From 7ec573a64d72a755a291cb9c28e476887a80c98b Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Wed, 20 Mar 2024 23:19:01 -0700 Subject: [PATCH 01/27] feat: add pathfinder templateGroups, templates for drug-disease --- data/templateGroups.json | 53 +++++++++++++++++++ .../Pathfinder/pf-drug-gene-cell-disease.json | 46 ++++++++++++++++ .../Pathfinder/pf-drug-gene-disease.json | 40 ++++++++++++++ .../pf-drug-gene-physioAndpath-disease.json | 49 +++++++++++++++++ 4 files changed, 188 insertions(+) create mode 100644 data/templates/Pathfinder/pf-drug-gene-cell-disease.json create mode 100644 data/templates/Pathfinder/pf-drug-gene-disease.json create mode 100644 data/templates/Pathfinder/pf-drug-gene-physioAndpath-disease.json diff --git a/data/templateGroups.json b/data/templateGroups.json index 3df3fd2e..afb5409c 100644 --- a/data/templateGroups.json +++ b/data/templateGroups.json @@ -51,5 +51,58 @@ "Chem-physically_interacts-GeneThatDownregs-Gene.json", "Chem-physically_interacts-Gene.json" ] + }, + { + "name": "Pathfinder: Drug-Disease", + "pathfinder": true, + "subject": ["Drug", "SmallMolecule", + "ChemicalEntity", "ComplexMolecularMixture", "MolecularMixture" + ], + "predicate": ["related_to"], + "object": ["Disease", "PhenotypicFeature", + "DiseaseOrPhenotypicFeature" + ], + "templates": [ + "pf-drug-gene-disease.json", + "pf-drug-gene-cell-disease.json", + "pf-drug-gene-physioAndpath-disease.json" + ] + }, + { + "name": "Pathfinder: Chem-Gene", + "subject": ["Drug", "SmallMolecule", + "ChemicalEntity", "ComplexMolecularMixture", "MolecularMixture" + ], + "predicate": ["related_to"], + "object": ["Gene", "Protein"], + "templates": [ + + ] + }, + { + "name": "Pathfinder: Disease-Disease", + "pathfinder": true, + "subject": ["Disease", "PhenotypicFeature", + "DiseaseOrPhenotypicFeature" + ], + "predicate": ["related_to"], + "object": ["Disease", "PhenotypicFeature", + "DiseaseOrPhenotypicFeature" + ], + "templates": [ + + ] + }, + { + "name": "Pathfinder: Gene-Disease", + "pathfinder": true, + "subject": ["Gene", "Protein"], + "predicate": ["related_to"], + "object": ["Disease", "PhenotypicFeature", + "DiseaseOrPhenotypicFeature" + ], + "templates": [ + + ] } ] diff --git a/data/templates/Pathfinder/pf-drug-gene-cell-disease.json b/data/templates/Pathfinder/pf-drug-gene-cell-disease.json new file mode 100644 index 00000000..c54e10d0 --- /dev/null +++ b/data/templates/Pathfinder/pf-drug-gene-cell-disease.json @@ -0,0 +1,46 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories":["biolink:ChemicalEntity"] + }, + "nA": { + "categories":["biolink:Gene"] + }, + "nB": { + "categories":["biolink:Cell"] + }, + "creativeQueryObject": { + "categories":["biolink:DiseaseOrPhenotypicFeature"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "nA", + "predicates": [ + "biolink:regulates", + "biolink:affects", + "biolink:interacts_with", + "biolink:associated_with" + ] + }, + "eB": { + "subject": "nA", + "object": "nB", + "predicates": [ + "biolink:related_to_at_instance_level" + ] + }, + "eC": { + "subject": "nB", + "object": "creativeQueryObject", + "predicates": [ + "biolink:related_to_at_instance_level" + ] + } + } + } + } +} \ No newline at end of file diff --git a/data/templates/Pathfinder/pf-drug-gene-disease.json b/data/templates/Pathfinder/pf-drug-gene-disease.json new file mode 100644 index 00000000..e5032697 --- /dev/null +++ b/data/templates/Pathfinder/pf-drug-gene-disease.json @@ -0,0 +1,40 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories":["biolink:ChemicalEntity"] + }, + "nA": { + "categories":["biolink:Gene"] + }, + "creativeQueryObject": { + "categories":["biolink:DiseaseOrPhenotypicFeature"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "nA", + "predicates": [ + "biolink:regulates", + "biolink:affects", + "biolink:interacts_with", + "biolink:associated_with" + ] + }, + "eB": { + "subject": "nA", + "object": "creativeQueryObject", + "predicates": [ + "biolink:gene_associated_with_condition", + "biolink:biomarker_for", + "biolink:affects", + "biolink:causes", + "biolink:contributes_to" + ] + } + } + } + } +} \ No newline at end of file diff --git a/data/templates/Pathfinder/pf-drug-gene-physioAndpath-disease.json b/data/templates/Pathfinder/pf-drug-gene-physioAndpath-disease.json new file mode 100644 index 00000000..5e738321 --- /dev/null +++ b/data/templates/Pathfinder/pf-drug-gene-physioAndpath-disease.json @@ -0,0 +1,49 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories":["biolink:ChemicalEntity"] + }, + "nA": { + "categories":["biolink:Gene"] + }, + "nB": { + "categories":["biolink:PhysiologicalProcess", "biolink:Pathway"] + }, + "creativeQueryObject": { + "categories":["biolink:DiseaseOrPhenotypicFeature"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "nA", + "predicates": [ + "biolink:regulates", + "biolink:affects", + "biolink:interacts_with", + "biolink:associated_with" + ] + }, + "eB": { + "subject": "nA", + "object": "nB", + "predicates": [ + "biolink:affects", + "biolink:contributes_to" + ] + }, + "eC": { + "subject": "nB", + "object": "creativeQueryObject", + "predicates": [ + "biolink:affects", + "biolink:affected_by", + "biolink:occurs_in" + ] + } + } + } + } +} \ No newline at end of file From 8deeada313e8547b43acb2074a95f6027eaa85e2 Mon Sep 17 00:00:00 2001 From: tokebe <43009413+tokebe@users.noreply.github.com> Date: Wed, 20 Dec 2023 13:19:19 -0500 Subject: [PATCH 02/27] feat: allow inferred explain-type queries --- src/inferred_mode/inferred_mode.ts | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/src/inferred_mode/inferred_mode.ts b/src/inferred_mode/inferred_mode.ts index 31b2169f..2b1e35bf 100644 --- a/src/inferred_mode/inferred_mode.ts +++ b/src/inferred_mode/inferred_mode.ts @@ -102,11 +102,9 @@ export default class InferredQueryHandler { return false; } - const tooManyIDs = - 1 < - Object.values(this.queryGraph.nodes).reduce((sum, node) => { - return typeof node.ids !== 'undefined' ? sum + node.ids.length : sum; - }, 0); + const tooManyIDs = Object.values(this.queryGraph.nodes).some((node) => { + return typeof node.ids !== 'undefined' && node.ids.length > 1; + }); if (tooManyIDs) { const message = 'Inferred Mode queries with multiple IDs are not supported. Your query terminates.'; this.logs.push(new LogEntry('WARNING', null, message).getLog()); From 52bc25d404416d7c297684b17c73091463f91e70 Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Fri, 22 Mar 2024 18:53:33 -0700 Subject: [PATCH 03/27] identify pathfinder queries. identify templates --- src/index.ts | 61 +++++++++++++++++++++++++++- src/inferred_mode/inferred_mode.ts | 7 +++- src/inferred_mode/template_lookup.ts | 4 +- src/query_graph.ts | 8 ++-- 4 files changed, 72 insertions(+), 8 deletions(-) diff --git a/src/index.ts b/src/index.ts index e0a029ad..7e16b003 100644 --- a/src/index.ts +++ b/src/index.ts @@ -413,7 +413,7 @@ export default class TRAPIQueryHandler { async _processQueryGraph(queryGraph: TrapiQueryGraph): Promise { try { - const queryGraphHandler = new QueryGraph(queryGraph, this.options.schema); + const queryGraphHandler = new QueryGraph(queryGraph, this.options.schema, this._queryIsPathfinder()); const queryEdges = await queryGraphHandler.calculateEdges(); this.logs = [...this.logs, ...queryGraphHandler.logs]; return queryEdges; @@ -509,6 +509,12 @@ export default class TRAPIQueryHandler { } } + _queryIsPathfinder(): boolean { + const inferredEdgeCount = Object.values(this.queryGraph.edges).reduce((i, edge) => i + (edge.knowledge_type === 'inferred' ? 1 : 0), 0); + const pinnedNodes = Object.values(this.queryGraph.nodes).reduce((i, node) => i + (node.ids != null ? 1 : 0), 0); + return inferredEdgeCount === 3 && pinnedNodes == 2 && Object.keys(this.queryGraph.edges).length === 3 && Object.keys(this.queryGraph.nodes).length === 3; + } + _queryUsesInferredMode(): boolean { const inferredEdge = Object.values(this.queryGraph.edges).some((edge) => edge.knowledge_type === 'inferred'); return inferredEdge; @@ -519,7 +525,50 @@ export default class TRAPIQueryHandler { return oneHop; } - async _handleInferredEdges(): Promise { + async _handlePathfinder(): Promise { + const [unpinnedNodeId, unpinnedNode] = Object.entries(this.queryGraph.nodes).find(([_, node]) => !node.ids); + // remove unpinned node & all edges involving unpinned node for now + delete this.queryGraph.nodes[unpinnedNodeId]; + const intermediateEdges = Object.entries(this.queryGraph.edges).filter(([_, edge]) => edge.subject === unpinnedNodeId || edge.object === unpinnedNodeId); + const mainEdge = Object.entries(this.queryGraph.edges).find(([_, edge]) => edge.subject !== unpinnedNodeId && edge.object !== unpinnedNodeId); + + // intermediateEdges should be in order of n0 -> un & un -> n1 + if (intermediateEdges[0][1].subject === unpinnedNodeId) { + let temp = intermediateEdges[0]; + intermediateEdges[0] = intermediateEdges[1]; + intermediateEdges[1] = temp; + } + + // remove intermediates for creative execution + intermediateEdges.forEach(([edgeId, _]) => delete this.queryGraph.edges[edgeId]); + + if (Object.keys(this.queryGraph.edges).length !== 1) { + const message = 'Pathfinder Mode needs exactly one edge between nodes with IDs. Your query terminates.'; + debug(message); + this.logs.push(new LogEntry('WARNING', null, message).getLog()); + return; + } + + if (intermediateEdges[0][1].subject !== mainEdge[1].subject || intermediateEdges[1][1].object !== mainEdge[1].object || intermediateEdges[0][1].object !== unpinnedNodeId || intermediateEdges[1][1].subject !== unpinnedNodeId) { + const message = 'Intermediate edges for Pathfinder are incorrect. Your query terminates.'; + debug(message); + this.logs.push(new LogEntry('WARNING', null, message).getLog()); + return; + } + + // test + console.log("recognized pathfinder"); + + // run creative mode + await this._handleInferredEdges(true); + const creativeResponse = this.getResponse(); + + // restore query graph + this.queryGraph.nodes[unpinnedNodeId] = unpinnedNode; + intermediateEdges.forEach(([edgeId, edge]) => this.queryGraph.edges[edgeId] = edge); + } + + async _handleInferredEdges(pathfinder = false): Promise { if (!this._queryIsOneHop()) { const message = 'Inferred Mode edges are only supported in single-edge queries. Your query terminates.'; debug(message); @@ -534,6 +583,7 @@ export default class TRAPIQueryHandler { this.path, this.predicatePath, this.includeReasoner, + pathfinder ); const inferredQueryResponse = await inferredQueryHandler.query(); if (inferredQueryResponse) { @@ -668,6 +718,13 @@ export default class TRAPIQueryHandler { } debug(`(3) All edges created ${JSON.stringify(queryEdges)} `); + if (this._queryIsPathfinder()) { + const span2 = Telemetry.startSpan({ description: 'pathfinderExecution' }); + await this._handlePathfinder(); + span2?.finish(); + return; + } + if (this._queryUsesInferredMode()) { const span2 = Telemetry.startSpan({ description: 'creativeExecution' }); await this._handleInferredEdges(); diff --git a/src/inferred_mode/inferred_mode.ts b/src/inferred_mode/inferred_mode.ts index 31b2169f..0a5e41fd 100644 --- a/src/inferred_mode/inferred_mode.ts +++ b/src/inferred_mode/inferred_mode.ts @@ -51,6 +51,7 @@ export default class InferredQueryHandler { path: string; predicatePath: string; includeReasoner: boolean; + pathfinder: boolean; CREATIVE_LIMIT: number; constructor( parent: TRAPIQueryHandler, @@ -60,6 +61,7 @@ export default class InferredQueryHandler { path: string, predicatePath: string, includeReasoner: boolean, + pathfinder: boolean ) { this.parent = parent; this.queryGraph = queryGraph; @@ -68,6 +70,7 @@ export default class InferredQueryHandler { this.path = path; this.predicatePath = predicatePath; this.includeReasoner = includeReasoner; + this.pathfinder = pathfinder; this.CREATIVE_LIMIT = process.env.CREATIVE_LIMIT ? parseInt(process.env.CREATIVE_LIMIT) : 500; } @@ -107,7 +110,7 @@ export default class InferredQueryHandler { Object.values(this.queryGraph.nodes).reduce((sum, node) => { return typeof node.ids !== 'undefined' ? sum + node.ids.length : sum; }, 0); - if (tooManyIDs) { + if (tooManyIDs && !this.pathfinder) { const message = 'Inferred Mode queries with multiple IDs are not supported. Your query terminates.'; this.logs.push(new LogEntry('WARNING', null, message).getLog()); debug(message); @@ -195,7 +198,7 @@ export default class InferredQueryHandler { }, []); return [...arr, ...objectCombos]; }, []); - const templates = await getTemplates(lookupObjects); + const templates = await getTemplates(lookupObjects, this.pathfinder); const logMessage = `Got ${templates.length} inferred query templates.`; debug(logMessage); diff --git a/src/inferred_mode/template_lookup.ts b/src/inferred_mode/template_lookup.ts index 100dc5cc..c525f6bb 100644 --- a/src/inferred_mode/template_lookup.ts +++ b/src/inferred_mode/template_lookup.ts @@ -25,6 +25,7 @@ export interface TemplateGroup { object: string[]; qualifiers?: CompactQualifiers; templates: string[]; + pathfinder: boolean; } export interface CompactEdge { @@ -34,7 +35,7 @@ export interface CompactEdge { qualifiers: CompactQualifiers; } -export async function getTemplates(lookups: TemplateLookup[]): Promise { +export async function getTemplates(lookups: TemplateLookup[], pathfinder = false): Promise { async function getFiles(dir: string): Promise { const rootFiles = await fs.readdir(path.resolve(dir)); return await async.reduce(rootFiles, [] as string[], async (arr, fname: string) => { @@ -57,6 +58,7 @@ export async function getTemplates(lookups: TemplateLookup[]): Promise { const lookupMatch = lookups.some((lookup) => { return ( + group.pathfinder === pathfinder && group.subject.includes(lookup.subject) && group.object.includes(lookup.object) && group.predicate.includes(lookup.predicate) && diff --git a/src/query_graph.ts b/src/query_graph.ts index 7a6f9d80..cb1a0c2b 100644 --- a/src/query_graph.ts +++ b/src/query_graph.ts @@ -15,11 +15,13 @@ export default class QueryGraph { queryGraph: TrapiQueryGraph; schema: any; logs: StampedLog[]; + skipCycleDetection: boolean; nodes: { [QNodeID: string]: QNode }; edges: { [QEdgeID: string]: QEdge }; - constructor(queryGraph: TrapiQueryGraph, schema: any) { + constructor(queryGraph: TrapiQueryGraph, schema: any, skipCycleDetection = false) { this.queryGraph = queryGraph; this.schema = schema; + this.skipCycleDetection = skipCycleDetection; this.logs = []; } @@ -93,7 +95,7 @@ export default class QueryGraph { } for (const firstNode in nodes) { - if (nodes[firstNode].visited === true) continue; + if (nodes[firstNode].visited == true) continue; const stack: { curNode: string; parent: string | number }[] = [{ curNode: firstNode, parent: -1 }]; nodes[firstNode].visited = true; while (stack.length !== 0) { @@ -191,7 +193,7 @@ export default class QueryGraph { this._validateNodeProperties(queryGraph); this._validateEdgeProperties(queryGraph); this._validateBatchSize(queryGraph); - this._validateCycles(queryGraph); + !this.skipCycleDetection && this._validateCycles(queryGraph); this._validateNoDuplicateQualifierTypes(queryGraph); } From 60dc949af23c282b8be7bfd300fc817a83dd50e1 Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Mon, 25 Mar 2024 18:12:44 -0700 Subject: [PATCH 04/27] create pathfinder intermediate aux graphs & results --- src/index.ts | 77 +++++++++++++++++++++++++++++- src/inferred_mode/inferred_mode.ts | 14 +++++- src/types.ts | 4 ++ 3 files changed, 92 insertions(+), 3 deletions(-) diff --git a/src/index.ts b/src/index.ts index 7e16b003..0bc55792 100644 --- a/src/index.ts +++ b/src/index.ts @@ -530,7 +530,7 @@ export default class TRAPIQueryHandler { // remove unpinned node & all edges involving unpinned node for now delete this.queryGraph.nodes[unpinnedNodeId]; const intermediateEdges = Object.entries(this.queryGraph.edges).filter(([_, edge]) => edge.subject === unpinnedNodeId || edge.object === unpinnedNodeId); - const mainEdge = Object.entries(this.queryGraph.edges).find(([_, edge]) => edge.subject !== unpinnedNodeId && edge.object !== unpinnedNodeId); + const [mainEdgeID, mainEdge] = Object.entries(this.queryGraph.edges).find(([_, edge]) => edge.subject !== unpinnedNodeId && edge.object !== unpinnedNodeId); // intermediateEdges should be in order of n0 -> un & un -> n1 if (intermediateEdges[0][1].subject === unpinnedNodeId) { @@ -549,7 +549,7 @@ export default class TRAPIQueryHandler { return; } - if (intermediateEdges[0][1].subject !== mainEdge[1].subject || intermediateEdges[1][1].object !== mainEdge[1].object || intermediateEdges[0][1].object !== unpinnedNodeId || intermediateEdges[1][1].subject !== unpinnedNodeId) { + if (intermediateEdges[0][1].subject !== mainEdge.subject || intermediateEdges[1][1].object !== mainEdge.object || intermediateEdges[0][1].object !== unpinnedNodeId || intermediateEdges[1][1].subject !== unpinnedNodeId) { const message = 'Intermediate edges for Pathfinder are incorrect. Your query terminates.'; debug(message); this.logs.push(new LogEntry('WARNING', null, message).getLog()); @@ -562,10 +562,83 @@ export default class TRAPIQueryHandler { // run creative mode await this._handleInferredEdges(true); const creativeResponse = this.getResponse(); + const originalAnalyses = (creativeResponse as any).original_analyses; + delete (creativeResponse as any).original_analyses; // restore query graph this.queryGraph.nodes[unpinnedNodeId] = unpinnedNode; intermediateEdges.forEach(([edgeId, edge]) => this.queryGraph.edges[edgeId] = edge); + + // set up a graph structure + const kgEdge = creativeResponse.message.results[0].analyses[0].edge_bindings[mainEdgeID][0].id; + const kgSrc = creativeResponse.message.results[0].node_bindings[mainEdge.subject][0].id; + const kgDst = creativeResponse.message.results[0].node_bindings[mainEdge.object][0].id; + const dfsNodes: {[node: string]: {dst: string, edge: string}[]} = {}; + for (const supportGraph of creativeResponse.message.knowledge_graph.edges[kgEdge].attributes.find(attr => attr.attribute_type_id === 'biolink:support_graphs').value as string[]) { + const auxGraph = creativeResponse.message.auxiliary_graphs[supportGraph]; + for (const subEdge of auxGraph.edges) { + const kgSubEdge = creativeResponse.message.knowledge_graph.edges[subEdge]; + if (!dfsNodes[kgSubEdge.subject]) { + dfsNodes[kgSubEdge.subject] = []; + } + dfsNodes[kgSubEdge.subject].push({ dst: kgSubEdge.object, edge: subEdge }); + } + } + + // perform dfs + const stack = [{ node: kgSrc, path: [kgSrc] }]; + const newResultObject: {[id: string]: TrapiResult} = {}; + const newAuxGraphs: {[id: string]: {edges: Set}} = {}; + while (stack.length !== 0) { + const { node, path } = stack.pop(); + if (node === kgDst) { + if (path.length > 3) { + // loop through all intermediate nodes (nodes are even indices) + for (let i = 2; i < path.length - 2; i += 2) { + const intermediateNode = path[i]; + if (!(`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}` in newResultObject)) { + newResultObject[`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}`] = { + node_bindings: { + [mainEdge.subject]: [{ id: kgSrc }], + [mainEdge.object]: [{ id: kgDst }], + [unpinnedNodeId]: [{ id: intermediateNode }] + }, + analyses: [{ + resource_id: "infores:biothings-explorer", + edge_bindings: { + [mainEdgeID]: [{ id: kgEdge }] + }, + score: 1 + }], + }; + newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}`] = { edges: new Set(path.slice(1, i).filter((_, ind) => ind % 2 == 0)) }; + newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}`] = { edges: new Set(path.slice(i + 1).filter((_, ind) => ind % 2 == 0)) }; + } else { + path.slice(1, i).filter((_, ind) => ind % 2 == 0).forEach(edge => newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}`].edges.add(edge)); + path.slice(i + 1).filter((_, ind) => ind % 2 == 0).forEach(edge => newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}`].edges.add(edge)); + } + } + } + } else { + for (const neighbor of dfsNodes[node]) { + if (!path.includes(neighbor.dst)) { + stack.push({ node: neighbor.dst, path: [...path, neighbor.edge, neighbor.dst ] }); + } + } + } + } + + creativeResponse.message.results = Object.values(newResultObject); + + const finalNewAuxGraphs: {[id: string]: {edges: string[]}} = newAuxGraphs as any; + for (const auxGraph in finalNewAuxGraphs) { + finalNewAuxGraphs[auxGraph].edges = Array.from(finalNewAuxGraphs[auxGraph].edges); + } + Object.assign(creativeResponse.message.auxiliary_graphs, finalNewAuxGraphs); + + // TODO: Add knowledge graph edges & combine scoring information + + this.getResponse = () => creativeResponse; } async _handleInferredEdges(pathfinder = false): Promise { diff --git a/src/inferred_mode/inferred_mode.ts b/src/inferred_mode/inferred_mode.ts index 0a5e41fd..919ae2ed 100644 --- a/src/inferred_mode/inferred_mode.ts +++ b/src/inferred_mode/inferred_mode.ts @@ -16,6 +16,8 @@ import { TrapiQueryGraph, TrapiResponse, TrapiResult, + TrapiAnalysis, + CreativePathfinderResponse } from '../types'; const debug = Debug('bte:biothings-explorer-trapi:inferred-mode'); @@ -31,6 +33,9 @@ export interface CombinedResponse { }; }; logs: StampedLog[]; + original_analyses?: { + [graphId: string]: TrapiAnalysis; + } } export interface CombinedResponseReport { @@ -260,7 +265,7 @@ export default class InferredQueryHandler { combinedResponse: CombinedResponse, ): CombinedResponseReport { const span = Telemetry.startSpan({ description: 'creativeCombineResponse' }); - const newResponse = handler.getResponse(); + const newResponse: CreativePathfinderResponse = handler.getResponse(); const report: CombinedResponseReport = { querySuccess: 0, queryHadResults: false, @@ -286,6 +291,7 @@ export default class InferredQueryHandler { combinedResponse.message.auxiliary_graphs[auxGraphID] = auxGraph; } }); + // add results newResponse.message.results.forEach((result) => { const translatedResult: TrapiResult = { @@ -302,6 +308,7 @@ export default class InferredQueryHandler { }, ], }; + const resultCreativeSubjectID = translatedResult.node_bindings[qEdge.subject] .map((binding) => binding.id) .join(','); @@ -356,6 +363,10 @@ export default class InferredQueryHandler { [] as string[], ), }; + + if (this.pathfinder) { + combinedResponse.original_analyses[auxGraphID] = translatedResult.analyses[0]; + } } if (resultID in combinedResponse.message.results) { @@ -511,6 +522,7 @@ export default class InferredQueryHandler { results: {}, }, logs: this.logs, + ...(this.pathfinder && { original_analyses: {} }) } as CombinedResponse; // add/combine nodes const resultQueries = []; diff --git a/src/types.ts b/src/types.ts index 5e02e4ad..a6fe069b 100644 --- a/src/types.ts +++ b/src/types.ts @@ -168,6 +168,10 @@ export interface TrapiResponse { logs: TrapiLog[]; } +export interface CreativePathfinderResponse extends TrapiResponse { + scores?: { [resID: string]: number }; +} + export type APIDefinition = { // Must have one of id or infores id?: string; // SmartAPI ID, takes priority over infores From f8fe4e2b5918c397c2059d2e26a7b23d6c80b01d Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Tue, 26 Mar 2024 16:39:49 -0700 Subject: [PATCH 05/27] add kg edges to pathfinder --- src/index.ts | 80 ++++++++++++++++++++++++++++++++++++++++++---------- 1 file changed, 65 insertions(+), 15 deletions(-) diff --git a/src/index.ts b/src/index.ts index 0bc55792..1d2f8b8a 100644 --- a/src/index.ts +++ b/src/index.ts @@ -573,15 +573,18 @@ export default class TRAPIQueryHandler { const kgEdge = creativeResponse.message.results[0].analyses[0].edge_bindings[mainEdgeID][0].id; const kgSrc = creativeResponse.message.results[0].node_bindings[mainEdge.subject][0].id; const kgDst = creativeResponse.message.results[0].node_bindings[mainEdge.object][0].id; - const dfsNodes: {[node: string]: {dst: string, edge: string}[]} = {}; + const dfsNodes: {[node: string]: {[dst: string]: string[]}} = {}; for (const supportGraph of creativeResponse.message.knowledge_graph.edges[kgEdge].attributes.find(attr => attr.attribute_type_id === 'biolink:support_graphs').value as string[]) { const auxGraph = creativeResponse.message.auxiliary_graphs[supportGraph]; for (const subEdge of auxGraph.edges) { const kgSubEdge = creativeResponse.message.knowledge_graph.edges[subEdge]; if (!dfsNodes[kgSubEdge.subject]) { - dfsNodes[kgSubEdge.subject] = []; + dfsNodes[kgSubEdge.subject] = {}; } - dfsNodes[kgSubEdge.subject].push({ dst: kgSubEdge.object, edge: subEdge }); + if (!dfsNodes[kgSubEdge.subject][kgSubEdge.object]) { + dfsNodes[kgSubEdge.subject][kgSubEdge.object] = []; + } + dfsNodes[kgSubEdge.subject][kgSubEdge.object].push(subEdge); } } @@ -592,10 +595,23 @@ export default class TRAPIQueryHandler { while (stack.length !== 0) { const { node, path } = stack.pop(); if (node === kgDst) { - if (path.length > 3) { - // loop through all intermediate nodes (nodes are even indices) - for (let i = 2; i < path.length - 2; i += 2) { + if (path.length > 2) { + // loop through all intermediate nodes + for (let i = 1; i < path.length - 1; i++) { const intermediateNode = path[i]; + const firstEdges = []; + const secondEdges = []; + for (let j = 0; j < i; j++) { + for (let edge of dfsNodes[path[j]][path[j+1]]) { + firstEdges.push(edge); + } + } + for (let j = i; j < path.length - 1; j++) { + for (let edge of dfsNodes[path[j]][path[j+1]]) { + secondEdges.push(edge); + } + } + if (!(`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}` in newResultObject)) { newResultObject[`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}`] = { node_bindings: { @@ -606,23 +622,54 @@ export default class TRAPIQueryHandler { analyses: [{ resource_id: "infores:biothings-explorer", edge_bindings: { - [mainEdgeID]: [{ id: kgEdge }] + [mainEdgeID]: [{ id: kgEdge }], + [intermediateEdges[0][0]]: [{ id: `pathfinder-${kgSrc}-${intermediateNode}` }], + [intermediateEdges[1][0]]: [{ id: `pathfinder-${intermediateNode}-${kgDst}` }], }, score: 1 }], }; - newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}`] = { edges: new Set(path.slice(1, i).filter((_, ind) => ind % 2 == 0)) }; - newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}`] = { edges: new Set(path.slice(i + 1).filter((_, ind) => ind % 2 == 0)) }; + creativeResponse.message.knowledge_graph.edges[`pathfinder-${kgSrc}-${intermediateNode}`] = { + predicate: 'biolink:related_to', + subject: kgSrc, + object: intermediateNode, + sources: [ + { + resource_id: this.options.provenanceUsesServiceProvider + ? 'infores:service-provider-trapi' + : 'infores:biothings-explorer', + resource_role: 'primary_knowledge_source', + }, + ], + attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${kgSrc}-${intermediateNode}-support`] }], + }; + creativeResponse.message.knowledge_graph.edges[`pathfinder-${intermediateNode}-${kgDst}`] = { + predicate: 'biolink:related_to', + subject: intermediateNode, + object: kgDst, + sources: [ + { + resource_id: this.options.provenanceUsesServiceProvider + ? 'infores:service-provider-trapi' + : 'infores:biothings-explorer', + resource_role: 'primary_knowledge_source', + }, + ], + attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${intermediateNode}-${kgDst}-support`] }], + }; + newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`] = { edges: new Set(firstEdges) }; + newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`] = { edges: new Set(secondEdges) }; + } else { - path.slice(1, i).filter((_, ind) => ind % 2 == 0).forEach(edge => newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}`].edges.add(edge)); - path.slice(i + 1).filter((_, ind) => ind % 2 == 0).forEach(edge => newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}`].edges.add(edge)); + firstEdges.forEach(edge => newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`].edges.add(edge)); + secondEdges.forEach(edge => newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`].edges.add(edge)); } } } } else { - for (const neighbor of dfsNodes[node]) { - if (!path.includes(neighbor.dst)) { - stack.push({ node: neighbor.dst, path: [...path, neighbor.edge, neighbor.dst ] }); + for (const neighbor in dfsNodes[node]) { + if (!path.includes(neighbor)) { + stack.push({ node: neighbor, path: [...path, neighbor ] }); } } } @@ -636,7 +683,10 @@ export default class TRAPIQueryHandler { } Object.assign(creativeResponse.message.auxiliary_graphs, finalNewAuxGraphs); - // TODO: Add knowledge graph edges & combine scoring information + // TODO: combine scoring information + // TODO: Fix 500 cap impl + // TODO: formatting + // TODO: move to a seperate file if this gets too big? this.getResponse = () => creativeResponse; } From 9e1e0f732c77da3e4fb417b0d935eed4242853b6 Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Tue, 26 Mar 2024 17:25:13 -0700 Subject: [PATCH 06/27] score pathfinder results --- src/index.ts | 21 ++++++++++++++++++++- 1 file changed, 20 insertions(+), 1 deletion(-) diff --git a/src/index.ts b/src/index.ts index 1d2f8b8a..7de0eb03 100644 --- a/src/index.ts +++ b/src/index.ts @@ -3,6 +3,7 @@ import path from 'path'; import QueryGraph from './query_graph'; import KnowledgeGraph from './graph/knowledge_graph'; import TrapiResultsAssembler from './results_assembly/query_results'; +import { scaled_sigmoid, inverse_scaled_sigmoid } from './results_assembly/score'; import InvalidQueryGraphError from './exceptions/invalid_query_graph_error'; import Debug from 'debug'; const debug = Debug('bte:biothings-explorer-trapi:main'); @@ -574,6 +575,7 @@ export default class TRAPIQueryHandler { const kgSrc = creativeResponse.message.results[0].node_bindings[mainEdge.subject][0].id; const kgDst = creativeResponse.message.results[0].node_bindings[mainEdge.object][0].id; const dfsNodes: {[node: string]: {[dst: string]: string[]}} = {}; + const supportGraphsPerNode: {[node: string]: Set} = {}; for (const supportGraph of creativeResponse.message.knowledge_graph.edges[kgEdge].attributes.find(attr => attr.attribute_type_id === 'biolink:support_graphs').value as string[]) { const auxGraph = creativeResponse.message.auxiliary_graphs[supportGraph]; for (const subEdge of auxGraph.edges) { @@ -585,6 +587,11 @@ export default class TRAPIQueryHandler { dfsNodes[kgSubEdge.subject][kgSubEdge.object] = []; } dfsNodes[kgSubEdge.subject][kgSubEdge.object].push(subEdge); + + if (!supportGraphsPerNode[kgSubEdge.subject]) { + supportGraphsPerNode[kgSubEdge.subject] = new Set(); + } + supportGraphsPerNode[kgSubEdge.subject].add(supportGraph); } } @@ -626,7 +633,7 @@ export default class TRAPIQueryHandler { [intermediateEdges[0][0]]: [{ id: `pathfinder-${kgSrc}-${intermediateNode}` }], [intermediateEdges[1][0]]: [{ id: `pathfinder-${intermediateNode}-${kgDst}` }], }, - score: 1 + score: undefined }], }; creativeResponse.message.knowledge_graph.edges[`pathfinder-${kgSrc}-${intermediateNode}`] = { @@ -660,6 +667,18 @@ export default class TRAPIQueryHandler { newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`] = { edges: new Set(firstEdges) }; newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`] = { edges: new Set(secondEdges) }; + // calculate score + if (supportGraphsPerNode[intermediateNode]?.size > 0) { + let score = undefined; + for (const supportGraph of supportGraphsPerNode[intermediateNode]) { + score = scaled_sigmoid( + inverse_scaled_sigmoid(score ?? 0) + + inverse_scaled_sigmoid(originalAnalyses[supportGraph].score), + ); + } + newResultObject[`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}`].analyses[0].score = score; + } + } else { firstEdges.forEach(edge => newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`].edges.add(edge)); secondEdges.forEach(edge => newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`].edges.add(edge)); From bd77b6d67c0952fda44d61e9f3a942108002365c Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Wed, 27 Mar 2024 17:33:22 -0700 Subject: [PATCH 07/27] implementation of creative limit for pathfinder --- src/index.ts | 21 ++++++++++++++------- src/inferred_mode/inferred_mode.ts | 23 +++++++++++++++++++---- 2 files changed, 33 insertions(+), 11 deletions(-) diff --git a/src/index.ts b/src/index.ts index 7de0eb03..33e1da7f 100644 --- a/src/index.ts +++ b/src/index.ts @@ -557,9 +557,6 @@ export default class TRAPIQueryHandler { return; } - // test - console.log("recognized pathfinder"); - // run creative mode await this._handleInferredEdges(true); const creativeResponse = this.getResponse(); @@ -569,6 +566,14 @@ export default class TRAPIQueryHandler { // restore query graph this.queryGraph.nodes[unpinnedNodeId] = unpinnedNode; intermediateEdges.forEach(([edgeId, edge]) => this.queryGraph.edges[edgeId] = edge); + creativeResponse.message.query_graph = this.queryGraph; + + // if no results then we are done + if (creativeResponse.message.results.length === 0) { + this.getResponse = () => creativeResponse; + return; + } + // set up a graph structure const kgEdge = creativeResponse.message.results[0].analyses[0].edge_bindings[mainEdgeID][0].id; @@ -694,18 +699,20 @@ export default class TRAPIQueryHandler { } } - creativeResponse.message.results = Object.values(newResultObject); - + creativeResponse.message.results = Object.values(newResultObject).sort((a, b) => (b.analyses[0].score ?? 0) - (a.analyses[0].score ?? 0)).slice(0, process.env.CREATIVE_LIMIT ? parseInt(process.env.CREATIVE_LIMIT) : 500); + creativeResponse.description = `Query processed successfully, retrieved ${creativeResponse.message.results.length} results.` + const finalNewAuxGraphs: {[id: string]: {edges: string[]}} = newAuxGraphs as any; for (const auxGraph in finalNewAuxGraphs) { finalNewAuxGraphs[auxGraph].edges = Array.from(finalNewAuxGraphs[auxGraph].edges); } Object.assign(creativeResponse.message.auxiliary_graphs, finalNewAuxGraphs); - // TODO: combine scoring information - // TODO: Fix 500 cap impl + // TODO: Add logs/debug statements in this function // TODO: formatting // TODO: move to a seperate file if this gets too big? + // TODO: test other templates + // TODO: make unit tests this.getResponse = () => creativeResponse; } diff --git a/src/inferred_mode/inferred_mode.ts b/src/inferred_mode/inferred_mode.ts index 919ae2ed..8911990f 100644 --- a/src/inferred_mode/inferred_mode.ts +++ b/src/inferred_mode/inferred_mode.ts @@ -292,6 +292,9 @@ export default class InferredQueryHandler { } }); + // modified count used for pathfinder + const pfIntermediateSet = new Set(); + // add results newResponse.message.results.forEach((result) => { const translatedResult: TrapiResult = { @@ -309,6 +312,17 @@ export default class InferredQueryHandler { ], }; + if (this.pathfinder) { + for (let [nodeID, bindings] of Object.entries(result.node_bindings)) { + if (nodeID === "creativeQuerySubject" || nodeID === "creativeQueryObject") { + continue; + } + for (const binding of bindings) { + pfIntermediateSet.add(binding.id); + } + } + } + const resultCreativeSubjectID = translatedResult.node_bindings[qEdge.subject] .map((binding) => binding.id) .join(','); @@ -436,8 +450,9 @@ export default class InferredQueryHandler { } report.querySuccess = 1; - if (Object.keys(combinedResponse.message.results).length >= this.CREATIVE_LIMIT && !report.creativeLimitHit) { - report.creativeLimitHit = Object.keys(newResponse.message.results).length; + const resSize = this.pathfinder ? pfIntermediateSet.size : Object.keys(combinedResponse.message.results).length; + if (resSize >= this.CREATIVE_LIMIT && !report.creativeLimitHit) { + report.creativeLimitHit = resSize; } span.finish(); return report; @@ -568,9 +583,9 @@ export default class InferredQueryHandler { stop = true; const message = [ `Addition of ${creativeLimitHit} results from Template ${i + 1}`, - Object.keys(combinedResponse.message.results).length === this.CREATIVE_LIMIT ? ' meets ' : ' exceeds ', + creativeLimitHit === this.CREATIVE_LIMIT ? ' meets ' : ' exceeds ', `creative result maximum of ${this.CREATIVE_LIMIT} (reaching ${ - Object.keys(combinedResponse.message.results).length + creativeLimitHit } merged). `, `Response will be truncated to top-scoring ${this.CREATIVE_LIMIT} results. Skipping remaining ${ subQueries.length - (i + 1) From 24eb56f63820dd5f6d58f97e2eee184b69619aff Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Thu, 28 Mar 2024 16:35:45 -0700 Subject: [PATCH 08/27] add debug statements --- src/index.ts | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/src/index.ts b/src/index.ts index 33e1da7f..73a6eb49 100644 --- a/src/index.ts +++ b/src/index.ts @@ -600,6 +600,10 @@ export default class TRAPIQueryHandler { } } + const message1 = '[Pathfinder]: Performing serach for intermediate nodes.'; + debug(message1); + this.logs.push(new LogEntry('INFO', null, message1).getLog()); + // perform dfs const stack = [{ node: kgSrc, path: [kgSrc] }]; const newResultObject: {[id: string]: TrapiResult} = {}; @@ -707,11 +711,13 @@ export default class TRAPIQueryHandler { finalNewAuxGraphs[auxGraph].edges = Array.from(finalNewAuxGraphs[auxGraph].edges); } Object.assign(creativeResponse.message.auxiliary_graphs, finalNewAuxGraphs); + + const message2 = `[Pathfinder]: Pathfinder found ${creativeResponse.message.results.length} intermediate nodes and created ${Object.keys(finalNewAuxGraphs).length} support graphs.