBIGene", "pubmed": "associations.publications.id", "relation": "associations.relation.label", "source": "associations.provided_by" @@ -71329,8 +71329,8 @@ "source": "associations.provided_by", "taxid": "associations.object.taxon.id" }, - "disease-gene-ncbigene": { - "NCBIGENE": "associations.object.NCBIGENE", + "disease-gene-NCBIGene": { + "NCBIGene": "associations.object.NCBIGene", "pubmed": "associations.publications.id", "relation": "associations.relation.label", "source": "associations.provided_by", @@ -71370,8 +71370,8 @@ "source": "associations.provided_by", "taxid": "associations.object.taxon.id" }, - "gene-interaction-ncbigene": { - "NCBIGENE": "associations.object.NCBIGENE", + "gene-interaction-NCBIGene": { + "NCBIGene": "associations.object.NCBIGene", "pubmed": "associations.publications.id", "relation": "associations.relation.label", "source": "associations.provided_by", @@ -71411,8 +71411,8 @@ "relation": "associations.relation.label", "source": "associations.provided_by" }, - "phenotype-gene-ncbigene": { - "NCBIGENE": "associations.object.NCBIGENE", + "phenotype-gene-NCBIGene": { + "NCBIGene": "associations.object.NCBIGene", "pubmed": "associations.publications.id", "relation": "associations.relation.label", "source": "associations.provided_by" @@ -71620,7 +71620,7 @@ "parameters": [ { "description": "CURIE identifier of gene IDs can be used with same results", - "example": "NCBIGENE:1017", + "example": "NCBIGene:1017", "in": "path", "name": "gene_id", "required": true, @@ -71660,7 +71660,7 @@ "parameters": [ { "description": "CURIE identifier of gene IDs can be used with same results", - "example": "NCBIGENE:1017", + "example": "NCBIGene:1017", "in": "path", "name": "gene_id", "required": true, @@ -71700,7 +71700,7 @@ "parameters": [ { "description": "CURIE identifier of gene IDs can be used with same results", - "example": "NCBIGENE:1017", + "example": "NCBIGene:1017", "in": "path", "name": "gene_id", "required": true, @@ -71740,7 +71740,7 @@ "parameters": [ { "description": "CURIE identifier of gene IDs can be used with same results", - "example": "NCBIGENE:1017", + "example": "NCBIGene:1017", "in": "path", "name": "gene_id", "required": true, From 866703c0191b098eab91d1b62863bb95ba105695 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 27 Apr 2021 07:49:37 -0700 Subject: [PATCH 58/68] chore(release): 1.12.1 --- CHANGELOG.md | 2 ++ package-lock.json | 2 +- package.json | 2 +- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d476159e..cd8f6e0a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,8 @@ 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. +### [1.12.1](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.12.0...v1.12.1) (2021-04-27) + ## [1.12.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.11.0...v1.12.0) (2021-04-27) ## [1.11.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.10.0...v1.11.0) (2021-04-27) diff --git a/package-lock.json b/package-lock.json index fb5ea2e9..12d14fab 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.12.0", + "version": "1.12.1", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index e2f6f710..cfad95f9 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.12.0", + "version": "1.12.1", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { From c26b317d5b70dbe2ffc18dd1a7c324a2e13f581e Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Wed, 28 Apr 2021 15:16:35 -0700 Subject: [PATCH 59/68] feat: :sparkles: expand predicate based on biolink model --- src/biolink.js | 8 ++++++++ src/query_edge.js | 13 +++++++++---- 2 files changed, 17 insertions(+), 4 deletions(-) diff --git a/src/biolink.js b/src/biolink.js index 905e791c..803fe47c 100644 --- a/src/biolink.js +++ b/src/biolink.js @@ -34,6 +34,14 @@ class BioLinkModel { } return className; } + + getDescendantPredicates(predicate) { + if (predicate in this.biolink.slotTree.objects) { + const descendants = this.biolink.slotTree.getDescendants(predicate).map((entity) => entity.name); + return [...descendants, ...