`; + debug(message2); + this.logs.push(new LogEntry('INFO', null, message2).getLog()); - // TODO: Add logs/debug statements in this function // TODO: formatting // TODO: move to a seperate file if this gets too big? - // TODO: test other templates // TODO: make unit tests this.getResponse = () => creativeResponse; From f2832f09362c89f3fac545281be4bcf1eecff9ce Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Fri, 29 Mar 2024 16:54:21 -0700 Subject: [PATCH 09/27] code reorganization for pathfinder --- src/index.ts | 229 ++----------------------- src/inferred_mode/inferred_mode.ts | 2 +- src/inferred_mode/pathfinder.ts | 261 +++++++++++++++++++++++++++++ 3 files changed, 280 insertions(+), 212 deletions(-) create mode 100644 src/inferred_mode/pathfinder.ts diff --git a/src/index.ts b/src/index.ts index 73a6eb49..e7ba0d7d 100644 --- a/src/index.ts +++ b/src/index.ts @@ -3,7 +3,6 @@ import path from 'path'; import QueryGraph from './query_graph'; import KnowledgeGraph from './graph/knowledge_graph'; import TrapiResultsAssembler from './results_assembly/query_results'; -import { scaled_sigmoid, inverse_scaled_sigmoid } from './results_assembly/score'; import InvalidQueryGraphError from './exceptions/invalid_query_graph_error'; import Debug from 'debug'; const debug = Debug('bte:biothings-explorer-trapi:main'); @@ -16,6 +15,7 @@ import { promises as fs } from 'fs'; import { getDescendants } from '@biothings-explorer/node-expansion'; import { resolveSRI, SRINodeNormFailure } from 'biomedical_id_resolver'; import InferredQueryHandler from './inferred_mode/inferred_mode'; +import PathfinderQueryHandler from './inferred_mode/pathfinder'; import KGNode from './graph/kg_node'; import KGEdge from './graph/kg_edge'; import { @@ -449,13 +449,11 @@ export default class TRAPIQueryHandler { let log_msg: string; if (currentQEdge.reverse) { - log_msg = `qEdge ${currentQEdge.id} (reversed): ${currentQEdge.object.categories} > ${ - currentQEdge.predicate ? `${currentQEdge.predicate} > ` : '' - }${currentQEdge.subject.categories}`; + log_msg = `qEdge ${currentQEdge.id} (reversed): ${currentQEdge.object.categories} > ${currentQEdge.predicate ? `${currentQEdge.predicate} > ` : '' + }${currentQEdge.subject.categories}`; } else { - log_msg = `qEdge ${currentQEdge.id}: ${currentQEdge.subject.categories} > ${ - currentQEdge.predicate ? `${currentQEdge.predicate} > ` : '' - }${currentQEdge.object.categories}`; + log_msg = `qEdge ${currentQEdge.id}: ${currentQEdge.subject.categories} > ${currentQEdge.predicate ? `${currentQEdge.predicate} > ` : '' + }${currentQEdge.object.categories}`; } this.logs.push(new LogEntry('INFO', null, log_msg).getLog()); @@ -496,9 +494,8 @@ export default class TRAPIQueryHandler { }); const qEdgesLogStr = qEdgesToLog.length > 1 ? `[${qEdgesToLog.join(', ')}]` : `${qEdgesToLog.join(', ')}`; if (len > 0) { - const terminateLog = `Query Edge${len !== 1 ? 's' : ''} ${qEdgesLogStr} ${ - len !== 1 ? 'have' : 'has' - } no MetaKG edges. Your query terminates.`; + const terminateLog = `Query Edge${len !== 1 ? 's' : ''} ${qEdgesLogStr} ${len !== 1 ? 'have' : 'has' + } no MetaKG edges. Your query terminates.`; debug(terminateLog); this.logs.push(new LogEntry('WARNING', null, terminateLog).getLog()); return false; @@ -527,203 +524,15 @@ export default class TRAPIQueryHandler { } async _handlePathfinder(): Promise { - const [unpinnedNodeId, unpinnedNode] = Object.entries(this.queryGraph.nodes).find(([_, node]) => !node.ids); - // remove unpinned node & all edges involving unpinned node for now - delete this.queryGraph.nodes[unpinnedNodeId]; - const intermediateEdges = Object.entries(this.queryGraph.edges).filter(([_, edge]) => edge.subject === unpinnedNodeId || edge.object === unpinnedNodeId); - const [mainEdgeID, mainEdge] = Object.entries(this.queryGraph.edges).find(([_, edge]) => edge.subject !== unpinnedNodeId && edge.object !== unpinnedNodeId); - - // intermediateEdges should be in order of n0 -> un & un -> n1 - if (intermediateEdges[0][1].subject === unpinnedNodeId) { - let temp = intermediateEdges[0]; - intermediateEdges[0] = intermediateEdges[1]; - intermediateEdges[1] = temp; - } - - // remove intermediates for creative execution - intermediateEdges.forEach(([edgeId, _]) => delete this.queryGraph.edges[edgeId]); - - if (Object.keys(this.queryGraph.edges).length !== 1) { - const message = 'Pathfinder Mode needs exactly one edge between nodes with IDs. Your query terminates.'; - debug(message); - this.logs.push(new LogEntry('WARNING', null, message).getLog()); - return; - } - - if (intermediateEdges[0][1].subject !== mainEdge.subject || intermediateEdges[1][1].object !== mainEdge.object || intermediateEdges[0][1].object !== unpinnedNodeId || intermediateEdges[1][1].subject !== unpinnedNodeId) { - const message = 'Intermediate edges for Pathfinder are incorrect. Your query terminates.'; - debug(message); - this.logs.push(new LogEntry('WARNING', null, message).getLog()); - return; - } - - // run creative mode - await this._handleInferredEdges(true); - const creativeResponse = this.getResponse(); - const originalAnalyses = (creativeResponse as any).original_analyses; - delete (creativeResponse as any).original_analyses; - - // restore query graph - this.queryGraph.nodes[unpinnedNodeId] = unpinnedNode; - intermediateEdges.forEach(([edgeId, edge]) => this.queryGraph.edges[edgeId] = edge); - creativeResponse.message.query_graph = this.queryGraph; - - // if no results then we are done - if (creativeResponse.message.results.length === 0) { - this.getResponse = () => creativeResponse; - return; - } - - - // set up a graph structure - const kgEdge = creativeResponse.message.results[0].analyses[0].edge_bindings[mainEdgeID][0].id; - const kgSrc = creativeResponse.message.results[0].node_bindings[mainEdge.subject][0].id; - const kgDst = creativeResponse.message.results[0].node_bindings[mainEdge.object][0].id; - const dfsNodes: {[node: string]: {[dst: string]: string[]}} = {}; - const supportGraphsPerNode: {[node: string]: Set} = {}; - for (const supportGraph of creativeResponse.message.knowledge_graph.edges[kgEdge].attributes.find(attr => attr.attribute_type_id === 'biolink:support_graphs').value as string[]) { - const auxGraph = creativeResponse.message.auxiliary_graphs[supportGraph]; - for (const subEdge of auxGraph.edges) { - const kgSubEdge = creativeResponse.message.knowledge_graph.edges[subEdge]; - if (!dfsNodes[kgSubEdge.subject]) { - dfsNodes[kgSubEdge.subject] = {}; - } - if (!dfsNodes[kgSubEdge.subject][kgSubEdge.object]) { - dfsNodes[kgSubEdge.subject][kgSubEdge.object] = []; - } - dfsNodes[kgSubEdge.subject][kgSubEdge.object].push(subEdge); - - if (!supportGraphsPerNode[kgSubEdge.subject]) { - supportGraphsPerNode[kgSubEdge.subject] = new Set(); - } - supportGraphsPerNode[kgSubEdge.subject].add(supportGraph); - } - } - - const message1 = '[Pathfinder]: Performing serach for intermediate nodes.'; - debug(message1); - this.logs.push(new LogEntry('INFO', null, message1).getLog()); - - // perform dfs - const stack = [{ node: kgSrc, path: [kgSrc] }]; - const newResultObject: {[id: string]: TrapiResult} = {}; - const newAuxGraphs: {[id: string]: {edges: Set}} = {}; - while (stack.length !== 0) { - const { node, path } = stack.pop(); - if (node === kgDst) { - if (path.length > 2) { - // loop through all intermediate nodes - for (let i = 1; i < path.length - 1; i++) { - const intermediateNode = path[i]; - const firstEdges = []; - const secondEdges = []; - for (let j = 0; j < i; j++) { - for (let edge of dfsNodes[path[j]][path[j+1]]) { - firstEdges.push(edge); - } - } - for (let j = i; j < path.length - 1; j++) { - for (let edge of dfsNodes[path[j]][path[j+1]]) { - secondEdges.push(edge); - } - } - - if (!(`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}` in newResultObject)) { - newResultObject[`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}`] = { - node_bindings: { - [mainEdge.subject]: [{ id: kgSrc }], - [mainEdge.object]: [{ id: kgDst }], - [unpinnedNodeId]: [{ id: intermediateNode }] - }, - analyses: [{ - resource_id: "infores:biothings-explorer", - edge_bindings: { - [mainEdgeID]: [{ id: kgEdge }], - [intermediateEdges[0][0]]: [{ id: `pathfinder-${kgSrc}-${intermediateNode}` }], - [intermediateEdges[1][0]]: [{ id: `pathfinder-${intermediateNode}-${kgDst}` }], - }, - score: undefined - }], - }; - creativeResponse.message.knowledge_graph.edges[`pathfinder-${kgSrc}-${intermediateNode}`] = { - predicate: 'biolink:related_to', - subject: kgSrc, - object: intermediateNode, - sources: [ - { - resource_id: this.options.provenanceUsesServiceProvider - ? 'infores:service-provider-trapi' - : 'infores:biothings-explorer', - resource_role: 'primary_knowledge_source', - }, - ], - attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${kgSrc}-${intermediateNode}-support`] }], - }; - creativeResponse.message.knowledge_graph.edges[`pathfinder-${intermediateNode}-${kgDst}`] = { - predicate: 'biolink:related_to', - subject: intermediateNode, - object: kgDst, - sources: [ - { - resource_id: this.options.provenanceUsesServiceProvider - ? 'infores:service-provider-trapi' - : 'infores:biothings-explorer', - resource_role: 'primary_knowledge_source', - }, - ], - attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${intermediateNode}-${kgDst}-support`] }], - }; - newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`] = { edges: new Set(firstEdges) }; - newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`] = { edges: new Set(secondEdges) }; - - // calculate score - if (supportGraphsPerNode[intermediateNode]?.size > 0) { - let score = undefined; - for (const supportGraph of supportGraphsPerNode[intermediateNode]) { - score = scaled_sigmoid( - inverse_scaled_sigmoid(score ?? 0) + - inverse_scaled_sigmoid(originalAnalyses[supportGraph].score), - ); - } - newResultObject[`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}`].analyses[0].score = score; - } - - } else { - firstEdges.forEach(edge => newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`].edges.add(edge)); - secondEdges.forEach(edge => newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`].edges.add(edge)); - } - } - } - } else { - for (const neighbor in dfsNodes[node]) { - if (!path.includes(neighbor)) { - stack.push({ node: neighbor, path: [...path, neighbor ] }); - } - } - } - } - - creativeResponse.message.results = Object.values(newResultObject).sort((a, b) => (b.analyses[0].score ?? 0) - (a.analyses[0].score ?? 0)).slice(0, process.env.CREATIVE_LIMIT ? parseInt(process.env.CREATIVE_LIMIT) : 500); - creativeResponse.description = `Query processed successfully, retrieved ${creativeResponse.message.results.length} results.` - - const finalNewAuxGraphs: {[id: string]: {edges: string[]}} = newAuxGraphs as any; - for (const auxGraph in finalNewAuxGraphs) { - finalNewAuxGraphs[auxGraph].edges = Array.from(finalNewAuxGraphs[auxGraph].edges); - } - Object.assign(creativeResponse.message.auxiliary_graphs, finalNewAuxGraphs); - - const message2 = `[Pathfinder]: Pathfinder found ${creativeResponse.message.results.length} intermediate nodes and created ${Object.keys(finalNewAuxGraphs).length} support graphs.`; - debug(message2); - this.logs.push(new LogEntry('INFO', null, message2).getLog()); - - // TODO: formatting - // TODO: move to a seperate file if this gets too big? // TODO: make unit tests + // TODO: add spans in the class + const pathfinderHandler = new PathfinderQueryHandler(this.logs, this.queryGraph, this); + const pathfinderResponse = await pathfinderHandler.query(); - this.getResponse = () => creativeResponse; + this.getResponse = () => pathfinderResponse; } - async _handleInferredEdges(pathfinder = false): Promise { + async _handleInferredEdges(): Promise { if (!this._queryIsOneHop()) { const message = 'Inferred Mode edges are only supported in single-edge queries. Your query terminates.'; debug(message); @@ -737,8 +546,7 @@ export default class TRAPIQueryHandler { this.options, this.path, this.predicatePath, - this.includeReasoner, - pathfinder + this.includeReasoner ); const inferredQueryResponse = await inferredQueryHandler.query(); if (inferredQueryResponse) { @@ -816,8 +624,7 @@ export default class TRAPIQueryHandler { new LogEntry( 'INFO', null, - `Execution Summary: (${KGNodes}) nodes / (${kgEdges}) edges / (${results}) results; (${resultQueries}/${queries}) queries${ - cached ? ` (${cached} cached qEdges)` : '' + `Execution Summary: (${KGNodes}) nodes / (${kgEdges}) edges / (${results}) results; (${resultQueries}/${queries}) queries${cached ? ` (${cached} cached qEdges)` : '' } returned results from(${sources.length}) unique API${sources.length === 1 ? 's' : ''}`, ).getLog(), new LogEntry('INFO', null, `APIs: ${sources.join(', ')} `).getLog(), @@ -874,10 +681,10 @@ export default class TRAPIQueryHandler { debug(`(3) All edges created ${JSON.stringify(queryEdges)} `); if (this._queryIsPathfinder()) { - const span2 = Telemetry.startSpan({ description: 'pathfinderExecution' }); - await this._handlePathfinder(); - span2?.finish(); - return; + const span2 = Telemetry.startSpan({ description: 'pathfinderExecution' }); + await this._handlePathfinder(); + span2?.finish(); + return; } if (this._queryUsesInferredMode()) { diff --git a/src/inferred_mode/inferred_mode.ts b/src/inferred_mode/inferred_mode.ts index 6b05d583..bddd3d38 100644 --- a/src/inferred_mode/inferred_mode.ts +++ b/src/inferred_mode/inferred_mode.ts @@ -66,7 +66,7 @@ export default class InferredQueryHandler { path: string, predicatePath: string, includeReasoner: boolean, - pathfinder: boolean + pathfinder = false ) { this.parent = parent; this.queryGraph = queryGraph; diff --git a/src/inferred_mode/pathfinder.ts b/src/inferred_mode/pathfinder.ts new file mode 100644 index 00000000..3d8cc815 --- /dev/null +++ b/src/inferred_mode/pathfinder.ts @@ -0,0 +1,261 @@ +import TRAPIQueryHandler, { QueryHandlerOptions } from '../index'; +import { TrapiResponse, TrapiQEdge, TrapiResult, TrapiQueryGraph, TrapiQNode, TrapiAnalysis } from '../types'; +import InferredQueryHandler from './inferred_mode'; +import { scaled_sigmoid, inverse_scaled_sigmoid } from '../results_assembly/score'; +import { LogEntry, StampedLog } from '@biothings-explorer/utils'; +import Debug from 'debug'; +const debug = Debug('bte:biothings-explorer-trapi:pathfinder'); + +interface ResultAuxObject { + results: ResultObject; + graphs: AuxGraphObject; +} + +interface ResultObject { + [id: string]: TrapiResult +} + +interface AuxGraphObject { + [id: string]: { edges: Set } +} + +interface DfsGraph { + [node: string]: { [dst: string]: string[] } +} + +export default class PathfinderQueryHandler { + logs: StampedLog[]; + CREATIVE_LIMIT: number; + options: QueryHandlerOptions; + queryGraph: TrapiQueryGraph; + parent: TRAPIQueryHandler; + + // assigned internally + unpinnedNodeId: string; + unpinnedNode: TrapiQNode; + intermediateEdges: [string, TrapiQEdge][]; + mainEdgeId: string; + mainEdge: TrapiQEdge; + originalAnalyses: { [id: string]: TrapiAnalysis }; + + constructor(logs: StampedLog[], queryGraph: TrapiQueryGraph, parent: TRAPIQueryHandler) { + this.logs = logs; + this.options = parent.options; + this.parent = parent; + this.queryGraph = queryGraph; + this.CREATIVE_LIMIT = process.env.CREATIVE_LIMIT ? parseInt(process.env.CREATIVE_LIMIT) : 500; + } + + async query() { + [this.unpinnedNodeId, this.unpinnedNode] = Object.entries(this.queryGraph.nodes).find(([_, node]) => !node.ids); + // remove unpinned node & all edges involving unpinned node for now + delete this.queryGraph.nodes[this.unpinnedNodeId]; + this.intermediateEdges = Object.entries(this.queryGraph.edges).filter(([_, edge]) => edge.subject === this.unpinnedNodeId || edge.object === this.unpinnedNodeId); + [this.mainEdgeId, this.mainEdge] = Object.entries(this.queryGraph.edges).find(([_, edge]) => edge.subject !== this.unpinnedNodeId && edge.object !== this.unpinnedNodeId); + + // intermediateEdges should be in order of n0 -> un & un -> n1 + if (this.intermediateEdges[0][1].subject === this.unpinnedNodeId) { + let temp = this.intermediateEdges[0]; + this.intermediateEdges[0] = this.intermediateEdges[1]; + this.intermediateEdges[1] = temp; + } + + // remove intermediates for creative execution + this.intermediateEdges.forEach(([edgeId, _]) => delete this.queryGraph.edges[edgeId]); + + if (Object.keys(this.queryGraph.edges).length !== 1) { + const message = 'Pathfinder Mode needs exactly one edge between nodes with IDs. Your query terminates.'; + debug(message); + this.logs.push(new LogEntry('WARNING', null, message).getLog()); + return; + } + + if (this.intermediateEdges[0][1].subject !== this.mainEdge.subject || this.intermediateEdges[1][1].object !== this.mainEdge.object || this.intermediateEdges[0][1].object !== this.unpinnedNodeId || this.intermediateEdges[1][1].subject !== this.unpinnedNodeId) { + const message = 'Intermediate edges for Pathfinder are incorrect. Your query terminates.'; + debug(message); + this.logs.push(new LogEntry('WARNING', null, message).getLog()); + return; + } + + // run creative mode + const inferredQueryHandler = new InferredQueryHandler( + this.parent, + this.queryGraph, + this.logs, + this.options, + this.parent.path, + this.parent.predicatePath, + this.parent.includeReasoner, + true + ); + const creativeResponse = await inferredQueryHandler.query(); + + // restore query graph + this.queryGraph.nodes[this.unpinnedNodeId] = this.unpinnedNode; + this.intermediateEdges.forEach(([edgeId, edge]) => this.queryGraph.edges[edgeId] = edge); + creativeResponse.message.query_graph = this.queryGraph; + + this.parse(creativeResponse); + + return creativeResponse; + } + + parse(creativeResponse: TrapiResponse) { + this.originalAnalyses = (creativeResponse as any).original_analyses; + delete (creativeResponse as any).original_analyses; + + // if no results then we are done + if (creativeResponse.message.results.length === 0) { + return creativeResponse; + } + + // set up a graph structure + const kgEdge = creativeResponse.message.results[0].analyses[0].edge_bindings[this.mainEdgeId][0].id; + const kgSrc = creativeResponse.message.results[0].node_bindings[this.mainEdge.subject][0].id; + const kgDst = creativeResponse.message.results[0].node_bindings[this.mainEdge.object][0].id; + const dfsNodes: DfsGraph = {}; + const supportGraphsPerNode: { [node: string]: Set } = {}; + for (const supportGraph of (creativeResponse.message.knowledge_graph.edges[kgEdge]?.attributes?.find(attr => attr.attribute_type_id === 'biolink:support_graphs')?.value ?? []) as string[]) { + const auxGraph = (creativeResponse.message.auxiliary_graphs ?? {})[supportGraph]; + for (const subEdge of auxGraph.edges) { + const kgSubEdge = creativeResponse.message.knowledge_graph.edges[subEdge]; + if (!dfsNodes[kgSubEdge.subject]) { + dfsNodes[kgSubEdge.subject] = {}; + } + if (!dfsNodes[kgSubEdge.subject][kgSubEdge.object]) { + dfsNodes[kgSubEdge.subject][kgSubEdge.object] = []; + } + dfsNodes[kgSubEdge.subject][kgSubEdge.object].push(subEdge); + + if (!supportGraphsPerNode[kgSubEdge.subject]) { + supportGraphsPerNode[kgSubEdge.subject] = new Set(); + } + supportGraphsPerNode[kgSubEdge.subject].add(supportGraph); + } + } + + const message1 = '[Pathfinder]: Performing serach for intermediate nodes.'; + debug(message1); + this.logs.push(new LogEntry('INFO', null, message1).getLog()); + + const { results: newResultObject, graphs: newAuxGraphs } = this._searchForIntermediates(creativeResponse, dfsNodes, supportGraphsPerNode, kgSrc, kgDst, kgEdge); + + creativeResponse.message.results = Object.values(newResultObject).sort((a, b) => (b.analyses[0].score ?? 0) - (a.analyses[0].score ?? 0)).slice(0, this.CREATIVE_LIMIT); + creativeResponse.description = `Query processed successfully, retrieved ${creativeResponse.message.results.length} results.` + + const finalNewAuxGraphs: { [id: string]: { edges: string[] } } = newAuxGraphs as any; + for (const auxGraph in finalNewAuxGraphs) { + finalNewAuxGraphs[auxGraph].edges = Array.from(finalNewAuxGraphs[auxGraph].edges); + } + Object.assign(creativeResponse.message.auxiliary_graphs!, finalNewAuxGraphs); + + const message2 = `[Pathfinder]: Pathfinder found ${creativeResponse.message.results.length} intermediate nodes and created ${Object.keys(finalNewAuxGraphs).length} support graphs.`; + debug(message2); + this.logs.push(new LogEntry('INFO', null, message2).getLog()); + + return creativeResponse; + } + + _searchForIntermediates(creativeResponse: TrapiResponse, dfsNodes: DfsGraph, supportGraphsPerNode: { [node: string]: Set }, kgSrc: string, kgDst: string, kgEdge: string): ResultAuxObject { + // perform dfs + const stack = [{ node: kgSrc, path: [kgSrc] }]; + const newResultObject: ResultObject = {}; + const newAuxGraphs: AuxGraphObject = {}; + while (stack.length !== 0) { + const { node, path } = stack.pop()!; + if (node === kgDst) { + if (path.length > 2) { + // loop through all intermediate nodes + for (let i = 1; i < path.length - 1; i++) { + const intermediateNode = path[i]; + const firstEdges: string[] = []; + const secondEdges: string[] = []; + for (let j = 0; j < i; j++) { + for (let edge of dfsNodes[path[j]][path[j + 1]]) { + firstEdges.push(edge); + } + } + for (let j = i; j < path.length - 1; j++) { + for (let edge of dfsNodes[path[j]][path[j + 1]]) { + secondEdges.push(edge); + } + } + + if (!(`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}` in newResultObject)) { + newResultObject[`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}`] = { + node_bindings: { + [this.mainEdge.subject]: [{ id: kgSrc }], + [this.mainEdge.object]: [{ id: kgDst }], + [this.unpinnedNodeId]: [{ id: intermediateNode }] + }, + analyses: [{ + resource_id: "infores:biothings-explorer", + edge_bindings: { + [this.mainEdgeId]: [{ id: kgEdge }], + [this.intermediateEdges[0][0]]: [{ id: `pathfinder-${kgSrc}-${intermediateNode}` }], + [this.intermediateEdges[1][0]]: [{ id: `pathfinder-${intermediateNode}-${kgDst}` }], + }, + score: undefined + }], + }; + creativeResponse.message.knowledge_graph.edges[`pathfinder-${kgSrc}-${intermediateNode}`] = { + predicate: 'biolink:related_to', + subject: kgSrc, + object: intermediateNode, + sources: [ + { + resource_id: this.options.provenanceUsesServiceProvider + ? 'infores:service-provider-trapi' + : 'infores:biothings-explorer', + resource_role: 'primary_knowledge_source', + }, + ], + attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${kgSrc}-${intermediateNode}-support`] }], + }; + creativeResponse.message.knowledge_graph.edges[`pathfinder-${intermediateNode}-${kgDst}`] = { + predicate: 'biolink:related_to', + subject: intermediateNode, + object: kgDst, + sources: [ + { + resource_id: this.options.provenanceUsesServiceProvider + ? 'infores:service-provider-trapi' + : 'infores:biothings-explorer', + resource_role: 'primary_knowledge_source', + }, + ], + attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${intermediateNode}-${kgDst}-support`] }], + }; + newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`] = { edges: new Set(firstEdges) }; + newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`] = { edges: new Set(secondEdges) }; + + // calculate score + if (supportGraphsPerNode[intermediateNode]?.size > 0) { + let score: number | undefined = undefined; + for (const supportGraph of supportGraphsPerNode[intermediateNode]) { + score = scaled_sigmoid( + inverse_scaled_sigmoid(score ?? 0) + + inverse_scaled_sigmoid(this.originalAnalyses[supportGraph].score), + ); + } + newResultObject[`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}`].analyses[0].score = score; + } + + } else { + firstEdges.forEach(edge => newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`].edges.add(edge)); + secondEdges.forEach(edge => newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`].edges.add(edge)); + } + } + } + } else { + for (const neighbor in dfsNodes[node]) { + if (!path.includes(neighbor)) { + stack.push({ node: neighbor, path: [...path, neighbor] }); + } + } + } + } + + return { results: newResultObject, graphs: newAuxGraphs }; + } +} \ No newline at end of file From 286dd473f1ed57f78164df793060aa251765087d Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Fri, 29 Mar 2024 17:16:49 -0700 Subject: [PATCH 10/27] logs & telemetry --- src/index.ts | 6 ++++-- src/inferred_mode/inferred_mode.ts | 4 +++- src/inferred_mode/pathfinder.ts | 15 +++++++++++++-- 3 files changed, 20 insertions(+), 5 deletions(-) diff --git a/src/index.ts b/src/index.ts index e7ba0d7d..3f7212bd 100644 --- a/src/index.ts +++ b/src/index.ts @@ -529,7 +529,9 @@ export default class TRAPIQueryHandler { const pathfinderHandler = new PathfinderQueryHandler(this.logs, this.queryGraph, this); const pathfinderResponse = await pathfinderHandler.query(); - this.getResponse = () => pathfinderResponse; + if (pathfinderResponse) { + this.getResponse = () => pathfinderResponse; + } } async _handleInferredEdges(): Promise { @@ -625,7 +627,7 @@ export default class TRAPIQueryHandler { 'INFO', null, `Execution Summary: (${KGNodes}) nodes / (${kgEdges}) edges / (${results}) results; (${resultQueries}/${queries}) queries${cached ? ` (${cached} cached qEdges)` : '' - } returned results from(${sources.length}) unique API${sources.length === 1 ? 's' : ''}`, + } returned results from(${sources.length}) unique API ${sources.length === 1 ? 's' : ''}`, ).getLog(), new LogEntry('INFO', null, `APIs: ${sources.join(', ')} `).getLog(), ]; diff --git a/src/inferred_mode/inferred_mode.ts b/src/inferred_mode/inferred_mode.ts index bddd3d38..81ddc655 100644 --- a/src/inferred_mode/inferred_mode.ts +++ b/src/inferred_mode/inferred_mode.ts @@ -645,7 +645,9 @@ export default class InferredQueryHandler { .getSummaryLog(response, response.logs as StampedLog[], resultQueries) .forEach((log) => response.logs.push(log)); } - response.logs = (response.logs as StampedLog[]).map((log) => log.toJSON()); + if (!this.pathfinder) { + response.logs = (response.logs as StampedLog[]).map((log) => log.toJSON()); + } return response; } diff --git a/src/inferred_mode/pathfinder.ts b/src/inferred_mode/pathfinder.ts index 3d8cc815..17a92a7c 100644 --- a/src/inferred_mode/pathfinder.ts +++ b/src/inferred_mode/pathfinder.ts @@ -2,7 +2,7 @@ import TRAPIQueryHandler, { QueryHandlerOptions } from '../index'; import { TrapiResponse, TrapiQEdge, TrapiResult, TrapiQueryGraph, TrapiQNode, TrapiAnalysis } from '../types'; import InferredQueryHandler from './inferred_mode'; import { scaled_sigmoid, inverse_scaled_sigmoid } from '../results_assembly/score'; -import { LogEntry, StampedLog } from '@biothings-explorer/utils'; +import { LogEntry, StampedLog, Telemetry } from '@biothings-explorer/utils'; import Debug from 'debug'; const debug = Debug('bte:biothings-explorer-trapi:pathfinder'); @@ -97,10 +97,15 @@ export default class PathfinderQueryHandler { this.parse(creativeResponse); + // logs + creativeResponse.logs = this.logs.map(log => log.toJSON()); + return creativeResponse; } parse(creativeResponse: TrapiResponse) { + const span = Telemetry.startSpan({ description: 'pathfinderParse' }); + this.originalAnalyses = (creativeResponse as any).original_analyses; delete (creativeResponse as any).original_analyses; @@ -134,7 +139,7 @@ export default class PathfinderQueryHandler { } } - const message1 = '[Pathfinder]: Performing serach for intermediate nodes.'; + const message1 = '[Pathfinder]: Performing search for intermediate nodes.'; debug(message1); this.logs.push(new LogEntry('INFO', null, message1).getLog()); @@ -153,10 +158,14 @@ export default class PathfinderQueryHandler { debug(message2); this.logs.push(new LogEntry('INFO', null, message2).getLog()); + span.finish(); + return creativeResponse; } _searchForIntermediates(creativeResponse: TrapiResponse, dfsNodes: DfsGraph, supportGraphsPerNode: { [node: string]: Set }, kgSrc: string, kgDst: string, kgEdge: string): ResultAuxObject { + const span = Telemetry.startSpan({ description: 'pathfinderIntermediateSearch' }); + // perform dfs const stack = [{ node: kgSrc, path: [kgSrc] }]; const newResultObject: ResultObject = {}; @@ -256,6 +265,8 @@ export default class PathfinderQueryHandler { } } + span.finish(); + return { results: newResultObject, graphs: newAuxGraphs }; } } \ No newline at end of file From aa26be6fac1567ae4ef8e7bdabb64e8b279ad50b Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Mon, 1 Apr 2024 17:24:19 -0700 Subject: [PATCH 11/27] bugfix for couting ids --- src/index.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/index.ts b/src/index.ts index 3f7212bd..9b0f85ef 100644 --- a/src/index.ts +++ b/src/index.ts @@ -509,7 +509,7 @@ export default class TRAPIQueryHandler { _queryIsPathfinder(): boolean { const inferredEdgeCount = Object.values(this.queryGraph.edges).reduce((i, edge) => i + (edge.knowledge_type === 'inferred' ? 1 : 0), 0); - const pinnedNodes = Object.values(this.queryGraph.nodes).reduce((i, node) => i + (node.ids != null ? 1 : 0), 0); + const pinnedNodes = Object.values(this.queryGraph.nodes).reduce((i, node) => i + (node.ids?.length > 0 ? 1 : 0), 0); return inferredEdgeCount === 3 && pinnedNodes == 2 && Object.keys(this.queryGraph.edges).length === 3 && Object.keys(this.queryGraph.nodes).length === 3; } From c94cdb506314dd1961c9fff7b51622fc41dac500 Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Mon, 1 Apr 2024 17:30:22 -0700 Subject: [PATCH 12/27] testing / function reorganization --- .../data/chemical_to_disease_pathfinder.json | 50 + ...hemical_to_disease_pf_creative_result.json | 199170 +++++++++++++++ __test__/unittest/pathfinder.test.ts | 75 + src/inferred_mode/pathfinder.ts | 57 +- 4 files changed, 199328 insertions(+), 24 deletions(-) create mode 100644 __test__/data/chemical_to_disease_pathfinder.json create mode 100644 __test__/data/chemical_to_disease_pf_creative_result.json create mode 100644 __test__/unittest/pathfinder.test.ts diff --git a/__test__/data/chemical_to_disease_pathfinder.json b/__test__/data/chemical_to_disease_pathfinder.json new file mode 100644 index 00000000..8a8e93a3 --- /dev/null +++ b/__test__/data/chemical_to_disease_pathfinder.json @@ -0,0 +1,50 @@ +{ + "message": { + "query_graph": { + "nodes": { + "n0": { + "ids": [ + "PUBCHEM.COMPOUND:5291" + ], + "categories": ["biolink:Drug"] + }, + "un": { + "categories": [ + "biolink:NamedThing" + ] + }, + "n2": { + "ids": [ + "MONDO:0004979" + ] + } + }, + "edges": { + "e0": { + "subject": "n0", + "object": "un", + "predicates": [ + "biolink:related_to" + ], + "knowledge_type": "inferred" + }, + "e1": { + "subject": "un", + "object": "n2", + "predicates": [ + "biolink:related_to" + ], + "knowledge_type": "inferred" + }, + "e2": { + "subject": "n0", + "object": "n2", + "predicates": [ + "biolink:related_to" + ], + "knowledge_type": "inferred" + } + } + } + } +} \ No newline at end of file diff --git a/__test__/data/chemical_to_disease_pf_creative_result.json b/__test__/data/chemical_to_disease_pf_creative_result.json new file mode 100644 index 00000000..8e434d01 --- /dev/null +++ b/__test__/data/chemical_to_disease_pf_creative_result.json @@ -0,0 +1,199170 @@ +{ + "status": "Success", + "description": "Query processed successfully, retrieved 1 results.", + "schema_version": "1.4.0", + "biolink_version": "4.1.6", + "workflow": [ + { + "id": "lookup" + } + ], + "message": { + "query_graph": { + "nodes": { + "n0": { + "ids": [ + "PUBCHEM.COMPOUND:5291" + ], + "categories": [ + "biolink:Drug", + "biolink:SmallMolecule" + ] + }, + "n2": { + "ids": [ + "MONDO:0004979" + ], + "categories": [ + "biolink:Disease" + ] + }, + "un": { + "categories": [ + "biolink:NamedThing" + ] + } + }, + "edges": { + "e2": { + "subject": "n0", + "object": "n2", + "predicates": [ + "biolink:related_to" + ], + "knowledge_type": "inferred" + }, + "e0": { + "subject": "n0", + "object": "un", + "predicates": [ + "biolink:related_to" + ], + "knowledge_type": "inferred" + }, + "e1": { + "subject": "un", + "object": "n2", + "predicates": [ + "biolink:related_to" + ], + "knowledge_type": "inferred" + } + } + }, + "knowledge_graph": { + "nodes": { + "PUBCHEM.COMPOUND:5291": { + "categories": [ + "biolink:SmallMolecule" + ], + "name": "Imatinib", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "PUBCHEM.COMPOUND:5291", + "CHEMBL.COMPOUND:CHEMBL941", + "UNII:BKJ8M8G5HI", + "CHEBI:45783", + "DRUGBANK:DB00619", + "MESH:C097613", + "CAS:1080014-82-9", + "CAS:152459-95-5", + "DrugCentral:1423", + "GTOPDB:5687", + "HMDB:HMDB0014757", + "INCHIKEY:KTUFNOKKBVMGRW-UHFFFAOYSA-N", + "UMLS:C0935989", + "RXCUI:282388", + "PUBCHEM.COMPOUND:123596", + "CHEMBL.COMPOUND:CHEMBL1642", + "UNII:8A1O1M485B", + "CHEBI:31690", + "MESH:D000068877", + "CAS:220127-57-1", + "INCHIKEY:YLMAHDNUQAMNNX-UHFFFAOYSA-N", + "UMLS:C0939537", + "RXCUI:284924", + "RXCUI:282386", + "UMLS:C0935987", + "RXCUI:284206", + "UMLS:C0938676", + "RXCUI:331600", + "UMLS:C1127612", + "RXCUI:376335", + "UMLS:C1250509", + "RXCUI:403878", + "UMLS:C1329083", + "RXCUI:403879", + "UMLS:C1329084", + "RXCUI:404588", + "UMLS:C1329793", + "RXCUI:404589", + "UMLS:C1329794", + "RXCUI:406050", + "UMLS:C1331283", + "RXCUI:406051", + "UMLS:C1331284", + "RXCUI:406060", + "UMLS:C1331293", + "RXCUI:411240", + "UMLS:C1340496", + "RXCUI:440549", + "UMLS:C1370586", + "RXCUI:483431", + "UMLS:C1532549", + "RXCUI:575017", + "UMLS:C1592742", + "RXCUI:576514", + "UMLS:C1594210", + "RXCUI:1160679", + "UMLS:C3215039", + "RXCUI:1160680", + "UMLS:C3215040", + "RXCUI:1171230", + "UMLS:C3225312", + "RXCUI:1171231", + "UMLS:C3225313" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "Imatinib", + "IMATINIB", + "imatinib", + "[OBSOLETE] imatinib", + "Imatinib Mesylate", + "IMATINIB MESYLATE", + "imatinib methanesulfonate", + "imatinib mesylate", + "Gleevec", + "imatinib 100 MG Oral Capsule", + "imatinib 100 MG", + "imatinib Oral Capsule", + "imatinib 100 MG Oral Tablet", + "imatinib 400 MG Oral Tablet", + "imatinib 100 MG Oral Tablet [Gleevec]", + "imatinib 400 MG Oral Tablet [Gleevec]", + "imatinib Oral Tablet", + "imatinib 400 MG", + "imatinib Oral Tablet [Gleevec]", + "imatinib 50 MG Oral Capsule", + "imatinib 50 MG", + "imatinib 400 MG Oral Capsule", + "imatinib 100 MG [Gleevec]", + "imatinib 400 MG [Gleevec]", + "imatinib Oral Product", + "imatinib Pill", + "Gleevec Oral Product", + "Gleevec Pill" + ] + } + ] + }, + "MONDO:0004979": { + "categories": [ + "biolink:Disease" + ], + "name": "asthma", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "MONDO:0004979", + "DOID:2841", + "EFO:0000270", + "UMLS:C0004096", + "UMLS:C0085129", + "UMLS:C0340062", + "UMLS:C3714497", + "MESH:D001249", + "MESH:D016535", + "MEDDRA:10003553", + "MEDDRA:10003555", + "MEDDRA:10003560", + "MEDDRA:10003561", + "MEDDRA:10003565", + "MEDDRA:10006450", + "MEDDRA:10037993", + "MEDDRA:10056285", + "MEDDRA:10066091", + "MEDDRA:10066863", + "MEDDRA:10082852", + "NCIT:C28397", + "SNOMEDCT:195967001", + "SNOMEDCT:991000119106", + "ICD10:J45", + "ICD9:493", + "KEGG.DISEASE:05310", + "HP:0002099" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "asthma", + "obsolete_asthma", + "Asthma", + "Bronchial Hyperreactivity", + "Hyperreactive airway disease", + "Reactive airway disease" + ] + } + ] + }, + "MONDO:0004765": { + "categories": [ + "biolink:Disease" + ], + "name": "intrinsic asthma", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "MONDO:0004765", + "DOID:9360", + "UMLS:C0155880", + "MEDDRA:10022847", + "SNOMEDCT:266361008", + "ICD9:493.1" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "intrinsic asthma", + "Intrinsic asthma" + ] + } + ] + }, + "MONDO:0004766": { + "categories": [ + "biolink:Disease" + ], + "name": "status asthmaticus", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "MONDO:0004766", + "DOID:9362", + "EFO:0008590", + "UMLS:C0038218", + "MESH:D013224", + "MEDDRA:10003562", + "MEDDRA:10041961", + "MEDDRA:10064823", + "NCIT:C122577", + "SNOMEDCT:708090002", + "ICD9:493.91", + "HP:0012653" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "status asthmaticus", + "Status Asthmaticus", + "Status asthmaticus" + ] + } + ] + }, + "MONDO:0004784": { + "categories": [ + "biolink:Disease" + ], + "name": "allergic asthma", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "MONDO:0004784", + "DOID:9415", + "UMLS:C0155877", + "MEDDRA:10001705", + "MEDDRA:10003558", + "MEDDRA:10003638", + "MEDDRA:10015888", + "SNOMEDCT:389145006", + "ICD9:493.0" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "allergic asthma", + "Allergic asthma" + ] + } + ] + }, + "MONDO:0005405": { + "categories": [ + "biolink:Disease" + ], + "name": "childhood onset asthma", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "MONDO:0005405", + "DOID:0080815", + "UMLS:C0264408", + "MEDDRA:10081274", + "SNOMEDCT:233678006" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "childhood onset asthma", + "childhood-onset asthma", + "Childhood asthma" + ] + } + ] + }, + "MONDO:0022742": { + "categories": [ + "biolink:Disease" + ], + "name": "occupational asthma", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "MONDO:0022742", + "DOID:0080820", + "UMLS:C0264423", + "MESH:D059366", + "MEDDRA:10070836", + "SNOMEDCT:57607007" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "occupational asthma", + "Asthma, Occupational" + ] + } + ] + }, + "NCBIGene:1509": { + "categories": [ + "biolink:Gene" + ], + "name": "CTSD", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1509", + "ENSEMBL:ENSG00000117984", + "HGNC:2529", + "OMIM:116840", + "UMLS:C1332805", + "UniProtKB:P07339", + "PR:P07339", + "ENSEMBL:ENSP00000236671", + "ENSEMBL:ENSP00000236671.2", + "UMLS:C2606220", + "UniProtKB:V9HWI3" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CTSD", + "CTSD gene", + "CATD_HUMAN Cathepsin D (sprot)", + "cathepsin D (human)", + "CTSD protein, human", + "V9HWI3_HUMAN Cathepsin D (trembl)" + ] + } + ] + }, + "NCBIGene:1666": { + "categories": [ + "biolink:Gene" + ], + "name": "DECR1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1666", + "ENSEMBL:ENSG00000104325", + "HGNC:2753", + "OMIM:222745", + "UMLS:C1413969", + "UniProtKB:A0A024R9D7", + "UniProtKB:Q16698", + "PR:Q16698" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "DECR1", + "DECR1 gene", + "A0A024R9D7_HUMAN 2,4-dienoyl CoA reductase 1, mitochondrial, isoform CRA_b (trembl)", + "DECR_HUMAN 2,4-dienoyl-CoA reductase [(3E)-enoyl-CoA-producing], mitochondrial (sprot)", + "2,4-dienoyl-CoA reductase [(3E)-enoyl-CoA-producing], mitochondrial (human)" + ] + } + ] + }, + "NCBIGene:5243": { + "categories": [ + "biolink:Gene" + ], + "name": "ABCB1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5243", + "ENSEMBL:ENSG00000085563", + "HGNC:40", + "OMIM:171050", + "UMLS:C0376622", + "UniProtKB:A4D1D2", + "UniProtKB:P08183", + "PR:P08183", + "UMLS:C1738970" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ABCB1", + "ABCB1 gene", + "A4D1D2_HUMAN ATP-binding cassette, sub-family B (MDR/TAP), member 1 (trembl)", + "MDR1_HUMAN ATP-dependent translocase ABCB1 (sprot)", + "ATP-dependent translocase ABCB1 (human)", + "ABCB1 protein, human" + ] + } + ] + }, + "NCBIGene:1576": { + "categories": [ + "biolink:Gene" + ], + "name": "CYP3A4", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1576", + "ENSEMBL:ENSG00000160868", + "HGNC:2637", + "OMIM:124010", + "UMLS:C1176140", + "UniProtKB:P08684", + "PR:P08684", + "ENSEMBL:ENSP00000498939", + "ENSEMBL:ENSP00000498939.1", + "UMLS:C1142644", + "UniProtKB:Q6GRK0" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CYP3A4", + "CYP3A4 gene", + "CP3A4_HUMAN Cytochrome P450 3A4 (sprot)", + "cytochrome P450 3A4 (human)", + "cytochrome P450 3A4 protein, human", + "Q6GRK0_HUMAN Cytochrome P450 3A (trembl)" + ] + } + ] + }, + "NCBIGene:23632": { + "categories": [ + "biolink:Gene" + ], + "name": "CA14", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:23632", + "ENSEMBL:ENSG00000118298", + "HGNC:1372", + "OMIM:604832", + "UMLS:C1413042", + "UniProtKB:A8K3J4", + "UniProtKB:Q9ULX7", + "PR:Q9ULX7", + "ENSEMBL:ENSP00000358107", + "ENSEMBL:ENSP00000358107.3", + "ENSEMBL:ENSP00000498013", + "ENSEMBL:ENSP00000498013.1" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CA14", + "CA14 gene", + "A8K3J4_HUMAN Carbonic anhydrase XIV, isoform CRA_d (trembl)", + "CAH14_HUMAN Carbonic anhydrase 14 (sprot)", + "carbonic anhydrase 14 (human)" + ] + } + ] + }, + "NCBIGene:1565": { + "categories": [ + "biolink:Gene" + ], + "name": "CYP2D6", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1565", + "ENSEMBL:ENSG00000100197", + "HGNC:2625", + "OMIM:124030", + "UMLS:C1332830", + "UniProtKB:C1ID52", + "UniProtKB:P10635", + "PR:P10635", + "ENSEMBL:ENSP00000483677", + "ENSEMBL:ENSP00000483677.1", + "UMLS:C3887685", + "UniProtKB:Q5Y7H2" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CYP2D6", + "CYP2D6 gene", + "C1ID52_HUMAN Cytochrome P450 (trembl)", + "CP2D6_HUMAN Cytochrome P450 2D6 (sprot)", + "cytochrome P450 2D6 (human)", + "Cytochrome P450 2D6, human", + "Q5Y7H2_HUMAN CYP2D variant (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:5004": { + "categories": [ + "biolink:Gene" + ], + "name": "ORM1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5004", + "ENSEMBL:ENSG00000229314", + "HGNC:8498", + "OMIM:138600", + "UMLS:C1418186", + "UniProtKB:P02763", + "PR:P02763", + "ENSEMBL:ENSP00000259396", + "ENSEMBL:ENSP00000259396.8", + "UMLS:C4283943" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ORM1", + "ORM1 gene", + "A1AG1_HUMAN Alpha-1-acid glycoprotein 1 (sprot)", + "alpha-1-acid glycoprotein 1 (human)", + "Alpha-1-Acid Glycoprotein 1, human" + ] + } + ] + }, + "NCBIGene:4914": { + "categories": [ + "biolink:Gene" + ], + "name": "NTRK1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4914", + "ENSEMBL:ENSG00000198400", + "HGNC:8031", + "OMIM:191315", + "UMLS:C0919487", + "UniProtKB:P04629", + "PR:P04629", + "UMLS:C3538924", + "UMLS:C3853565", + "UniProtKB:X5DR71" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "NTRK1", + "NTRK1 gene", + "NTRK1_HUMAN High affinity nerve growth factor receptor (sprot)", + "high affinity nerve growth factor receptor (human)", + "High Affinity Nerve Growth Factor Receptor Isoform TrkA-III, human", + "High Affinity Nerve Growth Factor Receptor, human", + "X5DR71_HUMAN Tyrosine-protein kinase receptor (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:6582": { + "categories": [ + "biolink:Gene" + ], + "name": "SLC22A2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6582", + "ENSEMBL:ENSG00000112499", + "HGNC:10966", + "OMIM:602608", + "UMLS:C1420137", + "UniProtKB:O15244", + "PR:O15244", + "UMLS:C1453694" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SLC22A2", + "SLC22A2 gene", + "S22A2_HUMAN Solute carrier family 22 member 2 (sprot)", + "solute carrier family 22 member 2 (human)", + "SLC22A2 protein, human" + ] + } + ] + }, + "NCBIGene:760": { + "categories": [ + "biolink:Gene" + ], + "name": "CA2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:760", + "ENSEMBL:ENSG00000104267", + "HGNC:1373", + "OMIM:611492", + "UMLS:C1413043", + "UniProtKB:P00918", + "PR:P00918", + "ENSEMBL:ENSP00000285379", + "ENSEMBL:ENSP00000285379.4", + "UMLS:C5196589", + "UniProtKB:V9HW21" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CA2", + "CA2 gene", + "CAH2_HUMAN Carbonic anhydrase 2 (sprot)", + "carbonic anhydrase 2 (human)", + "Carbonic Anhydrase 2", + "V9HW21_HUMAN Carbonic anhydrase (trembl)" + ] + } + ] + }, + "NCBIGene:1577": { + "categories": [ + "biolink:Gene" + ], + "name": "CYP3A5", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1577", + "ENSEMBL:ENSG00000106258", + "HGNC:2638", + "OMIM:605325", + "UMLS:C1413882", + "UniProtKB:B7Z3P6", + "UniProtKB:P20815", + "PR:P20815", + "UMLS:C0535996" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CYP3A5", + "CYP3A5 gene", + "B7Z3P6_HUMAN Cytochrome P450 3A (trembl)", + "CP3A5_HUMAN Cytochrome P450 3A5 (sprot)", + "cytochrome P450 3A5 (human)", + "CYP3A5 protein, human" + ] + } + ] + }, + "NCBIGene:1544": { + "categories": [ + "biolink:Gene" + ], + "name": "CYP1A2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1544", + "ENSEMBL:ENSG00000140505", + "HGNC:2596", + "OMIM:124060", + "UMLS:C1332826", + "UniProtKB:P05177", + "PR:P05177", + "ENSEMBL:ENSP00000342007", + "ENSEMBL:ENSP00000342007.4", + "UMLS:C1620185" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CYP1A2", + "CYP1A2 gene", + "CP1A2_HUMAN Cytochrome P450 1A2 (sprot)", + "cytochrome P450 1A2 (human)", + "CYP1A2 protein, human" + ] + } + ] + }, + "NCBIGene:780": { + "categories": [ + "biolink:Gene" + ], + "name": "DDR1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:780", + "ENSEMBL:ENSG00000204580", + "HGNC:2730", + "OMIM:600408", + "UMLS:C1333206", + "UniProtKB:A0A024RCJ0", + "UniProtKB:A0A024RCL1", + "UniProtKB:A0A024RCQ1", + "UniProtKB:A0A0A0MSX3", + "ENSEMBL:ENSP00000405998", + "ENSEMBL:ENSP00000405998.2", + "ENSEMBL:ENSP00000447357", + "ENSEMBL:ENSP00000447357.2", + "ENSEMBL:ENSP00000448460", + "ENSEMBL:ENSP00000448460.2", + "ENSEMBL:ENSP00000448797", + "ENSEMBL:ENSP00000448797.2", + "UniProtKB:Q08345", + "PR:Q08345", + "UMLS:C0294276", + "UniProtKB:Q96T61", + "UniProtKB:Q96T62" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "DDR1", + "DDR1 gene", + "A0A024RCJ0_HUMAN receptor protein-tyrosine kinase (trembl)", + "A0A024RCL1_HUMAN receptor protein-tyrosine kinase (trembl)", + "A0A024RCQ1_HUMAN receptor protein-tyrosine kinase (trembl)", + "A0A0A0MSX3_HUMAN receptor protein-tyrosine kinase (trembl)", + "DDR1_HUMAN Epithelial discoidin domain-containing receptor 1 (sprot)", + "epithelial discoidin domain-containing receptor 1 (human)", + "DDR1 protein, human", + "Q96T61_HUMAN Discoidin domain receptor DDR1e (Fragment) (trembl)", + "Q96T62_HUMAN Discoidin domain receptor DDR1d (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:6580": { + "categories": [ + "biolink:Gene" + ], + "name": "SLC22A1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6580", + "ENSEMBL:ENSG00000175003", + "HGNC:10963", + "OMIM:602607", + "UMLS:C1420134", + "UniProtKB:O15245", + "PR:O15245", + "UMLS:C3539830" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SLC22A1", + "SLC22A1 gene", + "S22A1_HUMAN Solute carrier family 22 member 1 (sprot)", + "solute carrier family 22 member 1 (human)", + "Solute Carrier Family 22 Member 1" + ] + } + ] + }, + "NCBIGene:3815": { + "categories": [ + "biolink:Gene" + ], + "name": "KIT", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3815", + "ENSEMBL:ENSG00000157404", + "HGNC:6342", + "OMIM:164920", + "UMLS:C1416655", + "UniProtKB:P10721", + "PR:P10721", + "UMLS:C3853650", + "UMLS:C5399841", + "UMLS:C5400043", + "UMLS:C5400044" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "KIT", + "KIT gene", + "KIT_HUMAN Mast/stem cell growth factor receptor Kit (sprot)", + "mast/stem cell growth factor receptor Kit (human)", + "Mast/Stem Cell Growth Factor Receptor Kit, human", + "Stem Cell Factor Receptor", + "Mast Cell Growth Factor Receptor", + "v-kit Hardy-Zuckerman 4 Feline Sarcoma Viral Oncogene Homolog" + ] + } + ] + }, + "NCBIGene:1557": { + "categories": [ + "biolink:Gene" + ], + "name": "CYP2C19", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1557", + "ENSEMBL:ENSG00000165841", + "HGNC:2621", + "OMIM:124020", + "UMLS:C1332828", + "UniProtKB:P33261", + "PR:P33261", + "ENSEMBL:ENSP00000360372", + "ENSEMBL:ENSP00000360372.3", + "UMLS:C0960580" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CYP2C19", + "CYP2C19 gene", + "CP2CJ_HUMAN Cytochrome P450 2C19 (sprot)", + "cytochrome P450 2C19 (human)", + "CYP2C19 protein, human" + ] + } + ] + }, + "NCBIGene:1551": { + "categories": [ + "biolink:Gene" + ], + "name": "CYP3A7", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1551", + "ENSEMBL:ENSG00000160870", + "HGNC:2640", + "OMIM:605340", + "UMLS:C1413884" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CYP3A7", + "CYP3A7 gene" + ] + } + ] + }, + "NCBIGene:5156": { + "categories": [ + "biolink:Gene" + ], + "name": "PDGFRA", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5156", + "ENSEMBL:ENSG00000134853", + "HGNC:8803", + "OMIM:173490", + "UMLS:C1335201", + "UniProtKB:P16234", + "PR:P16234", + "UMLS:C3853694" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PDGFRA", + "PDGFRA gene", + "PGFRA_HUMAN Platelet-derived growth factor receptor alpha (sprot)", + "platelet-derived growth factor receptor alpha (human)", + "Platelet-Derived Growth Factor Receptor Alpha, human" + ] + } + ] + }, + "NCBIGene:5742": { + "categories": [ + "biolink:Gene" + ], + "name": "PTGS1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5742", + "ENSEMBL:ENSG00000095303", + "HGNC:9604", + "OMIM:176805", + "UMLS:C1335271", + "UniProtKB:A0A087X296", + "ENSEMBL:ENSP00000483540", + "ENSEMBL:ENSP00000483540.2", + "UniProtKB:P23219", + "PR:P23219", + "UMLS:C1565830", + "UMLS:C5574837" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PTGS1", + "PTGS1 gene", + "A0A087X296_HUMAN Prostaglandin-endoperoxide synthase 1 (trembl)", + "PGH1_HUMAN Prostaglandin G/H synthase 1 (sprot)", + "prostaglandin G/H synthase 1 (human)", + "PTGS1 protein, human", + "Cyclooxygenase 3, human" + ] + } + ] + }, + "NCBIGene:5159": { + "categories": [ + "biolink:Gene" + ], + "name": "PDGFRB", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5159", + "ENSEMBL:ENSG00000113721", + "HGNC:8804", + "OMIM:173410", + "UMLS:C1335202", + "UniProtKB:P09619", + "PR:P09619", + "UMLS:C3853695", + "UniProtKB:Q59F04" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PDGFRB", + "PDGFRB gene", + "PGFRB_HUMAN Platelet-derived growth factor receptor beta (sprot)", + "platelet-derived growth factor receptor beta (human)", + "Platelet-Derived Growth Factor Receptor Beta, Human", + "Q59F04_HUMAN receptor protein-tyrosine kinase (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:1436": { + "categories": [ + "biolink:Gene" + ], + "name": "CSF1R", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1436", + "ENSEMBL:ENSG00000182578", + "HGNC:2433", + "OMIM:164770", + "UMLS:C0879468", + "UniProtKB:P07333", + "PR:P07333", + "UMLS:C4082532" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CSF1R", + "CSF1R gene", + "CSF1R_HUMAN Macrophage colony-stimulating factor 1 receptor (sprot)", + "macrophage colony-stimulating factor 1 receptor (human)", + "Macrophage Colony-Stimulating Factor 1 Receptor, human" + ] + } + ] + }, + "NCBIGene:6916": { + "categories": [ + "biolink:Gene" + ], + "name": "TBXAS1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6916", + "ENSEMBL:ENSG00000059377", + "HGNC:11609", + "OMIM:274180", + "UMLS:C1420620", + "UniProtKB:B4DVP1", + "UniProtKB:P24557", + "PR:P24557", + "UniProtKB:Q53F23" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TBXAS1", + "TBXAS1 gene", + "B4DVP1_HUMAN cDNA FLJ59444, highly similar to Thromboxane-A synthase (trembl)", + "THAS_HUMAN Thromboxane-A synthase (sprot)", + "thromboxane-A synthase (human)", + "Q53F23_HUMAN HCG14925, isoform CRA_a (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:6532": { + "categories": [ + "biolink:Gene" + ], + "name": "SLC6A4", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6532", + "ENSEMBL:ENSG00000108576", + "HGNC:11050", + "OMIM:182138", + "UMLS:C1420214", + "UniProtKB:B2R7Y7", + "UniProtKB:P31645", + "PR:P31645", + "UMLS:C1456457" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SLC6A4", + "SLC6A4 gene", + "B2R7Y7_HUMAN Transporter (trembl)", + "SC6A4_HUMAN Sodium-dependent serotonin transporter (sprot)", + "sodium-dependent serotonin transporter (human)", + "SLC6A4 protein, human" + ] + } + ] + }, + "NCBIGene:1432": { + "categories": [ + "biolink:Gene" + ], + "name": "MAPK14", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1432", + "ENSEMBL:ENSG00000112062", + "HGNC:6876", + "OMIM:600289", + "UMLS:C1366876", + "UniProtKB:A0A024RD15", + "UniProtKB:B4E0K5", + "ENSEMBL:ENSP00000419837", + "ENSEMBL:ENSP00000419837.1", + "UniProtKB:L7RSM2", + "UniProtKB:Q16539", + "PR:Q16539", + "UMLS:C1456380" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MAPK14", + "MAPK14 gene", + "A0A024RD15_HUMAN Mitogen-activated protein kinase 14 (trembl)", + "B4E0K5_HUMAN mitogen-activated protein kinase (trembl)", + "L7RSM2_HUMAN Mitogen-activated protein kinase 14 (trembl)", + "MK14_HUMAN Mitogen-activated protein kinase 14 (sprot)", + "mitogen-activated protein kinase 14 (human)", + "MAPK14 protein, human" + ] + } + ] + }, + "NCBIGene:7297": { + "categories": [ + "biolink:Gene" + ], + "name": "TYK2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:7297", + "ENSEMBL:ENSG00000105397", + "HGNC:12440", + "OMIM:176941", + "UMLS:C1421249", + "UniProtKB:A0A024R7E4", + "UniProtKB:P29597", + "PR:P29597", + "ENSEMBL:ENSP00000431885", + "ENSEMBL:ENSP00000431885.1", + "ENSEMBL:ENSP00000436175", + "ENSEMBL:ENSP00000436175.2", + "UMLS:C1448662" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TYK2", + "TYK2 gene", + "A0A024R7E4_HUMAN Tyrosine-protein kinase (trembl)", + "TYK2_HUMAN Non-receptor tyrosine-protein kinase TYK2 (sprot)", + "non-receptor tyrosine-protein kinase TYK2 (human)", + "TYK2 protein, human" + ] + } + ] + }, + "NCBIGene:3717": { + "categories": [ + "biolink:Gene" + ], + "name": "JAK2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3717", + "ENSEMBL:ENSG00000096968", + "HGNC:6192", + "OMIM:147796", + "UMLS:C1334291", + "UniProtKB:A8K910", + "UniProtKB:B4DYV1", + "UniProtKB:O60674", + "PR:O60674", + "ENSEMBL:ENSP00000371067", + "ENSEMBL:ENSP00000371067.4", + "UMLS:C1527617" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "JAK2", + "JAK2 gene", + "A8K910_HUMAN Tyrosine-protein kinase (trembl)", + "B4DYV1_HUMAN Tyrosine-protein kinase (trembl)", + "JAK2_HUMAN Tyrosine-protein kinase JAK2 (sprot)", + "tyrosine-protein kinase JAK2 (human)", + "JAK2 protein, human" + ] + } + ] + }, + "NCBIGene:4363": { + "categories": [ + "biolink:Gene" + ], + "name": "ABCC1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4363", + "ENSEMBL:ENSG00000103222", + "HGNC:51", + "OMIM:158343", + "UMLS:C0919458", + "UniProtKB:P33527", + "PR:P33527", + "UMLS:C1451297" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ABCC1", + "ABCC1 gene", + "MRP1_HUMAN Multidrug resistance-associated protein 1 (sprot)", + "multidrug resistance-associated protein 1 (human)", + "ABCC1 protein, human" + ] + } + ] + }, + "NCBIGene:1956": { + "categories": [ + "biolink:Gene" + ], + "name": "EGFR", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1956", + "ENSEMBL:ENSG00000146648", + "HGNC:3236", + "OMIM:131550", + "UMLS:C1414313", + "UniProtKB:B7Z2I3", + "UniProtKB:C9JYS6", + "ENSEMBL:ENSP00000413354", + "ENSEMBL:ENSP00000413354.2", + "UniProtKB:E7BSV0", + "UniProtKB:F2YGG7", + "UniProtKB:P00533", + "PR:P00533", + "UMLS:C1368111", + "UMLS:C1739039", + "UniProtKB:Q504U8", + "ENSEMBL:ENSP00000415559", + "ENSEMBL:ENSP00000415559.1" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "EGFR", + "EGFR gene", + "B7Z2I3_HUMAN Receptor protein-tyrosine kinase (trembl)", + "C9JYS6_HUMAN Receptor protein-tyrosine kinase (trembl)", + "E7BSV0_HUMAN Receptor protein-tyrosine kinase (trembl)", + "F2YGG7_HUMAN Receptor protein-tyrosine kinase (trembl)", + "EGFR_HUMAN Epidermal growth factor receptor (sprot)", + "epidermal growth factor receptor (human)", + "Soluble ErbB-1", + "EGFR protein, human", + "Q504U8_HUMAN Receptor protein-tyrosine kinase (trembl)" + ] + } + ] + }, + "NCBIGene:5601": { + "categories": [ + "biolink:Gene" + ], + "name": "MAPK9", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5601", + "ENSEMBL:ENSG00000050748", + "HGNC:6886", + "OMIM:602896", + "UMLS:C1334482", + "UniProtKB:D7R525", + "ENSEMBL:ENSP00000443149", + "ENSEMBL:ENSP00000443149.1", + "UniProtKB:P45984", + "PR:P45984", + "UMLS:C1367019" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MAPK9", + "MAPK9 gene", + "D7R525_HUMAN Stress-activated protein kinase JNK (trembl)", + "MK09_HUMAN Mitogen-activated protein kinase 9 (sprot)", + "mitogen-activated protein kinase 9 (human)", + "MAPK9 protein, human" + ] + } + ] + }, + "NCBIGene:5894": { + "categories": [ + "biolink:Gene" + ], + "name": "RAF1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5894", + "ENSEMBL:ENSG00000132155", + "HGNC:9829", + "OMIM:164760", + "UMLS:C0812215", + "UniProtKB:A0A0S2Z4L5", + "ENSEMBL:ENSP00000508794", + "ENSEMBL:ENSP00000508794.1", + "ENSEMBL:ENSP00000509612", + "ENSEMBL:ENSP00000509612.1", + "ENSEMBL:ENSP00000509669", + "ENSEMBL:ENSP00000509669.1", + "UniProtKB:L7RRS6", + "UniProtKB:P04049", + "PR:P04049", + "UMLS:C4706023" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "RAF1", + "RAF1 gene", + "A0A0S2Z4L5_HUMAN non-specific serine/threonine protein kinase (Fragment) (trembl)", + "L7RRS6_HUMAN non-specific serine/threonine protein kinase (trembl)", + "RAF1_HUMAN RAF proto-oncogene serine/threonine-protein kinase (sprot)", + "RAF proto-oncogene serine/threonine-protein kinase (human)", + "RAF1 protein, human" + ] + } + ] + }, + "NCBIGene:3654": { + "categories": [ + "biolink:Gene" + ], + "name": "IRAK1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3654", + "ENSEMBL:ENSG00000184216", + "HGNC:6112", + "OMIM:300283", + "UMLS:C1334134", + "UniProtKB:P51617", + "PR:P51617", + "UMLS:C1334201" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "IRAK1", + "IRAK1 gene", + "IRAK1_HUMAN Interleukin-1 receptor-associated kinase 1 (sprot)", + "interleukin-1 receptor-associated kinase 1 (human)", + "IRAK1 protein, human" + ] + } + ] + }, + "NCBIGene:6850": { + "categories": [ + "biolink:Gene" + ], + "name": "SYK", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6850", + "ENSEMBL:ENSG00000165025", + "HGNC:11491", + "OMIM:600085", + "UMLS:C1335892", + "UniProtKB:A0A024R244", + "UniProtKB:A0A024R273", + "UniProtKB:P43405", + "PR:P43405", + "UMLS:C0134982" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SYK", + "SYK gene", + "A0A024R244_HUMAN Tyrosine-protein kinase (trembl)", + "A0A024R273_HUMAN Tyrosine-protein kinase (trembl)", + "KSYK_HUMAN Tyrosine-protein kinase SYK (sprot)", + "tyrosine-protein kinase SYK (human)", + "SYK protein, human" + ] + } + ] + }, + "NCBIGene:640": { + "categories": [ + "biolink:Gene" + ], + "name": "BLK", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:640", + "ENSEMBL:ENSG00000136573", + "HGNC:1057", + "OMIM:191305", + "UMLS:C1332419", + "UniProtKB:E9PJX5", + "ENSEMBL:ENSP00000433663", + "ENSEMBL:ENSP00000433663.1", + "UniProtKB:P51451", + "PR:P51451", + "ENSEMBL:ENSP00000259089", + "ENSEMBL:ENSP00000259089.4", + "UMLS:C3713783", + "UniProtKB:Q05D26" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "BLK", + "BLK gene", + "E9PJX5_HUMAN Tyrosine-protein kinase (trembl)", + "BLK_HUMAN Tyrosine-protein kinase Blk (sprot)", + "tyrosine-protein kinase Blk (human)", + "BLK protein, human", + "Q05D26_HUMAN Tyrosine-protein kinase (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:2260": { + "categories": [ + "biolink:Gene" + ], + "name": "FGFR1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2260", + "ENSEMBL:ENSG00000077782", + "HGNC:3688", + "OMIM:136350", + "UMLS:C0919509", + "UniProtKB:A0A0S2Z3Q6", + "UniProtKB:A0A3B3ISD1", + "ENSEMBL:ENSP00000497266", + "ENSEMBL:ENSP00000497266.1", + "ENSEMBL:ENSP00000507997", + "ENSEMBL:ENSP00000507997.1", + "UniProtKB:P11362", + "PR:P11362", + "UMLS:C1527757" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "FGFR1", + "FGFR1 gene", + "A0A0S2Z3Q6_HUMAN Fibroblast growth factor receptor 1 (Fragment) (trembl)", + "A0A3B3ISD1_HUMAN Fibroblast growth factor receptor (trembl)", + "FGFR1_HUMAN Fibroblast growth factor receptor 1 (sprot)", + "fibroblast growth factor receptor 1 (human)", + "FGFR1 protein, human" + ] + } + ] + }, + "NCBIGene:3791": { + "categories": [ + "biolink:Gene" + ], + "name": "KDR", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3791", + "ENSEMBL:ENSG00000128052", + "HGNC:6307", + "OMIM:191306", + "UMLS:C1334306", + "UniProtKB:P35968", + "PR:P35968", + "UMLS:C3840403", + "UMLS:C3849882" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "KDR", + "KDR gene", + "VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (sprot)", + "vascular endothelial growth factor receptor 2 (human)", + "Soluble Vascular Endothelial Growth Factor Receptor 2, human", + "KDR protein, human" + ] + } + ] + }, + "NCBIGene:5599": { + "categories": [ + "biolink:Gene" + ], + "name": "MAPK8", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5599", + "ENSEMBL:ENSG00000107643", + "HGNC:6881", + "OMIM:601158", + "UMLS:C1367731", + "UniProtKB:A1L4K2", + "UniProtKB:P45983", + "PR:P45983", + "UMLS:C5441984" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MAPK8", + "MAPK8 gene", + "A1L4K2_HUMAN Stress-activated protein kinase JNK (trembl)", + "MK08_HUMAN Mitogen-activated protein kinase 8 (sprot)", + "mitogen-activated protein kinase 8 (human)", + "MAPK8 protein, human" + ] + } + ] + }, + "NCBIGene:2534": { + "categories": [ + "biolink:Gene" + ], + "name": "FYN", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2534", + "ENSEMBL:ENSG00000010810", + "HGNC:4037", + "OMIM:137025", + "UMLS:C0812303", + "UniProtKB:P06241", + "PR:P06241", + "UMLS:C1442788" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "FYN", + "FYN gene", + "FYN_HUMAN Tyrosine-protein kinase Fyn (sprot)", + "tyrosine-protein kinase Fyn (human)", + "FYN protein, human" + ] + } + ] + }, + "NCBIGene:5347": { + "categories": [ + "biolink:Gene" + ], + "name": "PLK1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5347", + "ENSEMBL:ENSG00000166851", + "HGNC:9077", + "OMIM:602098", + "UMLS:C1335227", + "UniProtKB:P53350", + "PR:P53350", + "ENSEMBL:ENSP00000300093", + "ENSEMBL:ENSP00000300093.4", + "UMLS:C0290178" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PLK1", + "PLK1 gene", + "PLK1_HUMAN Serine/threonine-protein kinase PLK1 (sprot)", + "serine/threonine-protein kinase PLK1 (human)", + "PLK1 protein, human" + ] + } + ] + }, + "NCBIGene:92": { + 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"M0R0W6_HUMAN receptor protein-tyrosine kinase (trembl)", + "UFO_HUMAN Tyrosine-protein kinase receptor UFO (sprot)", + "tyrosine-protein kinase receptor UFO (human)", + "AXL protein, human" + ] + } + ] + }, + "NCBIGene:5294": { + "categories": [ + "biolink:Gene" + ], + "name": "PIK3CG", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5294", + "ENSEMBL:ENSG00000105851", + "HGNC:8978", + "OMIM:601232", + "UMLS:C1335214", + "UniProtKB:A0A024R720", + "UniProtKB:A8K9G9", + "UniProtKB:P48736", + "PR:P48736", + "ENSEMBL:ENSP00000352121", + "ENSEMBL:ENSP00000352121.3", + "ENSEMBL:ENSP00000392258", + "ENSEMBL:ENSP00000392258.2", + "ENSEMBL:ENSP00000419260", + "ENSEMBL:ENSP00000419260.1", + "UMLS:C2713509" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PIK3CG", + "PIK3CG gene", + "A0A024R720_HUMAN phosphatidylinositol-4,5-bisphosphate 3-kinase (trembl)", + "A8K9G9_HUMAN phosphatidylinositol-4,5-bisphosphate 3-kinase (trembl)", + "PK3CG_HUMAN Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform (sprot)", + "phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform (human)", + "PIK3CG protein, human" + ] + } + ] + }, + "NCBIGene:9261": { + "categories": [ + "biolink:Gene" + ], + "name": "MAPKAPK2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:9261", + "ENSEMBL:ENSG00000162889", + "HGNC:6887", + "OMIM:602006", + "UMLS:C1442514", + "UniProtKB:P49137", + "PR:P49137", + "UMLS:C1452441" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MAPKAPK2", + "MAPKAPK2 gene", + "MAPK2_HUMAN MAP kinase-activated protein kinase 2 (sprot)", + "MAP kinase-activated protein kinase 2 (human)", + "MAPKAPK2 protein, human" + ] + } + ] + }, + "NCBIGene:695": { + "categories": [ + "biolink:Gene" + ], + "name": "BTK", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:695", + "ENSEMBL:ENSG00000010671", + "HGNC:1133", + "OMIM:300300", + "UMLS:C1412841", + "UniProtKB:Q06187", + "PR:Q06187", + "UMLS:C1528376", + "UniProtKB:Q5JY90", + "ENSEMBL:ENSP00000512057", + "ENSEMBL:ENSP00000512057.1" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "BTK", + "BTK gene", + "BTK_HUMAN Tyrosine-protein kinase BTK (sprot)", + "tyrosine-protein kinase BTK (human)", + "BTK protein, human", + "Q5JY90_HUMAN Tyrosine-protein kinase (trembl)" + ] + } + ] + }, + "NCBIGene:659": { + "categories": [ + "biolink:Gene" + ], + "name": "BMPR2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:659", + "ENSEMBL:ENSG00000204217", + "HGNC:1078", + "OMIM:600799", + "UMLS:C1332431", + "UniProtKB:Q13873", + "PR:Q13873", + "UMLS:C1312154" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "BMPR2", + "BMPR2 gene", + "BMPR2_HUMAN Bone morphogenetic protein receptor type-2 (sprot)", + "bone morphogenetic protein receptor type-2 (human)", + "BMPR2 protein, human" + ] + } + ] + }, + "NCBIGene:2185": { + "categories": [ + "biolink:Gene" + ], + "name": "PTK2B", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2185", + "ENSEMBL:ENSG00000120899", + "HGNC:9612", + "OMIM:601212", + "UMLS:C1335273", + "UniProtKB:Q14289", + "PR:Q14289", + "UMLS:C1430595" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PTK2B", + "PTK2B gene", + "FAK2_HUMAN Protein-tyrosine kinase 2-beta (sprot)", + "protein-tyrosine kinase 2-beta (human)", + "PTK2B protein, human" + ] + } + ] + }, + "NCBIGene:2011": { + "categories": [ + "biolink:Gene" + ], + "name": "MARK2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2011", + "ENSEMBL:ENSG00000072518", + "HGNC:3332", + "OMIM:600526", + "UMLS:C1414387", + "UniProtKB:A0A140VJP1", + "UniProtKB:A8K2S4", + "UniProtKB:Q7KZI7", + "PR:Q7KZI7", + "UMLS:C0299851" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MARK2", + "MARK2 gene", + "A0A140VJP1_HUMAN non-specific serine/threonine protein kinase (trembl)", + "A8K2S4_HUMAN non-specific serine/threonine protein kinase (trembl)", + "MARK2_HUMAN Serine/threonine-protein kinase MARK2 (sprot)", + "serine/threonine-protein kinase MARK2 (human)", + "MARK2 protein, human" + ] + } + ] + }, + "NCBIGene:1244": { + "categories": [ + "biolink:Gene" + ], + "name": "ABCC2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1244", + "ENSEMBL:ENSG00000023839", + "HGNC:53", + "OMIM:601107", + "UMLS:C1412077", + "UniProtKB:Q92887", + "PR:Q92887", + "ENSEMBL:ENSP00000497274", + "ENSEMBL:ENSP00000497274.1", + "UMLS:C3540577" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ABCC2", + "ABCC2 gene", + "MRP2_HUMAN ATP-binding cassette sub-family C member 2 (sprot)", + "ATP-binding cassette sub-family C member 2 (human)", + "Canalicular Multispecific Organic Anion 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"value": [ + "MUSK", + "MUSK gene", + "A0A087WSY1_HUMAN receptor protein-tyrosine kinase (trembl)", + "MUSK_HUMAN Muscle, skeletal receptor tyrosine-protein kinase (sprot)", + "muscle, skeletal receptor tyrosine-protein kinase (human)", + "MUSK protein, human" + ] + } + ] + }, + "NCBIGene:2042": { + "categories": [ + "biolink:Gene" + ], + "name": "EPHA3", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2042", + "ENSEMBL:ENSG00000044524", + "HGNC:3387", + "OMIM:179611", + "UMLS:C0812263", + "UniProtKB:A0A140VJJ0", + "UniProtKB:P29320", + "PR:P29320", + "UMLS:C1452792", + "UniProtKB:Q6P4R6" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "EPHA3", + "EPHA3 gene", + "A0A140VJJ0_HUMAN receptor protein-tyrosine kinase (trembl)", + "EPHA3_HUMAN Ephrin type-A receptor 3 (sprot)", + "ephrin type-A receptor 3 (human)", + "EPHA3 protein, human", + "Q6P4R6_HUMAN receptor protein-tyrosine kinase (trembl)" + ] + } + ] + }, + "NCBIGene:208": 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controller), isoform CRA_a (trembl)", + "CDK13_HUMAN Cyclin-dependent kinase 13 (sprot)", + "cyclin-dependent kinase 13 (human)", + "Q9BVE2_HUMAN CDC2L5 protein (trembl)" + ] + } + ] + }, + "NCBIGene:6794": { + "categories": [ + "biolink:Gene" + ], + "name": "STK11", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6794", + "ENSEMBL:ENSG00000118046", + "HGNC:11389", + "OMIM:602216", + "UMLS:C0694883", + "UniProtKB:A0A0S2Z4D1", + "UniProtKB:Q15831", + "PR:Q15831", + "UMLS:C1431123" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "STK11", + "STK11 gene", + "A0A0S2Z4D1_HUMAN non-specific serine/threonine protein kinase (Fragment) (trembl)", + "STK11_HUMAN Serine/threonine-protein kinase STK11 (sprot)", + "serine/threonine-protein kinase STK11 (human)", + "STK11 protein, human" + ] + } + ] + }, + "NCBIGene:85443": { + "categories": [ + "biolink:Gene" + ], + "name": "DCLK3", + "attributes": [ + { + "attribute_type_id": 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"CDC42BPB gene", + "A0A024R6N2_HUMAN non-specific serine/threonine protein kinase (trembl)", + "Q86XZ8_HUMAN CDC42BPB protein (Fragment) (trembl)", + "MRCKB_HUMAN Serine/threonine-protein kinase MRCK beta (sprot)", + "serine/threonine-protein kinase MRCK beta (human)" + ] + } + ] + }, + "NCBIGene:3718": { + "categories": [ + "biolink:Gene" + ], + "name": "JAK3", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3718", + "ENSEMBL:ENSG00000105639", + "HGNC:6193", + "OMIM:600173", + "UMLS:C1334292", + "UniProtKB:A0A024R7M7", + "UniProtKB:P52333", + "PR:P52333", + "UMLS:C0253456" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "JAK3", + "JAK3 gene", + "A0A024R7M7_HUMAN Tyrosine-protein kinase (trembl)", + "JAK3_HUMAN Tyrosine-protein kinase JAK3 (sprot)", + "tyrosine-protein kinase JAK3 (human)", + "JAK3 protein, human" + ] + } + ] + }, + "NCBIGene:5588": { + "categories": [ + "biolink:Gene" + ], + "name": "PRKCQ", + "attributes": [ 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+ "TYRO3_HUMAN Tyrosine-protein kinase receptor TYRO3 (sprot)", + "tyrosine-protein kinase receptor TYRO3 (human)", + "TYRO3 protein, human" + ] + } + ] + }, + "NCBIGene:814": { + "categories": [ + "biolink:Gene" + ], + "name": "CAMK4", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:814", + "ENSEMBL:ENSG00000152495", + "HGNC:1464", + "OMIM:114080", + "UMLS:C1413103", + "UniProtKB:Q16566", + "PR:Q16566", + "ENSEMBL:ENSP00000282356", + "ENSEMBL:ENSP00000282356.4", + "ENSEMBL:ENSP00000422634", + "ENSEMBL:ENSP00000422634.1" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CAMK4", + "CAMK4 gene", + "KCC4_HUMAN Calcium/calmodulin-dependent protein kinase type IV (sprot)", + "calcium/calmodulin-dependent protein kinase type IV (human)" + ] + } + ] + }, + "NCBIGene:91754": { + "categories": [ + "biolink:Gene" + ], + "name": "NEK9", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:91754", + "ENSEMBL:ENSG00000119638", + "HGNC:18591", + "OMIM:609798", + "UMLS:C1425629", + "UniProtKB:A0A7I2V454", + "ENSEMBL:ENSP00000503827", + "ENSEMBL:ENSP00000503827.1", + "ENSEMBL:ENSP00000504104", + "ENSEMBL:ENSP00000504104.1", + "UniProtKB:A0A7I2V5R1", + "ENSEMBL:ENSP00000504620", + "ENSEMBL:ENSP00000504620.1", + "UniProtKB:Q6PKF2", + "UniProtKB:Q8TD19", + "PR:Q8TD19", + "ENSEMBL:ENSP00000238616", + "ENSEMBL:ENSP00000238616.5", + "UMLS:C1138216" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "NEK9", + "NEK9 gene", + "A0A7I2V454_HUMAN NIMA related kinase 9 (trembl)", + "A0A7I2V5R1_HUMAN NIMA related kinase 9 (trembl)", + "Q6PKF2_HUMAN NEK9 protein (Fragment) (trembl)", + "NEK9_HUMAN Serine/threonine-protein kinase Nek9 (sprot)", + "serine/threonine-protein kinase Nek9 (human)", + "NEK9 protein, human" + ] + } + ] + }, + "NCBIGene:27148": { + "categories": [ + "biolink:Gene" + ], + "name": "STK36", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:27148", + "ENSEMBL:ENSG00000163482", + "HGNC:17209", + "OMIM:607652", + "UMLS:C1424823", + "UniProtKB:A0A140VJW1", + "UniProtKB:Q9NRP7", + "PR:Q9NRP7", + "UMLS:C1565882" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "STK36", + "STK36 gene", + "A0A140VJW1_HUMAN Testicular tissue protein Li 188 (trembl)", + "STK36_HUMAN Serine/threonine-protein kinase 36 (sprot)", + "serine/threonine-protein kinase 36 (human)", + "STK36 protein, human" + ] + } + ] + }, + "NCBIGene:658": { + "categories": [ + "biolink:Gene" + ], + "name": "BMPR1B", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:658", + "ENSEMBL:ENSG00000138696", + "HGNC:1077", + "OMIM:603248", + "UMLS:C1412807", + "UniProtKB:A8KAE3", + "UniProtKB:O00238", + "PR:O00238", + "UMLS:C1312140" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "BMPR1B", + "BMPR1B gene", + "A8KAE3_HUMAN receptor protein serine/threonine kinase (trembl)", + "BMR1B_HUMAN Bone morphogenetic protein receptor type-1B (sprot)", + "bone morphogenetic protein receptor type-1B (human)", + "BMPR1B protein, human" + ] + } + ] + }, + "NCBIGene:6793": { + "categories": [ + "biolink:Gene" + ], + "name": "STK10", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6793", + "ENSEMBL:ENSG00000072786", + "HGNC:11388", + "OMIM:603919", + "UMLS:C1420463", + "UniProtKB:O94804", + "PR:O94804", + "ENSEMBL:ENSP00000176763", + "ENSEMBL:ENSP00000176763.5" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "STK10", + "STK10 gene", + "STK10_HUMAN Serine/threonine-protein kinase 10 (sprot)", + "serine/threonine-protein kinase 10 (human)" + ] + } + ] + }, + "NCBIGene:2241": { + "categories": [ + "biolink:Gene" + ], + "name": "FER", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2241", + "ENSEMBL:ENSG00000151422", + "HGNC:3655", + "OMIM:176942", + "UMLS:C0812288", + "UniProtKB:P16591", + "PR:P16591", + "UMLS:C1570097", + "UniProtKB:Q6PEJ9", + "UniProtKB:W0S0X4", + "UniProtKB:W0S1B5" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "FER", + "FER gene", + "FER_HUMAN Tyrosine-protein kinase Fer (sprot)", + "tyrosine-protein kinase Fer (human)", + "FER protein, human", + "Q6PEJ9_HUMAN FER protein (trembl)", + "W0S0X4_HUMAN Tyrosine-protein kinase (trembl)", + "W0S1B5_HUMAN Tyrosine-protein kinase (trembl)" + ] + } + ] + }, + "NCBIGene:2321": { + "categories": [ + "biolink:Gene" + ], + "name": "FLT1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2321", + "ENSEMBL:ENSG00000102755", + "HGNC:3763", + "OMIM:165070", + "UMLS:C0812298", + "UniProtKB:L7RSL3", + "UniProtKB:P17948", + "PR:P17948", + "UMLS:C1568520" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "FLT1", + "FLT1 gene", + "L7RSL3_HUMAN receptor protein-tyrosine kinase (trembl)", + "VGFR1_HUMAN Vascular endothelial growth factor receptor 1 (sprot)", + "vascular endothelial growth factor receptor 1 (human)", + "FLT1 protein, human" + ] + } + ] + }, + "NCBIGene:5610": { + "categories": [ + "biolink:Gene" + ], + "name": "EIF2AK2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5610", + "ENSEMBL:ENSG00000055332", + "HGNC:9437", + "OMIM:176871", + "UMLS:C1539341", + "UniProtKB:P19525", + "PR:P19525", + "UMLS:C3710914", + "UniProtKB:Q8IW76" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "EIF2AK2", + "EIF2AK2 gene", + "E2AK2_HUMAN Interferon-induced, double-stranded RNA-activated protein kinase (sprot)", + "interferon-induced, double-stranded RNA-activated protein kinase (human)", + "EIF2AK2 protein, human", + "Q8IW76_HUMAN eIF2AK2 protein (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:5606": { + "categories": [ + "biolink:Gene" + ], + "name": "MAP2K3", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5606", + "ENSEMBL:ENSG00000034152", + "HGNC:6843", + "OMIM:602315", + "UMLS:C1456386", + "UniProtKB:P46734", + "PR:P46734", + "UMLS:C1434650", + "UniProtKB:Q6FI23" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MAP2K3", + "MAP2K3 gene", + "MP2K3_HUMAN Dual specificity mitogen-activated protein kinase kinase 3 (sprot)", + "dual specificity mitogen-activated protein kinase kinase 3 (human)", + "MAP2K3 protein, human", + "Q6FI23_HUMAN MAP2K3 protein (trembl)" + ] + } + ] + }, + "NCBIGene:1025": { + "categories": [ + "biolink:Gene" + ], + "name": "CDK9", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1025", + "ENSEMBL:ENSG00000136807", + "HGNC:1780", + "OMIM:603251", + "UMLS:C1413290", + "UniProtKB:A0A024R880", + "UniProtKB:P50750", + "PR:P50750", + "UMLS:C1172090" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CDK9", + "CDK9 gene", + "A0A024R880_HUMAN Cyclin-dependent kinase 9 (CDC2-related kinase), isoform CRA_a (trembl)", + "CDK9_HUMAN Cyclin-dependent kinase 9 (sprot)", + "cyclin-dependent kinase 9 (human)", + "CDK9 protein, human" + ] + } + ] + }, + "NCBIGene:5747": { + "categories": [ + "biolink:Gene" + ], + "name": "PTK2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5747", + "ENSEMBL:ENSG00000169398", + "HGNC:9611", + "OMIM:600758", + "UMLS:C1366894", + "UniProtKB:Q05397", + "PR:Q05397", + "UMLS:C1565427", + "UniProtKB:Q59GM6", + "UniProtKB:Q59GN8", + "UniProtKB:Q658W2" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PTK2", + "PTK2 gene", + "FAK1_HUMAN Focal adhesion kinase 1 (sprot)", + "focal adhesion kinase 1 (human)", + "PTK2 protein, human", + "Q59GM6_HUMAN non-specific protein-tyrosine kinase (Fragment) (trembl)", + "Q59GN8_HUMAN non-specific protein-tyrosine kinase (Fragment) (trembl)", + "Q658W2_HUMAN non-specific protein-tyrosine kinase (trembl)" + ] + } + ] + }, + "NCBIGene:5058": { + "categories": [ + "biolink:Gene" + ], + "name": "PAK1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5058", + "ENSEMBL:ENSG00000149269", + "HGNC:8590", + "OMIM:602590", + "UMLS:C1418259", + "UniProtKB:A0A024R5P0", + "UniProtKB:Q13153", + "PR:Q13153", + "UMLS:C1505379" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PAK1", + "PAK1 gene", + "A0A024R5P0_HUMAN non-specific serine/threonine protein kinase (trembl)", + "PAK1_HUMAN Serine/threonine-protein kinase PAK 1 (sprot)", + "serine/threonine-protein kinase PAK 1 (human)", + "PAK1 protein, human" + ] + } + ] + }, + "NCBIGene:4214": { + "categories": [ + "biolink:Gene" + ], + "name": "MAP3K1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4214", + "ENSEMBL:ENSG00000095015", + "HGNC:6848", + "OMIM:600982", + "UMLS:C1367675", + "UniProtKB:Q13233", + "PR:Q13233", + "ENSEMBL:ENSP00000382423", + "ENSEMBL:ENSP00000382423.3", + "UMLS:C1367798" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MAP3K1", + "MAP3K1 gene", + "M3K1_HUMAN Mitogen-activated protein kinase kinase kinase 1 (sprot)", + "mitogen-activated protein kinase kinase kinase 1 (human)", + "MAP3K1 protein, human" + ] + } + ] + }, + "NCBIGene:51135": { + "categories": [ + "biolink:Gene" + ], + "name": "IRAK4", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:51135", + "ENSEMBL:ENSG00000198001", + "HGNC:17967", + "OMIM:606883", + "UMLS:C1334137", + "UniProtKB:B2RAP9", + "UniProtKB:B4E359", + "UniProtKB:Q69FE3", + "UniProtKB:Q9NWZ3", + "PR:Q9NWZ3", + "UMLS:C1334203" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "IRAK4", + "IRAK4 gene", + "B2RAP9_HUMAN Interleukin-1 