[predicate]]; + } + return [predicate]; + } } const BioLinkModelInstance = new BioLinkModel(); diff --git a/src/query_edge.js b/src/query_edge.js index dc149fcb..f27a0359 100644 --- a/src/query_edge.js +++ b/src/query_edge.js @@ -26,15 +26,20 @@ module.exports = class QEdge { return new helper()._generateHash(toBeHashed); } + expandPredicates(predicates) { + const reducer = (acc, cur) => [...acc, ...reverse.getDescendantPredicates(cur)]; + return Array.from(new Set(predicates.reduce(reducer, []))); + } + getPredicate() { if (this.predicate === undefined) { return undefined; } - const predicates = utils.toArray(this.predicate); - return predicates + const predicates = utils.toArray(this.predicate).map(item => utils.removeBioLinkPrefix(item)); + const expandedPredicates = this.expandPredicates(predicates); + return expandedPredicates .map((predicate) => { - const predicateWithOutPrefix = utils.removeBioLinkPrefix(predicate); - return this.isReversed() === true ? reverse.reverse(predicateWithOutPrefix) : predicateWithOutPrefix; + return this.isReversed() === true ? reverse.reverse(predicate) : predicate; }) .filter((item) => !(typeof item === 'undefined')); } From 3ec3af2fbbfc4cf3222f3ed2326d2084cf17c4fc Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Wed, 28 Apr 2021 15:16:51 -0700 Subject: [PATCH 60/68] test: :white_check_mark: update test for expanding predicates --- __test__/integration/QueryEdge.test.js | 35 +++++++++++++++++++++++++- __test__/integration/biolink.test.js | 20 +++++++++++++++ __test__/unittest/QueryEdge.test.js | 9 ++++--- 3 files changed, 59 insertions(+), 5 deletions(-) diff --git a/__test__/integration/QueryEdge.test.js b/__test__/integration/QueryEdge.test.js index ddccc034..daa517c9 100644 --- a/__test__/integration/QueryEdge.test.js +++ b/__test__/integration/QueryEdge.test.js @@ -127,7 +127,40 @@ describe("Testing QueryEdge Module", () => { test("test get reverse predicate if query is reversed", () => { const edge = new QEdge("e01", { subject: type_node, object: disease1_node, predicate: "biolink:treats" }); const res = edge.getPredicate(); - expect(res).toEqual(["treated_by"]); + expect(res).toContain("treated_by"); + }); + + test("test get reverse predicate if query is reversed and expanded", () => { + const edge = new QEdge("e01", { subject: type_node, object: disease1_node, predicate: "biolink:affects" }); + const res = edge.getPredicate(); + expect(res).toContain("affected_by"); + expect(res).toContain("disrupted_by"); + }); + }) + + describe("Testing expandPredicates function", () => { + test("All predicates are correctly expanded if in biolink model", () => { + const edge = new QEdge("e01", { subject: type_node, object: disease1_node, predicate: "biolink:contributes_to" }); + const res = edge.expandPredicates(["contributes_to"]) + expect(res).toContain("contributes_to"); + expect(res).toContain("causes"); + }); + + test("Multiple predicates can be resolved", () => { + const edge = new QEdge("e01", { subject: type_node, object: disease1_node, predicate: "biolink:contributes_to" }); + const res = edge.expandPredicates(["contributes_to", "ameliorates"]) + expect(res).toContain("contributes_to"); + expect(res).toContain("causes"); + expect(res).toContain("ameliorates"); + expect(res).toContain("treats"); + }); + + test("Predicates not in biolink model should return itself", () => { + const edge = new QEdge("e01", { subject: type_node, object: disease1_node, predicate: "biolink:contributes_to" }); + const res = edge.expandPredicates(["contributes_to", "amelio"]) + expect(res).toContain("contributes_to"); + expect(res).toContain("causes"); + expect(res).toContain("amelio"); }); }) diff --git a/__test__/integration/biolink.test.js b/__test__/integration/biolink.test.js index b7daf73e..8fa07dd4 100644 --- a/__test__/integration/biolink.test.js +++ b/__test__/integration/biolink.test.js @@ -50,4 +50,24 @@ describe("Test BioLinkModel class", () => { }) }) + + describe("Test getDescendantPredicates function", () => { + test("if input is in biolink model, return all its desendants and itself", () => { + const res = biolink.getDescendantPredicates('related_to'); + expect(res).toContain("subclass_of"); + expect(res).toContain("superclass_of"); + expect(res).toContain("related_to"); + }) + + test("if input is in biolink model but doesn't have descendants, return itself", () => { + const res = biolink.getDescendantPredicates('subclass_of'); + expect(res).toEqual(["subclass_of"]) + }) + + test("if input is not in biolink, return itself", () => { + const res = biolink.getDescendantPredicates('Gene1'); + expect(res).toEqual(["Gene1"]) + }) + + }) }) diff --git a/__test__/unittest/QueryEdge.test.js b/__test__/unittest/QueryEdge.test.js index d1c52ae5..c12a6058 100644 --- a/__test__/unittest/QueryEdge.test.js +++ b/__test__/unittest/QueryEdge.test.js @@ -19,7 +19,7 @@ describe("Test QEdge class", () => { } }) const res = edge.getPredicate(); - expect(res).toEqual(['treats']); + expect(res).toContain("treats"); }) test("Undefined predicate should return itself", () => { @@ -44,7 +44,8 @@ describe("Test QEdge class", () => { } }) const res = edge.getPredicate(); - expect(res).toEqual(['treats', 'targets']); + expect(res).toContain("treats"); + expect(res).toContain("targets"); }) test("An array of non-undefined predicates with reverse edge should exclude return value if undefined", () => { @@ -63,7 +64,7 @@ describe("Test QEdge class", () => { } }) const res = edge.getPredicate(); - expect(res).toEqual(['treated_by']); + expect(res).toContain("treated_by") }) test("An array of non-undefined predicates with reverse edge should return reversed predicates if not undefined", () => { @@ -81,7 +82,7 @@ describe("Test QEdge class", () => { } }) const res = edge.getPredicate(); - expect(res).toEqual(['treated_by']); + expect(res).toContain("treated_by"); }) }) From deb1a200d4caa23f46a19a8764fc8640a95ab8a7 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Wed, 28 Apr 2021 15:17:00 -0700 Subject: [PATCH 61/68] chore(release): 1.13.0 --- 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 cd8f6e0a..3745a4e7 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. +## [1.13.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.12.1...v1.13.0) (2021-04-28) + + +### Features + +* :sparkles: expand predicate based on biolink model ([c26b317](https://github.com/kevinxin90/bte_trapi_query_graph_handler/commit/c26b317d5b70dbe2ffc18dd1a7c324a2e13f581e)) + ### [1.12.1](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.12.0...v1.12.1) (2021-04-27) ## [1.12.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.11.0...v1.12.0) (2021-04-27) diff --git a/package-lock.json b/package-lock.json index 12d14fab..defd12b2 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.12.1", + "version": "1.13.0", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index cfad95f9..2094ba72 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.12.1", + "version": "1.13.0", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { From 72254376b2414a382331f22d9ac86faec101c344 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Wed, 28 Apr 2021 15:17:18 -0700 Subject: [PATCH 62/68] style: :art: style code --- src/query_edge.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/query_edge.js b/src/query_edge.js index f27a0359..415539fc 100644 --- a/src/query_edge.js +++ b/src/query_edge.js @@ -35,7 +35,7 @@ module.exports = class QEdge { if (this.predicate === undefined) { return undefined; } - const predicates = utils.toArray(this.predicate).map(item => utils.removeBioLinkPrefix(item)); + const predicates = utils.toArray(this.predicate).map((item) => utils.removeBioLinkPrefix(item)); const expandedPredicates = this.expandPredicates(predicates); return expandedPredicates .map((predicate) => { From a11c01230760c488c3566a3090527185b4a32c02 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Wed, 28 Apr 2021 17:13:29 -0700 Subject: [PATCH 63/68] refactor: :recycle: add debug message for expanded edges --- src/query_edge.js | 1 + 1 file changed, 1 insertion(+) diff --git a/src/query_edge.js b/src/query_edge.js index 415539fc..72207862 100644 --- a/src/query_edge.js +++ b/src/query_edge.js @@ -37,6 +37,7 @@ module.exports = class QEdge { } const predicates = utils.toArray(this.predicate).map((item) => utils.removeBioLinkPrefix(item)); const expandedPredicates = this.expandPredicates(predicates); + debug(`Expanded edges: ${expandedPredicates}`); return expandedPredicates .map((predicate) => { return this.isReversed() === true ? reverse.reverse(predicate) : predicate; From 8862ca6f5be513fe656aeac57fb63d558735b859 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Wed, 28 Apr 2021 17:13:36 -0700 Subject: [PATCH 64/68] chore(release): 1.13.1 --- CHANGELOG.md | 2 ++ package-lock.json | 2 +- package.json | 2 +- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3745a4e7..95e1adf5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,8 @@ 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. +### [1.13.1](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.13.0...v1.13.1) (2021-04-29) + ## [1.13.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.12.1...v1.13.0) (2021-04-28) diff --git a/package-lock.json b/package-lock.json index defd12b2..49d06dca 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.13.0", + "version": "1.13.1", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index 2094ba72..c6e87bdb 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.13.0", + "version": "1.13.1", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { From 6345571e60998a403c946aabed2fc4a07d8ebbdd Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Wed, 28 Apr 2021 17:19:50 -0700 Subject: [PATCH 65/68] feat: :sparkles: support expanding predicates based on biolink hierarchy --- src/query_execution_edge.js | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/src/query_execution_edge.js b/src/query_execution_edge.js index 03f33b1d..63944f8b 100644 --- a/src/query_execution_edge.js +++ b/src/query_execution_edge.js @@ -27,15 +27,21 @@ module.exports = class QExeEdge { return new helper()._generateHash(toBeHashed); } + expandPredicates(predicates) { + const reducer = (acc, cur) => [...acc, ...reverse.getDescendantPredicates(cur)]; + return Array.from(new Set(predicates.reduce(reducer, []))); + } + getPredicate() { - if (this.qEdge.predicate === undefined) { + if (this.predicate === undefined) { return undefined; } - const predicates = utils.toArray(this.qEdge.predicate); - return predicates + const predicates = utils.toArray(this.predicate).map((item) => utils.removeBioLinkPrefix(item)); + const expandedPredicates = this.expandPredicates(predicates); + debug(`Expanded edges: ${expandedPredicates}`); + return expandedPredicates .map((predicate) => { - const predicateWithOutPrefix = utils.removeBioLinkPrefix(predicate); - return this.reverse === true ? reverse.reverse(predicateWithOutPrefix) : predicateWithOutPrefix; + return this.isReversed() === true ? reverse.reverse(predicate) : predicate; }) .filter((item) => !(typeof item === 'undefined')); } From ce1b9a44f5add5df8b65802974de5a3fd8aa17d3 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Wed, 28 Apr 2021 17:19:57 -0700 Subject: [PATCH 66/68] chore(release): 1.14.0 --- 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 95e1adf5..e18c6df9 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. +## [1.14.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.13.1...v1.14.0) (2021-04-29) + + +### Features + +* :sparkles: support expanding predicates based on biolink hierarchy ([6345571](https://github.com/kevinxin90/bte_trapi_query_graph_handler/commit/6345571e60998a403c946aabed2fc4a07d8ebbdd)) + ### [1.13.1](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.13.0...v1.13.1) (2021-04-29) ## [1.13.