receptor-associated kinase 4 (trembl)", + "B4E359_HUMAN Interleukin-1 receptor-associated kinase 4 (trembl)", + "Q69FE3_HUMAN Interleukin-1 receptor-associated kinase 4 (trembl)", + "IRAK4_HUMAN Interleukin-1 receptor-associated kinase 4 (sprot)", + "interleukin-1 receptor-associated kinase 4 (human)", + "IRAK4 protein, human" + ] + } + ] + }, + "NCBIGene:11040": { + "categories": [ + "biolink:Gene" + ], + "name": "PIM2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:11040", + "ENSEMBL:ENSG00000102096", + "HGNC:8987", + "OMIM:300295", + "UMLS:C1418581", + "UniProtKB:A0A024QYW7", + "UniProtKB:Q9P1W9", + "PR:Q9P1W9", + "ENSEMBL:ENSP00000365692", + "ENSEMBL:ENSP00000365692.4", + "UMLS:C1453189" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PIM2", + "PIM2 gene", + "A0A024QYW7_HUMAN Serine/threonine-protein kinase (trembl)", + "PIM2_HUMAN Serine/threonine-protein kinase pim-2 (sprot)", + "serine/threonine-protein kinase pim-2 (human)", + "PIM2 protein, human" + ] + } + ] + }, + "NCBIGene:29110": { + "categories": [ + "biolink:Gene" + ], + "name": "TBK1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:29110", + "ENSEMBL:ENSG00000183735", + "HGNC:11584", + "OMIM:604834", + "UMLS:C1336579", + "UniProtKB:Q9UHD2", + "PR:Q9UHD2", + "ENSEMBL:ENSP00000329967", + "ENSEMBL:ENSP00000329967.5", + "ENSEMBL:ENSP00000498995", + "ENSEMBL:ENSP00000498995.1", + "UMLS:C1449326" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TBK1", + "TBK1 gene", + "TBK1_HUMAN Serine/threonine-protein kinase TBK1 (sprot)", + "serine/threonine-protein kinase TBK1 (human)", + "TBK1 protein, human" + ] + } + ] + }, + "NCBIGene:10257": { + "categories": [ + "biolink:Gene" + ], + "name": "ABCC4", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:10257", + "ENSEMBL:ENSG00000125257", + "HGNC:55", + "OMIM:605250", + "UMLS:C1412079", + "UniProtKB:A8K2Q2", + "UniProtKB:O15439", + "PR:O15439", + "UMLS:C3538745" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ABCC4", + "ABCC4 gene", + "A8K2Q2_HUMAN cDNA FLJ77042, highly similar to Homo sapiens ATP-binding cassette, sub-family C (CFTR/MRP), member 4, mRNA (trembl)", + "MRP4_HUMAN ATP-binding cassette sub-family C member 4 (sprot)", + "ATP-binding cassette sub-family C member 4 (human)", + "Multidrug Resistance-Associated Protein 4" + ] + } + ] + }, + "NCBIGene:11213": { + "categories": [ + "biolink:Gene" + ], + "name": "IRAK3", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:11213", + "ENSEMBL:ENSG00000090376", + "HGNC:17020", + "OMIM:604459", + "UMLS:C1334136", + "UniProtKB:Q9Y616", + "PR:Q9Y616", + "UMLS:C1334202" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "IRAK3", + "IRAK3 gene", + "IRAK3_HUMAN Interleukin-1 receptor-associated kinase 3 (sprot)", + "interleukin-1 receptor-associated kinase 3 (human)", + "IRAK3 protein, human" + ] + } + ] + }, + "NCBIGene:1017": { + "categories": [ + "biolink:Gene" + ], + "name": "CDK2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1017", + "ENSEMBL:ENSG00000123374", + "HGNC:1771", + "OMIM:116953", + "UMLS:C1332733", + "UniProtKB:A0A024RB10", + "UniProtKB:A0A024RB77", + "UniProtKB:B4DDL9", + "UniProtKB:E7ESI2", + "ENSEMBL:ENSP00000393605", + "ENSEMBL:ENSP00000393605.2", + "UniProtKB:G3V5T9", + "ENSEMBL:ENSP00000452514", + "ENSEMBL:ENSP00000452514.1", + "UniProtKB:P24941", + "PR:P24941", + "UMLS:C0108855" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CDK2", + "CDK2 gene", + "A0A024RB10_HUMAN Cyclin-dependent kinase 2, isoform CRA_a (trembl)", + "A0A024RB77_HUMAN Cyclin-dependent kinase 2, isoform CRA_b (trembl)", + "B4DDL9_HUMAN cDNA FLJ54979, highly similar to Homo sapiens cyclin-dependent kinase 2 (CDK2), transcript variant 2, mRNA (trembl)", + "E7ESI2_HUMAN Cyclin dependent kinase 2 (trembl)", + "G3V5T9_HUMAN Cyclin dependent kinase 2 (trembl)", + "CDK2_HUMAN Cyclin-dependent kinase 2 (sprot)", + "cyclin-dependent kinase 2 (human)", + "CDK2 protein, human" + ] + } + ] + }, + "NCBIGene:5578": { + "categories": [ + "biolink:Gene" + ], + "name": "PRKCA", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5578", + "ENSEMBL:ENSG00000154229", + "HGNC:9393", + "OMIM:176960", + "UMLS:C1335261", + "UniProtKB:L7RSM7", + "UniProtKB:P17252", + "PR:P17252", + "ENSEMBL:ENSP00000408695", + "ENSEMBL:ENSP00000408695.3", + "UMLS:C1565919", + "UniProtKB:Q7Z727" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PRKCA", + "PRKCA gene", + "L7RSM7_HUMAN Protein kinase C (trembl)", + "KPCA_HUMAN Protein kinase C alpha type (sprot)", + "protein kinase C alpha type (human)", + "PRKCA protein, human", + "Q7Z727_HUMAN PRKCA protein (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:898": { + "categories": [ + "biolink:Gene" + ], + "name": "CCNE1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:898", + "ENSEMBL:ENSG00000105173", + "HGNC:1589", + "OMIM:123837", + "UMLS:C1332697", + "UniProtKB:A0A0G3DHS8", + "UniProtKB:P24864", + "PR:P24864", + "UMLS:C1259807", + "UniProtKB:V5W5X2" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CCNE1", + "CCNE1 gene", + "A0A0G3DHS8_HUMAN Pluripotent specific cyclin E1 (trembl)", + "CCNE1_HUMAN G1/S-specific cyclin-E1 (sprot)", + "G1/S-specific cyclin-E1 (human)", + "CCNE1 protein, human", + "V5W5X2_HUMAN Cyclin E variant ex5del (trembl)" + ] + } + ] + }, + "NCBIGene:3480": { + "categories": [ + "biolink:Gene" + ], + "name": "IGF1R", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3480", + "ENSEMBL:ENSG00000140443", + "HGNC:5465", + "OMIM:147370", + "UMLS:C1334088", + "UniProtKB:C9J5X1", + "ENSEMBL:ENSP00000496919", + "ENSEMBL:ENSP00000496919.1", + "UniProtKB:P08069", + "PR:P08069", + "ENSEMBL:ENSP00000497069", + "ENSEMBL:ENSP00000497069.1", + "UMLS:C4044495", + "UMLS:C4049897" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "IGF1R", + "IGF1R gene", + "C9J5X1_HUMAN Tyrosine-protein kinase receptor (trembl)", + "IGF1R_HUMAN Insulin-like growth factor 1 receptor (sprot)", + "insulin-like growth factor 1 receptor (human)", + "IGF1R protein, human", + "Insulin-Like Growth Factor 1 Receptor Beta Chain, Human" + ] + } + ] + }, + "NCBIGene:3645": { + "categories": [ + "biolink:Gene" + ], + "name": "INSRR", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3645", + "ENSEMBL:ENSG00000027644", + "HGNC:6093", + "OMIM:147671", + "UMLS:C1416459", + "UniProtKB:P14616", + "PR:P14616", + "ENSEMBL:ENSP00000357178", + "ENSEMBL:ENSP00000357178.3", + "UMLS:C4082285" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "INSRR", + "INSRR gene", + "INSRR_HUMAN Insulin receptor-related protein (sprot)", + "insulin receptor-related protein (human)", + "Insulin Receptor-Related Receptor, human" + ] + } + ] + }, + "NCBIGene:5594": { + "categories": [ + "biolink:Gene" + ], + "name": "MAPK1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5594", + "ENSEMBL:ENSG00000100030", + "HGNC:6871", + "OMIM:176948", + "UMLS:C1366882", + "UniProtKB:P28482", + "PR:P28482", + "UMLS:C2713871", + "UniProtKB:Q1HBJ4", + "UniProtKB:Q499G7" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MAPK1", + "MAPK1 gene", + "MK01_HUMAN Mitogen-activated protein kinase 1 (sprot)", + "mitogen-activated protein kinase 1 (human)", + "MAPK1 protein, human", + "Q1HBJ4_HUMAN Mitogen-activated protein kinase (trembl)", + "Q499G7_HUMAN Mitogen-activated protein kinase (trembl)" + ] + } + ] + }, + "NCBIGene:207": { + "categories": [ + "biolink:Gene" + ], + "name": "AKT1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:207", + "ENSEMBL:ENSG00000142208", + "HGNC:391", + "OMIM:164730", + "UMLS:C0812228", + "UniProtKB:B0LPE5", + "UniProtKB:B3KVH4", + "UniProtKB:P31749", + "PR:P31749", + "UMLS:C0668624" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "AKT1", + "AKT1 gene", + "B0LPE5_HUMAN RAC-alpha serine/threonine-protein kinase (trembl)", + "B3KVH4_HUMAN RAC-alpha serine/threonine-protein kinase (trembl)", + "AKT1_HUMAN RAC-alpha serine/threonine-protein kinase (sprot)", + "RAC-alpha serine/threonine-protein kinase (human)", + "AKT1 protein, human" + ] + } + ] + }, + "NCBIGene:91": { + "categories": [ + "biolink:Gene" + ], + "name": "ACVR1B", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:91", + "ENSEMBL:ENSG00000135503", + "HGNC:172", + "OMIM:601300", + "UMLS:C1332011", + "UniProtKB:P36896", + "PR:P36896", + "UMLS:C0663443" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ACVR1B", + "ACVR1B gene", + "ACV1B_HUMAN Activin receptor type-1B (sprot)", + "activin receptor type-1B (human)", + "ACVR1B protein, human" + ] + } + ] + }, + "NCBIGene:5581": { + "categories": [ + "biolink:Gene" + ], + "name": "PRKCE", + 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"ENSEMBL:ENSP00000427638", + "ENSEMBL:ENSP00000427638.1", + "UniProtKB:F8W9W0", + "ENSEMBL:ENSP00000389208", + "ENSEMBL:ENSP00000389208.2", + "UniProtKB:P54756", + "PR:P54756", + "UMLS:C1435808", + "UniProtKB:Q59FT4" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "EPHA5", + "EPHA5 gene", + "A0A384MU00_HUMAN receptor protein-tyrosine kinase (trembl)", + "B7ZKJ3_HUMAN receptor protein-tyrosine kinase (trembl)", + "B7ZKW7_HUMAN receptor protein-tyrosine kinase (trembl)", + "F8VP57_HUMAN receptor protein-tyrosine kinase (trembl)", + "F8W9W0_HUMAN receptor protein-tyrosine kinase (trembl)", + "EPHA5_HUMAN Ephrin type-A receptor 5 (sprot)", + "ephrin type-A receptor 5 (human)", + "EPHA5 protein, human", + "Q59FT4_HUMAN receptor protein-tyrosine kinase (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:2066": { + "categories": [ + "biolink:Gene" + ], + "name": "ERBB4", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2066", + "ENSEMBL:ENSG00000178568", + "HGNC:3432", + "OMIM:600543", + "UMLS:C0812267", + "UniProtKB:Q15303", + "PR:Q15303", + "UMLS:C3853568" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ERBB4", + "ERBB4 gene", + "ERBB4_HUMAN Receptor tyrosine-protein kinase erbB-4 (sprot)", + "receptor tyrosine-protein kinase erbB-4 (human)", + "Receptor Tyrosine-Protein Kinase ErbB-4, human" + ] + } + ] + }, + "NCBIGene:8767": { + "categories": [ + "biolink:Gene" + ], + "name": "RIPK2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:8767", + "ENSEMBL:ENSG00000104312", + "HGNC:10020", + "OMIM:603455", + "UMLS:C1335624", + "UniProtKB:A0A0S2Z4Z8", + "UniProtKB:O43353", + "PR:O43353", + "UMLS:C1447644" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "RIPK2", + "RIPK2 gene", + "A0A0S2Z4Z8_HUMAN Receptor-interacting serine-threonine kinase 2 isoform 1 (Fragment) (trembl)", + "RIPK2_HUMAN Receptor-interacting serine/threonine-protein kinase 2 (sprot)", + "receptor-interacting serine/threonine-protein kinase 2 (human)", + "RIPK2 protein, human" + ] + } + ] + }, + "NCBIGene:2064": { + "categories": [ + "biolink:Gene" + ], + "name": "ERBB2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2064", + "ENSEMBL:ENSG00000141736", + "HGNC:3430", + "OMIM:164870", + "UMLS:C0242957", + "UniProtKB:F5H1T4", + "ENSEMBL:ENSP00000462808", + "ENSEMBL:ENSP00000462808.1", + "UniProtKB:J3QLU9", + "ENSEMBL:ENSP00000463714", + "ENSEMBL:ENSP00000463714.1", + "UniProtKB:P04626", + "PR:P04626", + "UMLS:C1506592", + "UMLS:C1702024", + "UMLS:C4320090", + "UniProtKB:X5DNK3" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ERBB2", + "ERBB2 gene", + "F5H1T4_HUMAN receptor protein-tyrosine kinase (trembl)", + "J3QLU9_HUMAN Receptor protein-tyrosine kinase (trembl)", + "ERBB2_HUMAN Receptor tyrosine-protein kinase erbB-2 (sprot)", + "receptor tyrosine-protein kinase erbB-2 (human)", + "herstatin protein, human", + "ERBB2 protein, human", + "Receptor Tyrosine-Protein Kinase erbB-2 Carboxyl Terminal Fragment, human", + "X5DNK3_HUMAN receptor protein-tyrosine kinase (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:6098": { + "categories": [ + "biolink:Gene" + ], + "name": "ROS1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6098", + "ENSEMBL:ENSG00000047936", + "HGNC:10261", + "OMIM:165020", + "UMLS:C0812281", + "UniProtKB:P08922", + "PR:P08922", + "ENSEMBL:ENSP00000357494", + "ENSEMBL:ENSP00000357494.3", + "UMLS:C1310668" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ROS1", + "ROS1 gene", + "ROS1_HUMAN Proto-oncogene tyrosine-protein kinase ROS (sprot)", + "proto-oncogene tyrosine-protein kinase ROS (human)", + "ROS1 protein, human" + ] + } + ] + }, + "NCBIGene:2065": { + "categories": [ + "biolink:Gene" + ], + "name": "ERBB3", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2065", + "ENSEMBL:ENSG00000065361", + "HGNC:3431", + "OMIM:190151", + "UMLS:C0812265", + "UniProtKB:P21860", + "PR:P21860", + "UMLS:C3657415" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ERBB3", + "ERBB3 gene", + "ERBB3_HUMAN Receptor tyrosine-protein kinase erbB-3 (sprot)", + "receptor tyrosine-protein kinase erbB-3 (human)", + "ERBB3 protein, human" + ] + } + ] + }, + "NCBIGene:5595": { + "categories": [ + "biolink:Gene" + ], + "name": "MAPK3", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5595", + "ENSEMBL:ENSG00000102882", + "HGNC:6877", + "OMIM:601795", + "UMLS:C1366765", + "UniProtKB:L7RXH5", + "UniProtKB:P27361", + "PR:P27361", + "UMLS:C4082284", + "UniProtKB:Q9BWJ1" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MAPK3", + "MAPK3 gene", + "L7RXH5_HUMAN Mitogen-activated protein kinase (trembl)", + "MK03_HUMAN Mitogen-activated protein kinase 3 (sprot)", + "mitogen-activated protein kinase 3 (human)", + "Mitogen-Activated Protein Kinase 3, human", + "Q9BWJ1_HUMAN MAPK3 protein (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:5291": { + "categories": [ + "biolink:Gene" + ], + "name": "PIK3CB", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5291", + "ENSEMBL:ENSG00000051382", + "HGNC:8976", + "OMIM:602925", + "UMLS:C1335213", + "UniProtKB:B4DER4", + "UniProtKB:P42338", + "PR:P42338", + "ENSEMBL:ENSP00000289153", + "ENSEMBL:ENSP00000289153.2", + "ENSEMBL:ENSP00000418143", + "ENSEMBL:ENSP00000418143.1", + "ENSEMBL:ENSP00000501150", + "ENSEMBL:ENSP00000501150.1", + "UMLS:C1566348" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PIK3CB", + "PIK3CB gene", + "B4DER4_HUMAN cDNA FLJ57102, highly similar to Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta isoform (trembl)", + "PK3CB_HUMAN Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform (sprot)", + "phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform (human)", + "PIK3CB protein, human" + ] + } + ] + }, + "NCBIGene:2475": { + "categories": [ + "biolink:Gene" + ], + "name": "MTOR", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2475", + "ENSEMBL:ENSG00000198793", + "HGNC:3942", + "OMIM:601231", + "UMLS:C1414805", + "UniProtKB:A0A8V8TQ52", + "ENSEMBL:ENSP00000515198", + "ENSEMBL:ENSP00000515198.1", + "UniProtKB:P42345", + "PR:P42345", + "ENSEMBL:ENSP00000354558", + "ENSEMBL:ENSP00000354558.4", + "UMLS:C1307407" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MTOR", + "MTOR gene", + "A0A8V8TQ52_HUMAN Serine/threonine-protein kinase mTOR (trembl)", + "MTOR_HUMAN Serine/threonine-protein kinase mTOR (sprot)", + "serine/threonine-protein kinase mTOR (human)", + "FRAP1 protein, human" + ] + } + ] + }, + "NCBIGene:1111": { + "categories": [ + "biolink:Gene" + ], + "name": "CHEK1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1111", + "ENSEMBL:ENSG00000149554", + "HGNC:1925", + "OMIM:603078", + "UMLS:C1332753", + "UniProtKB:B4DT73", + "UniProtKB:E7EPP6", + "ENSEMBL:ENSP00000391090", + "ENSEMBL:ENSP00000391090.2", + "UniProtKB:O14757", + "PR:O14757", + "UMLS:C0659150" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CHEK1", + "CHEK1 gene", + "B4DT73_HUMAN cDNA FLJ56409, highly similar to Serine/threonine-protein kinase Chk1 (trembl)", + "E7EPP6_HUMAN Checkpoint kinase 1 (trembl)", + "CHK1_HUMAN Serine/threonine-protein kinase Chk1 (sprot)", + "serine/threonine-protein kinase Chk1 (human)", + "CHEK1 protein, human" + ] + } + ] + }, + "NCBIGene:5592": { + "categories": [ + "biolink:Gene" + ], + "name": "PRKG1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5592", + "ENSEMBL:ENSG00000185532", + "HGNC:9414", + "OMIM:176894", + "UMLS:C1418929", + "UniProtKB:Q13976", + "PR:Q13976", + "UMLS:C3489929" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PRKG1", + "PRKG1 gene", + "KGP1_HUMAN cGMP-dependent protein kinase 1 (sprot)", + "cGMP-dependent protein kinase 1 (human)", + "PRKG1 protein, human" + ] + } + ] + }, + "NCBIGene:4638": { + "categories": [ + "biolink:Gene" + ], + "name": "MYLK", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4638", + "ENSEMBL:ENSG00000065534", + "HGNC:7590", + "OMIM:600922", + "UMLS:C1334539", + "UniProtKB:A0A8I5KTQ1", + "ENSEMBL:ENSP00000510593", + "ENSEMBL:ENSP00000510593.1", + "UniProtKB:Q05B97", + "UniProtKB:Q05B98", + "UniProtKB:Q15746", + "PR:Q15746", + "UMLS:C1567740" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MYLK", + "MYLK gene", + "A0A8I5KTQ1_HUMAN Myosin light chain kinase (trembl)", + "Q05B97_HUMAN MYLK protein (Fragment) (trembl)", + "Q05B98_HUMAN MYLK protein (Fragment) (trembl)", + "MYLK_HUMAN Myosin light chain kinase, smooth muscle (sprot)", + "myosin light chain kinase, smooth muscle (human)", + "MYLK protein, human" + ] + } + ] + }, + "NCBIGene:120892": { + "categories": [ + "biolink:Gene" + ], + "name": "LRRK2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:120892", + "ENSEMBL:ENSG00000188906", + "HGNC:18618", + "OMIM:609007", + "UMLS:C1425650", + "UniProtKB:Q17RV3", + "UniProtKB:Q5S007", + "PR:Q5S007", + "ENSEMBL:ENSP00000298910", + "ENSEMBL:ENSP00000298910.7", + "UMLS:C1531201" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "LRRK2", + "LRRK2 gene", + "Q17RV3_HUMAN non-specific serine/threonine protein kinase (trembl)", + "LRRK2_HUMAN Leucine-rich repeat serine/threonine-protein kinase 2 (sprot)", + "leucine-rich repeat serine/threonine-protein kinase 2 (human)", + "LRRK2 protein, human" + ] + } + ] + }, + "NCBIGene:5879": { + "categories": [ + "biolink:Gene" + ], + "name": "RAC1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5879", + "ENSEMBL:ENSG00000136238", + "HGNC:9801", + "OMIM:602048", + "UMLS:C1419227", + "UniProtKB:A4D2P0", + "UniProtKB:A4D2P1", + "UniProtKB:P63000", + "PR:P63000", + "UMLS:C1430928" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "RAC1", + "RAC1 gene", + "A4D2P0_HUMAN Ras-related C3 botulinum toxin substrate 1 (Rho family, small GTP binding protein Rac1) (trembl)", + "A4D2P1_HUMAN Ras-related C3 botulinum toxin substrate 1 (Rho family, small GTP binding protein Rac1) (trembl)", + "RAC1_HUMAN Ras-related C3 botulinum toxin substrate 1 (sprot)", + "Ras-related C3 botulinum toxin substrate 1 (human)", + "RAC1 protein, human" + ] + } + ] + }, + "NCBIGene:10413": { + "categories": [ + "biolink:Gene" + ], + "name": "YAP1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:10413", + "ENSEMBL:ENSG00000137693", + "HGNC:16262", + "OMIM:606608", + "UMLS:C1424135", + "UniProtKB:A0A024R3E4", + "UniProtKB:K0KVU2", + "UniProtKB:P46937", + "PR:P46937", + "UMLS:C1318127", + "UniProtKB:Q86T74" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "YAP1", + "YAP1 gene", + "A0A024R3E4_HUMAN Yes-associated protein 1, 65kDa, isoform CRA_b (trembl)", + "K0KVU2_HUMAN Yes-associated protein isoform 9 (Fragment) (trembl)", + "YAP1_HUMAN Transcriptional coactivator YAP1 (sprot)", + "transcriptional coactivator YAP1 (human)", + "YAP1 protein, human", + "Q86T74_HUMAN Uncharacterized protein DKFZp451O0517 (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:5295": { + "categories": [ + "biolink:Gene" + ], + "name": "PIK3R1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5295", + "ENSEMBL:ENSG00000145675", + "HGNC:8979", + "OMIM:171833", + "UMLS:C1418576", + "UniProtKB:A0A2X0SFG1", + "UniProtKB:P27986", + "PR:P27986", + "UMLS:C3273598" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PIK3R1", + "PIK3R1 gene", + "A0A2X0SFG1_HUMAN Phosphatidylinositol 3-kinase regulatory subunit alpha (Fragment) (trembl)", + "P85A_HUMAN Phosphatidylinositol 3-kinase regulatory subunit alpha (sprot)", + "phosphatidylinositol 3-kinase regulatory subunit alpha (human)", + "Phosphatidylinositol 3-Kinase Regulatory Subunit Alpha" + ] + } + ] + }, + "NCBIGene:7037": { + "categories": [ + "biolink:Gene" + ], + "name": "TFRC", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:7037", + "ENSEMBL:ENSG00000072274", + "HGNC:11763", + "OMIM:190010", + "UMLS:C1420708", + "UniProtKB:A0A8V8TM46", + "ENSEMBL:ENSP00000513650", + "ENSEMBL:ENSP00000513650.1", + "ENSEMBL:ENSP00000513651", + "ENSEMBL:ENSP00000513651.1", + "UniProtKB:A8K6Q8", + "UniProtKB:B7Z2I6", + "UniProtKB:G3V0E5", + "ENSEMBL:ENSP00000390133", + "ENSEMBL:ENSP00000390133.1", + "UniProtKB:P02786", + "PR:P02786", + "ENSEMBL:ENSP00000353224", + "ENSEMBL:ENSP00000353224.4", + "ENSEMBL:ENSP00000376197", + "ENSEMBL:ENSP00000376197.3", + "ENSEMBL:ENSP00000513646", + "ENSEMBL:ENSP00000513646.1", + "ENSEMBL:ENSP00000513654", + "ENSEMBL:ENSP00000513654.1", + "UMLS:C0108801", + "UniProtKB:Q7Z3E0" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TFRC", + "TFRC gene", + "A0A8V8TM46_HUMAN Transferrin receptor protein 1 (trembl)", + "A8K6Q8_HUMAN Transferrin receptor protein 1 (trembl)", + "B7Z2I6_HUMAN Transferrin receptor protein 1 (trembl)", + "G3V0E5_HUMAN Transferrin receptor protein 1 (trembl)", + "TFR1_HUMAN Transferrin receptor protein 1 (sprot)", + "transferrin receptor protein 1 (human)", + "TFRC protein, human", + "Q7Z3E0_HUMAN Uncharacterized protein DKFZp686O0451 (trembl)" + ] + } + ] + }, + "NCBIGene:2638": { + "categories": [ + "biolink:Gene" + ], + "name": "GC", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2638", + "ENSEMBL:ENSG00000145321", + "HGNC:4187", + "OMIM:139200", + "UMLS:C1367452", + "UniProtKB:P02774", + "PR:P02774", + "UMLS:C4281799" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "GC", + "GC gene", + "VTDB_HUMAN Vitamin D-binding protein (sprot)", + "vitamin D-binding protein (human)", + "GC, vitamin D binding protein, human" + ] + } + ] + }, + "NCBIGene:7042": { + "categories": [ + "biolink:Gene" + ], + "name": "TGFB2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:7042", + "ENSEMBL:ENSG00000092969", + "HGNC:11768", + "OMIM:190220", + "UMLS:C1336621", + "UniProtKB:P61812", + "PR:P61812", + "UMLS:C1699342", + "UniProtKB:Q59EG9" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TGFB2", + "TGFB2 gene", + "TGFB2_HUMAN Transforming growth factor beta-2 proprotein (sprot)", + "transforming growth factor beta-2 (human)", + "TGFB2 protein, human", + "Q59EG9_HUMAN Transforming growth factor, beta 2 variant (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:5154": { + "categories": [ + "biolink:Gene" + ], + "name": "PDGFA", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5154", + "ENSEMBL:ENSG00000197461", + "HGNC:8799", + "OMIM:173430", + "UMLS:C1335200", + "UniProtKB:P04085", + "PR:P04085", + "UMLS:C1335430" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PDGFA", + "PDGFA gene", + "PDGFA_HUMAN Platelet-derived growth factor subunit A (sprot)", + "platelet-derived growth factor subunit A (human)", + "PDGFA protein, human" + ] + } + ] + }, + "NCBIGene:59067": { + "categories": [ + "biolink:Gene" + ], + "name": "IL21", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:59067", + "ENSEMBL:ENSG00000138684", + "HGNC:6005", + "OMIM:605384", + "UMLS:C1416406", + "UniProtKB:A0A224B028", + "UniProtKB:Q9HBE4", + "PR:Q9HBE4", + "UMLS:C1698797" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "IL21", + "IL21 gene", + "A0A224B028_HUMAN Interleukin (trembl)", + "IL21_HUMAN Interleukin-21 (sprot)", + "interleukin-21 (human)", + "IL21 protein, human" + ] + } + ] + }, + "NCBIGene:50616": { + "categories": [ + "biolink:Gene" + ], + "name": "IL22", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:50616", + "ENSEMBL:ENSG00000127318", + "HGNC:14900", + "OMIM:605330", + "UMLS:C1423038", + "UniProtKB:A0A7R8C389", + "UniProtKB:Q9GZX6", + "PR:Q9GZX6", + "ENSEMBL:ENSP00000329384", + "ENSEMBL:ENSP00000329384.4", + "ENSEMBL:ENSP00000442424", + "ENSEMBL:ENSP00000442424.1", + "UMLS:C1700909" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "IL22", + "IL22 gene", + "A0A7R8C389_HUMAN Interferon 2B1 (trembl)", + "IL22_HUMAN Interleukin-22 (sprot)", + "interleukin-22 (human)", + "IL22 protein, human" + ] + } + ] + }, + "NCBIGene:3605": { + "categories": [ + "biolink:Gene" + ], + "name": "IL17A", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3605", + "ENSEMBL:ENSG00000112115", + "HGNC:5981", + "OMIM:603149", + "UMLS:C1825592", + "UniProtKB:Q16552", + "PR:Q16552", + "ENSEMBL:ENSP00000497968", + "ENSEMBL:ENSP00000497968.1", + "UMLS:C1701790" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "IL17A", + "IL17A gene", + "IL17_HUMAN Interleukin-17A (sprot)", + "interleukin-17A (human)", + "IL17A protein, human" + ] + } + ] + }, + "NCBIGene:7049": { + "categories": [ + "biolink:Gene" + ], + "name": "TGFBR3", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:7049", + "ENSEMBL:ENSG00000069702", + "HGNC:11774", + "OMIM:600742", + "UMLS:C1336625", + "UniProtKB:A0A0A8KWK3", + "UniProtKB:Q03167", + "PR:Q03167", + "UMLS:C1700222" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TGFBR3", + "TGFBR3 gene", + "A0A0A8KWK3_HUMAN Transforming growth factor, beta receptor III (trembl)", + "TGBR3_HUMAN Transforming growth factor beta receptor type 3 (sprot)", + "transforming growth factor beta receptor type 3 (human)", + "TGFBR3 protein, human" + ] + } + ] + }, + "NCBIGene:10673": { + "categories": [ + "biolink:Gene" + ], + "name": "TNFSF13B", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:10673", + "ENSEMBL:ENSG00000102524", + "HGNC:11929", + "OMIM:603969", + "UMLS:C1420816", + "UniProtKB:A0A0U5J7Q1", + "UniProtKB:Q9Y275", + "PR:Q9Y275", + "UMLS:C1682317" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TNFSF13B", + "TNFSF13B gene", + "A0A0U5J7Q1_HUMAN Epididymis secretory sperm binding protein (trembl)", + "TN13B_HUMAN Tumor necrosis factor ligand superfamily member 13B (sprot)", + "tumor necrosis factor ligand superfamily member 13B (human)", + "TNFSF13B protein, human" + ] + } + ] + }, + "NCBIGene:931": { + "categories": [ + "biolink:Gene" + ], + "name": "MS4A1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:931", + "ENSEMBL:ENSG00000156738", + "HGNC:7315", + "OMIM:112210", + 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mRNA (trembl)", + "SPD2A_HUMAN SH3 and PX domain-containing protein 2A (sprot)", + "SH3 and PX domain-containing protein 2A (human)", + "SH3 and PX Domain-Containing Protein 2A, Human" + ] + } + ] + }, + "NCBIGene:6500": { + "categories": [ + "biolink:Gene" + ], + "name": "SKP1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6500", + "ENSEMBL:ENSG00000113558", + "HGNC:10899", + "OMIM:601434", + "UMLS:C1420081", + "UniProtKB:P63208", + "PR:P63208", + "UMLS:C0385145" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SKP1", + "SKP1 gene", + "SKP1_HUMAN S-phase kinase-associated protein 1 (sprot)", + "S-phase kinase-associated protein 1 (human)", + "SKP1 protein, human" + ] + } + ] + }, + "NCBIGene:4524": { + "categories": [ + "biolink:Gene" + ], + "name": "MTHFR", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4524", + "ENSEMBL:ENSG00000177000", + "HGNC:7436", + "OMIM:607093", + 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"name": "ITSN2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:50618", + "ENSEMBL:ENSG00000198399", + "HGNC:6184", + "OMIM:604464", + "UMLS:C1416521" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ITSN2", + "ITSN2 gene" + ] + } + ] + }, + "NCBIGene:55824": { + "categories": [ + "biolink:Gene" + ], + "name": "PAG1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:55824", + "ENSEMBL:ENSG00000076641", + "HGNC:30043", + "OMIM:605767", + "UMLS:C1538565", + "UniProtKB:Q9NWQ8", + "PR:Q9NWQ8", + "ENSEMBL:ENSP00000220597", + "ENSEMBL:ENSP00000220597.3" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PAG1", + "PAG1 gene", + "PHAG1_HUMAN Phosphoprotein associated with glycosphingolipid-enriched microdomains 1 (sprot)", + "phosphoprotein associated with glycosphingolipid-enriched microdomains 1 (human)" + ] + } + ] + }, + "NCBIGene:23387": { + "categories": [ + "biolink:Gene" + ], + "name": "SIK3", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:23387", + "ENSEMBL:ENSG00000160584", + "HGNC:29165", + "OMIM:614776", + "UMLS:C2828701", + "UniProtKB:A1A5A9", + "UniProtKB:Q9Y2K2", + "PR:Q9Y2K2" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SIK3", + "SIK3 gene", + "A1A5A9_HUMAN KIAA0999 protein (trembl)", + "SIK3_HUMAN Serine/threonine-protein kinase SIK3 (sprot)", + "serine/threonine-protein kinase SIK3 (human)" + ] + } + ] + }, + "NCBIGene:72": { + "categories": [ + "biolink:Gene" + ], + "name": "ACTG2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:72", + "ENSEMBL:ENSG00000163017", + "HGNC:145", + "OMIM:102545", + "UMLS:C1332010", + "UniProtKB:P63267", + "PR:P63267", + "UMLS:C1332142" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ACTG2", + "ACTG2 gene", + "ACTH_HUMAN Actin, gamma-enteric smooth muscle (sprot)", + "actin, gamma-enteric smooth muscle (human)", + "Actin, Gamma 2" + ] + } + ] + }, + "NCBIGene:867": { + "categories": [ + "biolink:Gene" + ], + "name": "CBL", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:867", + "ENSEMBL:ENSG00000110395", + "HGNC:1541", + "OMIM:165360", + "UMLS:C0812242" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CBL", + "CBL gene" + ] + } + ] + }, + "NCBIGene:60": { + "categories": [ + "biolink:Gene" + ], + "name": "ACTB", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:60", + "ENSEMBL:ENSG00000075624", + "HGNC:132", + "OMIM:102630", + "UMLS:C1384510", + "UniProtKB:P60709", + "PR:P60709", + "ENSEMBL:ENSP00000494269", + "ENSEMBL:ENSP00000494269.1", + "ENSEMBL:ENSP00000494750", + "ENSEMBL:ENSP00000494750.1", + "ENSEMBL:ENSP00000495995", + "ENSEMBL:ENSP00000495995.2", + "ENSEMBL:ENSP00000501862", + "ENSEMBL:ENSP00000501862.1", + "ENSEMBL:ENSP00000502821", + "ENSEMBL:ENSP00000502821.1", + "UMLS:C3542398", + "UniProtKB:Q1KLZ0" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ACTB", + "ACTB gene", + "ACTB_HUMAN Actin, cytoplasmic 1 (sprot)", + "actin, cytoplasmic 1 (human)", + "Actin, Cytoplasmic 1", + "Q1KLZ0_HUMAN HCG15971, isoform CRA_a (trembl)" + ] + } + ] + }, + "NCBIGene:799": { + "categories": [ + "biolink:Gene" + ], + "name": "CALCR", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:799", + "ENSEMBL:ENSG00000004948", + "HGNC:1440", + "OMIM:114131", + "UMLS:C1413085", + "UniProtKB:P30988", + "PR:P30988" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CALCR", + "CALCR gene", + "CALCR_HUMAN Calcitonin receptor (sprot)", + "calcitonin receptor (human)" + ] + } + ] + }, + "NCBIGene:2017": { + "categories": [ + "biolink:Gene" + ], + "name": "CTTN", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2017", + "ENSEMBL:ENSG00000085733", + "HGNC:3338", + "OMIM:164765", + "UMLS:C0812261", + "UniProtKB:A0A024R5M3", + "UniProtKB:Q14247", + "PR:Q14247", + "UMLS:C1533647", + "UniProtKB:Q53HG7" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CTTN", + "CTTN gene", + "A0A024R5M3_HUMAN Cortactin, isoform CRA_c (trembl)", + "SRC8_HUMAN Src substrate cortactin (sprot)", + "Src substrate cortactin (human)", + "CTTN protein, human", + "Q53HG7_HUMAN Cortactin isoform a variant (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:6469": { + "categories": [ + "biolink:Gene" + ], + "name": "SHH", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6469", + "ENSEMBL:ENSG00000164690", + "HGNC:10848", + "OMIM:600725", + "UMLS:C1335824", + "UniProtKB:Q15465", + "PR:Q15465", + "ENSEMBL:ENSP00000297261", + "ENSEMBL:ENSP00000297261.2", + "UMLS:C0258846" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SHH", + "SHH gene", + "SHH_HUMAN Sonic hedgehog protein (sprot)", + "sonic hedgehog protein (human)", + "SHH protein, human" + ] + } + ] + }, + "NCBIGene:51684": { + "categories": [ + "biolink:Gene" + ], + "name": "SUFU", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:51684", + "ENSEMBL:ENSG00000107882", + "HGNC:16466", + "OMIM:607035", + "UMLS:C1424302", + "UniProtKB:A0A223LX15", + "UniProtKB:Q9UMX1", + "PR:Q9UMX1", + "UMLS:C3273645" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SUFU", + "SUFU gene", + "A0A223LX15_HUMAN Suppressor of fused homolog (trembl)", + "SUFU_HUMAN Suppressor of fused homolog (sprot)", + "suppressor of fused homolog (human)", + "Suppressor of Fused Homolog" + ] + } + ] + }, + "NCBIGene:3624": { + "categories": [ + "biolink:Gene" + ], + "name": "INHBA", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3624", + "ENSEMBL:ENSG00000122641", + "HGNC:6066", + "OMIM:147290", + "UMLS:C1334131", + "UniProtKB:A4D1W7", + "UniProtKB:P08476", + "PR:P08476", + "ENSEMBL:ENSP00000242208", + "ENSEMBL:ENSP00000242208.4", + "ENSEMBL:ENSP00000397197", + "ENSEMBL:ENSP00000397197.1", + "ENSEMBL:ENSP00000490646", + "ENSEMBL:ENSP00000490646.1", + "UMLS:C1570131" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "INHBA", + "INHBA gene", + "A4D1W7_HUMAN Inhibin beta A chain (trembl)", + "INHBA_HUMAN Inhibin beta A chain (sprot)", + "inhibin beta A chain (human)", + "INHBA protein, human" + ] + } + ] + }, + "NCBIGene:8205": { + "categories": [ + "biolink:Gene" + ], + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:8205" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "NCBIGene:8205" + ] + } + ] + }, + "NCBIGene:6786": { + "categories": [ + "biolink:Gene" + ], + "name": "STIM1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6786", + "ENSEMBL:ENSG00000167323", + "HGNC:11386", + "OMIM:605921", + "UMLS:C1335879", + "UniProtKB:G0XQ39", + "ENSEMBL:ENSP00000478059", + "ENSEMBL:ENSP00000478059.1", + "UniProtKB:Q13586", + "PR:Q13586", + "UMLS:C1430594" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "STIM1", + "STIM1 gene", + "G0XQ39_HUMAN STIM1L (trembl)", + "STIM1_HUMAN Stromal interaction molecule 1 (sprot)", + "stromal interaction molecule 1 (human)", + "STIM1 protein, human" + ] + } + ] + }, + "NCBIGene:4240": { + "categories": [ + "biolink:Gene" + ], + "name": "MFGE8", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4240", + "ENSEMBL:ENSG00000140545", + "HGNC:7036", + "OMIM:602281", + "UMLS:C1334502", + "UniProtKB:A0A8Q3SIZ9", + "ENSEMBL:ENSP00000512163", + "ENSEMBL:ENSP00000512163.1", + "UniProtKB:B3KTQ2", + "UniProtKB:B4E396", + "UniProtKB:H0YKB5", + "ENSEMBL:ENSP00000452734", + "ENSEMBL:ENSP00000452734.2", + "UniProtKB:Q08431", + "PR:Q08431", + "UMLS:C0388561" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MFGE8", + "MFGE8 gene", + "A0A8Q3SIZ9_HUMAN Milk fat globule EGF and factor V/VIII domain containing (trembl)", + "B3KTQ2_HUMAN cDNA FLJ38589 fis, clone HCHON2010074, highly similar to LACTADHERIN (trembl)", + "B4E396_HUMAN cDNA FLJ59612, highly similar to Lactadherin (trembl)", + "H0YKB5_HUMAN Milk fat globule EGF and factor V/VIII domain containing (trembl)", + "MFGM_HUMAN Lactadherin (sprot)", + "lactadherin (human)", + "MFGE8 protein, human" + ] + } + ] + }, + "NCBIGene:2736": { + "categories": [ + "biolink:Gene" + ], + "name": "GLI2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2736", + "ENSEMBL:ENSG00000074047", + "HGNC:4318", + "OMIM:165230", + "UMLS:C0812306", + "UniProtKB:P10070", + "PR:P10070", + "UMLS:C0218975", + "UniProtKB:Q1PSW9", + "ENSEMBL:ENSP00000398992", + "ENSEMBL:ENSP00000398992.1", + "UniProtKB:Q59FV5" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "GLI2", + "GLI2 gene", + "GLI2_HUMAN Zinc finger protein GLI2 (sprot)", + "zinc finger protein GLI2 (human)", + "GLI2 protein, human", + "Q1PSW9_HUMAN GLI family zinc finger 2 (Fragment) (trembl)", + "Q59FV5_HUMAN GLI-Kruppel family member GLI2 isoform beta variant (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:5727": { + "categories": [ + "biolink:Gene" + ], + "name": "PTCH1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5727", + "ENSEMBL:ENSG00000185920", + "HGNC:9585", + "OMIM:601309", + "UMLS:C1826732", + "UniProtKB:Q13635", + "PR:Q13635", + "UMLS:C4308013" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PTCH1", + "PTCH1 gene", + "PTC1_HUMAN Protein patched homolog 1 (sprot)", + "protein patched homolog 1 (human)", + "PTCH1 protein, human" + ] + } + ] + }, + "NCBIGene:3569": { + "categories": [ + "biolink:Gene" + ], + "name": "IL6", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3569", + "ENSEMBL:ENSG00000136244", + "HGNC:6018", + "OMIM:147620", + "UMLS:C1334122", + "UniProtKB:B4DNQ5", + "UniProtKB:B4DVM1", + "UniProtKB:B5MC21", + "ENSEMBL:ENSP00000385043", + "ENSEMBL:ENSP00000385043.1", + "UniProtKB:P05231", + "PR:P05231", + "ENSEMBL:ENSP00000258743", + "ENSEMBL:ENSP00000258743.5", + "ENSEMBL:ENSP00000385675", + "ENSEMBL:ENSP00000385675.1", + "UMLS:C0878479", + "UMLS:C1527132", + "UMLS:C1698754", + "UniProtKB:Q75MH2" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "IL6", + "IL6 gene", + "B4DNQ5_HUMAN Interleukin-6 (trembl)", + "B4DVM1_HUMAN Interleukin-6 (trembl)", + "B5MC21_HUMAN Interleukin-6 (trembl)", + "IL6_HUMAN Interleukin-6 (sprot)", + "interleukin-6 (human)", + "Sigosix", + "Recombinant Interleukin-6", + "IL6 protein, human", + "Q75MH2_HUMAN Interleukin-6 (trembl)" + ] + } + ] + }, + "NCBIGene:3479": { + "categories": [ + "biolink:Gene" + ], + "name": "IGF1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3479", + "ENSEMBL:ENSG00000017427", + "HGNC:5464", + "OMIM:147440", + "UMLS:C1334089", + "UniProtKB:P05019", + "PR:P05019", + "UMLS:C3712803", + "UniProtKB:Q13429", + "UniProtKB:Q59GC5", + "UniProtKB:Q5U743" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "IGF1", + "IGF1 gene", + "IGF1_HUMAN Insulin-like growth factor I (sprot)", + "insulin-like growth factor I (human)", + "IGF1 protein, human", + "Q13429_HUMAN Insulin-like growth factor I (Fragment) (trembl)", + "Q59GC5_HUMAN Insulin-like growth factor I (Fragment) (trembl)", + "Q5U743_HUMAN Insulin-like growth factor I (trembl)" + ] + } + ] + }, + "NCBIGene:11127": { + "categories": [ + "biolink:Gene" + ], + "name": "KIF3A", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:11127", + "ENSEMBL:ENSG00000131437", + "HGNC:6319", + "OMIM:604683", + "UMLS:C1416634", + "UniProtKB:B4DHG8", + "UniProtKB:E9PES4", + "ENSEMBL:ENSP00000385808", + "ENSEMBL:ENSP00000385808.1", + "UniProtKB:J3KPF9", + "ENSEMBL:ENSP00000368009", + "ENSEMBL:ENSP00000368009.1", + "UniProtKB:Q05CT3", + "UniProtKB:Q9Y496", + "PR:Q9Y496", + "ENSEMBL:ENSP00000368020", + "ENSEMBL:ENSP00000368020.3" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "KIF3A", + "KIF3A gene", + "B4DHG8_HUMAN Kinesin-like protein (trembl)", + "E9PES4_HUMAN Kinesin-like protein (trembl)", + "J3KPF9_HUMAN Kinesin-like protein (trembl)", + "Q05CT3_HUMAN Kinesin-like protein (Fragment) (trembl)", + "KIF3A_HUMAN Kinesin-like protein KIF3A (sprot)", + "kinesin-like protein KIF3A (human)" + ] + } + ] + }, + "NCBIGene:501": { + "categories": [ + "biolink:Gene" + ], + "name": "ALDH7A1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:501", + "ENSEMBL:ENSG00000164904", + "HGNC:877", + "OMIM:107323", + "UMLS:C1412691", + "UniProtKB:P49419", + "PR:P49419" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ALDH7A1", + "ALDH7A1 gene", + "AL7A1_HUMAN Alpha-aminoadipic semialdehyde dehydrogenase (sprot)", + "alpha-aminoadipic semialdehyde dehydrogenase (human)" + ] + } + ] + }, + "NCBIGene:224": { + "categories": [ + "biolink:Gene" + ], + "name": "ALDH3A2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:224", + "ENSEMBL:ENSG00000072210", + "HGNC:403", + "OMIM:609523", + "UMLS:C1412334", + "UniProtKB:P51648", + "PR:P51648" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ALDH3A2", + "ALDH3A2 gene", + "AL3A2_HUMAN Aldehyde dehydrogenase family 3 member A2 (sprot)", + "aldehyde dehydrogenase family 3 member A2 (human)" + ] + } + ] + }, + "NCBIGene:637": { + "categories": [ + "biolink:Gene" + ], + "name": "BID", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:637", + "ENSEMBL:ENSG00000015475", + "HGNC:1050", + "OMIM:601997", + "UMLS:C1332410", + "UniProtKB:A8ASI8", + "UniProtKB:B2ZP79", + "UniProtKB:B3KT21", + "UniProtKB:P55957", + "PR:P55957", + "UMLS:C1530795", + "UMLS:C3641819" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "BID", + "BID gene", + "A8ASI8_HUMAN BH3-interacting domain death agonist (trembl)", + "B2ZP79_HUMAN BH3-interacting domain death agonist (trembl)", + "B3KT21_HUMAN BH3-interacting domain death agonist (trembl)", + "BID_HUMAN BH3-interacting domain death agonist (sprot)", + "BH3-interacting domain death agonist (human)", + "BID protein, human", + "Truncated BID" + ] + } + ] + }, + "NCBIGene:6280": { + "categories": [ + "biolink:Gene" + ], + "name": "S100A9", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6280", + "ENSEMBL:ENSG00000163220", + "HGNC:10499", + "OMIM:123886", + "UMLS:C1335798", + "UniProtKB:P06702", + "PR:P06702", + "ENSEMBL:ENSP00000357727", + "ENSEMBL:ENSP00000357727.3", + "UMLS:C4281724" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "S100A9", + "S100A9 gene", + "S10A9_HUMAN Protein S100-A9 (sprot)", + "protein S100-A9 (human)", + "Protein S100-A9" + ] + } + ] + }, + "NCBIGene:9446": { + "categories": [ + "biolink:Gene" + ], + "name": "GSTO1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:9446", + "ENSEMBL:ENSG00000148834", + "HGNC:13312", + "OMIM:605482", + "UMLS:C1421933", + "UniProtKB:P78417", + "PR:P78417", + "UniProtKB:V9HWG9" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "GSTO1", + "GSTO1 gene", + "GSTO1_HUMAN Glutathione S-transferase omega-1 (sprot)", + "glutathione S-transferase omega-1 (human)", + "V9HWG9_HUMAN Glutathione S-transferase omega (trembl)" + ] + } + ] + }, + "NCBIGene:7291": { + "categories": [ + "biolink:Gene" + ], + "name": "TWIST1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:7291", + "ENSEMBL:ENSG00000122691", + "HGNC:12428", + "OMIM:601622", + "UMLS:C1421244", + "UniProtKB:Q15672", + "PR:Q15672", + "ENSEMBL:ENSP00000242261", + "ENSEMBL:ENSP00000242261.5", + "UMLS:C0533325" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TWIST1", + "TWIST1 gene", + "TWST1_HUMAN Twist-related protein 1 (sprot)", + "twist-related protein 1 (human)", + "TWIST1 protein, human" + ] + } + ] + }, + "NCBIGene:4790": { + "categories": [ + "biolink:Gene" + ], + "name": "NFKB1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4790", + "ENSEMBL:ENSG00000109320", + "HGNC:7794", + "OMIM:164011", + "UMLS:C1417708", + "UniProtKB:P19838", + "PR:P19838", + "UMLS:C1452413", + "UMLS:C2986465" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "NFKB1", + "NFKB1 gene", + "NFKB1_HUMAN Nuclear factor NF-kappa-B p105 subunit (sprot)", + "nuclear factor NF-kappa-B p105 subunit (human)", + "NFKB1 protein, human", + "Nuclear Factor NF-kappa-B p105 Subunit" + ] + } + ] + }, + "NCBIGene:7157": { + "categories": [ + "biolink:Gene" + ], + "name": "TP53", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:7157", + "ENSEMBL:ENSG00000141510", + "HGNC:11998", + "OMIM:191170", + "UMLS:C0079419", + "UniProtKB:A0A087WT22", + "ENSEMBL:ENSP00000477531", + "ENSEMBL:ENSP00000477531.1", + "UniProtKB:A0A087WXZ1", + "ENSEMBL:ENSP00000481401", + "ENSEMBL:ENSP00000481401.1", + "UniProtKB:A0A087X1Q1", + "ENSEMBL:ENSP00000484375", + "ENSEMBL:ENSP00000484375.1", + "UniProtKB:H2EHT1", + "UniProtKB:K7PPA8", + "UniProtKB:P04637", + "PR:P04637", + "UMLS:C0146283", + "UniProtKB:Q53GA5" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TP53", + "TP53 gene", + "A0A087WT22_HUMAN Cellular tumor antigen p53 (trembl)", + "A0A087WXZ1_HUMAN Cellular tumor antigen p53 (trembl)", + "A0A087X1Q1_HUMAN Cellular tumor antigen p53 (trembl)", + "H2EHT1_HUMAN Cellular tumor antigen p53 (trembl)", + "K7PPA8_HUMAN Cellular tumor antigen p53 (trembl)", + "P53_HUMAN Cellular tumor antigen p53 (sprot)", + "cellular tumor antigen p53 (human)", + "TP53 protein, human", + "Q53GA5_HUMAN Tumor protein p53 variant (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:4851": { + "categories": [ + "biolink:Gene" + ], + "name": "NOTCH1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4851", + "ENSEMBL:ENSG00000148400", + "HGNC:7881", + "OMIM:190198", + "UMLS:C1334889", + "UniProtKB:P46531", + "PR:P46531", + "ENSEMBL:ENSP00000498587", + "ENSEMBL:ENSP00000498587.1", + "UMLS:C1335068" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "NOTCH1", + "NOTCH1 gene", + "NOTC1_HUMAN Neurogenic locus notch homolog protein 1 (sprot)", + "neurogenic locus notch homolog protein 1 (human)", + "NOTCH1 protein, human" + ] + } + ] + }, + "NCBIGene:3091": { + "categories": [ + "biolink:Gene" + ], + "name": "HIF1A", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3091", + "ENSEMBL:ENSG00000100644", + "HGNC:4910", + "OMIM:603348", + "UMLS:C1333897", + "UniProtKB:D0VY79", + "UniProtKB:Q16665", + "PR:Q16665", + "UMLS:C1528322" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "HIF1A", + "HIF1A gene", + "D0VY79_HUMAN Hypoxia-inducible factor 1-alpha (trembl)", + "HIF1A_HUMAN Hypoxia-inducible factor 1-alpha (sprot)", + "hypoxia-inducible factor 1-alpha (human)", + "HIF1A protein, human" + ] + } + ] + }, + "NCBIGene:5624": { + "categories": [ + "biolink:Gene" + ], + "name": "PROC", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5624", + "ENSEMBL:ENSG00000115718", + "HGNC:9451", + "OMIM:612283", + "UMLS:C1418943", + "UniProtKB:B4DPC8", + "UniProtKB:P04070", + "PR:P04070", + "UMLS:C1949480" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PROC", + "PROC gene", + "B4DPC8_HUMAN cDNA FLJ51023, highly similar to Vitamin K-dependent protein C (trembl)", + "PROC_HUMAN Vitamin K-dependent protein C (sprot)", + "vitamin K-dependent protein C (human)", + "protein C, human" + ] + } + ] + }, + "NCBIGene:6584": { + "categories": [ + "biolink:Gene" + ], + "name": "SLC22A5", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6584", + "ENSEMBL:ENSG00000197375", + "HGNC:10969", + "OMIM:603377", + "UMLS:C1420140", + "UniProtKB:O76082", + "PR:O76082" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SLC22A5", + "SLC22A5 gene", + "OCTN2_HUMAN Organic cation/carnitine transporter 2 (sprot)", + "organic cation/carnitine transporter 2 (human)" + ] + } + ] + }, + "NCBIGene:7480": { + "categories": [ + "biolink:Gene" + ], + "name": "WNT10B", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:7480", + "ENSEMBL:ENSG00000169884", + "HGNC:12775", + "OMIM:601906", + "UMLS:C1421511", + "UniProtKB:O00744", + "PR:O00744", + "UMLS:C1454716" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "WNT10B", + "WNT10B gene", + "WN10B_HUMAN Protein Wnt-10b (sprot)", + "protein Wnt-10b (human)", + "WNT10B protein, human" + ] + } + ] + }, + "NCBIGene:999": { + "categories": [ + "biolink:Gene" + ], + "name": "CDH1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:999", + "ENSEMBL:ENSG00000039068", + "HGNC:1748", + "OMIM:192090", + "UMLS:C0694872", + "UniProtKB:A0A0U2ZQU7", + "UniProtKB:B3GN61", + "UniProtKB:P12830", + "PR:P12830", + "UMLS:C1739912", + "UniProtKB:Q9UII7" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CDH1", + "CDH1 gene", + "A0A0U2ZQU7_HUMAN E-cadherin 1 (trembl)", + "B3GN61_HUMAN Truncated E-cadherin (trembl)", + "CADH1_HUMAN Cadherin-1 (sprot)", + "cadherin-1 (human)", + "CDH1 protein, human", + "Q9UII7_HUMAN E-cadherin (trembl)" + ] + } + ] + }, + "NCBIGene:7178": { + "categories": [ + "biolink:Gene" + ], + "name": "TPT1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:7178", + "ENSEMBL:ENSG00000133112", + "HGNC:12022", + "OMIM:600763", + "UMLS:C1420882", + "UniProtKB:A0A024RDY2", + "UniProtKB:A0A0B4J2C3", + "ENSEMBL:ENSP00000477781", + "ENSEMBL:ENSP00000477781.1", + "UniProtKB:A0A0P1J1R0", + "UniProtKB:P13693", + "PR:P13693", + "UMLS:C1100850" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TPT1", + "TPT1 gene", + "A0A024RDY2_HUMAN Tumor protein, translationally-controlled 1, isoform CRA_a (trembl)", + "A0A0B4J2C3_HUMAN Tumor protein, translationally-controlled 1 (trembl)", + "A0A0P1J1R0_HUMAN Translationally-controlled tumor protein (trembl)", + "TCTP_HUMAN Translationally-controlled tumor protein (sprot)", + "translationally-controlled tumor protein (human)", + "TPT1 protein, human" + ] + } + ] + }, + "NCBIGene:1977": { + "categories": [ + "biolink:Gene" + ], + "name": "EIF4E", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1977", + "ENSEMBL:ENSG00000151247", + "HGNC:3287", + "OMIM:133440", + "UMLS:C1414351", + "UniProtKB:D6RBW1", + "ENSEMBL:ENSP00000423977", + "ENSEMBL:ENSP00000423977.1", + "UniProtKB:P06730", + "PR:P06730", + "UMLS:C3539642", + "UniProtKB:Q32Q75", + "UniProtKB:X5D7E3" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "EIF4E", + "EIF4E gene", + "D6RBW1_HUMAN Eukaryotic translation initiation factor 4E (trembl)", + "IF4E_HUMAN Eukaryotic translation initiation factor 4E (sprot)", + "eukaryotic translation initiation factor 4E (human)", + "Eukaryotic Translation Initiation Factor 4E, human", + "Q32Q75_HUMAN Eukaryotic translation initiation factor 4E (trembl)", + "X5D7E3_HUMAN Eukaryotic translation initiation factor 4E isoform A (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:2938": { + "categories": [ + "biolink:Gene" + ], + "name": "GSTA1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2938", + "ENSEMBL:ENSG00000243955", + "HGNC:4626", + "OMIM:138359", + "UMLS:C1415328", + "UniProtKB:A0A140VJK4", + "UniProtKB:B7Z1F9", + "UniProtKB:P08263", + "PR:P08263", + "ENSEMBL:ENSP00000335620", + "ENSEMBL:ENSP00000335620.5", + "UMLS:C1436224" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "GSTA1", + "GSTA1 gene", + "A0A140VJK4_HUMAN Glutathione S-transferase (trembl)", + "B7Z1F9_HUMAN Glutathione S-transferase (trembl)", + "GSTA1_HUMAN Glutathione S-transferase A1 (sprot)", + "glutathione S-transferase A1 (human)", + "Glutathione S-Transferase A1, Human" + ] + } + ] + }, + "NCBIGene:4035": { + "categories": [ + "biolink:Gene" + ], + "name": "LRP1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4035", + "ENSEMBL:ENSG00000123384", + "HGNC:6692", + "OMIM:107770", + "UMLS:C1416912", + "UniProtKB:Q07954", + "PR:Q07954", + "UMLS:C2987172", + "UniProtKB:Q59FG2" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "LRP1", + "LRP1 gene", + "LRP1_HUMAN Prolow-density lipoprotein receptor-related protein 1 (sprot)", + "prolow-density lipoprotein receptor-related protein 1 (human)", + "Prolow-Density Lipoprotein Receptor-Related Protein 1", + "Q59FG2_HUMAN Low density lipoprotein-related protein 1 variant (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:217": { + "categories": [ + "biolink:Gene" + ], + "name": "ALDH2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:217", + "ENSEMBL:ENSG00000111275", + "HGNC:404", + "OMIM:100650", + "UMLS:C1412335", + "UniProtKB:A0A384NPN7", + "UniProtKB:P05091", + "PR:P05091", + "UMLS:C4083146" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ALDH2", + "ALDH2 gene", + "A0A384NPN7_HUMAN Aldehyde dehydrogenase 2 family (Mitochondrial), isoform CRA_c (trembl)", + "ALDH2_HUMAN Aldehyde dehydrogenase, mitochondrial (sprot)", + "aldehyde dehydrogenase, mitochondrial (human)", + "Aldehyde Dehydrogenase, Mitochondrial, human" + ] + } + ] + }, + "NCBIGene:596": { + "categories": [ + "biolink:Gene" + ], + "name": "BCL2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:596", + "ENSEMBL:ENSG00000171791", + "HGNC:990", + "OMIM:151430", + "UMLS:C0376515", + "UniProtKB:A0A024R2B3", + "UniProtKB:A0A024R2C4", + "UniProtKB:A0A7I2V3S7", + "ENSEMBL:ENSP00000503628", + "ENSEMBL:ENSP00000503628.1", + "UniProtKB:P10415", + "PR:P10415", + "UMLS:C4042483" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "BCL2", + "BCL2 gene", + "A0A024R2B3_HUMAN Apoptosis regulator Bcl-2 (trembl)", + "A0A024R2C4_HUMAN Apoptosis regulator Bcl-2 (trembl)", + "A0A7I2V3S7_HUMAN Apoptosis regulator Bcl-2 (trembl)", + "BCL2_HUMAN Apoptosis regulator Bcl-2 (sprot)", + "apoptosis regulator Bcl-2 (human)", + "BCL2 protein, human" + ] + } + ] + }, + "NCBIGene:5970": { + "categories": [ + "biolink:Gene" + ], + "name": "RELA", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5970", + "ENSEMBL:ENSG00000173039", + "HGNC:9955", + "OMIM:164014", + "UMLS:C1335610", + "UniProtKB:A0A087X0W8", + "ENSEMBL:ENSP00000483705", + "ENSEMBL:ENSP00000483705.1", + "UniProtKB:Q04206", + "PR:Q04206", + "UMLS:C1567060" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "RELA", + "RELA gene", + "A0A087X0W8_HUMAN RELA proto-oncogene, NF-kB subunit (trembl)", + "TF65_HUMAN Transcription factor p65 (sprot)", + "transcription factor p65 (human)", + "RELA protein, human" + ] + } + ] + }, + "NCBIGene:2012": { + "categories": [ + "biolink:Gene" + ], + "name": "EMP1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2012", + "ENSEMBL:ENSG00000134531", + "HGNC:3333", + "OMIM:602333", + "UMLS:C0812384", + "UniProtKB:A0A024RAT0", + "UniProtKB:P54849", + "PR:P54849", + "UMLS:C1259382" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "EMP1", + "EMP1 gene", + "A0A024RAT0_HUMAN Epithelial membrane protein 1 (trembl)", + "EMP1_HUMAN Epithelial membrane protein 1 (sprot)", + "epithelial membrane protein 1 (human)", + "EMP1 protein, human" + ] + } + ] + }, + "NCBIGene:3921": { + "categories": [ + "biolink:Gene" + ], + "name": "RPSA", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3921", + "ENSEMBL:ENSG00000168028", + "HGNC:6502", + "OMIM:150370", + "UMLS:C1539696", + "UniProtKB:A0A024R2L6", + "UniProtKB:A0A0C4DG17", + "ENSEMBL:ENSP00000389351", + "ENSEMBL:ENSP00000389351.1", + "UniProtKB:P08865", + "PR:P08865", + "ENSEMBL:ENSP00000346067", + "ENSEMBL:ENSP00000346067.4", + "ENSEMBL:ENSP00000410848", + "ENSEMBL:ENSP00000410848.2", + "ENSEMBL:ENSP00000513423", + "ENSEMBL:ENSP00000513423.1", + "ENSEMBL:ENSP00000513424", + "ENSEMBL:ENSP00000513424.1", + "ENSEMBL:ENSP00000513425", + "ENSEMBL:ENSP00000513425.1", + "UMLS:C2001624", + "UMLS:C3816725" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "RPSA", + "RPSA gene", + "A0A024R2L6_HUMAN Small ribosomal subunit protein uS2 (trembl)", + "A0A0C4DG17_HUMAN Small ribosomal subunit protein uS2 (trembl)", + "RSSA_HUMAN Small ribosomal subunit protein uS2 (sprot)", + "40S ribosomal protein SA (human)", + "Lamr1 protein, human", + "67 kDa Laminin Receptor" + ] + } + ] + }, + "NCBIGene:4855": { + "categories": [ + "biolink:Gene" + ], + "name": "NOTCH4", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4855", + "ENSEMBL:ENSG00000204301", + "HGNC:7884", + "OMIM:164951", + "UMLS:C0812223", + "UniProtKB:A0A1U9X983", + "UniProtKB:Q99466", + "PR:Q99466", + "ENSEMBL:ENSP00000401321", + "ENSEMBL:ENSP00000401321.1", + "ENSEMBL:ENSP00000408335", + "ENSEMBL:ENSP00000408335.2", + "UMLS:C0539211" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "NOTCH4", + "NOTCH4 gene", + "A0A1U9X983_HUMAN NOTCH4 (trembl)", + "NOTC4_HUMAN Neurogenic locus notch homolog protein 4 (sprot)", + "neurogenic locus notch homolog protein 4 (human)", + "NOTCH4 protein, human" + ] + } + ] + }, + "NCBIGene:378938": { + "categories": [ + "biolink:Gene" + ], + "name": "MALAT1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:378938", + "ENSEMBL:ENSG00000251562", + "HGNC:29665", + "OMIM:607924", + "UMLS:C1537647" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MALAT1", + "MALAT1 gene" + ] + } + ] + }, + "NCBIGene:8626": { + "categories": [ + "biolink:Gene" + ], + "name": "TP63", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:8626", + "ENSEMBL:ENSG00000073282", + "HGNC:15979", + "OMIM:603273", + "UMLS:C1422009", + "UniProtKB:A0A0S2Z4N5", + "UniProtKB:A0A0S2Z4N6", + "UniProtKB:A0A141PNN3", + "UniProtKB:A0A141PNN4", + "UniProtKB:B7Z8X6", + "UniProtKB:C9D7D0", + "UniProtKB:Q9H3D4", + "PR:Q9H3D4", + "UMLS:C1431519", + "UMLS:C4284135" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TP63", + "TP63 gene", + "A0A0S2Z4N5_HUMAN Tumor protein 63 (p63) (Fragment) (trembl)", + "A0A0S2Z4N6_HUMAN Tumor protein 63 (p63) (Fragment) (trembl)", + "A0A141PNN3_HUMAN Cellular tumor antigen p53 (trembl)", + "A0A141PNN4_HUMAN Cellular tumor antigen p53 (trembl)", + "B7Z8X6_HUMAN Cellular tumor antigen p53 (trembl)", + "C9D7D0_HUMAN Cellular tumor antigen p53 (trembl)", + "P63_HUMAN Tumor protein 63 (sprot)", + "tumor protein 63 (human)", + "TP63 protein, human", + "Tumor Protein 63 Isoform 2, human" + ] + } + ] + }, + "NCBIGene:928": { + "categories": [ + "biolink:Gene" + ], + "name": "CD9", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:928", + "ENSEMBL:ENSG00000010278", + "HGNC:1709", + "OMIM:143030", + "UMLS:C1413246", + "UniProtKB:A6NNI4", + "ENSEMBL:ENSP00000371955", + "ENSEMBL:ENSP00000371955.2", + "ENSEMBL:ENSP00000494858", + "ENSEMBL:ENSP00000494858.1", + "ENSEMBL:ENSP00000495090", + "ENSEMBL:ENSP00000495090.1", + "ENSEMBL:ENSP00000502917", + "ENSEMBL:ENSP00000502917.1", + "UniProtKB:B4DK09", + "UniProtKB:P21926", + "PR:P21926", + "ENSEMBL:ENSP00000009180", + "ENSEMBL:ENSP00000009180.4", + "ENSEMBL:ENSP00000371958", + "ENSEMBL:ENSP00000371958.1", + "ENSEMBL:ENSP00000496639", + "ENSEMBL:ENSP00000496639.1", + "UMLS:C1701084" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CD9", + "CD9 gene", + "A6NNI4_HUMAN CD9 molecule (trembl)", + "B4DK09_HUMAN cDNA FLJ56697, highly similar to CD9 antigen (trembl)", + "CD9_HUMAN CD9 antigen (sprot)", + "CD9 antigen (human)", + "CD9 protein, human" + ] + } + ] + }, + "NCBIGene:1499": { + "categories": [ + "biolink:Gene" + ], + "name": "CTNNB1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1499", + "ENSEMBL:ENSG00000168036", + "HGNC:2514", + "OMIM:116806", + "UMLS:C1332803", + "UniProtKB:A0A024R2Q3", + "UniProtKB:B4DGU4", + "ENSEMBL:ENSP00000411226", + "ENSEMBL:ENSP00000411226.1", + "ENSEMBL:ENSP00000494467", + "ENSEMBL:ENSP00000494467.1", + "ENSEMBL:ENSP00000494780", + "ENSEMBL:ENSP00000494780.1", + 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"ENSEMBL:ENSG00000026508", + "HGNC:1681", + "OMIM:107269", + "UMLS:C1332712", + "UniProtKB:P16070", + "PR:P16070", + "UMLS:C1097299" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CD44", + "CD44 gene", + "CD44_HUMAN CD44 antigen (sprot)", + "CD44 antigen (human)", + "CD44 protein, human" + ] + } + ] + }, + "NCBIGene:218": { + "categories": [ + "biolink:Gene" + ], + "name": "ALDH3A1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:218", + "ENSEMBL:ENSG00000108602", + "HGNC:405", + "OMIM:100660", + "UMLS:C1412336", + "UniProtKB:I3L3I9", + "ENSEMBL:ENSP00000460482", + "ENSEMBL:ENSP00000460482.2", + "UniProtKB:P30838", + "PR:P30838", + "ENSEMBL:ENSP00000225740", + "ENSEMBL:ENSP00000225740.6", + "ENSEMBL:ENSP00000388469", + "ENSEMBL:ENSP00000388469.1", + "ENSEMBL:ENSP00000411821", + "ENSEMBL:ENSP00000411821.2", + "UniProtKB:Q6PKA6" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ALDH3A1", + "ALDH3A1 gene", 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(Fragment) (trembl)", + "Q5ZPJ1_HUMAN Bax protein (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:7476": { + "categories": [ + "biolink:Gene" + ], + "name": "WNT7A", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:7476", + "ENSEMBL:ENSG00000154764", + "HGNC:12786", + "OMIM:601570", + "UMLS:C1337005", + "UniProtKB:O00755", + "PR:O00755", + "ENSEMBL:ENSP00000285018", + "ENSEMBL:ENSP00000285018.4", + "UMLS:C0295892" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "WNT7A", + "WNT7A gene", + "WNT7A_HUMAN Protein Wnt-7a (sprot)", + "protein Wnt-7a (human)", + "WNT7A protein, human" + ] + } + ] + }, + "NCBIGene:100526842": { + "categories": [ + "biolink:Gene" + ], + "name": "RPL17-C18orf32", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:100526842", + "ENSEMBL:ENSG00000215472", + "HGNC:44661", + "UMLS:C3539211", + "UniProtKB:A0A0A0MRF8", + "ENSEMBL:ENSP00000352143", + 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to T-cell-specific surface glycoprotein CD28 (trembl)", + "CD28_HUMAN T-cell-specific surface glycoprotein CD28 (sprot)", + "T-cell-specific surface glycoprotein CD28 (human)", + "T-Cell-Specific Surface Glycoprotein CD28, human" + ] + } + ] + }, + "NCBIGene:6139": { + "categories": [ + "biolink:Gene" + ], + "name": "RPL17", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6139", + "ENSEMBL:ENSG00000265681", + "HGNC:10307", + "OMIM:603661", + "UMLS:C1419633", + "UniProtKB:A0A024R261", + "UniProtKB:P18621", + "PR:P18621" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "RPL17", + "RPL17 gene", + "A0A024R261_HUMAN Large ribosomal subunit protein uL22 (trembl)", + "RL17_HUMAN Large ribosomal subunit protein uL22 (sprot)", + "60S ribosomal protein L17 (human)" + ] + } + ] + }, + "NCBIGene:5728": { + "categories": [ + "biolink:Gene" + ], + "name": "PTEN", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5728", + "ENSEMBL:ENSG00000171862", + "HGNC:9588", + "OMIM:601728", + "UMLS:C0694888", + "UniProtKB:P60484", + "PR:P60484", + "UMLS:C1430988" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PTEN", + "PTEN gene", + "PTEN_HUMAN Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN (sprot)", + "phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN (human)", + "PTEN protein, human" + ] + } + ] + }, + "NCBIGene:134391": { + "categories": [ + "biolink:Gene" + ], + "name": "GPR151", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:134391", + "ENSEMBL:ENSG00000173250", + "HGNC:23624", + "OMIM:618487", + "UMLS:C1428170" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "GPR151", + "GPR151 gene" + ] + } + ] + }, + "NCBIGene:6374": { + "categories": [ + "biolink:Gene" + ], + "name": "CXCL5", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6374", + "ENSEMBL:ENSG00000163735", + "HGNC:10642", + "OMIM:600324", + "UMLS:C1332819", + "UniProtKB:P42830", + "PR:P42830", + "ENSEMBL:ENSP00000296027", + "ENSEMBL:ENSP00000296027.4", + "UMLS:C1435946", + "UniProtKB:Q6I9S7" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CXCL5", + "CXCL5 gene", + "CXCL5_HUMAN C-X-C motif chemokine 5 (sprot)", + "C-X-C motif chemokine 5 (human)", + "CXCL5 protein, human", + "Q6I9S7_HUMAN C-X-C motif chemokine (trembl)" + ] + } + ] + }, + "NCBIGene:4283": { + "categories": [ + "biolink:Gene" + ], + "name": "CXCL9", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4283", + "ENSEMBL:ENSG00000138755", + "HGNC:7098", + "OMIM:601704", + "UMLS:C1332821", + "UniProtKB:Q07325", + "PR:Q07325", + "ENSEMBL:ENSP00000354901", + "ENSEMBL:ENSP00000354901.4", + "UMLS:C0215469" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CXCL9", + "CXCL9 gene", + "CXCL9_HUMAN C-X-C motif chemokine 9 (sprot)", + "C-X-C motif chemokine 9 (human)", + "CXCL9 protein, human" + ] + } + ] + }, + "NCBIGene:8322": { + "categories": [ + "biolink:Gene" + ], + "name": "FZD4", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:8322", + "ENSEMBL:ENSG00000174804", + "HGNC:4042", + "OMIM:604579", + "UMLS:C1333586", + "UniProtKB:Q9ULV1", + "PR:Q9ULV1", + "ENSEMBL:ENSP00000434034", + "ENSEMBL:ENSP00000434034.1", + "UMLS:C1333639" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "FZD4", + "FZD4 gene", + "FZD4_HUMAN Frizzled-4 (sprot)", + "frizzled-4 (human)", + "FZD4 protein, human" + ] + } + ] + }, + "NCBIGene:2920": { + "categories": [ + "biolink:Gene" + ], + "name": "CXCL2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2920", + "ENSEMBL:ENSG00000081041", + "HGNC:4603", + "OMIM:139110", + "UMLS:C0812310", + "UniProtKB:A0A024RDD9", + "UniProtKB:P19875", + "PR:P19875", + "ENSEMBL:ENSP00000427279", + "ENSEMBL:ENSP00000427279.1", + "UMLS:C0245297" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CXCL2", + "CXCL2 gene", + "A0A024RDD9_HUMAN C-X-C motif chemokine (trembl)", + "CXCL2_HUMAN C-X-C motif chemokine 2 (sprot)", + "C-X-C motif chemokine 2 (human)", + "CXCL2 protein, human" + ] + } + ] + }, + "NCBIGene:259249": { + "categories": [ + "biolink:Gene" + ], + "name": "MRGPRX1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:259249", + "ENSEMBL:ENSG00000170255", + "HGNC:17962", + "OMIM:607227", + "UMLS:C1826279", + "UniProtKB:Q96LB2", + "PR:Q96LB2", + "ENSEMBL:ENSP00000305766", + "ENSEMBL:ENSP00000305766.3", + "ENSEMBL:ENSP00000499076", + "ENSEMBL:ENSP00000499076.2", + "UniProtKB:W8W3P5" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MRGPRX1", + "MRGPRX1 gene", + "MRGX1_HUMAN Mas-related G-protein coupled receptor member X1 (sprot)", 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"HGNC:17980", + "OMIM:607229", + "UMLS:C1826281", + "UniProtKB:Q96LB0", + "PR:Q96LB0", + "ENSEMBL:ENSP00000379571", + "ENSEMBL:ENSP00000379571.2", + "ENSEMBL:ENSP00000481943", + "ENSEMBL:ENSP00000481943.1" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MRGPRX3", + "MRGPRX3 gene", + "MRGX3_HUMAN Mas-related G-protein coupled receptor member X3 (sprot)", + "Mas-related G-protein coupled receptor member X3 (human)" + ] + } + ] + }, + "NCBIGene:9547": { + "categories": [ + "biolink:Gene" + ], + "name": "CXCL14", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:9547", + "ENSEMBL:ENSG00000145824", + "HGNC:10640", + "OMIM:604186", + "UMLS:C1332818", + "UniProtKB:O95715", + "PR:O95715", + "ENSEMBL:ENSP00000337065", + "ENSEMBL:ENSP00000337065.5", + "UMLS:C1335988" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CXCL14", + "CXCL14 gene", + "CXL14_HUMAN C-X-C motif chemokine 14 (sprot)", + "C-X-C motif chemokine 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"NCBIGene:10563", + "ENSEMBL:ENSG00000156234", + "HGNC:10639", + "OMIM:605149", + "UMLS:C1366572", + "UniProtKB:O43927", + "PR:O43927", + "ENSEMBL:ENSP00000286758", + "ENSEMBL:ENSP00000286758.4", + "ENSEMBL:ENSP00000507688", + "ENSEMBL:ENSP00000507688.1", + "UMLS:C0963811", + "UniProtKB:Q53X90" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CXCL13", + "CXCL13 gene", + "CXL13_HUMAN C-X-C motif chemokine 13 (sprot)", + "C-X-C motif chemokine 13 (human)", + "CXCL13 protein, human", + "Q53X90_HUMAN C-X-C motif chemokine (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:59352": { + "categories": [ + "biolink:Gene" + ], + "name": "LGR6", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:59352", + "ENSEMBL:ENSG00000133067", + "HGNC:19719", + "OMIM:606653", + "UMLS:C1426357", + "UniProtKB:Q9HBX8", + "PR:Q9HBX8", + "UMLS:C0962886" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "LGR6", + "LGR6 gene", + "LGR6_HUMAN Leucine-rich repeat-containing G-protein coupled receptor 6 (sprot)", + "leucine-rich repeat-containing G-protein coupled receptor 6 (human)", + "LGR6 protein, human" + ] + } + ] + }, + "NCBIGene:2919": { + "categories": [ + "biolink:Gene" + ], + "name": "CXCL1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2919", + "ENSEMBL:ENSG00000163739", + "HGNC:4602", + "OMIM:155730", + "UMLS:C0812445", + "UniProtKB:P09341", + "PR:P09341", + "ENSEMBL:ENSP00000379110", + "ENSEMBL:ENSP00000379110.3", + "UMLS:C0131875" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CXCL1", + "CXCL1 gene", + "GROA_HUMAN Growth-regulated alpha protein (sprot)", + "growth-regulated alpha protein (human)", + "CXCL1 protein, human" + ] + } + ] + }, + "NCBIGene:5473": { + "categories": [ + "biolink:Gene" + ], + "name": "PPBP", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5473", + "ENSEMBL:ENSG00000163736", + 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}, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MIR145", + "MIR145 gene" + ] + } + ] + }, + "NCBIGene:407008": { + "categories": [ + "biolink:Gene" + ], + "name": "MIR223", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:407008", + "ENSEMBL:ENSG00000284567", + "HGNC:31603", + "OMIM:300694", + "UMLS:C1537861" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MIR223", + "MIR223 gene" + ] + } + ] + }, + "NCBIGene:6583": { + "categories": [ + "biolink:Gene" + ], + "name": "SLC22A4", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6583", + "ENSEMBL:ENSG00000197208", + "HGNC:10968", + "OMIM:604190", + "UMLS:C1420139", + "UniProtKB:Q9H015", + "PR:Q9H015", + "ENSEMBL:ENSP00000200652", + "ENSEMBL:ENSP00000200652.3" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SLC22A4", + "SLC22A4 gene", + "S22A4_HUMAN Solute carrier family 22 member 4 (sprot)", + "solute 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"E7EPT6_HUMAN Transforming growth factor alpha (trembl)", + "F8VNR3_HUMAN Transforming growth factor alpha (trembl)", + "TGFA_HUMAN Protransforming growth factor alpha (sprot)", + "protransforming growth factor alpha (human)", + "Protransforming Growth Factor Alpha, human", + "TGFA protein, human" + ] + } + ] + }, + "NCBIGene:1950": { + "categories": [ + "biolink:Gene" + ], + "name": "EGF", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1950", + "ENSEMBL:ENSG00000138798", + "HGNC:3229", + "OMIM:131530", + "UMLS:C1367721", + "UniProtKB:P01133", + "PR:P01133", + "UMLS:C0242275", + "UMLS:C1509244", + "UMLS:C2825836", + "UMLS:C3897855" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "EGF", + "EGF gene", + "EGF_HUMAN Pro-epidermal growth factor (sprot)", + "pro-epidermal growth factor (human)", + "epidermal growth factor", + "human epidermal growth factor", + "Recombinant Human Epidermal Growth Factor", + "Pro-Epidermal Growth 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gene", + "CMA1_HUMAN Chymase (sprot)", + "chymase (human)", + "CMA1 protein, human", + "Q4FEB3_HUMAN Chymase 1 preproprotein transcript E (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:4547": { + "categories": [ + "biolink:Gene" + ], + "name": "MTTP", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4547", + "ENSEMBL:ENSG00000138823", + "HGNC:7467", + "OMIM:157147", + "UMLS:C1826328", + "UniProtKB:B7Z7X3", + "UniProtKB:P55157", + "PR:P55157", + "UMLS:C1741347" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MTTP", + "MTTP gene", + "B7Z7X3_HUMAN Microsomal triglyceride transfer protein large subunit (trembl)", + "MTP_HUMAN Microsomal triglyceride transfer protein large subunit (sprot)", + "microsomal triglyceride transfer protein large subunit (human)", + "MTTP protein, human" + ] + } + ] + }, + "NCBIGene:2778": { + "categories": [ + "biolink:Gene" + ], + "name": "GNAS", + "attributes": [ + { + "attribute_type_id": 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element-binding protein 1 (human)", + "CREB1 protein, human", + "Q53X93_HUMAN CREB1 protein (Fragment) (trembl)", + "Q5U0J5_HUMAN cAMP responsive element binding protein 1 (trembl)" + ] + } + ] + }, + "NCBIGene:2355": { + "categories": [ + "biolink:Gene" + ], + "name": "FOSL2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2355", + "ENSEMBL:ENSG00000075426", + "HGNC:3798", + "OMIM:601575", + "UMLS:C0812302", + "UniProtKB:P15408", + "PR:P15408", + "UMLS:C1312389", + "UniProtKB:Q9H5M2" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "FOSL2", + "FOSL2 gene", + "FOSL2_HUMAN Fos-related antigen 2 (sprot)", + "Fos-related antigen 2 (human)", + "FOSL2 protein, human", + "Q9H5M2_HUMAN Alternative protein FOSL2 (trembl)" + ] + } + ] + }, + "NCBIGene:2775": { + "categories": [ + "biolink:Gene" + ], + "name": "GNAO1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2775", + 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"OMIM:602354", + "UMLS:C1425844", + "UniProtKB:A0A024QZD6", + "UniProtKB:O43561", + "PR:O43561", + "UMLS:C5444101" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "LAT", + "LAT gene", + "A0A024QZD6_HUMAN Linker for activation of T cells, isoform CRA_f (trembl)", + "LAT_HUMAN Linker for activation of T-cells family member 1 (sprot)", + "linker for activation of T-cells family member 1 (human)", + "Linker for Activation of T-Cells Family Member 1, Human" + ] + } + ] + }, + "NCBIGene:2100": { + "categories": [ + "biolink:Gene" + ], + "name": "ESR2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2100", + "ENSEMBL:ENSG00000140009", + "HGNC:3468", + "OMIM:601663", + "UMLS:C1414462", + "UniProtKB:A0A348FV93", + "UniProtKB:F1D8N3", + "UniProtKB:Q0PTK2", + "UniProtKB:Q7LCB3", + "UniProtKB:Q92731", + "PR:Q92731", + "UMLS:C1523984" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ESR2", + "ESR2 gene", + "A0A348FV93_HUMAN Estrogen receptor beta (trembl)", + "F1D8N3_HUMAN Estrogen receptor beta (trembl)", + "Q0PTK2_HUMAN Estrogen receptor beta (trembl)", + "Q7LCB3_HUMAN Estrogen receptor beta (trembl)", + "ESR2_HUMAN Estrogen receptor beta (sprot)", + "estrogen receptor beta (human)", + "estrogen receptor beta, human" + ] + } + ] + }, + "NCBIGene:4609": { + "categories": [ + "biolink:Gene" + ], + "name": "MYC", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4609", + "ENSEMBL:ENSG00000136997", + "HGNC:7553", + "OMIM:190080", + "UMLS:C0086661", + "UniProtKB:P01106", + "PR:P01106", + "UMLS:C1454487" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MYC", + "MYC gene", + "MYC_HUMAN Myc proto-oncogene protein (sprot)", + "Myc proto-oncogene protein (human)", + "MYC protein, human" + ] + } + ] + }, + "NCBIGene:3727": { + "categories": [ + "biolink:Gene" + ], + "name": "JUND", + "attributes": [ + { + "attribute_type_id": 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"ENSEMBL:ENSP00000303315.4", + "UMLS:C1442793", + "UniProtKB:Q5U079" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "JUNB", + "JUNB gene", + "JUNB_HUMAN Transcription factor JunB (sprot)", + "transcription factor JunB (human)", + "JUNB protein, human", + "Q5U079_HUMAN Jun B proto-oncogene (trembl)" + ] + } + ] + }, + "NCBIGene:2770": { + "categories": [ + "biolink:Gene" + ], + "name": "GNAI1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2770", + "ENSEMBL:ENSG00000127955", + "HGNC:4384", + "OMIM:139310", + "UMLS:C1415142", + "UniProtKB:P63096", + "PR:P63096", + "UMLS:C1517337" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "GNAI1", + "GNAI1 gene", + "GNAI1_HUMAN Guanine nucleotide-binding protein G(i) subunit alpha-1 (sprot)", + "guanine nucleotide-binding protein G(i) subunit alpha-1 (human)", + "GNAI1 protein, human" + ] + } + ] + }, + "NCBIGene:2776": { + "categories": [ + "biolink:Gene" + ], + 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"PR:Q13451", + "UMLS:C1741214", + "UniProtKB:Q2TA84" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "FKBP5", + "FKBP5 gene", + "FKBP5_HUMAN Peptidyl-prolyl cis-trans isomerase FKBP5 (sprot)", + "peptidyl-prolyl cis-trans isomerase FKBP5 (human)", + "FKBP5 protein, human", + "Q2TA84_HUMAN peptidylprolyl isomerase (trembl)" + ] + } + ] + }, + "NCBIGene:2099": { + "categories": [ + "biolink:Gene" + ], + "name": "ESR1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2099", + "ENSEMBL:ENSG00000091831", + "HGNC:3467", + "OMIM:133430", + "UMLS:C1414461", + "UniProtKB:A0A125SXW3", + "UniProtKB:A8KAF4", + "UniProtKB:G4XH65", + "UniProtKB:H0Y4W6", + "UniProtKB:P03372", + "PR:P03372", + "UMLS:C1521863", + "UniProtKB:Q9UBT1" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ESR1", + "ESR1 gene", + "A0A125SXW3_HUMAN Estrogen receptor (trembl)", + "A8KAF4_HUMAN Estrogen receptor (trembl)", + "G4XH65_HUMAN Estrogen 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"NCBIGene:1490", + "ENSEMBL:ENSG00000118523", + "HGNC:2500", + "OMIM:121009", + "UMLS:C1413791", + "UniProtKB:P29279", + "PR:P29279", + "UMLS:C1137457", + "UniProtKB:Q5M8T4" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CCN2", + "CCN2 gene", + "CCN2_HUMAN CCN family member 2 (sprot)", + "CCN family member 2 (human)", + "CTGF protein, human", + "Q5M8T4_HUMAN Connective tissue growth factor (trembl)" + ] + } + ] + }, + "NCBIGene:4092": { + "categories": [ + "biolink:Gene" + ], + "name": "SMAD7", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4092", + "ENSEMBL:ENSG00000101665", + "HGNC:6773", + "OMIM:602932", + "UMLS:C1334470", + "UniProtKB:B3KYA8", + "UniProtKB:O15105", + "PR:O15105", + "UMLS:C1566818" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SMAD7", + "SMAD7 gene", + "B3KYA8_HUMAN cDNA FLJ16482 fis, clone BRTHA2017972, highly similar to Mothers against decapentaplegic homolog 7 (SMAD 7) (trembl)", + "SMAD7_HUMAN Mothers against decapentaplegic homolog 7 (sprot)", + "mothers against decapentaplegic homolog 7 (human)", + "SMAD7 protein, human" + ] + } + ] + }, + "NCBIGene:4089": { + "categories": [ + "biolink:Gene" + ], + "name": "SMAD4", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4089", + "ENSEMBL:ENSG00000141646", + "HGNC:6770", + "OMIM:600993", + "UMLS:C0694891", + "UniProtKB:A0A024R274", + "UniProtKB:Q13485", + "PR:Q13485", + "ENSEMBL:ENSP00000341551", + "ENSEMBL:ENSP00000341551.3", + "ENSEMBL:ENSP00000381452", + "ENSEMBL:ENSP00000381452.1", + "UMLS:C0385939" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SMAD4", + "SMAD4 gene", + "A0A024R274_HUMAN Mothers against decapentaplegic homolog (trembl)", + "SMAD4_HUMAN Mothers against decapentaplegic homolog 4 (sprot)", + "mothers against decapentaplegic homolog 4 (human)", + "SMAD4 protein, human" + ] + } + ] + }, + "NCBIGene:2258": { + "categories": [ + 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sorting-associated protein 51 homolog (sprot)", + "vacuolar protein sorting-associated protein 51 homolog (human)" + ] + } + ] + }, + "NCBIGene:7108": { + "categories": [ + "biolink:Gene" + ], + "name": "TM7SF2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:7108", + "ENSEMBL:ENSG00000149809", + "HGNC:11863", + "OMIM:603414", + "UMLS:C1420771", + "UniProtKB:A0A024R577", + "UniProtKB:O76062", + "PR:O76062" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TM7SF2", + "TM7SF2 gene", + "A0A024R577_HUMAN Transmembrane 7 superfamily member 2, isoform CRA_a (trembl)", + "ERG24_HUMAN Delta(14)-sterol