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.12.1...v1.13.0) (2021-04-28) diff --git a/package-lock.json b/package-lock.json index 49d06dca..279a13ca 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.13.1", + "version": "1.14.0", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index c6e87bdb..8a5d3dd7 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.13.1", + "version": "1.14.0", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": { From 2e111088cfe53dc50a993bb5ded692929bdc5c08 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 4 May 2021 09:42:23 -0700 Subject: [PATCH 67/68] build: :arrow_up: support customized transformation of EBI Protein API --- package-lock.json | 64 ++++++----------------------------------------- package.json | 2 +- 2 files changed, 8 insertions(+), 58 deletions(-) diff --git a/package-lock.json b/package-lock.json index 279a13ca..7e02aba7 100644 --- a/package-lock.json +++ b/package-lock.json @@ -427,9 +427,9 @@ "dev": true }, "@biothings-explorer/api-response-transform": { - "version": "1.10.1", - "resolved": "https://registry.npmjs.org/@biothings-explorer/api-response-transform/-/api-response-transform-1.10.1.tgz", - "integrity": "sha512-9/mPSkjf8TscSHdqrDsz1Ov112j/CHYdUdndxTqRTKKrDObOCJlSt6krU8S8G7vmgrc8BAJh3PnH+eLlj0At4Q==", + "version": "1.11.0", + "resolved": "https://registry.npmjs.org/@biothings-explorer/api-response-transform/-/api-response-transform-1.11.0.tgz", + "integrity": "sha512-AKYBjJgNF27dwOIAPtPU9BP0aMdsqN7bIr9+Q34F24zr3ihAN/H6SYp52NDaqcJXVBctengLmxPMUUUngWFi1g==", "requires": { "@biothings-explorer/json-transformer": "^1.0.2", "@commitlint/cli": "^11.0.0", @@ -450,65 +450,15 @@ } }, "@biothings-explorer/call-apis": { - "version": "1.20.0", - "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.20.0.tgz", - "integrity": "sha512-WF6+QEdnY3HmQhbHl6PKOAmNjhoIOpXmAhxlqYL39V2BlHlz7joY7PSebYkW+lQxLBjQjeDam5RaVYXXmfnCYQ==", + "version": "1.21.0", + "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.21.0.tgz", + "integrity": "sha512-7P9/WwnegO4kqidYHO5HobpSwuxPWdC2GoWxQN6FRHv9CPACcAkin9DCdoktj2B0FI1IRJumtQmnuO7dRxSnZw==", "requires": { - "@biothings-explorer/api-response-transform": "^1.10.1", + "@biothings-explorer/api-response-transform": "^1.11.0", "axios": "^0.21.1", "biomedical_id_resolver": "^3.9.0", "debug": "^4.3.1", "husky": "^4.3.8" - }, - "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==" - }, - "biolink-model": { - "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", - "js-yaml": "^4.0.0", - "pascal-case": "^3.1.2" - } - }, - "biomedical_id_resolver": { - "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": "^0.3.1", - "debug": "^4.3.1", - "husky": "^4.3.8", - "lodash": "^4.17.21" - }, - "dependencies": { - "axios": { - "version": "0.19.2", - "resolved": "https://registry.npmjs.org/axios/-/axios-0.19.2.tgz", - "integrity": "sha512-fjgm5MvRHLhx+osE2xoekY70AhARk3a6hkN+3Io1jc00jtquGvxYlKlsFUhmUET0V5te6CcZI7lcv2Ym61mjHA==", - "requires": { - "follow-redirects": "1.5.10" - } - } - } - }, - "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" - } - } } }, "@biothings-explorer/json-transformer": { diff --git a/package.json b/package.json index 8a5d3dd7..6dd4be83 100644 --- a/package.json +++ b/package.json @@ -50,7 +50,7 @@ "typescript": "^4.2.3" }, "dependencies": { - "@biothings-explorer/call-apis": "^1.20.0", + "@biothings-explorer/call-apis": "^1.21.0", "@biothings-explorer/smartapi-kg": "^3.7.0", "biolink-model": "^0.3.0", "biomedical_id_resolver": "^3.9.0", From 49e58782a232e37d909c2e59709362a1d0c88415 Mon Sep 17 00:00:00 2001 From: jiwen xin Date: Tue, 4 May 2021 09:42:37 -0700 Subject: [PATCH 68/68] chore(release): 1.15.0 --- CHANGELOG.md | 2 ++ package-lock.json | 2 +- package.json | 2 +- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e18c6df9..1b732d31 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,8 @@ 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. +## [1.15.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.14.0...v1.15.0) (2021-05-04) + ## [1.14.0](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.13.1...v1.14.0) (2021-04-29) diff --git a/package-lock.json b/package-lock.json index 7e02aba7..2e6444be 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.14.0", + "version": "1.15.0", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index 6dd4be83..cbc844c7 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.14.0", + "version": "1.15.0", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", "scripts": {