reductase TM7SF2 (sprot)", + "Delta(14)-sterol reductase TM7SF2 (human)" + ] + } + ] + }, + "NCBIGene:7010": { + "categories": [ + "biolink:Gene" + ], + "name": "TEK", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:7010", + "ENSEMBL:ENSG00000120156", + "HGNC:11724", + "OMIM:600221", + 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"UniProtKB:Q4W251" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "GSTT1", + "GSTT1 gene", + "A0A0G2JRN4_HUMAN Glutathione S-transferase theta 1, isoform CRA_a (trembl)", + "A0A0G2JRQ5_HUMAN glutathione transferase (trembl)", + "GSTT1_HUMAN Glutathione S-transferase theta-1 (sprot)", + "glutathione S-transferase theta-1 (human)", + "Glutathione S-Transferase Theta-1, Human", + "Q4GZS9_HUMAN Glutathione S-transferase theta 1 (Fragment) (trembl)", + "Q4W251_HUMAN Glutathione S-transferase theta 1 (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:331": { + "categories": [ + "biolink:Gene" + ], + "name": "XIAP", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:331", + "ENSEMBL:ENSG00000101966", + "HGNC:592", + "OMIM:300079", + "UMLS:C1337109", + "UniProtKB:B2R9R2", + "UniProtKB:P98170", + "PR:P98170", + "ENSEMBL:ENSP00000347858", + "ENSEMBL:ENSP00000347858.3", + "ENSEMBL:ENSP00000360242", + "ENSEMBL:ENSP00000360242.3", + "ENSEMBL:ENSP00000405529", + "ENSEMBL:ENSP00000405529.2", + "UMLS:C1173600" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "XIAP", + "XIAP gene", + "B2R9R2_HUMAN cDNA, FLJ94517, highly similar to Homo sapiens baculoviral IAP repeat-containing 4 (BIRC4), mRNA (trembl)", + "XIAP_HUMAN E3 ubiquitin-protein ligase XIAP (sprot)", + "E3 ubiquitin-protein ligase XIAP (human)", + "BIRC4 protein, human" + ] + } + ] + }, + "NCBIGene:959": { + "categories": [ + "biolink:Gene" + ], + "name": "CD40LG", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:959", + "ENSEMBL:ENSG00000102245", + "HGNC:11935", + "OMIM:300386", + "UMLS:C1539082", + "UniProtKB:P29965", + "PR:P29965", + "ENSEMBL:ENSP00000359663", + "ENSEMBL:ENSP00000359663.2", + "UMLS:C0167627", + "UMLS:C3887583" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CD40LG", + "CD40LG gene", + "CD40L_HUMAN CD40 ligand (sprot)", + "CD40 ligand (human)", + "CD40 Ligand", + "CD40 Ligand, human" + ] + } + ] + }, + "NCBIGene:3574": { + "categories": [ + "biolink:Gene" + ], + "name": "IL7", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3574", + "ENSEMBL:ENSG00000104432", + "HGNC:6023", + "OMIM:146660", + "UMLS:C1334124", + "UniProtKB:A0A0A0MTG5", + "ENSEMBL:ENSP00000438922", + "ENSEMBL:ENSP00000438922.2", + "UniProtKB:A8K673", + "UniProtKB:P13232", + "PR:P13232", + "UMLS:C1699239", + "UniProtKB:Q5FBX5", + "ENSEMBL:ENSP00000368408", + "ENSEMBL:ENSP00000368408.3" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "IL7", + "IL7 gene", + "A0A0A0MTG5_HUMAN Interleukin-7 (trembl)", + "A8K673_HUMAN Interleukin-7 (trembl)", + "IL7_HUMAN Interleukin-7 (sprot)", + "interleukin-7 (human)", + "IL7 protein, human", + "Q5FBX5_HUMAN Interleukin-7 (trembl)" + ] + } + ] + }, + "NCBIGene:3952": { + "categories": [ + "biolink:Gene" + ], + "name": "LEP", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3952", + "ENSEMBL:ENSG00000174697", + "HGNC:6553", + "OMIM:164160", + "UMLS:C1416825", + "UniProtKB:A4D0Y8", + "UniProtKB:P41159", + "PR:P41159", + "ENSEMBL:ENSP00000312652", + "ENSEMBL:ENSP00000312652.4", + "UMLS:C4742979" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "LEP", + "LEP gene", + "A4D0Y8_HUMAN Leptin (trembl)", + "LEP_HUMAN Leptin (sprot)", + "leptin (human)", + "LEP protein, human" + ] + } + ] + }, + "NCBIGene:8678": { + "categories": [ + "biolink:Gene" + ], + "name": "BECN1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:8678", + "ENSEMBL:ENSG00000126581", + "HGNC:1034", + "OMIM:604378", + "UMLS:C1412785", + "UniProtKB:A0A024R1X5", + "UniProtKB:B4DQ36", + "UniProtKB:E7EV84", + "ENSEMBL:ENSP00000416173", + "ENSEMBL:ENSP00000416173.2", + "UniProtKB:Q14457", + "PR:Q14457", + "ENSEMBL:ENSP00000355231", + "ENSEMBL:ENSP00000355231.3", + "ENSEMBL:ENSP00000465364", + "ENSEMBL:ENSP00000465364.1", + "UMLS:C1453431", + "UniProtKB:W0FFG4" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "BECN1", + "BECN1 gene", + "A0A024R1X5_HUMAN Beclin-1 (trembl)", + "B4DQ36_HUMAN cDNA FLJ52719, moderately similar to Beclin-1 (trembl)", + "E7EV84_HUMAN Beclin 1 (trembl)", + "BECN1_HUMAN Beclin-1 (sprot)", + "beclin-1 (human)", + "BECN1 protein, human", + "W0FFG4_HUMAN Beclin-1 (trembl)" + ] + } + ] + }, + "NCBIGene:60468": { + "categories": [ + "biolink:Gene" + ], + "name": "BACH2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:60468", + "ENSEMBL:ENSG00000112182", + "HGNC:14078", + "OMIM:605394", + "UMLS:C1422394", + "UniProtKB:Q9BYV9", + "PR:Q9BYV9", + "ENSEMBL:ENSP00000257749", + "ENSEMBL:ENSP00000257749.4", + "ENSEMBL:ENSP00000345642", + "ENSEMBL:ENSP00000345642.3", + "ENSEMBL:ENSP00000384145", + "ENSEMBL:ENSP00000384145.3", + "ENSEMBL:ENSP00000397668", + "ENSEMBL:ENSP00000397668.2", + "ENSEMBL:ENSP00000512284", + "ENSEMBL:ENSP00000512284.1", + "UMLS:C1453878" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "BACH2", + "BACH2 gene", + "BACH2_HUMAN Transcription regulator protein BACH2 (sprot)", + "transcription regulator protein BACH2 (human)", + "BACH2 protein, human" + ] + } + ] + }, + "NCBIGene:6347": { + "categories": [ + "biolink:Gene" + ], + "name": "CCL2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6347", + "ENSEMBL:ENSG00000108691", + "HGNC:10618", + "OMIM:158105", + "UMLS:C1337092", + "UniProtKB:P13500", + "PR:P13500", + "ENSEMBL:ENSP00000225831", + "ENSEMBL:ENSP00000225831.4", + "UMLS:C1449159" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CCL2", + "CCL2 gene", + "CCL2_HUMAN C-C motif chemokine 2 (sprot)", + "C-C motif chemokine 2 (human)", + "CCL2 protein, human" + ] + } + ] + }, + "NCBIGene:10058": { + "categories": [ + "biolink:Gene" + ], + "name": "ABCB6", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:10058", + "ENSEMBL:ENSG00000115657", + "HGNC:47", + "OMIM:605452", + "UMLS:C1332001", + "UniProtKB:Q9NP58", + "PR:Q9NP58", + "UMLS:C1447552" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ABCB6", + "ABCB6 gene", + "ABCB6_HUMAN ATP-binding cassette sub-family B member 6 (sprot)", + "ATP-binding cassette sub-family B member 6 (human)", + "ABCB6 protein, human" + ] + } + ] + }, + "NCBIGene:51497": { + "categories": [ + "biolink:Gene" + ], + "name": "NELFCD", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:51497", + "ENSEMBL:ENSG00000101158", + "HGNC:15934", + "OMIM:605297", + "UMLS:C1423842", + "UniProtKB:H0UI80", + "ENSEMBL:ENSP00000473290", + "ENSEMBL:ENSP00000473290.1", + "UniProtKB:Q8IXH7", + "PR:Q8IXH7", + "UMLS:C3537293" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "NELFCD", + "NELFCD gene", + "H0UI80_HUMAN Negative elongation factor complex member C/D (trembl)", + "NELFD_HUMAN Negative elongation factor C/D (sprot)", + "negative elongation factor C/D (human)", + "Negative Elongation Factor C/D" + ] + } + ] + }, + "NCBIGene:5743": { + "categories": [ + "biolink:Gene" + ], + "name": "PTGS2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5743", + "ENSEMBL:ENSG00000073756", + "HGNC:9605", + "OMIM:600262", + "UMLS:C1367485", + "UniProtKB:P35354", + "PR:P35354", + "ENSEMBL:ENSP00000356438", + "ENSEMBL:ENSP00000356438.5", + "ENSEMBL:ENSP00000506242", + "ENSEMBL:ENSP00000506242.1", + "UMLS:C1565860" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PTGS2", + "PTGS2 gene", + "PGH2_HUMAN Prostaglandin G/H synthase 2 (sprot)", + "prostaglandin G/H synthase 2 (human)", + "PTGS2 protein, human" + ] + } + ] + }, + "NCBIGene:468": { + "categories": [ + "biolink:Gene" + ], + "name": "ATF4", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:468", + "ENSEMBL:ENSG00000128272", + "HGNC:786", + "OMIM:604064", + "UMLS:C1412617", + "UniProtKB:P18848", + "PR:P18848", + "ENSEMBL:ENSP00000336790", + "ENSEMBL:ENSP00000336790.2", + "ENSEMBL:ENSP00000379912", + "ENSEMBL:ENSP00000379912.1", + "ENSEMBL:ENSP00000384587", + "ENSEMBL:ENSP00000384587.2", + "ENSEMBL:ENSP00000501783", + "ENSEMBL:ENSP00000501783.2", + "ENSEMBL:ENSP00000501863", + "ENSEMBL:ENSP00000501863.1", + "ENSEMBL:ENSP00000502400", + "ENSEMBL:ENSP00000502400.2", + "ENSEMBL:ENSP00000502610", + "ENSEMBL:ENSP00000502610.2", + "ENSEMBL:ENSP00000505360", + "ENSEMBL:ENSP00000505360.1", + "UMLS:C1566322" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ATF4", + "ATF4 gene", + "ATF4_HUMAN Cyclic AMP-dependent transcription factor ATF-4 (sprot)", + "cyclic AMP-dependent transcription factor ATF-4 (human)", + "ATF4 protein, human" + ] + } + ] + }, + "NCBIGene:6932": { + "categories": [ + "biolink:Gene" + ], + "name": "TCF7", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6932", + "ENSEMBL:ENSG00000081059", + "HGNC:11639", + "OMIM:189908", + "UMLS:C1420642", + "UniProtKB:B3KQ75", + "UniProtKB:P36402", + "PR:P36402", + "UMLS:C0286910" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TCF7", + "TCF7 gene", + "B3KQ75_HUMAN cDNA FLJ33018 fis, clone THYMU1000459, highly similar to Homo sapiens transcription factor 7 (T-cell specific, HMG-box) (TCF7), transcript variant 5, mRNA (trembl)", + "TCF7_HUMAN Transcription factor 7 (sprot)", + "transcription factor 7 (human)", + "TCF7 protein, human" + ] + } + ] + }, + "NCBIGene:2697": { + "categories": [ + "biolink:Gene" + ], + "name": "GJA1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2697", + "ENSEMBL:ENSG00000152661", + "HGNC:4274", + "OMIM:121014", + "UMLS:C1415068", + "UniProtKB:A0A654IBU3", + "UniProtKB:P17302", + "PR:P17302", + "ENSEMBL:ENSP00000282561", + "ENSEMBL:ENSP00000282561.3", + "ENSEMBL:ENSP00000497283", + "ENSEMBL:ENSP00000497283.1", + "ENSEMBL:ENSP00000497367", + "ENSEMBL:ENSP00000497367.1", + "ENSEMBL:ENSP00000497565", + "ENSEMBL:ENSP00000497565.1", + "UMLS:C1568716" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "GJA1", + "GJA1 gene", + "A0A654IBU3_HUMAN Gap junction protein (trembl)", + "CXA1_HUMAN Gap junction alpha-1 protein (sprot)", + "gap junction alpha-1 protein (human)", + "GJA1 protein, human" + ] + } + ] + }, + "NCBIGene:5468": { + "categories": [ + "biolink:Gene" + ], + "name": "PPARG", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5468", + "ENSEMBL:ENSG00000132170", + "HGNC:9236", + "OMIM:601487", + "UMLS:C1335238", + "UniProtKB:A0A494C1F9", + "UniProtKB:D2KUA6", + "UniProtKB:E9PFV2", + "ENSEMBL:ENSP00000312472", + "ENSEMBL:ENSP00000312472.7", + "ENSEMBL:ENSP00000380205", + "ENSEMBL:ENSP00000380205.3", + "ENSEMBL:ENSP00000380210", + "ENSEMBL:ENSP00000380210.3", + "ENSEMBL:ENSP00000380221", + "ENSEMBL:ENSP00000380221.3", + "ENSEMBL:ENSP00000494873", + "ENSEMBL:ENSP00000494873.2", + "ENSEMBL:ENSP00000494934", + "ENSEMBL:ENSP00000494934.2", + "ENSEMBL:ENSP00000495840", + "ENSEMBL:ENSP00000495840.2", + "ENSEMBL:ENSP00000498313", + "ENSEMBL:ENSP00000498313.1", + "ENSEMBL:ENSP00000506813", + "ENSEMBL:ENSP00000506813.1", + "ENSEMBL:ENSP00000507893", + "ENSEMBL:ENSP00000507893.1", + "ENSEMBL:ENSP00000508065", + "ENSEMBL:ENSP00000508065.1", + "UniProtKB:E9PFX5", + "ENSEMBL:ENSP00000380196", + "ENSEMBL:ENSP00000380196.2", + "UniProtKB:P37231", + "PR:P37231", + "UMLS:C3887582" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PPARG", + "PPARG gene", + "A0A494C1F9_HUMAN Peroxisome proliferator-activated receptor gamma (Fragment) (trembl)", + "D2KUA6_HUMAN Peroxisome proliferator-activated receptor gamma (trembl)", + "E9PFV2_HUMAN Peroxisome proliferator-activated receptor gamma (trembl)", + "E9PFX5_HUMAN Peroxisome proliferator-activated receptor gamma (trembl)", + "PPARG_HUMAN Peroxisome proliferator-activated receptor gamma (sprot)", + "peroxisome proliferator-activated receptor gamma (human)", + "Peroxisome Proliferator-Activated Receptor Gamma, human" + ] + } + ] + }, + "NCBIGene:3394": { + "categories": [ + "biolink:Gene" + ], + "name": "IRF8", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3394", + "ENSEMBL:ENSG00000140968", + "HGNC:5358", + "OMIM:601565", + "UMLS:C1537422", + "UniProtKB:Q02556", + "PR:Q02556", + "ENSEMBL:ENSP00000268638", + "ENSEMBL:ENSP00000268638.4", + "ENSEMBL:ENSP00000456992", + "ENSEMBL:ENSP00000456992.2", + "ENSEMBL:ENSP00000512953", + "ENSEMBL:ENSP00000512953.1", + "UMLS:C1450600" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "IRF8", + "IRF8 gene", + "IRF8_HUMAN Interferon regulatory factor 8 (sprot)", + "interferon regulatory factor 8 (human)", + "IRF8 protein, human" + ] + } + ] + }, + "NCBIGene:3565": { + "categories": [ + "biolink:Gene" + ], + "name": "IL4", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3565", + "ENSEMBL:ENSG00000113520", + "HGNC:6014", + "OMIM:147780", + "UMLS:C1334119", + "UniProtKB:D4HNR6", + "UniProtKB:P05112", + "PR:P05112", + "UMLS:C1701589", + "UniProtKB:Q5FC01" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "IL4", + "IL4 gene", + "D4HNR6_HUMAN Interleukin-4 (trembl)", + "IL4_HUMAN Interleukin-4 (sprot)", + "interleukin-4 (human)", + "interleukin-4, human", + "Q5FC01_HUMAN Interleukin-4 (trembl)" + ] + } + ] + }, + "NCBIGene:2549": { + "categories": [ + "biolink:Gene" + ], + "name": "GAB1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2549", + "ENSEMBL:ENSG00000109458", + "HGNC:4066", + "OMIM:604439", + "UMLS:C1414900", + "UniProtKB:Q13480", + "PR:Q13480", + "UMLS:C1447432", + "UniProtKB:Q9HA84" + ] + }, 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"attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5265", + "ENSEMBL:ENSG00000197249", + "HGNC:8941", + "OMIM:107400", + "UniProtKB:E9KL23", + "UniProtKB:P01009", + "PR:P01009", + "UMLS:C1455316" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SERPINA1", + "E9KL23_HUMAN Epididymis secretory sperm binding protein Li 44a (trembl)", + "A1AT_HUMAN Alpha-1-antitrypsin (sprot)", + "alpha-1-antitrypsin (human)", + "SERPINA1 protein, human" + ] + } + ] + }, + "NCBIGene:1234": { + "categories": [ + "biolink:Gene" + ], + "name": "CCR5", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1234", + "ENSEMBL:ENSG00000160791", + "HGNC:1606", + "OMIM:601373", + "UMLS:C1332700", + "UniProtKB:P51681", + "PR:P51681", + "ENSEMBL:ENSP00000292303", + "ENSEMBL:ENSP00000292303.4", + "ENSEMBL:ENSP00000404881", + "ENSEMBL:ENSP00000404881.1", + "UMLS:C3711103", + "UniProtKB:Q38L21" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CCR5", + "CCR5 gene", + "CCR5_HUMAN C-C chemokine receptor type 5 (sprot)", + "C-C chemokine receptor type 5 (human)", + "CCR5 protein, human", + "Q38L21_HUMAN C-C chemokine receptor type 5 (trembl)" + ] + } + ] + }, + "NCBIGene:1027": { + "categories": [ + "biolink:Gene" + ], + "name": "CDKN1B", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1027", + "ENSEMBL:ENSG00000111276", + "HGNC:1785", + "OMIM:600778", + "UMLS:C1332737", + "UniProtKB:P46527", + "PR:P46527", + "ENSEMBL:ENSP00000228872", + "ENSEMBL:ENSP00000228872.4", + "ENSEMBL:ENSP00000507272", + "ENSEMBL:ENSP00000507272.1", + "UMLS:C1504812", + "UniProtKB:Q6I9V6" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CDKN1B", + "CDKN1B gene", + "CDN1B_HUMAN Cyclin-dependent kinase inhibitor 1B (sprot)", + "cyclin-dependent kinase inhibitor 1B (human)", + "CDKN1B protein, human", + "Q6I9V6_HUMAN CDKN1B protein (trembl)" + ] + } + ] + }, + "NCBIGene:7292": { + "categories": [ + "biolink:Gene" + ], + "name": "TNFSF4", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:7292", + "ENSEMBL:ENSG00000117586", + "HGNC:11934", + "OMIM:603594", + "UMLS:C1336648", + "UniProtKB:A0A024R937", + "UniProtKB:P23510", + "PR:P23510", + "UMLS:C0257572" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TNFSF4", + "TNFSF4 gene", + "A0A024R937_HUMAN Tumor necrosis factor (Ligand) superfamily, member 4 (Tax-transcriptionally activated glycoprotein 1, 34kDa), isoform CRA_a (trembl)", + "TNFL4_HUMAN Tumor necrosis factor ligand superfamily member 4 (sprot)", + "tumor necrosis factor ligand superfamily member 4 (human)", + "TNFSF4 protein, human" + ] + } + ] + }, + "NCBIGene:362": { + "categories": [ + "biolink:Gene" + ], + "name": "AQP5", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:362", + "ENSEMBL:ENSG00000161798", + "HGNC:638", + "OMIM:600442", + "UMLS:C1412495", + 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"UMLS:C4759837", + "UniProtKB:V9HWB4" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "HSPA5", + "HSPA5 gene", + "BIP_HUMAN Endoplasmic reticulum chaperone BiP (sprot)", + "endoplasmic reticulum chaperone BiP (human)", + "78 kDa Glucose-Regulated Protein", + "V9HWB4_HUMAN 78 kDa glucose-regulated protein (trembl)" + ] + } + ] + }, + "NCBIGene:6362": { + "categories": [ + "biolink:Gene" + ], + "name": "CCL18", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6362", + "ENSEMBL:ENSG00000275385", + "HGNC:10616", + "OMIM:603757", + "UMLS:C1332681", + "UniProtKB:P55774", + "PR:P55774", + "ENSEMBL:ENSP00000479955", + "ENSEMBL:ENSP00000479955.1", + "ENSEMBL:ENSP00000483144", + "ENSEMBL:ENSP00000483144.1", + "ENSEMBL:ENSP00000483347", + "ENSEMBL:ENSP00000483347.1", + "UMLS:C0541270" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CCL18", + "CCL18 gene", + "CCL18_HUMAN C-C motif chemokine 18 (sprot)", + "C-C motif 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} + ] + }, + "NCBIGene:3315": { + "categories": [ + "biolink:Gene" + ], + "name": "HSPB1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3315", + "ENSEMBL:ENSG00000106211", + "HGNC:5246", + "OMIM:602195", + "UMLS:C1333928", + "UniProtKB:P04792", + "PR:P04792", + "ENSEMBL:ENSP00000248553", + "ENSEMBL:ENSP00000248553.6", + "UMLS:C1447061", + "UniProtKB:V9HW43" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "HSPB1", + "HSPB1 gene", + "HSPB1_HUMAN Heat shock protein beta-1 (sprot)", + "heat shock protein beta-1 (human)", + "HSPB1 protein, human", + "V9HW43_HUMAN Heat shock protein beta-1 (trembl)" + ] + } + ] + }, + "NCBIGene:6376": { + "categories": [ + "biolink:Gene" + ], + "name": "CX3CL1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6376", + "ENSEMBL:ENSG00000006210", + "HGNC:10647", + "OMIM:601880", + "UMLS:C1332814", + "UniProtKB:A0N0N7", + "UniProtKB:P78423", + "PR:P78423", + 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FMR1-interacting protein 2 (sprot)", + "cytoplasmic FMR1-interacting protein 2 (human)" + ] + } + ] + }, + "NCBIGene:860": { + "categories": [ + "biolink:Gene" + ], + "name": "RUNX2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:860", + "ENSEMBL:ENSG00000124813", + "HGNC:10472", + "OMIM:600211", + "UMLS:C1419771", + "UniProtKB:A0A0D9SEN7", + "ENSEMBL:ENSP00000485863", + "ENSEMBL:ENSP00000485863.1", + "UniProtKB:Q13950", + "PR:Q13950", + "UMLS:C1529564", + "UniProtKB:Q32MY8" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "RUNX2", + "RUNX2 gene", + "A0A0D9SEN7_HUMAN Runt-related transcription factor (trembl)", + "RUNX2_HUMAN Runt-related transcription factor 2 (sprot)", + "runt-related transcription factor 2 (human)", + "RUNX2 protein, human", + "Q32MY8_HUMAN RUNX2 protein (trembl)" + ] + } + ] + }, + "NCBIGene:5657": { + "categories": [ + "biolink:Gene" + ], + "name": "PRTN3", + "attributes": [ + { + "attribute_type_id": 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Human" + ] + } + ] + }, + "NCBIGene:4982": { + "categories": [ + "biolink:Gene" + ], + "name": "TNFRSF11B", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4982", + "ENSEMBL:ENSG00000164761", + "HGNC:11909", + "OMIM:602643", + "UMLS:C1336645", + "UniProtKB:O00300", + "PR:O00300", + "ENSEMBL:ENSP00000297350", + "ENSEMBL:ENSP00000297350.4", + "UMLS:C1308614" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TNFRSF11B", + "TNFRSF11B gene", + "TR11B_HUMAN Tumor necrosis factor receptor superfamily member 11B (sprot)", + "tumor necrosis factor receptor superfamily member 11B (human)", + "TNFRSF11B protein, human" + ] + } + ] + }, + "NCBIGene:4739": { + "categories": [ + "biolink:Gene" + ], + "name": "NEDD9", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4739", + "ENSEMBL:ENSG00000111859", + "HGNC:7733", + "OMIM:602265", + "UMLS:C1417664", + "UniProtKB:A0A024QZV9", + "UniProtKB:A0A087WUD2", + 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"value": [ + "HMOX1", + "HMOX1 gene", + "HMOX1_HUMAN Heme oxygenase 1 (sprot)", + "heme oxygenase 1 (human)", + "HMOX1 protein, human", + "Q6FH11_HUMAN Heme oxygenase (trembl)" + ] + } + ] + }, + "NCBIGene:1015": { + "categories": [ + "biolink:Gene" + ], + "name": "CDH17", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1015", + "ENSEMBL:ENSG00000079112", + "HGNC:1756", + "OMIM:603017", + "UMLS:C1413274", + "UniProtKB:Q12864", + "PR:Q12864", + "ENSEMBL:ENSP00000027335", + "ENSEMBL:ENSP00000027335.3", + "ENSEMBL:ENSP00000401468", + "ENSEMBL:ENSP00000401468.2", + "UMLS:C0246443" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CDH17", + "CDH17 gene", + "CAD17_HUMAN Cadherin-17 (sprot)", + "cadherin-17 (human)", + "CDH17 protein, human" + ] + } + ] + }, + "NCBIGene:4485": { + "categories": [ + "biolink:Gene" + ], + "name": "MST1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4485", + "ENSEMBL:ENSG00000173531", + "HGNC:7380", + "OMIM:142408", + "UMLS:C1417377", + "UniProtKB:G3XAK1", + "ENSEMBL:ENSP00000414287", + "ENSEMBL:ENSP00000414287.2", + "UniProtKB:P26927", + "PR:P26927", + "UMLS:C1567781", + "UniProtKB:Q53GN8" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MST1", + "MST1 gene", + "G3XAK1_HUMAN Macrophage stimulating 1 (trembl)", + "HGFL_HUMAN Hepatocyte growth factor-like protein (sprot)", + "hepatocyte growth factor-like protein (human)", + "MST1 protein, human", + "Q53GN8_HUMAN Macrophage stimulating 1 (Hepatocyte growth factor-like) variant (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:50943": { + "categories": [ + "biolink:Gene" + ], + "name": "FOXP3", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:50943", + "ENSEMBL:ENSG00000049768", + "HGNC:6106", + "OMIM:300292", + "UMLS:C1416467", + "UniProtKB:Q9BZS1", + "PR:Q9BZS1", + "UMLS:C3539868" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "FOXP3", + "FOXP3 gene", + "FOXP3_HUMAN Forkhead box protein P3 (sprot)", + "forkhead box protein P3 (human)", + "Forkhead Box Protein P3" + ] + } + ] + }, + "NCBIGene:5741": { + "categories": [ + "biolink:Gene" + ], + "name": "PTH", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5741", + "ENSEMBL:ENSG00000152266", + "HGNC:9606", + "OMIM:168450", + "UMLS:C1419072", + "UniProtKB:P01270", + "PR:P01270", + "ENSEMBL:ENSP00000282091", + "ENSEMBL:ENSP00000282091.1", + "ENSEMBL:ENSP00000433208", + "ENSEMBL:ENSP00000433208.1", + "UMLS:C0020063", + "UMLS:C0071935" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PTH", + "PTH gene", + "PTHY_HUMAN Parathyroid hormone (sprot)", + "parathyroid hormone (human)", + "PTH protein, human", + "preproparathormone" + ] + } + ] + }, + "NCBIGene:2876": { + "categories": [ + "biolink:Gene" + ], + "name": "GPX1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2876", + "ENSEMBL:ENSG00000233276", + "HGNC:4553", + "OMIM:138320", + "UMLS:C1415275", + "UniProtKB:A0A2R8Y6B6", + "ENSEMBL:ENSP00000495108", + "ENSEMBL:ENSP00000495108.1", + "UniProtKB:P07203", + "PR:P07203", + "UMLS:C1568555", + "UniProtKB:Q7L4Q3" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "GPX1", + "GPX1 gene", + "A0A2R8Y6B6_HUMAN Glutathione peroxidase 1 (trembl)", + "GPX1_HUMAN Glutathione peroxidase 1 (sprot)", + "glutathione peroxidase 1 (human)", + "GPX1 protein, human", + "Q7L4Q3_HUMAN Glutathione peroxidase (trembl)" + ] + } + ] + }, + "NCBIGene:2006": { + "categories": [ + "biolink:Gene" + ], + "name": "ELN", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2006", + "ENSEMBL:ENSG00000049540", + "HGNC:3327", + "OMIM:130160", + "UMLS:C1414382", + "UniProtKB:B3KRT8", + "ENSEMBL:ENSP00000480955", + "ENSEMBL:ENSP00000480955.1", + "UniProtKB:B4E3S4", + "UniProtKB:E7EN65", + "ENSEMBL:ENSP00000403162", + "ENSEMBL:ENSP00000403162.1", + "UniProtKB:E7ENM0", + "ENSEMBL:ENSP00000389857", + "ENSEMBL:ENSP00000389857.1", + "UniProtKB:G3V0G6", + "ENSEMBL:ENSP00000392575", + "ENSEMBL:ENSP00000392575.1", + "UniProtKB:G5E950", + "ENSEMBL:ENSP00000315607", + "ENSEMBL:ENSP00000315607.7", + "UniProtKB:P15502", + "PR:P15502", + "UniProtKB:Q59H17", + "UniProtKB:Q6ZUN2", + "UniProtKB:Q8NBI4" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ELN", + "ELN gene", + "B3KRT8_HUMAN Elastin (trembl)", + "B4E3S4_HUMAN Elastin (trembl)", + "E7EN65_HUMAN Elastin (trembl)", + "E7ENM0_HUMAN Elastin (trembl)", + "G3V0G6_HUMAN Elastin (trembl)", + "G5E950_HUMAN Elastin (trembl)", + "ELN_HUMAN Elastin (sprot)", + "elastin (human)", + "Q59H17_HUMAN Elastin variant (Fragment) (trembl)", + "Q6ZUN2_HUMAN Elastin (trembl)", + "Q8NBI4_HUMAN Elastin (trembl)" + ] + } + ] + }, + "NCBIGene:2335": { + "categories": [ + "biolink:Gene" + ], + "name": "FN1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2335", + "ENSEMBL:ENSG00000115414", + "HGNC:3778", + "OMIM:135600", + "UMLS:C1367472", + "UniProtKB:B7ZLE5", + "UniProtKB:P02751", + "PR:P02751", + "UMLS:C1570610", + "UniProtKB:Q6MZF4", + "UniProtKB:Q6MZM7", + "UniProtKB:Q6N084", + "UniProtKB:Q9UQS6" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "FN1", + "FN1 gene", + "B7ZLE5_HUMAN Fibronectin (trembl)", + "FINC_HUMAN Fibronectin (sprot)", + "fibronectin (human)", + "FN1 protein, human", + "Q6MZF4_HUMAN Fibronectin (Fragment) (trembl)", + "Q6MZM7_HUMAN Fibronectin (Fragment) (trembl)", + "Q6N084_HUMAN Fibronectin (Fragment) (trembl)", + "Q9UQS6_HUMAN Fibronectin (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:6401": { + "categories": [ + "biolink:Gene" + ], + "name": "SELE", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6401", + "ENSEMBL:ENSG00000007908", + "HGNC:10718", + "OMIM:131210", + "UMLS:C1337114", + "UniProtKB:P16581", + "PR:P16581", + "ENSEMBL:ENSP00000331736", + "ENSEMBL:ENSP00000331736.7", + "UMLS:C2742136" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SELE", + "SELE gene", + "LYAM2_HUMAN E-selectin (sprot)", + "E-selectin (human)", + "SELE protein, human" + ] + } + ] + }, + "NCBIGene:10533": { + "categories": [ + "biolink:Gene" + ], + "name": "ATG7", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:10533", + "ENSEMBL:ENSG00000197548", + "HGNC:16935", + "OMIM:608760", + "UMLS:C1825498", + "UniProtKB:B3KQM6", + "UniProtKB:O95352", + "PR:O95352", + "UMLS:C1701777" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ATG7", + "ATG7 gene", + "B3KQM6_HUMAN Ubiquitin-like modifier-activating enzyme ATG7 (trembl)", + "ATG7_HUMAN Ubiquitin-like modifier-activating enzyme ATG7 (sprot)", + "ubiquitin-like modifier-activating enzyme ATG7 (human)", + "Atg7 protein, human" + ] + } + ] + }, + "NCBIGene:2621": { + "categories": [ + "biolink:Gene" + ], + "name": "GAS6", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2621", + "ENSEMBL:ENSG00000183087", + "HGNC:4168", + "OMIM:600441", + "UMLS:C1414991", + "UniProtKB:Q14393", + "PR:Q14393", + "UMLS:C1567829" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "GAS6", + "GAS6 gene", + "GAS6_HUMAN Growth arrest-specific protein 6 (sprot)", + "growth arrest-specific protein 6 (human)", + "GAS6 protein, human" + ] + } + ] + }, + "NCBIGene:6886": { + "categories": [ + "biolink:Gene" + ], + "name": "TAL1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6886", + "ENSEMBL:ENSG00000162367", + "HGNC:11556", + "OMIM:187040", + "UMLS:C0796355", + "UniProtKB:P17542", + "PR:P17542", + "UMLS:C0378781", + "UniProtKB:Q16509" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TAL1", + "TAL1 gene", + "TAL1_HUMAN T-cell acute lymphocytic leukemia protein 1 (sprot)", + "T-cell acute lymphocytic leukemia protein 1 (human)", + "TAL1 protein, human", + "Q16509_HUMAN TAL-1 (trembl)" + ] + } + ] + }, + "NCBIGene:2623": { + "categories": [ + "biolink:Gene" + ], + "name": "GATA1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2623", + "ENSEMBL:ENSG00000102145", + "HGNC:4170", + "OMIM:305371", + "UMLS:C1333663", + "UniProtKB:P15976", + "PR:P15976", + "UMLS:C1530719" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "GATA1", + "GATA1 gene", + "GATA1_HUMAN Erythroid transcription factor (sprot)", + "erythroid transcription factor (human)", + "GATA1 protein, human" + ] + } + ] + }, + "NCBIGene:947": { + "categories": [ + "biolink:Gene" + ], + "name": "CD34", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:947", + "ENSEMBL:ENSG00000174059", + "HGNC:1662", + "OMIM:142230", + "UMLS:C1332710", + "UniProtKB:P28906", + "PR:P28906", + "UMLS:C5441748" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CD34", + "CD34 gene", + "CD34_HUMAN Hematopoietic progenitor cell antigen CD34 (sprot)", + "hematopoietic progenitor cell antigen CD34 (human)", + "CD34 protein, human" + ] + } + ] + }, + "NCBIGene:6320": { + "categories": [ + "biolink:Gene" + ], + "name": "CLEC11A", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6320", + "ENSEMBL:ENSG00000105472", + "HGNC:10576", + "OMIM:604713", + "UMLS:C1539105", + "UniProtKB:Q9Y240", + "PR:Q9Y240", + "ENSEMBL:ENSP00000250340", + "ENSEMBL:ENSP00000250340.3", + "UMLS:C0671154", + "UMLS:C3888289" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CLEC11A", + "CLEC11A gene", + "CLC11_HUMAN C-type lectin domain family 11 member A (sprot)", + "C-type lectin domain family 11 member A (human)", + "CLEC11A protein, human", + "Stem Cell Growth Factor Beta, human" + ] + } + ] + }, + "NCBIGene:386653": { + "categories": [ + "biolink:Gene" 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(trembl)", + "CIB1_HUMAN Calcium and integrin-binding protein 1 (sprot)", + "calcium and integrin-binding protein 1 (human)", + "Calcium and Integrin-Binding Protein 1" + ] + } + ] + }, + "NCBIGene:3579": { + "categories": [ + "biolink:Gene" + ], + "name": "CXCR2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3579", + "ENSEMBL:ENSG00000180871", + "HGNC:6027", + "OMIM:146928", + "UMLS:C1334126", + "UniProtKB:P25025", + "PR:P25025", + "ENSEMBL:ENSP00000319635", + "ENSEMBL:ENSP00000319635.2", + "UMLS:C4082290", + "UniProtKB:Q53PC4" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CXCR2", + "CXCR2 gene", + "CXCR2_HUMAN C-X-C chemokine receptor type 2 (sprot)", + "C-X-C chemokine receptor type 2 (human)", + "C-X-C Chemokine Receptor Type 2, human", + "Q53PC4_HUMAN C-X-C chemokine receptor type 2 (trembl)" + ] + } + ] + }, + "NCBIGene:4513": { + "categories": [ + "biolink:Gene" + ], + "name": "COX2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4513", + "ENSEMBL:ENSG00000198712", + "HGNC:7421", + "OMIM:516040", + "UMLS:C1537986", + "UniProtKB:P00403", + "PR:P00403", + "ENSEMBL:ENSP00000354876", + "ENSEMBL:ENSP00000354876.1", + "UniProtKB:U5Z487" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "COX2", + "MT-CO2", + "MT-CO2 gene", + "COX2_HUMAN Cytochrome c oxidase subunit 2 (sprot)", + "cytochrome c oxidase subunit 2 (human)", + "U5Z487_HUMAN Cytochrome c oxidase subunit 2 (trembl)" + ] + } + ] + }, + "NCBIGene:1536": { + "categories": [ + "biolink:Gene" + ], + "name": "CYBB", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1536", + "ENSEMBL:ENSG00000165168", + "HGNC:2578", + "OMIM:300481", + "UMLS:C1413844", + "UniProtKB:A0A0S2Z3S6", + "UniProtKB:P04839", + "PR:P04839", + "ENSEMBL:ENSP00000367851", + "ENSEMBL:ENSP00000367851.4", + "UMLS:C1429424" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CYBB", + "CYBB gene", + "A0A0S2Z3S6_HUMAN Cytochrome b-245 beta polypeptide isoform 1 (Fragment) (trembl)", + "CY24B_HUMAN Cytochrome b-245 heavy chain (sprot)", + "cytochrome b-245 heavy chain (human)", + "CYBB protein, human" + ] + } + ] + }, + "NCBIGene:847": { + "categories": [ + "biolink:Gene" + ], + "name": "CAT", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:847", + "ENSEMBL:ENSG00000121691", + "HGNC:1516", + "OMIM:115500", + "UMLS:C1413138", + "UniProtKB:A0A384P5Q0", + "UniProtKB:P04040", + "PR:P04040", + "ENSEMBL:ENSP00000241052", + "ENSEMBL:ENSP00000241052.4", + "UMLS:C3530118" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CAT", + "CAT gene", + "A0A384P5Q0_HUMAN Catalase (trembl)", + "CATA_HUMAN Catalase (sprot)", + "catalase (human)", + "CAT protein, human" + ] + } + ] + }, + "NCBIGene:54738": { + "categories": [ + "biolink:Gene" + ], + "name": "FEV", + "attributes": [ + { + "attribute_type_id": 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"value": [ + "NCBIGene:9141", + "ENSEMBL:ENSG00000105185", + "HGNC:8764", + "OMIM:604583", + "UMLS:C1418405", + "UniProtKB:O14737", + "PR:O14737", + "UMLS:C1431691" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PDCD5", + "PDCD5 gene", + "PDCD5_HUMAN Programmed cell death protein 5 (sprot)", + "programmed cell death protein 5 (human)", + "PDCD5 protein, human" + ] + } + ] + }, + "NCBIGene:1649": { + "categories": [ + "biolink:Gene" + ], + "name": "DDIT3", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1649", + "ENSEMBL:ENSG00000175197", + "HGNC:2726", + "OMIM:126337", + "UMLS:C1413947", + "UniProtKB:P35638", + "PR:P35638", + "UMLS:C0170521", + "UniProtKB:Q53YD1" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "DDIT3", + "DDIT3 gene", + "DDIT3_HUMAN DNA damage-inducible transcript 3 protein (sprot)", + "DNA damage-inducible transcript 3 protein (human)", + "DDIT3 protein, human", + "Q53YD1_HUMAN DNA damage-inducible transcript 3 protein (trembl)" + ] + } + ] + }, + "NCBIGene:1440": { + "categories": [ + "biolink:Gene" + ], + "name": "CSF3", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1440", + "ENSEMBL:ENSG00000108342", + "HGNC:2438", + "OMIM:138970", + "UMLS:C1332793", + "UniProtKB:P09919", + "PR:P09919", + "UMLS:C5441740", + "UniProtKB:Q6FH65", + "UniProtKB:Q8N4W3", + "ENSEMBL:ENSP00000327766", + "ENSEMBL:ENSP00000327766.2" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CSF3", + "CSF3 gene", + "CSF3_HUMAN Granulocyte colony-stimulating factor (sprot)", + "granulocyte colony-stimulating factor (human)", + "CSF3 protein, human", + "Q6FH65_HUMAN Granulocyte colony-stimulating factor (Fragment) (trembl)", + "Q8N4W3_HUMAN Granulocyte colony-stimulating factor (trembl)" + ] + } + ] + }, + "NCBIGene:23037": { + "categories": [ + "biolink:Gene" + ], + "name": "PDZD2", + "attributes": [ + { + "attribute_type_id": 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human" + ] + } + ] + }, + "NCBIGene:604": { + "categories": [ + "biolink:Gene" + ], + "name": "BCL6", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:604", + "ENSEMBL:ENSG00000113916", + "HGNC:1001", + "OMIM:109565", + "UMLS:C1332399", + "UniProtKB:B5B0A5", + "UniProtKB:P41182", + "PR:P41182", + "UMLS:C1448774" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "BCL6", + "BCL6 gene", + "B5B0A5_HUMAN Zinc finger transcription factor BCL6S (trembl)", + "BCL6_HUMAN B-cell lymphoma 6 protein (sprot)", + "B-cell lymphoma 6 protein (human)", + "BCL6 protein, human" + ] + } + ] + }, + "NCBIGene:7412": { + "categories": [ + "biolink:Gene" + ], + "name": "VCAM1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:7412", + "ENSEMBL:ENSG00000162692", + "HGNC:12663", + "OMIM:192225", + "UMLS:C1421435", + "UniProtKB:P19320", + "PR:P19320", + "UMLS:C3853651" + ] + }, + { + "attribute_type_id": 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"ENSEMBL:ENSP00000330341.2", + "UMLS:C3275257", + "UniProtKB:Q6FI39" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SOCS3", + "SOCS3 gene", + "SOCS3_HUMAN Suppressor of cytokine signaling 3 (sprot)", + "suppressor of cytokine signaling 3 (human)", + "Suppressor of Cytokine Signaling 3", + "Q6FI39_HUMAN Suppressor of cytokine signaling 3 (trembl)" + ] + } + ] + }, + "NCBIGene:301": { + "categories": [ + "biolink:Gene" + ], + "name": "ANXA1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:301", + "ENSEMBL:ENSG00000135046", + "HGNC:533", + "OMIM:151690", + "UMLS:C1412417", + "UniProtKB:P04083", + "PR:P04083", + "ENSEMBL:ENSP00000257497", + "ENSEMBL:ENSP00000257497.6", + "ENSEMBL:ENSP00000366109", + "ENSEMBL:ENSP00000366109.1", + "UniProtKB:Q5TZZ9" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ANXA1", + "ANXA1 gene", + "ANXA1_HUMAN Annexin A1 (sprot)", + "annexin A1 (human)", + "Q5TZZ9_HUMAN Annexin 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] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ALOX15", + "ALOX15 gene", + "LOX15_HUMAN Polyunsaturated fatty acid lipoxygenase ALOX15 (sprot)", + "polyunsaturated fatty acid lipoxygenase ALOX15 (human)", + "ALOX15 protein, human" + ] + } + ] + }, + "NCBIGene:2624": { + "categories": [ + "biolink:Gene" + ], + "name": "GATA2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2624", + "ENSEMBL:ENSG00000179348", + "HGNC:4171", + "OMIM:137295", + "UMLS:C1414993", + "UniProtKB:P23769", + "PR:P23769", + "UMLS:C1506956" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "GATA2", + "GATA2 gene", + "GATA2_HUMAN Endothelial transcription factor GATA-2 (sprot)", + "endothelial transcription factor GATA-2 (human)", + "GATA2 protein, human" + ] + } + ] + }, + "NCBIGene:4311": { + "categories": [ + "biolink:Gene" + ], + "name": "MME", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4311", + "ENSEMBL:ENSG00000196549", + "HGNC:7154", + "OMIM:120520", + "UMLS:C1366499", + "UniProtKB:P08473", + "PR:P08473", + "ENSEMBL:ENSP00000353679", + "ENSEMBL:ENSP00000353679.2", + "ENSEMBL:ENSP00000417079", + "ENSEMBL:ENSP00000417079.1", + "ENSEMBL:ENSP00000418525", + "ENSEMBL:ENSP00000418525.1", + "ENSEMBL:ENSP00000418791", + "ENSEMBL:ENSP00000418791.2", + "ENSEMBL:ENSP00000419653", + "ENSEMBL:ENSP00000419653.1", + "ENSEMBL:ENSP00000420389", + "ENSEMBL:ENSP00000420389.1", + "ENSEMBL:ENSP00000420542", + "ENSEMBL:ENSP00000420542.2", + "ENSEMBL:ENSP00000502021", + "ENSEMBL:ENSP00000502021.2", + "ENSEMBL:ENSP00000505211", + "ENSEMBL:ENSP00000505211.1", + "ENSEMBL:ENSP00000505690", + "ENSEMBL:ENSP00000505690.1", + "UMLS:C3887624" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MME", + "MME gene", + "NEP_HUMAN Neprilysin (sprot)", + "neprilysin (human)", + "Human Neprilysin" + ] + } + ] + }, + "NCBIGene:8744": { + "categories": [ + "biolink:Gene" + ], 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"UniProtKB:Q15910", + "PR:Q15910", + "UMLS:C1172384", + "UniProtKB:S4S3R8" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "EZH2", + "EZH2 gene", + "A0A090N8E9_HUMAN Histone-lysine N-methyltransferase EZH2 (trembl)", + "EZH2_HUMAN Histone-lysine N-methyltransferase EZH2 (sprot)", + "histone-lysine N-methyltransferase EZH2 (human)", + "EZH2 protein, human", + "S4S3R8_HUMAN Histone-lysine N-methyltransferase EZH2 (trembl)" + ] + } + ] + }, + "NCBIGene:3684": { + "categories": [ + "biolink:Gene" + ], + "name": "ITGAM", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3684", + "ENSEMBL:ENSG00000169896", + "HGNC:6149", + "OMIM:120980", + "UMLS:C1366562", + "UniProtKB:P11215", + "PR:P11215", + "UMLS:C1701032" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ITGAM", + "ITGAM gene", + "ITAM_HUMAN Integrin alpha-M (sprot)", + "integrin alpha-M (human)", + "ITGAM protein, human" + ] + } + ] + }, + "NCBIGene:1896": { 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cDNA FLJ51025, highly similar to NADPH oxidase 4 (trembl)", + "B7Z529_HUMAN cDNA FLJ51027, highly similar to NADPH oxidase 4 (trembl)", + "NOX4_HUMAN NADPH oxidase 4 (sprot)", + "NADPH oxidase 4 (human)", + "NOX4 protein, human" + ] + } + ] + }, + "NCBIGene:8829": { + "categories": [ + "biolink:Gene" + ], + "name": "NRP1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:8829", + "ENSEMBL:ENSG00000099250", + "HGNC:8004", + "OMIM:602069", + "UMLS:C1334905", + "UniProtKB:A8K9V7", + "UniProtKB:O14786", + "PR:O14786", + "UMLS:C4281812", + "UniProtKB:Q59F20", + "UniProtKB:Q68DN3", + "UniProtKB:Q6AWA9", + "UniProtKB:Q6X907" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "NRP1", + "NRP1 gene", + "A8K9V7_HUMAN Neuropilin (trembl)", + "NRP1_HUMAN Neuropilin-1 (sprot)", + "neuropilin-1 (human)", + "Neuropilin-1, Human", + "Q59F20_HUMAN Neuropilin-1 variant (Fragment) (trembl)", + "Q68DN3_HUMAN Neuropilin (trembl)", + "Q6AWA9_HUMAN Uncharacterized protein DKFZp686A03134 (Fragment) (trembl)", + "Q6X907_HUMAN Neuropilin (trembl)" + ] + } + ] + }, + "NCBIGene:384": { + "categories": [ + "biolink:Gene" + ], + "name": "ARG2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:384", + "ENSEMBL:ENSG00000081181", + "HGNC:664", + "OMIM:107830", + "UMLS:C1412516", + "UniProtKB:A0A024R6A0", + "UniProtKB:P78540", + "PR:P78540", + "ENSEMBL:ENSP00000261783", + "ENSEMBL:ENSP00000261783.3" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ARG2", + "ARG2 gene", + "A0A024R6A0_HUMAN Arginase (trembl)", + "ARGI2_HUMAN Arginase-2, mitochondrial (sprot)", + "arginase-2, mitochondrial (human)" + ] + } + ] + }, + "NCBIGene:3953": { + "categories": [ + "biolink:Gene" + ], + "name": "LEPR", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3953", + "ENSEMBL:ENSG00000116678", + "HGNC:6554", + "OMIM:601007", + "UMLS:C1366515", + "UniProtKB:P48357", + "PR:P48357", + "UMLS:C1144168", + "UniProtKB:Q4G138" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "LEPR", + "LEPR gene", + "LEPR_HUMAN Leptin receptor (sprot)", + "leptin receptor (human)", + "leptin receptor, human", + "Q4G138_HUMAN LEPR protein (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:4481": { + "categories": [ + "biolink:Gene" + ], + "name": "MSR1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4481", + "ENSEMBL:ENSG00000038945", + "HGNC:7376", + "OMIM:153622", + "UMLS:C1417374", + "UniProtKB:P21757", + "PR:P21757", + "UMLS:C3811790" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MSR1", + "MSR1 gene", + "MSRE_HUMAN Macrophage scavenger receptor types I and II (sprot)", + "macrophage scavenger receptor types I and II (human)", + "Macrophage Scavenger Receptor Types I and II" + ] + } + ] + }, + "NCBIGene:10891": { + "categories": [ + "biolink:Gene" + ], + "name": "PPARGC1A", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:10891", + "ENSEMBL:ENSG00000109819", + "HGNC:9237", + "OMIM:604517", + "UMLS:C1418779", + "UniProtKB:A0A024R9Q9", + "UniProtKB:Q9UBK2", + "PR:Q9UBK2", + "UMLS:C1452082", + "UMLS:C4054191" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PPARGC1A", + "PPARGC1A gene", + "A0A024R9Q9_HUMAN Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (trembl)", + "PRGC1_HUMAN Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (sprot)", + "peroxisome proliferator-activated receptor gamma coactivator 1-alpha (human)", + "PPARGC1A protein, human", + "Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-Alpha Isoform 4" + ] + } + ] + }, + "NCBIGene:595": { + "categories": [ + "biolink:Gene" + ], + "name": "CCND1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:595", + "ENSEMBL:ENSG00000110092", + "HGNC:1582", + "OMIM:168461", + "UMLS:C1413172", + "UniProtKB:P24385", + "PR:P24385", + "ENSEMBL:ENSP00000227507", + "ENSEMBL:ENSP00000227507.2", + "UMLS:C0388730", + "UMLS:C1741716", + "UMLS:C3893229", + "UniProtKB:Q6FI00" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CCND1", + "CCND1 gene", + "CCND1_HUMAN G1/S-specific cyclin-D1 (sprot)", + "G1/S-specific cyclin-D1 (human)", + "Cyclin D", + "CCND1 protein, human", + "G1/S-Specific Cyclin-D1b, human", + "Q6FI00_HUMAN CCND1 protein (trembl)" + ] + } + ] + }, + "NCBIGene:1906": { + "categories": [ + "biolink:Gene" + ], + "name": "EDN1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1906", + "ENSEMBL:ENSG00000078401", + "HGNC:3176", + "OMIM:131240", + "UMLS:C1414260", + "UniProtKB:P05305", + "PR:P05305", + "ENSEMBL:ENSP00000368683", + "ENSEMBL:ENSP00000368683.5", + "UMLS:C4316927", + "UniProtKB:Q6FH53" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "EDN1", + "EDN1 gene", + "EDN1_HUMAN Endothelin-1 (sprot)", + "endothelin-1 (human)", + "Endothelin-1, human", + "Q6FH53_HUMAN EDN1 protein (trembl)" + ] + } + ] + }, + "NCBIGene:7494": { + "categories": [ + "biolink:Gene" + ], + "name": "XBP1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:7494", + "ENSEMBL:ENSG00000100219", + "HGNC:12801", + "OMIM:194355", + "UMLS:C1421527", + "UniProtKB:A0A024R1F0", + "UniProtKB:P17861", + "PR:P17861", + "UMLS:C4083144" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "XBP1", + "XBP1 gene", + "A0A024R1F0_HUMAN X-box binding protein 1, isoform CRA_b (trembl)", + "XBP1_HUMAN X-box-binding protein 1 (sprot)", + "X-box-binding protein 1 (human)", + "X-Box Binding Protein 1, Human" + ] + } + ] + }, + "NCBIGene:3559": { + "categories": [ + "biolink:Gene" + ], + "name": "IL2RA", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3559", + "ENSEMBL:ENSG00000134460", + "HGNC:6008", + "OMIM:147730", + "UMLS:C1334114", + "UniProtKB:H0Y5Z0", + "ENSEMBL:ENSP00000402024", + "ENSEMBL:ENSP00000402024.2", + "UniProtKB:P01589", + "PR:P01589", + "ENSEMBL:ENSP00000369293", + "ENSEMBL:ENSP00000369293.3", + "UMLS:C1700887", + "UniProtKB:Q5W005", + "ENSEMBL:ENSP00000369287", + "ENSEMBL:ENSP00000369287.1" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "IL2RA", + "IL2RA gene", + "H0Y5Z0_HUMAN Interleukin 2 receptor subunit alpha (trembl)", + "IL2RA_HUMAN Interleukin-2 receptor subunit alpha (sprot)", + "interleukin-2 receptor subunit alpha (human)", + "IL2RA protein, human", + "Q5W005_HUMAN Interleukin 2 receptor subunit alpha (trembl)" + ] + } + ] + }, + "NCBIGene:3280": { + "categories": [ + "biolink:Gene" + ], + "name": "HES1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3280", + "ENSEMBL:ENSG00000114315", + "HGNC:5192", + "OMIM:139605", + "UMLS:C1415725", + "UniProtKB:Q14469", + "PR:Q14469", + "ENSEMBL:ENSP00000232424", + "ENSEMBL:ENSP00000232424.3", + "UMLS:C0539029" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "HES1", + "HES1 gene", + "HES1_HUMAN Transcription factor HES-1 (sprot)", + "transcription factor HES-1 (human)", + "HES1 protein, human" + ] + } + ] + }, + "NCBIGene:5465": { + "categories": [ + "biolink:Gene" + ], + "name": "PPARA", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5465", + "ENSEMBL:ENSG00000186951", + "HGNC:9232", + "OMIM:170998", + "UMLS:C1418776", + "UniProtKB:F1D8S4", + "UniProtKB:Q07869", + "PR:Q07869", + "UMLS:C4551616" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PPARA", + "PPARA gene", + "F1D8S4_HUMAN Peroxisome proliferator-activated receptor alpha (trembl)", + "PPARA_HUMAN Peroxisome proliferator-activated receptor alpha (sprot)", + "peroxisome proliferator-activated receptor alpha (human)", + "Peroxisome Proliferator-Activated Receptor Alpha, human" + ] + } + ] + }, + "NCBIGene:283": { + "categories": [ + "biolink:Gene" + ], + "name": "ANG", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:283", + "ENSEMBL:ENSG00000214274", + "HGNC:483", + "OMIM:105850", + "UMLS:C1367482", + "UniProtKB:P03950", + "PR:P03950", + "ENSEMBL:ENSP00000336762", + "ENSEMBL:ENSP00000336762.6", + "ENSEMBL:ENSP00000381077", + "ENSEMBL:ENSP00000381077.4", + "UMLS:C3179204", + "UniProtKB:W0UV28" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ANG", + "ANG gene", + "ANGI_HUMAN Angiogenin (sprot)", + "angiogenin (human)", + "ANG protein, human", + "W0UV28_HUMAN Ribonuclease A A1 (trembl)" + ] + } + ] + }, + "NCBIGene:26033": { + "categories": [ + "biolink:Gene" + ], + "name": "ATRNL1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:26033", + "ENSEMBL:ENSG00000107518", + "HGNC:29063", + "OMIM:612869", + "UMLS:C1428783", + "UniProtKB:Q4G0Y2", + "UniProtKB:Q5VV63", + "PR:Q5VV63" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ATRNL1", + "ATRNL1 gene", + "Q4G0Y2_HUMAN ATRNL1 protein (trembl)", + "ATRN1_HUMAN Attractin-like protein 1 (sprot)", + "attractin-like protein 1 (human)" + ] + } + ] + }, + "NCBIGene:8741": { + "categories": [ + "biolink:Gene" + ], + "name": "TNFSF13", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:8741", + "ENSEMBL:ENSG00000161955", + "HGNC:11928", + "OMIM:604472", + "UMLS:C1420815", + "UniProtKB:B3KR02", + "UniProtKB:O75888", + "PR:O75888", + "UMLS:C0757844", + "UniProtKB:Q2QBA2", + "ENSEMBL:ENSP00000369908", + "ENSEMBL:ENSP00000369908.5" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TNFSF13", + "TNFSF13 gene", + "B3KR02_HUMAN HCG2045906, isoform CRA_c (trembl)", + "TNF13_HUMAN Tumor necrosis factor ligand superfamily member 13 (sprot)", + "tumor necrosis factor ligand superfamily member 13 isoforms alpha/beta/gamma/4/5 (human)", + "TNFSF13 protein, human", + "Q2QBA2_HUMAN TNF superfamily member 13 (trembl)" + ] + } + ] + }, + "NCBIGene:1958": { + "categories": [ + "biolink:Gene" + ], + "name": "EGR1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1958", + "ENSEMBL:ENSG00000120738", + "HGNC:3238", + "OMIM:128990", + "UMLS:C1414314", + "UniProtKB:P18146", + "PR:P18146", + "ENSEMBL:ENSP00000239938", + "ENSEMBL:ENSP00000239938.4", + "UMLS:C1447045", + "UniProtKB:Q546S1" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "EGR1", + "EGR1 gene", + "EGR1_HUMAN Early growth response protein 1 (sprot)", + "early growth response protein 1 (human)", + "EGR1 protein, human", + "Q546S1_HUMAN Early growth response protein (trembl)" + ] + } + ] + }, + "NCBIGene:3066": { + "categories": [ + "biolink:Gene" + ], + "name": "HDAC2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3066", + "ENSEMBL:ENSG00000196591", + "HGNC:4853", + "OMIM:605164", + "UMLS:C1333892", + "UniProtKB:Q92769", + "PR:Q92769", + "UMLS:C2713652" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "HDAC2", + "HDAC2 gene", + "HDAC2_HUMAN Histone deacetylase 2 (sprot)", + "histone deacetylase 2 (human)", + "HDAC2 protein, human" + ] + } + ] + }, + "NCBIGene:4314": { + "categories": [ + "biolink:Gene" + ], + "name": "MMP3", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4314", + "ENSEMBL:ENSG00000149968", + "HGNC:7173", + "OMIM:185250", + "UMLS:C1366358", + "UniProtKB:P08254", + "PR:P08254", + "ENSEMBL:ENSP00000299855", + "ENSEMBL:ENSP00000299855.5", + "UMLS:C1723257" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "MMP3", + "MMP3 gene", + "MMP3_HUMAN Stromelysin-1 (sprot)", + "stromelysin-1 (human)", + "MMP3 protein, human" + ] + } + ] + }, + "NCBIGene:79813": { + "categories": [ + "biolink:Gene" + ], + "name": "EHMT1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:79813", + "ENSEMBL:ENSG00000181090", + "HGNC:24650", + "OMIM:607001", + "UMLS:C1539338", + "UniProtKB:A0A1B0GV09", + "ENSEMBL:ENSP00000490328", + "ENSEMBL:ENSP00000490328.1", + "UniProtKB:Q9H9B1", + "PR:Q9H9B1", + "UMLS:C2350813" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "EHMT1", + "EHMT1 gene", + "A0A1B0GV09_HUMAN Euchromatic histone lysine methyltransferase 1 (trembl)", + "EHMT1_HUMAN Histone-lysine N-methyltransferase EHMT1 (sprot)", + "histone-lysine N-methyltransferase EHMT1 (human)", + "EHMT1 protein, human" + ] + } + ] + }, + "NCBIGene:4838": { + "categories": [ + "biolink:Gene" + ], + "name": "NODAL", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:4838", + "ENSEMBL:ENSG00000156574", + "HGNC:7865", + "OMIM:601265", + "UMLS:C1417752", + "UniProtKB:Q96S42", + "PR:Q96S42", + "ENSEMBL:ENSP00000287139", + "ENSEMBL:ENSP00000287139.3", + "UMLS:C3272515" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "NODAL", + "NODAL gene", + "NODAL_HUMAN Nodal homolog (sprot)", + "nodal homolog (human)", + "Nodal Homolog" + ] + } + ] + }, + "NCBIGene:1361": { + "categories": [ + "biolink:Gene" + ], + "name": "CPB2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1361", + "ENSEMBL:ENSG00000080618", + "HGNC:2300", + "OMIM:603101", + "UMLS:C1413666", + "UniProtKB:A0A087WSY5", + "ENSEMBL:ENSP00000400714", + "ENSEMBL:ENSP00000400714.3", + "UniProtKB:Q96IY4", + "PR:Q96IY4", + "UMLS:C3710898" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CPB2", + "CPB2 gene", + "A0A087WSY5_HUMAN Carboxypeptidase B2 (trembl)", + "CBPB2_HUMAN Carboxypeptidase B2 (sprot)", + "carboxypeptidase B2 (human)", + "CPB2 protein, human" + ] + } + ] + }, + "NCBIGene:23411": { + "categories": [ + "biolink:Gene" + ], + "name": "SIRT1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:23411", + "ENSEMBL:ENSG00000096717", + "HGNC:14929", + "OMIM:604479", + "UMLS:C1423062", + "UniProtKB:A0A024QZQ1", + "UniProtKB:A8K128", + "UniProtKB:B0QZ35", + "ENSEMBL:ENSP00000384063", + "ENSEMBL:ENSP00000384063.1", + "ENSEMBL:ENSP00000384508", + "ENSEMBL:ENSP00000384508.1", + "UniProtKB:E9PC49", + "ENSEMBL:ENSP00000409208", + "ENSEMBL:ENSP00000409208.1", + "UniProtKB:Q96EB6", + "PR:Q96EB6", + "UMLS:C1101544" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SIRT1", + "SIRT1 gene", + "A0A024QZQ1_HUMAN Sirtuin (Silent mating type information regulation 2 homolog) 1 (S. cerevisiae), isoform CRA_a (trembl)", + "A8K128_HUMAN cDNA FLJ76335, highly similar to Homo sapiens sirtuin (silent mating type information regulation 2 homolog) 1 (S. cerevisiae), mRNA (trembl)", + "B0QZ35_HUMAN Sirtuin 1 (trembl)", + "E9PC49_HUMAN Sirtuin 1 (trembl)", + "SIR1_HUMAN NAD-dependent protein deacetylase sirtuin-1 (sprot)", + "NAD-dependent protein deacetylase sirtuin-1 (human)", + "SIRT1 protein, human" + ] + } + ] + }, + "NCBIGene:3689": { + "categories": [ + "biolink:Gene" + ], + "name": "ITGB2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3689", + "ENSEMBL:ENSG00000160255", + "HGNC:6155", + "OMIM:600065", + "UMLS:C1334146", + "UniProtKB:A0A494C0X7", + "ENSEMBL:ENSP00000498780", + "ENSEMBL:ENSP00000498780.1", + "UniProtKB:B4E0R1", + "UniProtKB:P05107", + "PR:P05107", + "ENSEMBL:ENSP00000303242", + "ENSEMBL:ENSP00000303242.6", + "ENSEMBL:ENSP00000347279", + "ENSEMBL:ENSP00000347279.4", + "ENSEMBL:ENSP00000380948", + "ENSEMBL:ENSP00000380948.2", + "ENSEMBL:ENSP00000380950", + "ENSEMBL:ENSP00000380950.1", + "ENSEMBL:ENSP00000380955", + "ENSEMBL:ENSP00000380955.1", + "UMLS:C4082564" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ITGB2", + "ITGB2 gene", + "A0A494C0X7_HUMAN Integrin beta (trembl)", + "B4E0R1_HUMAN Integrin beta (trembl)", + "ITB2_HUMAN Integrin beta-2 (sprot)", + "integrin beta-2 (human)", + "Integrin Beta-2, human" + ] + } + ] + }, + "NCBIGene:6439": { + "categories": [ + "biolink:Gene" + ], + "name": "SFTPB", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6439", + "ENSEMBL:ENSG00000168878", + "HGNC:10801", + "OMIM:178640", + "UMLS:C1442757", + "UniProtKB:D6W5L6", + "UniProtKB:P07988", + "PR:P07988", + "ENSEMBL:ENSP00000377409", + "ENSEMBL:ENSP00000377409.4", + "ENSEMBL:ENSP00000386346", + "ENSEMBL:ENSP00000386346.2", + "ENSEMBL:ENSP00000428719", + "ENSEMBL:ENSP00000428719.2", + "UMLS:C3849523" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SFTPB", + "SFTPB gene", + "D6W5L6_HUMAN Surfactant, pulmonary-associated protein B, isoform CRA_a (trembl)", + "PSPB_HUMAN Pulmonary surfactant-associated protein B (sprot)", + "pulmonary surfactant-associated protein B (human)", + "SFTPB protein, human" + ] + } + ] + }, + "NCBIGene:998": { + "categories": [ + "biolink:Gene" + ], + "name": "CDC42", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:998", + "ENSEMBL:ENSG00000070831", + "HGNC:1736", + "OMIM:116952", + "UMLS:C1366537", + "UniProtKB:A0A024RAA5", + "UniProtKB:A0A024RAA6", + "UniProtKB:P60953", + "PR:P60953", + "UMLS:C4705281" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CDC42", + "CDC42 gene", + "A0A024RAA5_HUMAN Cell division control protein 42 homolog (trembl)", + "A0A024RAA6_HUMAN Cell division control protein 42 homolog (trembl)", + "CDC42_HUMAN Cell division control protein 42 homolog (sprot)", + "cell division control protein 42 homolog (human)", + "CDC42 protein, human" + ] + } + ] + }, + "NCBIGene:6614": { + "categories": [ + "biolink:Gene" + ], + "name": "SIGLEC1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6614", + "ENSEMBL:ENSG00000088827", + "HGNC:11127", + "OMIM:600751", + "UMLS:C1420266", + "UniProtKB:Q9BZZ2", + "PR:Q9BZZ2" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SIGLEC1", + "SIGLEC1 gene", + "SN_HUMAN Sialoadhesin (sprot)", + "sialoadhesin (human)" + ] + } + ] + }, + "NCBIGene:54498": { + "categories": [ + "biolink:Gene" + ], + "name": "SMOX", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:54498", + "ENSEMBL:ENSG00000088826", + "HGNC:15862", + "OMIM:615854", + "UMLS:C1423784", + "UniProtKB:Q9NWM0", + "PR:Q9NWM0" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SMOX", + "SMOX gene", + "SMOX_HUMAN Spermine oxidase (sprot)", + "spermine oxidase (human)" + ] + } + ] + }, + "NCBIGene:2023": { + "categories": [ + "biolink:Gene" + ], + "name": "ENO1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2023", + "ENSEMBL:ENSG00000074800", + "HGNC:3350", + "OMIM:172430", + "UMLS:C1414402", + "UniProtKB:A0A024R4F1", + "UniProtKB:P06733", + "PR:P06733", + "UMLS:C0300895" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ENO1", + "ENO1 gene", + "A0A024R4F1_HUMAN phosphopyruvate hydratase (trembl)", + "ENOA_HUMAN Alpha-enolase (sprot)", + "alpha-enolase (human)", + "ENO1 protein, human" + ] + } + ] + }, + "NCBIGene:2539": { + "categories": [ + "biolink:Gene" + ], + "name": "G6PD", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2539", + "ENSEMBL:ENSG00000160211", + "HGNC:4057", + "OMIM:305900", + "UMLS:C1333652", + "UniProtKB:A0A384NL00", + "UniProtKB:P11413", + "PR:P11413", + "UMLS:C4742874" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "G6PD", + "G6PD gene", + "A0A384NL00_HUMAN Glucose-6-phosphate 1-dehydrogenase (trembl)", + "G6PD_HUMAN Glucose-6-phosphate 1-dehydrogenase (sprot)", + "glucose-6-phosphate 1-dehydrogenase (human)", + "G6PD protein, human" + ] + } + ] + }, + "NCBIGene:6346": { + "categories": [ + "biolink:Gene" + ], + "name": "CCL1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6346", + "ENSEMBL:ENSG00000108702", + "HGNC:10609", + "OMIM:182281", + "UMLS:C1332683", + "UniProtKB:P22362", + "PR:P22362", + "ENSEMBL:ENSP00000225842", + "ENSEMBL:ENSP00000225842.3", + "UMLS:C1447090" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CCL1", + "CCL1 gene", + "CCL1_HUMAN C-C motif chemokine 1 (sprot)", + "C-C motif chemokine 1 (human)", + "CCL1 protein, human" + ] + } + ] + }, + "NCBIGene:8013": { + "categories": [ + "biolink:Gene" + ], + "name": "NR4A3", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:8013", + "ENSEMBL:ENSG00000119508", + "HGNC:7982", + "OMIM:600542", + "UMLS:C1417837", + "UniProtKB:A0A024R168", + "UniProtKB:Q92570", + "PR:Q92570", + "UMLS:C1453685" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "NR4A3", + "NR4A3 gene", + "A0A024R168_HUMAN Nuclear receptor subfamily 4, group A, member 3, isoform CRA_c (trembl)", + "NR4A3_HUMAN Nuclear receptor subfamily 4 group A member 3 (sprot)", + "nuclear receptor subfamily 4 group A member 3 (human)", + "NR4A3 protein, human" + ] + } + ] + }, + "UniProtKB:P13236": { + "categories": [ + "biolink:Protein" + ], + "name": "CCL4_HUMAN C-C motif chemokine 4 (sprot)", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "UniProtKB:P13236", + "PR:P13236", + "ENSEMBL:ENSP00000478708", + "ENSEMBL:ENSP00000478708.1", + "ENSEMBL:ENSP00000480345", + "ENSEMBL:ENSP00000480345.1", + "ENSEMBL:ENSP00000482259", + "ENSEMBL:ENSP00000482259.1", + "UMLS:C1429582" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CCL4_HUMAN C-C motif chemokine 4 (sprot)", + "C-C motif chemokine 4 (human)", + "CCL4 protein, human" + ] + } + ] + }, + "NCBIGene:6513": { + "categories": [ + "biolink:Gene" + ], + "name": "SLC2A1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6513", + "ENSEMBL:ENSG00000117394", + "HGNC:11005", + "OMIM:138140", + "UMLS:C1335837", + "UniProtKB:P11166", + "PR:P11166", + "ENSEMBL:ENSP00000416293", + "ENSEMBL:ENSP00000416293.2", + "UMLS:C1504631", + "UniProtKB:Q59GX2" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SLC2A1", + "SLC2A1 gene", + "GTR1_HUMAN Solute carrier family 2, facilitated glucose transporter member 1 (sprot)", + "solute carrier family 2, facilitated glucose transporter member 1 (human)", + "SLC2A1 protein, human", + "Q59GX2_HUMAN Solute carrier family 2, facilitated glucose transporter member 1 (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:1080": { + "categories": [ + "biolink:Gene" + ], + "name": "CFTR", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1080", + "ENSEMBL:ENSG00000001626", + "HGNC:1884", + "OMIM:602421", + "UMLS:C1413365", + "UniProtKB:A0A024R730", + "UniProtKB:P13569", + "PR:P13569", + "UMLS:C1612819" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CFTR", + "CFTR gene", + "A0A024R730_HUMAN Cystic fibrosis transmembrane conductance regulator (trembl)", + "CFTR_HUMAN Cystic fibrosis transmembrane conductance regulator (sprot)", + "cystic fibrosis transmembrane conductance regulator (human)", + "CFTR protein, human" + ] + } + ] + }, + "NCBIGene:7448": { + "categories": [ + "biolink:Gene" + ], + "name": "VTN", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:7448", + "ENSEMBL:ENSG00000109072", + "HGNC:12724", + "OMIM:193190", + "UMLS:C1336937", + "UniProtKB:D9ZGG2", + "UniProtKB:P04004", + "PR:P04004", + "ENSEMBL:ENSP00000226218", + "ENSEMBL:ENSP00000226218.4", + "UMLS:C4281807" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "VTN", + "VTN gene", + "D9ZGG2_HUMAN Vitronectin (trembl)", + "VTNC_HUMAN Vitronectin (sprot)", + "vitronectin (human)", + "Vitronectin, human" + ] + } + ] + }, + "NCBIGene:5175": { + "categories": [ + "biolink:Gene" + ], + "name": "PECAM1", + "attributes": [ + { 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chemokine 22 (human)", + "CCL22 protein, human" + ] + } + ] + }, + "NCBIGene:5972": { + "categories": [ + "biolink:Gene" + ], + "name": "REN", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5972", + "ENSEMBL:ENSG00000143839", + "HGNC:9958", + "OMIM:179820", + "UMLS:C1419338", + "UniProtKB:P00797", + "PR:P00797", + "UMLS:C5441729" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "REN", + "REN gene", + "RENI_HUMAN Renin (sprot)", + "renin (human)", + "REN protein, human" + ] + } + ] + }, + "NCBIGene:1153": { + "categories": [ + "biolink:Gene" + ], + "name": "CIRBP", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1153", + "ENSEMBL:ENSG00000099622", + "HGNC:1982", + "OMIM:602649", + "UMLS:C1413426", + "UniProtKB:D6W5Y5", + "ENSEMBL:ENSP00000465077", + "ENSEMBL:ENSP00000465077.1", + "ENSEMBL:ENSP00000465558", + "ENSEMBL:ENSP00000465558.1", + "ENSEMBL:ENSP00000466025", + 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"attribute_type_id": "biolink:synonym", + "value": [ + "SERPINE1", + "SERPINE1 gene", + "A0A024QYT5_HUMAN Serpin peptidase inhibitor, clade E (Nexin, plasminogen activator inhibitor type 1), member 1, isoform CRA_b (trembl)", + "PAI1_HUMAN Plasminogen activator inhibitor 1 (sprot)", + "plasminogen activator inhibitor 1 (human)", + "SERPINE1 protein, human" + ] + } + ] + }, + "NCBIGene:9700": { + "categories": [ + "biolink:Gene" + ], + "name": "ESPL1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:9700", + "ENSEMBL:ENSG00000135476", + "HGNC:16856", + "OMIM:604143", + "UMLS:C1424597", + "UniProtKB:Q14674", + "PR:Q14674" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ESPL1", + "ESPL1 gene", + "ESPL1_HUMAN Separin (sprot)", + "separin (human)" + ] + } + ] + }, + "NCBIGene:54884": { + "categories": [ + "biolink:Gene" + ], + "name": "RETSAT", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:54884", + "ENSEMBL:ENSG00000042445", + "HGNC:25991", + "OMIM:617597", + "UMLS:C1826796", + "UniProtKB:Q6NUM9", + "PR:Q6NUM9" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "RETSAT", + "RETSAT gene", + "RETST_HUMAN All-trans-retinol 13,14-reductase (sprot)", + "all-trans-retinol 13,14-reductase (human)" + ] + } + ] + }, + "NCBIGene:1311": { + "categories": [ + "biolink:Gene" + ], + "name": "COMP", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1311", + "ENSEMBL:ENSG00000105664", + "HGNC:2227", + "OMIM:600310", + "UMLS:C1456376", + "UniProtKB:P49747", + "PR:P49747", + "UMLS:C3711580" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "COMP", + "COMP gene", + "COMP_HUMAN Cartilage oligomeric matrix protein (sprot)", + "cartilage oligomeric matrix protein (human)", + "human COMP protein" + ] + } + ] + }, + "NCBIGene:6590": { + "categories": [ + "biolink:Gene" + ], + "name": "SLPI", + "attributes": [ 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Tumor necrosis factor ligand 2A (trembl)", + "TNF18_HUMAN Tumor necrosis factor ligand superfamily member 18 (sprot)", + "tumor necrosis factor ligand superfamily member 18 (human)", + "TNFSF18 protein, human" + ] + } + ] + }, + "NCBIGene:970": { + "categories": [ + "biolink:Gene" + ], + "name": "CD70", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:970", + "ENSEMBL:ENSG00000125726", + "HGNC:11937", + "OMIM:602840", + "UMLS:C1824671", + "UniProtKB:A0A0U5JA32", + "UniProtKB:P32970", + "PR:P32970", + "UMLS:C1664176" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CD70", + "CD70 gene", + "A0A0U5JA32_HUMAN Tumor necrosis factor ligand 8A (trembl)", + "CD70_HUMAN CD70 antigen (sprot)", + "CD70 antigen (human)", + "CD70 protein, human" + ] + } + ] + }, + "NCBIGene:284217": { + "categories": [ + "biolink:Gene" + ], + "name": "LAMA1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:284217", + "ENSEMBL:ENSG00000101680", + "HGNC:6481", + "OMIM:150320", + "UMLS:C1416775", + "UniProtKB:P25391", + "PR:P25391", + "ENSEMBL:ENSP00000374309", + "ENSEMBL:ENSP00000374309.3" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "LAMA1", + "LAMA1 gene", + "LAMA1_HUMAN Laminin subunit alpha-1 (sprot)", + "laminin subunit alpha-1 (human)" + ] + } + ] + }, + "NCBIGene:55540": { + "categories": [ + "biolink:Gene" + ], + "name": "IL17RB", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:55540", + "ENSEMBL:ENSG00000056736", + "HGNC:18015", + "OMIM:605458", + "UMLS:C1425241", + "UniProtKB:Q9NRM6", + "PR:Q9NRM6", + "UMLS:C1312816" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "IL17RB", + "IL17RB gene", + "I17RB_HUMAN Interleukin-17 receptor B (sprot)", + "interleukin-17 receptor B (human)", + "IL17RB protein, human" + ] + } + ] + }, + "NCBIGene:930": { + "categories": [ + "biolink:Gene" + ], + "name": "CD19", + 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"OMIM:106150", + "UMLS:C1366631", + "UniProtKB:B0ZBE2", + "UniProtKB:B2R5S1", + "UniProtKB:P01019", + "PR:P01019", + "ENSEMBL:ENSP00000355627", + "ENSEMBL:ENSP00000355627.5", + "ENSEMBL:ENSP00000504866", + "ENSEMBL:ENSP00000504866.1", + "ENSEMBL:ENSP00000505063", + "ENSEMBL:ENSP00000505063.1", + "ENSEMBL:ENSP00000505963", + "ENSEMBL:ENSP00000505963.1", + "ENSEMBL:ENSP00000505985", + "ENSEMBL:ENSP00000505985.1", + "UMLS:C2713666", + "UMLS:C3714928", + "UMLS:C4521302" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "AGT", + "AGT gene", + "B0ZBE2_HUMAN Angiotensinogen (trembl)", + "B2R5S1_HUMAN Angiotensinogen (trembl)", + "ANGT_HUMAN Angiotensinogen (sprot)", + "angiotensinogen (human)", + "AGT protein, human", + "Angiotensin-2, Human", + "Angiotensin-1, human" + ] + } + ] + }, + "NCBIGene:7077": { + "categories": [ + "biolink:Gene" + ], + "name": "TIMP2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:7077", + "ENSEMBL:ENSG00000035862", + "HGNC:11821", + "OMIM:188825", + "UMLS:C1336629", + "UniProtKB:A0A140VK57", + "UniProtKB:P16035", + "PR:P16035", + "ENSEMBL:ENSP00000262768", + "ENSEMBL:ENSP00000262768.6", + "UMLS:C3178655" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TIMP2", + "TIMP2 gene", + "A0A140VK57_HUMAN Testicular secretory protein Li 57 (trembl)", + "TIMP2_HUMAN Metalloproteinase inhibitor 2 (sprot)", + "metalloproteinase inhibitor 2 (human)", + "TIMP2 protein, human" + ] + } + ] + }, + "NCBIGene:2056": { + "categories": [ + "biolink:Gene" + ], + "name": "EPO", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2056", + "ENSEMBL:ENSG00000130427", + "HGNC:3415", + "OMIM:133170", + "UMLS:C1366564", + "UniProtKB:G9JKG7", + "UniProtKB:P01588", + "PR:P01588", + "ENSEMBL:ENSP00000252723", + "ENSEMBL:ENSP00000252723.2", + "UMLS:C2976467" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "EPO", + "EPO gene", 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"UMLS:C3491277", + "UniProtKB:Q546G0" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CD33", + "CD33 gene", + "CD33_HUMAN Myeloid cell surface antigen CD33 (sprot)", + "myeloid cell surface antigen CD33 (human)", + "CD33 protein, human", + "Q546G0_HUMAN CD33 antigen (Gp67) (trembl)" + ] + } + ] + }, + "NCBIGene:1524": { + "categories": [ + "biolink:Gene" + ], + "name": "CX3CR1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1524", + "ENSEMBL:ENSG00000168329", + "HGNC:2558", + "OMIM:601470", + "UMLS:C1439296", + "UniProtKB:P49238", + "PR:P49238", + "UMLS:C1143767" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "CX3CR1", + "CX3CR1 gene", + "CX3C1_HUMAN CX3C chemokine receptor 1 (sprot)", + "CX3C chemokine receptor 1 (human)", + "CX3CR1 protein, human" + ] + } + ] + }, + "NCBIGene:6667": { + "categories": [ + "biolink:Gene" + ], + "name": "SP1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6667", + "ENSEMBL:ENSG00000185591", + "HGNC:11205", + "OMIM:189906", + "UMLS:C1335858", + "UniProtKB:P08047", + "PR:P08047", + "UMLS:C1308232" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SP1", + "SP1 gene", + "SP1_HUMAN Transcription factor Sp1 (sprot)", + "transcription factor Sp1 (human)", + "Sp1 protein, human" + ] + } + ] + }, + "NCBIGene:7442": { + "categories": [ + "biolink:Gene" + ], + "name": "TRPV1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:7442", + "ENSEMBL:ENSG00000196689", + "HGNC:12716", + "OMIM:602076", + "UMLS:C1421467", + "UniProtKB:Q8NER1", + "PR:Q8NER1" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TRPV1", + "TRPV1 gene", + "TRPV1_HUMAN Transient receptor potential cation channel subfamily V member 1 (sprot)", + "transient receptor potential cation channel subfamily V member 1 (human)" + ] + } + ] + }, + "NCBIGene:1831": { + 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"LOX12_HUMAN Polyunsaturated fatty acid lipoxygenase ALOX12 (sprot)", + "polyunsaturated fatty acid lipoxygenase ALOX12 (human)", + "Arachidonate 12-Lipoxygenase, 12S-Type" + ] + } + ] + }, + "NCBIGene:10318": { + "categories": [ + "biolink:Gene" + ], + "name": "TNIP1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:10318", + "ENSEMBL:ENSG00000145901", + "HGNC:16903", + "OMIM:607714", + "UMLS:C1424624", + "UniProtKB:A0A0A0MRZ4", + "ENSEMBL:ENSP00000374029", + "ENSEMBL:ENSP00000374029.3", + "UniProtKB:A8K4N4", + "UniProtKB:B7Z8K2", + "UniProtKB:Q15025", + "PR:Q15025", + "UMLS:C4724734" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TNIP1", + "TNIP1 gene", + "A0A0A0MRZ4_HUMAN TNFAIP3 interacting protein 1 (trembl)", + "A8K4N4_HUMAN cDNA FLJ77844, highly similar to Homo sapiens TNFAIP3 interacting protein 1, mRNA (trembl)", + "B7Z8K2_HUMAN cDNA FLJ61022, highly similar to Nef-associated factor 1 (trembl)", + "TNIP1_HUMAN TNFAIP3-interacting protein 1 (sprot)", + "TNFAIP3-interacting protein 1 (human)", + "TNFAIP3-Interacting Protein 1" + ] + } + ] + }, + "NCBIGene:2936": { + "categories": [ + "biolink:Gene" + ], + "name": "GSR", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2936", + "ENSEMBL:ENSG00000104687", + "HGNC:4623", + "OMIM:138300", + "UMLS:C1415326", + "UniProtKB:P00390", + "PR:P00390", + "UMLS:C4721873", + "UniProtKB:V9HW90" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "GSR", + "GSR gene", + "GSHR_HUMAN Glutathione reductase, mitochondrial (sprot)", + "glutathione reductase, mitochondrial (human)", + "Glutathione Reductase, Mitochondrial, Human", + "V9HW90_HUMAN Glutathione reductase (trembl)" + ] + } + ] + }, + "NCBIGene:6283": { + "categories": [ + "biolink:Gene" + ], + "name": "S100A12", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6283", + "ENSEMBL:ENSG00000163221", + "HGNC:10489", + "OMIM:603112", + "UMLS:C1335796", + "UniProtKB:P80511", + "PR:P80511", + "ENSEMBL:ENSP00000357726", + "ENSEMBL:ENSP00000357726.3", + "UMLS:C0389073" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "S100A12", + "S100A12 gene", + "S10AC_HUMAN Protein S100-A12 (sprot)", + "protein S100-A12 (human)", + "S100A12 protein, human" + ] + } + ] + }, + "NCBIGene:355": { + "categories": [ + "biolink:Gene" + ], + "name": "FAS", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:355", + "ENSEMBL:ENSG00000026103", + "HGNC:11920", + "OMIM:134637", + "UMLS:C1539477", + "UniProtKB:K9J972", + "ENSEMBL:ENSP00000347979", + "ENSEMBL:ENSP00000347979.3", + "UniProtKB:P25445", + "PR:P25445", + "UMLS:C1454645", + "UniProtKB:Q59FU8", + "ENSEMBL:ENSP00000509810", + "ENSEMBL:ENSP00000509810.1" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "FAS", + "FAS gene", + "K9J972_HUMAN FAS receptor variant 9 (trembl)", + "TNR6_HUMAN Tumor necrosis factor receptor superfamily member 6 (sprot)", + "tumor necrosis factor receptor superfamily member 6 (human)", + "FAS protein, human", + "Q59FU8_HUMAN Tumor necrosis factor receptor superfamily member 6 (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:6892": { + "categories": [ + "biolink:Gene" + ], + "name": "TAPBP", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6892", + "ENSEMBL:ENSG00000206208", + "HGNC:11566", + "OMIM:601962", + "UMLS:C1420583", + "UniProtKB:A0A024RCT1", + "UniProtKB:A0A0A0MSV9", + "UniProtKB:A0A0A0MT98", + "UniProtKB:O15533", + "PR:O15533", + "ENSEMBL:ENSP00000363700", + "ENSEMBL:ENSP00000363700.3", + "ENSEMBL:ENSP00000372684", + "ENSEMBL:ENSP00000372684.4", + "ENSEMBL:ENSP00000372685", + "ENSEMBL:ENSP00000372685.2", + "ENSEMBL:ENSP00000378546", + "ENSEMBL:ENSP00000378546.3", + "ENSEMBL:ENSP00000402087", + "ENSEMBL:ENSP00000402087.1", + "ENSEMBL:ENSP00000407195", + "ENSEMBL:ENSP00000407195.2", + "UMLS:C1313790" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TAPBP", + "TAPBP gene", + "A0A024RCT1_HUMAN TAP binding protein (Tapasin), isoform CRA_c (trembl)", + "A0A0A0MSV9_HUMAN Tapasin (trembl)", + "A0A0A0MT98_HUMAN Tapasin (trembl)", + "TPSN_HUMAN Tapasin (sprot)", + "tapasin (human)", + "TAPBP protein, human" + ] + } + ] + }, + "NCBIGene:473": { + "categories": [ + "biolink:Gene" + ], + "name": "RERE", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:473", + "ENSEMBL:ENSG00000142599", + "HGNC:9965", + "OMIM:605226", + "UMLS:C1419345", + "UniProtKB:Q9P2R6", + "PR:Q9P2R6" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "RERE", + "RERE gene", + "RERE_HUMAN Arginine-glutamic acid dipeptide repeats protein (sprot)", + "arginine-glutamic acid dipeptide repeats protein (human)" + ] + } + ] + }, + "NCBIGene:10371": { + "categories": [ + "biolink:Gene" + ], + "name": "SEMA3A", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:10371", + "ENSEMBL:ENSG00000075213", + "HGNC:10723", + "OMIM:603961", + "UMLS:C1419942", + "UniProtKB:Q14563", + "PR:Q14563", + "ENSEMBL:ENSP00000265362", + "ENSEMBL:ENSP00000265362.3", + "ENSEMBL:ENSP00000415260", + "ENSEMBL:ENSP00000415260.1" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SEMA3A", + "SEMA3A gene", + "SEM3A_HUMAN Semaphorin-3A (sprot)", + "semaphorin-3A (human)" + ] + } + ] + }, + "NCBIGene:7874": { + "categories": [ + "biolink:Gene" + ], + "name": "USP7", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:7874", + "ENSEMBL:ENSG00000187555", + "HGNC:12630", + "OMIM:602519", + "UMLS:C1421408", + "UniProtKB:B7Z855", + "UniProtKB:B7ZAX6", + "UniProtKB:Q6U8A4", + "UniProtKB:Q93009", + "PR:Q93009", + "UMLS:C1142946" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "USP7", + "USP7 gene", + "B7Z855_HUMAN Ubiquitin carboxyl-terminal hydrolase 7 (trembl)", + "B7ZAX6_HUMAN Ubiquitin carboxyl-terminal hydrolase 7 (trembl)", + "Q6U8A4_HUMAN Ubiquitin carboxyl-terminal hydrolase 7 (Fragment) (trembl)", + "UBP7_HUMAN Ubiquitin carboxyl-terminal hydrolase 7 (sprot)", + "ubiquitin carboxyl-terminal hydrolase 7 (human)", + "USP7 protein, human" + ] + } + ] + }, + "NCBIGene:57410": { + "categories": [ + "biolink:Gene" + ], + "name": "SCYL1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:57410", + "ENSEMBL:ENSG00000142186", + "HGNC:14372", + "OMIM:607982", + "UMLS:C1422597", + "UniProtKB:Q96KG9", + "PR:Q96KG9" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SCYL1", + "SCYL1 gene", + "SCYL1_HUMAN N-terminal kinase-like protein (sprot)", + "N-terminal kinase-like protein (human)" + ] + } + ] + }, + "NCBIGene:64129": { + "categories": [ + "biolink:Gene" + ], + "name": "TINAGL1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:64129", + "ENSEMBL:ENSG00000142910", + "HGNC:19168", + "OMIM:616064", + "UMLS:C1823280", + "UniProtKB:F6SDV2", + "ENSEMBL:ENSP00000445392", + "ENSEMBL:ENSP00000445392.2", + "UniProtKB:Q9GZM7", + "PR:Q9GZM7", + "UMLS:C4761441" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TINAGL1", + "TINAGL1 gene", + "F6SDV2_HUMAN Tubulointerstitial nephritis antigen like 1 (trembl)", + "TINAL_HUMAN Tubulointerstitial nephritis antigen-like (sprot)", + "tubulointerstitial nephritis antigen-like (human)", + "Tubulointerstitial Nephritis Antigen-Like, Human" + ] + } + ] + }, + "NCBIGene:5266": { + "categories": [ + "biolink:Gene" + ], + "name": "PI3", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5266", + "ENSEMBL:ENSG00000124102", + "HGNC:8947", + "OMIM:182257", + "UMLS:C1418549", + "UniProtKB:P19957", + "PR:P19957", + "ENSEMBL:ENSP00000243924", + "ENSEMBL:ENSP00000243924.3", + "UMLS:C0142580" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PI3", + "PI3 gene", + "ELAF_HUMAN Elafin (sprot)", + "elafin (human)", + "PI3 protein, human" + ] + } + ] + }, + "NCBIGene:6876": { + "categories": [ + "biolink:Gene" + ], + "name": "TAGLN", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:6876", + "ENSEMBL:ENSG00000149591", + "HGNC:11553", + "OMIM:600818", + "UMLS:C1420578", + "UniProtKB:Q01995", + "PR:Q01995", + "ENSEMBL:ENSP00000278968", + "ENSEMBL:ENSP00000278968.6", + "ENSEMBL:ENSP00000376678", + "ENSEMBL:ENSP00000376678.4", + "ENSEMBL:ENSP00000431941", + "ENSEMBL:ENSP00000431941.1", + "ENSEMBL:ENSP00000432054", + "ENSEMBL:ENSP00000432054.1", + "ENSEMBL:ENSP00000432282", + "ENSEMBL:ENSP00000432282.1", + "UMLS:C1429758", + "UniProtKB:Q5U0D2" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "TAGLN", + "TAGLN gene", + "TAGL_HUMAN Transgelin (sprot)", + "transgelin (human)", + "TAGLN protein, human", + "Q5U0D2_HUMAN Transgelin (trembl)" + ] + } + ] + }, + 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"ENSEMBL:ENSG00000102393", + "HGNC:4296", + "OMIM:300644", + "UMLS:C1439334", + "UniProtKB:P06280", + "PR:P06280", + "ENSEMBL:ENSP00000218516", + "ENSEMBL:ENSP00000218516.4", + "UniProtKB:Q53Y83" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "GLA", + "GLA gene", + "AGAL_HUMAN Alpha-galactosidase A (sprot)", + "alpha-galactosidase A (human)", + "Q53Y83_HUMAN Alpha-galactosidase (trembl)" + ] + } + ] + }, + "NCBIGene:240": { + "categories": [ + "biolink:Gene" + ], + "name": "ALOX5", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:240", + "ENSEMBL:ENSG00000012779", + "HGNC:435", + "OMIM:152390", + "UMLS:C1412361", + "UniProtKB:P09917", + "PR:P09917", + "UMLS:C3711265" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ALOX5", + "ALOX5 gene", + "LOX5_HUMAN Polyunsaturated fatty acid 5-lipoxygenase (sprot)", + "polyunsaturated fatty acid 5-lipoxygenase (human)", + "ALOX5 protein, human" + ] + } + ] + }, + "NCBIGene:54658": { + "categories": [ + "biolink:Gene" + ], + "name": "UGT1A1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:54658", + "ENSEMBL:ENSG00000241635", + "HGNC:12530", + "OMIM:191740", + "UMLS:C0537026", + "UniProtKB:P22309", + "PR:P22309", + "UMLS:C1567723", + "UniProtKB:Q5DT03" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "UGT1A1", + "UGT1A1 gene", + "UD11_HUMAN UDP-glucuronosyltransferase 1A1 (sprot)", + "UDP-glucuronosyltransferase 1A1 (human)", + "UGT1A1 protein, human", + "Q5DT03_HUMAN UDP-glucuronosyltransferase (trembl)" + ] + } + ] + }, + "NCBIGene:1786": { + "categories": [ + "biolink:Gene" + ], + "name": "DNMT1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:1786", + "ENSEMBL:ENSG00000130816", + "HGNC:2976", + "OMIM:126375", + "UMLS:C1414121", + "UniProtKB:I6L9H2", + "UniProtKB:P26358", + "PR:P26358", + "UMLS:C4548354", + "UniProtKB:Q59FP7" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "DNMT1", + "DNMT1 gene", + "I6L9H2_HUMAN DNA (cytosine-5)-methyltransferase (trembl)", + "DNMT1_HUMAN DNA (cytosine-5)-methyltransferase 1 (sprot)", + "DNA (cytosine-5)-methyltransferase 1 (human)", + "DNMT1 protein, human", + "Q59FP7_HUMAN DNA (cytosine-5)-methyltransferase 1 (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:3832": { + "categories": [ + "biolink:Gene" + ], + "name": "KIF11", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3832", + "ENSEMBL:ENSG00000138160", + "HGNC:6388", + "OMIM:148760", + "UMLS:C1416693", + "UniProtKB:P52732", + "PR:P52732", + "ENSEMBL:ENSP00000260731", + "ENSEMBL:ENSP00000260731.3", + "UMLS:C1173400" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "KIF11", + "KIF11 gene", + "KIF11_HUMAN Kinesin-like protein KIF11 (sprot)", + "kinesin-like protein KIF11 (human)", + "KIF11 protein, human" + ] + } + ] + }, + "NCBIGene:5345": { + "categories": [ + "biolink:Gene" + ], + "name": "SERPINF2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5345", + "ENSEMBL:ENSG00000167711", + "HGNC:9075", + "OMIM:613168", + "UMLS:C1418648", + "UniProtKB:P08697", + "PR:P08697", + "ENSEMBL:ENSP00000479005", + "ENSEMBL:ENSP00000479005.1", + "ENSEMBL:ENSP00000481874", + "ENSEMBL:ENSP00000481874.1", + "UMLS:C2713682" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "SERPINF2", + "SERPINF2 gene", + "A2AP_HUMAN Alpha-2-antiplasmin (sprot)", + "alpha-2-antiplasmin (human)", + "SERPINF2 protein, human" + ] + } + ] + }, + "NCBIGene:3156": { + "categories": [ + "biolink:Gene" + ], + "name": "HMGCR", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:3156", + "ENSEMBL:ENSG00000113161", + "HGNC:5006", + "OMIM:142910", + "UMLS:C1415615", + "UniProtKB:A0A024RAP2", + "UniProtKB:P04035", + "PR:P04035", + "UMLS:C2975999" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "HMGCR", + "HMGCR gene", + "A0A024RAP2_HUMAN 3-hydroxy-3-methylglutaryl coenzyme A reductase (trembl)", + "HMDH_HUMAN 3-hydroxy-3-methylglutaryl-coenzyme A reductase (sprot)", + "3-hydroxy-3-methylglutaryl-coenzyme A reductase (human)", + "HMGCR protein, human" + ] + } + ] + }, + "NCBIGene:302": { + "categories": [ + "biolink:Gene" + ], + "name": "ANXA2", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:302", + "ENSEMBL:ENSG00000182718", + "HGNC:537", + "OMIM:151740", + "UMLS:C1412420", + "UniProtKB:A0A024R5Z7", + "UniProtKB:H0YL33", + "ENSEMBL:ENSP00000453039", + "ENSEMBL:ENSP00000453039.2", + "ENSEMBL:ENSP00000453869", + "ENSEMBL:ENSP00000453869.2", + "UniProtKB:P07355", + "PR:P07355", + "UMLS:C1175494" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ANXA2", + "ANXA2 gene", + "A0A024R5Z7_HUMAN Annexin (trembl)", + "H0YL33_HUMAN Annexin (trembl)", + "ANXA2_HUMAN Annexin A2 (sprot)", + "annexin A2 (human)", + "ANXA2 protein, human" + ] + } + ] + }, + "NCBIGene:5328": { + "categories": [ + "biolink:Gene" + ], + "name": "PLAU", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:5328", + "ENSEMBL:ENSG00000122861", + "HGNC:9052", + "OMIM:191840", + "UMLS:C1335224", + "UniProtKB:A0A024QZM9", + "UniProtKB:B4DNJ4", + "UniProtKB:P00749", + "PR:P00749", + "UMLS:C4548357", + "UniProtKB:Q59GZ8" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "PLAU", + "PLAU gene", + "A0A024QZM9_HUMAN Plasminogen activator, urokinase, isoform CRA_a (trembl)", + "B4DNJ4_HUMAN cDNA FLJ53742, highly similar to Urokinase-type plasminogen activator (trembl)", + "UROK_HUMAN Urokinase-type plasminogen activator (sprot)", + "urokinase-type plasminogen activator (human)", + "PLAU protein, human", + "Q59GZ8_HUMAN Urokinase plasminogen activator preproprotein variant (Fragment) (trembl)" + ] + } + ] + }, + "NCBIGene:2150": { + "categories": [ + "biolink:Gene" + ], + "name": "F2RL1", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2150", + "ENSEMBL:ENSG00000164251", + "HGNC:3538", + "OMIM:600933", + "UMLS:C1414506", + "UniProtKB:P55085", + "PR:P55085", + "ENSEMBL:ENSP00000296677", + "ENSEMBL:ENSP00000296677.4" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "F2RL1", + "F2RL1 gene", + "PAR2_HUMAN Proteinase-activated receptor 2 (sprot)", + "proteinase-activated receptor 2 (human)" + ] + } + ] + }, + "NCBIGene:2118": { + "categories": [ + "biolink:Gene" + ], + "name": "ETV4", + "attributes": [ + { + "attribute_type_id": "biolink:xref", + "value": [ + "NCBIGene:2118", + "ENSEMBL:ENSG00000175832", + "HGNC:3493", + "OMIM:600711", + "UMLS:C1333362", + "UniProtKB:P43268", + "PR:P43268", + "UMLS:C1333479" + ] + }, + { + "attribute_type_id": "biolink:synonym", + "value": [ + "ETV4", + "ETV4 gene", + "ETV4_HUMAN ETS translocation variant 4 (sprot)", + "ETS translocation variant 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synaptic genes, increasing their expression; (4) c-Abl induces tyrosine phosphorylation of HDAC2, a posttranslational modification, affecting both its stability and repression activity; and (5) treatment with Imatinib decreases HDAC2 levels in a transgenic mice model of AD.", + "The tyrosine kinase inhibitor imatinib, which inhibits PDGFR and c-Abl, and which has previously been reported to counteract beta-cell death and diabetes, has been suggested to reduce atherosclerosis by inhibiting PDGFR-induced LRP1 phosphorylation.", + "In vitro treatment of human CML cell lines with imatinib or siRNA directed against BCR-ABL significantly reduced BCR-ABL while increasing CCN3 expression.", + "The tyrosine kinase inhibitors imatinib, nilotinib, and dasatinib block the BCR-ABL protein and prevent activation of the transformation pathways.", + "The tyrosine kinase inhibitor imatinib (STI571, Glivec) blocks the activity of the BCR/ABL oncogene and induces hematologic remissions in the majority of patients with chronic myeloid leukemia (CML).", + "Based on these observations, imatinib was developed as a specific inhibitor for the Bcr-Abl protein tyrosine kinase.", + "Imatinib also inhibits the c-abl, platelet derived growth factor receptor (PDGFR), abl-related gene and stem cell factor receptor, c-kit, protein tyrosine kinases.", + "In obstructed kidneys, PAK2 and c-abl activity were increased but only c-abl activation was blocked by imatinib.", + "Imatinib is a molecularly targeted therapy that inhibits the oncogenic fusion protein BCR-ABL, the tyrosine kinase involved in the pathogenesis of chronic myelogenous leukemia (CML).", + "Thus, cardiotoxicity is an unanticipated side effect of inhibition of c-Abl by imatinib.", + "Imatinib also blocks c-Abl, a physiological tyrosine kinase activated by a variety of stress signals including damaged DNA.", + "Inhibition of c-Abl caused an enhanced irradiation-induced mutation frequency and slowdown of DNA repair, whereas imatinib was ineffective in cells expressing a T315I variant of c-Abl.", + "Imatinib also inhibits the c-abl, platelet-derived growth factor (PDGF) receptor, abl-related gene (ARG) and stem-cell factor (SCF) receptor tyrosine kinases, and has been used clinically to inhibit the growth of malignant cells in patients with CML and gastrointestinal stromal tumors (GISTs).", + "Pharmacological inhibition of c-Abl by Imatinib (STI571) protects the ovarian reserve from the toxic effect of cisplatin.", + "Considering the high morbidity associated with cGvHD, the lack of efficient molecular therapies for clinical use, and first positive signals from uncontrolled studies of imatinib, combined inhibition of c-Abl and PDGFR might be a promising future strategy for treatment of sclerodermatous cGvHD.", + "In marked contrast, the alpha6 integrin(high+)/CD44(+) cells were sensitive to apoptosis induced by the cross-linking agent cisplatin, and imatinib inhibition of c-Abl blocked the ability of cisplatin to kill alpha6 integrin(high+)/CD44(+) cells.", + "In this study, we show that inhibition of Bcr-Abl oncogene by imatinib induces down-regulation of Jab1 in Bcr-Abl-positive K562, Ku812, and MEG01 leukemia cells suggesting Bcr-Abl may regulate Jab1 expression.", + "Imatinib is a receptor tyrosine kinase inhibitor that blocks the activity of c-Abl, c-Kit, and PDGF receptors.", + "Chronic myeloid leukemia has changed its natural history thanks to imatinib and dasatinib, both of which inhibit the intracellular bcr/abl protein derived from the alteration in the Philadelphia chromosome.", + "Specific inhibition of c-Abl by imatinib, siRNA, or c-Abl kinase dead drastically reduces high NaCl-induced TonEBP/OREBP activity by reducing its nuclear location and transactivating activity. c-Abl associates with TonEBP/OREBP (coimmunoprecipitation) and phosphorylates TonEBP/OREBP-Y143 both in cell and in vitro.", + "The combination of imatinib and CAI also down-regulated bcr-abl protein levels.", + "There is a controversy in literature as to whether c-Abl is crucial for the induction of TAp63-mediated apoptosis and whether that inhibition of c-Abl with imatinib, which was designed to inhibit the oncogenic kinase BCR-ABL and c-kit, protects oocytes from chemotherapy-induced apoptosis in mice.", + "We therefore aimed to explore whether genomic damage induced by chemotherapy drug cisplatin activates c-Abl along with TAp63 and the inhibition of c-Abl with imatinib prevents cisplatin-induced oocyte death and follicle loss in human ovary.", + "RESULTS: Removal of imatinib from culture medium led to a decrease in Bcr-Abl protein expression by Day 5, which was sustained for > or = 3 weeks of imatinib deprivation.", + "c-Abl co-immunoprecipitated with SHIP2 and its binding to SHIP2 was largely reduced by imatinib but not by sunitinib.", + "CONCLUSIONS/INTERPRETATION: Imatinib inhibition of c-Abl in beta cells decreases SHIP2 activity, which results in enhanced signalling downstream of PI3 kinase.", + "Imatinib inhibits c-Abl, c-Kit, and PDGFRs.", + "Imatinib and Stattic were used to inhibit c-Abl and STAT3 activation, respectively.", + "More importantly, we found that c-Abl inhibition by Imatinib significantly inhibits the interaction between APP and BACE1.", + "Imatinib also inhibited differentiation of fibrocytes via suppression of c-Abl activity that was essential for the differentiation of monocytes to fibrocytes.", + "Cotreatment of neferine and imatinib significantly decreased the expression of BCR-ABL protein and its molecular chaperone heat shock protein 90 (Hsp90) mRNA and protein levels, and further decreased phospho-extracellular regulated protein kinase 1/2 (p-Erk1/2) and myeloid cell leukemia (Mcl-1) expression.", + "Collectively, our data show that combination of chidamide and imatinib synergistically targets tyrosine kinase inhibitor (TKI) -resistant BC-CML cells via inhibition of Bcr-Abl and beta-catenin signaling, suggesting that this combination has the potential for treating TKI-resistant CML and improving clinical outcomes of BC-CML patients.", + "In the present study, we by undertaking a direct comparison of inducible NOS (iNOS) status in neutrophils from healthy volunteers, newly diagnosed, imatinib responder, and resistant CML patients as well as by conducting in vitro studies in K562 cells demonstrated that inhibition of BCR-ABL by imatinib or siRNA significantly enhanced NO generation and iNOS expression.", + "Novel alpha-Aminophosphonates of imatinib Intermediate: Synthesis, anticancer Activity, human Abl tyrosine kinase Inhibition, ADME and toxicity prediction.", + "Imatinib is one of the most effective therapeutic strategies to inhibit the BCR-ABL tyrosine Kinase in patients with CML, but resistance is increasingly encountered.", + "Besides, compound 6l enhanced apoptosis in CML cells with 52.4 % when compared with imatinib (61.8 %) and inhibited Abl TK significantly with an IC 50 value of 13.04 +/- 2.48 MUM in a large panel of kinases accentuating Abl TK-mediated apoptosis of compound 6l in CML cells.", + "Selective inhibition of c-Abl by Imatinib also showed anti-inflammatory activity marked with suppressed levels of NF-kB and pro-inflammatory mediators (TNF-alpha, IL-1beta, and IL-6) suggesting the neuroprotective effect of Imatinib same as valproate (standard drug) in epilepsy.", + "Discovery of imatinib mesylate (IM) as the targeted BCR-ABL protein tyrosine kinase inhibitor (TKI) has resulted in its use as the frontline therapy for chronic myeloid leukemia (CML) across the world.", + "The tyrosine kinase inhibitor imatinib mesylate (formerly STI571, [Gleevec]; Novartis Pharmaceuticals Corp, East Hanover, NJ) blocks activity of the Bcr-Abl oncoprotein, and was recently approved for several indications in the treatment of chronic myeloid leukemia.", + "The tyrosine kinase inhibitor imatinib mesylate (formerly STI571, Gleevec, Novartis Pharmaceuticals Corp, East Hanover, NJ) blocks activity of the Bcr-Abl oncoprotein and the cell surface tyrosine kinase receptor c-Kit, and as such was recently approved for several indications in the treatment on chronic myeloid leukemia and gastrointestinal stromal tumors.", + "More recently, the clinical success of imatinib mesylate (STI571), potent competitive inhibitor of the Bcr/Abl protein tyrosine kinase, in the treatment of CML has focused enthusiasm toward molecular targeted therapy for the hematological malignancies.", + "Inhibition of c-abl activity with imatinib mesylate ameliorates experimental renal fibrosis in rats.", + "Imatinib mesylate has become a therapy of interest for the treatment of systemic sclerosis because of its ability to inhibit c-Abl and platelet-derived growth factor receptor, tyrosine kinases involved in profibrotic pathways.", + "Imatinib mesylate, a BCR/ABL fusion protein inhibitor, is the first-line treatment against chronic myelogenous leukemia.", + "Imatinib mesylate, commercially known as Gleevec/Glivec, is the first targeted anticancer drug that inhibits activity of the tyrosine kinases, c-ABL, c-KIT, and PDGFR.", + "The authors recently have shown that a tyrosine kinase inhibitor, imatinib mesylate, induces clearance of PrP(Sc) via specific inhibition of c-Abl in prion-infected cell culture models.", + "Imatinib mesylate is a specific inhibitor of the Bcr-Abl protein tyrosine kinase that competes with ATP for its specific binding site in the kinase domain.", + "We explored the effects of imatinib mesylate, an inhibitor of Bcr-Abl protein used in front-line CML therapy, on the adhesivity of JURL-MK1 cells to fibronectin and searched for underlying changes in the cell proteome.", + "PURPOSE: The tyrosine kinase inhibitor imatinib mesylate inhibits the function of the Bcr-Abl oncoprotein associated with Philadelphia-positive chronic myelogenous leukemia (CML).", + "BACKGROUND: Imatinib mesylate (Gleevec) is a selective Bcr-Abl protein tyrosine-kinase inhibitor, and it also inhibits the receptor tyrosine kinases for stem cell factor (c-kit) and platelet-derived growth factor (PDGFR).", + "PURPOSE: Imatinib mesylate (Imatinib), clinically employed for chronic myeloid leukemia and gastrointestinal stromal tumors, is a selective inhibitor of the tyrosine kinases, c-abl, c-kit and PDGFRs.", + "BACKGROUND: Chronic myeloid leukemia is associated with a BCR/ABL oncoprotein inhibited by imatinib mesylate, the first tyrosine kinase inhibitor.", + "INTRODUCTION: Imatinib mesylate, an orally active inhibitor of the c-abl, c-kit, and platelet-derived growth factor receptor (PDGFR) tyrosine kinases, is in clinical use for the treatment of chronic myeloid leukemia (CML) and gastrointestinal stromal cell tumors.", + "First-line therapy for CML consists of treatment with imatinib mesylate, which selectively inhibits the BCR-ABL protein by competing for its ATP-binding site.", + "Combined Therapy of ATRA and Imatinib Mesylate Decreases BCR-ABL and ABCB1/MDR1 Expression Through Cellular Differentiation in a Chronic Myeloid Leukemia Model.", + "Therefore, K-562 cells transfected with RNAifect deliver Bcr-Abl siRNA efficiently and the Bcr-Abl siRNA decreased the IC(50) of Gleevec required to inhibit the high levels of Bcr-Abl protein found in K-562 cells.", + "Suppression of c-Abl or PKCdelta expression using SiRNAs impaired PARP cleavage, Gleevec and/or rottlerin inhibited the induction of the subG1 phase and the increase of reactive oxygen species level.", + "Gleevec is a relatively specific inhibitor of c-Abl, a tyrosine kinase that can play a role in the regulation Rad51.", + "These effects could not be mirrored by the use of Gleevec, a potent inhibitor of c-Abl and PDGFR kinases that are also inhibited by PP2.", + "This downregulation can be explained by Gleevec's inhibition of c-Abl, which destabilizes p63." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-semmeddb" + ] + } + ] + }, + "32b9232e40c5846d3deb1a8b9f1d82bb": { + "predicate": "biolink:affects", + "subject": "PUBCHEM.COMPOUND:5291", + "object": "NCBIGene:1436", + "qualifiers": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "activity_or_abundance" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + }, + { + "qualifier_type_id": "biolink:qualified_predicate", + "qualifier_value": "biolink:causes" + } + ], + "attributes": [ + { + "attribute_type_id": "biolink:publications", + "value": [ + "PMID:16449525", + "PMID:15917650", + "PMID:15637141", + "PMID:24718867" + ], + "value_type_id": "linkml:Uriorcurie" + }, + { + "attribute_type_id": "biolink:supporting_text", + "value": [ + "Since we have previously demonstrated inhibition of c-fms by imatinib, we examined the effect of imatinib on OC formation and activity.", + "Inhibition of c-fms by imatinib: expanding the spectrum of treatment.", + "Imatinib was also found to inhibit M-CSF-induced proliferation of a cytokine-dependent cell line, further supporting the hypothesis that imatinib affects the growth and development of monocyte and/or macrophages through inhibition of c-fms signaling.", + "However, in vivo studies clearly demonstrate that compared with imatinib, PLX3397 results in sustained blockade of c-Kit, c-Fms, and PDGFRbeta, resulting in significant suppression of tumor growth." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-semmeddb" + ] + } + ] + }, + "4e6dfeb6a4232e289223ae4a2b3b7489": { + "predicate": "biolink:affects", + "subject": "PUBCHEM.COMPOUND:5291", + "object": "NCBIGene:3815", + "qualifiers": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "activity_or_abundance" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + }, + { + "qualifier_type_id": "biolink:qualified_predicate", + "qualifier_value": "biolink:causes" + } + ], + "attributes": [ + { + "attribute_type_id": "biolink:publications", + "value": [ + "PMID:16629079", + "PMID:16498290", + "PMID:12672043", + "PMID:12481435", + "PMID:18648736", + "PMID:15123459", + "PMID:17546049", + "PMID:17032555", + "PMID:17101065", + "PMID:17298867", + "PMID:21561667", + "PMID:22652566", + "PMID:22153896", + "PMID:21768379", + "PMID:28403213", + "PMID:26779374", + "PMID:26056505", + "PMID:29100343", + "PMID:29196126", + "PMID:16242052", + "PMID:19383029", + "PMID:30523507", + "PMID:29704617", + "PMID:20736294", + "PMID:20883053", + "PMID:25684098", + "PMID:12952023", + "PMID:14760098", + "PMID:18559612", + "PMID:24434430", + "PMID:28315973", + "PMID:19047099", + "PMID:16619531", + "PMID:18413817", + "PMID:27563456", + "PMID:20033343", + "PMID:28514613", + "PMID:12824897", + "PMID:15853160", + "PMID:15471556", + "PMID:15188667", + "PMID:16397263", + "PMID:15070706", + "PMID:16910417", + "PMID:19193436", + "PMID:26428235", + "PMID:16740725", + "PMID:15372471", + "PMID:18553235", + "PMID:26576593", + "PMID:12912938", + "PMID:16572634" + ], + "value_type_id": "linkml:Uriorcurie" + }, + { + "attribute_type_id": "biolink:supporting_text", + "value": [ + "The treatment options have evolved rapidly with the discovery of imatinib (Gleevec) that selectively inhibits KIT.", + "The treatment of localized GIST is surgical resection, which must be complete; that of advanced or unresectable GIST is based on the use of a targeted therapy, imatinib, which is a pharmacological antagonist of the KIT protein.", + "Imatinib could inhibit the KIT, MAP and Akt phosphorylation of all the transfectants but had a weaker effect on KIT(820Tyr).", + "In signaling studies, addition of stem cell factor (SCF) induced phosphorylation of ERK and Akt by WTKit, and ERK, Akt and STAT3 by V560GKit, which were all blocked by Imatinib.", + "When we reported gain-of-function mutations of the Kit gene in GISTs, the inhibitory effect of imatinib on KIT was already known.", + "Imatinib is a potent, specific inhibitor of KIT that has demonstrated significant activity and tolerability in the treatment of malignant unresectable or metastatic GIST, inducing tumor shrinkage of 50% or more or stabilizing disease in most patients.", + "Most gastrointestinal stromal tumor (GIST) patients respond to KIT inhibition with imatinib, yet will eventually exhibit resistance.", + "Imatinib, a potent inhibitor of KIT activity, is now standard front-line therapy for advanced GIST.", + "Imatinib, a specific inhibitor of the aberrant KIT protein, is an approved, well-tolerated oral drug for the management of metastatic or inoperable GIST.", + "Imatinib is a selective inhibitor of KIT, PDGFR, and ABL tyrosine kinase activity and exerts different anti-tumor effects according to the regions of mutations in c-kit and PDGFR genes.", + "From these findings, imatinib was considered to elicit a clinical response in a canine case of MCT via inhibition of the constitutively activated KIT caused by a c-kit c.1523A>T mutation.", + "In contrast to the single-mutant Kit(V558/+) control mice, treatment of the Kit(V558;T669I/+) mice with either imatinib or dasatinib failed to inhibit oncogenic Kit signaling and GIST growth.", + "This mutation caused ligand-independent phosphorylation of KIT, which was suppressed by imatinib.", + "Imatinib, which disrupts Kit signaling, also abrogated AHR in A/J mice.", + "The drug imatinib, a selective inhibitor of Kit, is used for treatment of mutant Kit-positive cancers.", + "In recent years, imatinib, a PDGFbetaR, ABL and KIT inhibitor, has revolutionized systemic therapy in DFSP.", + "Successful targeting of tyrosine-protein kinase Kit with imatinib, a tyrosine kinase inhibitor, has had a major impact in the survival of patients with GIST in both the adjuvant and metastatic setting.", + "Imatinib inhibited the KIT pathway in imatinib-sensitive GIST-T1 but not GIST-RX1, RX2, and RX4.", + "The drug imatinib, a specific Kit inhibitor, improves the prognosis of metastatic GIST patients, but these patients become resistant to the drug by acquiring secondary mutations in the Kit kinase domain.", + "Because imatinib could also inhibit the activity of KIT, a 145-kD transmembrane glycoprotein, and because gastrointestinal stromal tumors (GISTs), the most common mesenchymal tumors of the digestive tract, are characterized by expression of a gain-of-function mutation in KIT, imatinib was used in therapeutic trials of GISTs beginning in 1999.", + "In addition to the inhibitory effect on KIT, imatinib also inhibits the activity of mutant platelet-derived growth factor receptor-alpha (PDGFRalpha) found in a subset of GIST.", + "Most of the constitutively active KIT can be inhibited by imatinib; D816V KIT cannot.", + "Imatinib, a potent inhibitor of mutated KIT, has revolutionized the clinical management of advanced, metastatic GIST.", + "Based upon the X-ray crystallographic structures, imatinib, sunitinib, and ponatinib are Type II Kit inhibitors.", + "Imatinib inhibits Kit and is front-line therapy for GIST.", + "Imatinib binds to and inhibits KIT and platelet-derived growth factor receptor (PDGFR)-alpha tyrosine kinases, interfering with their downstream tumourogenic processes.", + "KIT and ERK were constitutively phosphorylated in both sublines, and their phosphorylation was suppressed by 10 MUM imatinib in rVI-MC1 cells.", + "The mechanism of action is not known, but one possible target for the action of imatinib is inhibition of the KIT receptor on mast cells.", + "We analyzed the in vitro impact of KIT blockade by imatinib in Ewing tumor cell lines.", + "The tyrosine kinase (TK) inhibitor dasatinib is 325-fold more potent against Bcr-Abl TK than imatinib in vitro, significantly inhibiting wild-type KIT and platelet-derived growth factor receptor beta TKs, and is active against cells carrying the mutant KIT-D816V gene.", + "Pharmacologically active concentrations of panobinostat and IM were achieved as evidenced by histone H3 acetylation in blood mononuclear cells in vivo and inhibition of the IM-resistant KIT (D816) mutation in vitro.", + "Exposure to imatinib, a Kit receptor inhibitor, for 3 days from P4 phenocopied the effect of hypoxia on the neonatal pups that resulted in inhibited intestinal motilities and decreased Kit+ ICC numbers.", + "Imatinib targeting of KIT-mutant oncoprotein in melanoma.", + "As resistance to imatinib causes therapy failure, our aim was to develop an in vivo GIST model to evaluate KIT inhibitors and monitor therapy with small animal positron emission tomography (PET).", + "PURPOSE: Gastrointestinal stromal tumors (GIST) are frequently associated with gain-of-function mutations of KIT, which can be inhibited by imatinib both in vitro and in vivo.", + "Sunitinib and regorafenib are approved options for patients progressing on imatinib, but with markedly decreased survival. pazopanib is a broad spectrum TKI targeting KIT, PDGFR and VEGFR receptors and has shown promising activity in phase 2 trials in GIST.", + "Emergence of imatinib resistance associated with downregulation of c-kit expression in recurrent gastrointestinal stromal tumor (GIST): optimal timing of resection.", + "KIT Inhibition by Imatinib in Patients with Severe Refractory Asthma.", + "We conducted a proof-of-principle trial to evaluate the effect of imatinib, a KIT inhibitor, on airway hyperresponsiveness, a physiological marker of severe asthma, as well as on airway mast-cell numbers and activation in patients with severe asthma.", + "Imatinib mesylate also inhibits the mutated KIT observed in most GISTs, and this explains the effectiveness of Imatinib mesylate on GISTs.", + "Imatinib mesylate is an oral drug designed to inhibit the kinase enzyme activity of KIT.", + "Moreover, molecular targeting drugs such as imatinib mesylate (STI571), which is a selective inhibitor of KIT, might be promising agents for the treatment of intracranial germinomas with c-kit gene mutations.", + "Most GISTs respond to imatinib mesylate, which selectively inhibits both KIT and PDGFRA, and is now considered as the standard systemic therapy for advanced GIST.", + "The small-molecule tyrosine kinase inhibitor imatinib mesylate is a potent inhibitor of wild-type (WT) KIT and certain mutant KIT isoforms and has become the standard of care for treating patients with metastatic GIST.", + "Transfection experiments revealed that the mutation caused ligand-independent autophosphorylation of Kit, which was inhibited by the tyrosine kinase inhibitor imatinib mesylate.", + "Most GISTs respond to imatinib mesylate, which selectively inhibits both KIT and PDGFRalpha, and is now considered standard systemic therapy for advanced GIST.", + "Twenty patients with SM were enrolled during 2003-2005 in phase II clinical trial with imatinib mesylate (400mg daily), a KIT inhibitor.", + "Although targeted therapy involving tyrosine kinase inhibitors (TKIs) such as imatinib mesylate is highly effective for gastrointestinal stromal tumor carrying V560G c-kit mutation, it does not show much potential for targeting wild-type KIT (WT-KIT).", + "Imatinib mesylate has been shown to effectively block constitutively active KIT and delay tumor growth.", + "Imatinib mesylate is a tyrosine kinase inhibitor targeting platelet-derived growth factor receptor-beta (PDGFRB), BCR-ABL, and KIT.", + "BACKGROUND: Imatinib mesylate, an inhibitor of KIT, ABL protein, and platelet-derived growth factor receptor alpha (PDGFRalpha) tyrosine kinase, has recently been found to have a dramatic antitumor effect on gastrointestinal stromal tumor (GIST).", + "BACKGROUND: Imatinib mesylate, a potent inhibitor of the KIT and PDGFR tyrosine kinases, is highly effective in the treatment of advanced gastrointestinal stromal tumors (GISTs).", + "Success of inhibition of KIT in malignant gastrointestinal stromal tumors with imatinib mesylate seems mutation-dependent, with a favorable response in the presence of exon 11 mutations.", + "The authors investigated the mutation of c-kit and the expression of its product KIT in IGCTs to identify tumors susceptible to imatinib mesylate, a synthetic agent targeting KIT.", + "BACKGROUND: Gastrointestinal stromal tumours (GIST) predominantly express activating mutations of the KIT tyrosine kinase receptor and are successfully treated with imatinib mesylate, a KIT inhibitor." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-semmeddb" + ] + } + ] + }, + "9c0a8941484a0c617912ce08cb4df25a": { + "predicate": "biolink:affects", + "subject": "PUBCHEM.COMPOUND:5291", + "object": "NCBIGene:5159", + "qualifiers": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "activity_or_abundance" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + }, + { + "qualifier_type_id": "biolink:qualified_predicate", + "qualifier_value": "biolink:causes" + } + ], + "attributes": [ + { + "attribute_type_id": "biolink:publications", + "value": [ + "PMID:24212821", + "PMID:28726812", + "PMID:15492236", + "PMID:18561944", + "PMID:17003785", + "PMID:18472395", + "PMID:17298867", + "PMID:22100984", + "PMID:22833213", + "PMID:28570599", + "PMID:20610572", + "PMID:18216472", + "PMID:24718867", + "PMID:27151023", + "PMID:27563456", + "PMID:23505219", + "PMID:12908555", + "PMID:16373964", + "PMID:17131346", + "PMID:30396570", + "PMID:14760091" + ], + "value_type_id": "linkml:Uriorcurie" + }, + { + "attribute_type_id": "biolink:supporting_text", + "value": [ + "Inhibition of the stromal PDGFr-beta with imatinib activates human PDGFr-beta/PDGF-B signaling loop, silent in untreated xenografts, via an apparent paracrine rescue pathway.", + "We describe a 10-year-old child with a germ-line PDGFRB p.N666H mutation who responded to the tyrosine kinase inhibitor imatinib by inhibition of PDGFRB.MethodsThe impact of p.N666H on PDGFRB function and sensitivity to imatinib was studied in cell culture.ResultsCells expressing the p.N666H mutation showed constitutive PDGFRB tyrosine phosphorylation.", + "Imatinib, a known inhibitor of PDGFRbeta, blocked the growth of patient colony-forming unit, granulocyte-macrophage in vitro and produced a clinically significant response before relapse and subsequent death with imatinib-resistant disease.", + "The protein levels of Rho were increased in aortae of diabetic rats, which were abolished by the treatment of Imatinib, the inhibitor of PDGFR.", + "We hypothesised that Imatinib, a specific PDGFR-beta inhibitor will, in addition to p-PDGFR-beta inhibition, downregulate VEGF, decrease IFP and improve tumour oxygenation.", + "Adult reproductive functions after early postnatal inhibition by imatinib of the two receptor tyrosine kinases, c-kit and PDGFR, in the rat testis.", + "Imatinib is a selective inhibitor of KIT, PDGFR, and ABL tyrosine kinase activity and exerts different anti-tumor effects according to the regions of mutations in c-kit and PDGFR genes.", + "Imatinib, a PDGFR inhibitor, significantly enhanced the anti-proliferative effect of ZM447439, an Aurora B specific inhibitor, and PHA-739358, a pan-Aurora kinase inhibitor.", + "A comparative study of PDGFR inhibition with imatinib on radiolabeled antibody targeting and clearance in two pathologically distinct models of colon adenocarcinoma.", + "Moreover, the expression of fibrosis related genes, and the phosphorylation of PDGFRs in ISO-treated mice hearts were inhibited by IMA as well.", + "In high-fat-fed apolipoprotein E(-/-) mice, inhibition of PDGFRbeta activity by imatinib reduced aortic total lipid staining area by 35% (P < 0.05).", + "OBJECTIVE: Imatinib being an inhibitor of tyrosine kinase receptors such as PDGFR, its effect on scleroderma fibroblasts was evaluated in vitro as a preclinical therapeutic step.", + "However, in vivo studies clearly demonstrate that compared with imatinib, PLX3397 results in sustained blockade of c-Kit, c-Fms, and PDGFRbeta, resulting in significant suppression of tumor growth.", + "Imatinib may have a therapeutical effect on ET via blocking of PDGFR.", + "Sunitinib and regorafenib are approved options for patients progressing on imatinib, but with markedly decreased survival. pazopanib is a broad spectrum TKI targeting KIT, PDGFR and VEGFR receptors and has shown promising activity in phase 2 trials in GIST.", + "Fibroblast migration was potently induced by PDGF-D and CCA conditioned medium and was significantly inhibited by PDGFRbeta blockade with Imatinib and by silencing PDGF-D expression in CCA cells.", + "Imatinib mesylate is also a potent inhibitor of PDGFR kinase and is currently being evaluated for the treatment of chronic myelomonocytic leukemia and glioblastoma multiforme, based upon evidence in these diseases of activating mutations in PDGFR.", + "In addition, signal transduction mediated by activating mutations of c-Kit and PDGFR can be effectively blocked by specific tyrosine kinase inhibitors, such as Imatinib mesylate.", + "To date however, there are no reports on the activity of imatinib mesylate, a selective PDGFR inhibitor, in RMS preclinical models.", + "Imatinib mesylate, commercially known as Gleevec/Glivec, is the first targeted anticancer drug that inhibits activity of the tyrosine kinases, c-ABL, c-KIT, and PDGFR.", + "The purpose of this study is to evaluate whether disruption of the platelet-derived growth factor-regulated growth pathway by Imatinib mesylate (Gleevec), a partially selective PDGFR inhibitor, inhibits growth of ovarian cancer cells expressing PDGFR." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-semmeddb" + ] + } + ] + }, + "dc401090860f91a37a93a90736ce6865": { + "predicate": "biolink:affects", + "subject": "PUBCHEM.COMPOUND:5291", + "object": "NCBIGene:5154", + "qualifiers": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "activity_or_abundance" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + }, + { + "qualifier_type_id": "biolink:qualified_predicate", + "qualifier_value": "biolink:causes" + } + ], + "attributes": [ + { + "attribute_type_id": "biolink:publications", + "value": [ + "PMID:17614352", + "PMID:18312355", + "PMID:20518073", + "PMID:18794084", + "PMID:16033874" + ], + "value_type_id": "linkml:Uriorcurie" + }, + { + "attribute_type_id": "biolink:supporting_text", + "value": [ + "Interestingly, phosphorylated-PDGFRalpha expression was significantly downregulated by imatinib.", + "Imatinib, KIT and PDGFRA inhibitor, has been successfully used in the treatment of metastatic GISTs.", + "Imatinib further inhibited PDGFRalpha expression and activity, as confirmed by the down-regulation of downstream Erk signaling pathway.", + "Imatinib efficiently inhibits the juxtamembrane PDGFRA mutations, whereas many tyrosine kinase domain activation loop PDGFRA mutations confer primary resistance to imatinib.", + "Imatinib, an inhibitor of PDGF receptors alpha and beta, as well as other selected tyrosine kinases, is indicated for treatment of chronic myelogenous leukemia (CML) and gastrointestinal stromal tumor (GIST)." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-semmeddb" + ] + } + ] + }, + "77fde41c19cd406e02f6834d0e8a6921": { + "predicate": "biolink:affects", + "subject": "PUBCHEM.COMPOUND:5291", + "object": "NCBIGene:207", + "qualifiers": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "activity_or_abundance" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + }, + { + "qualifier_type_id": "biolink:qualified_predicate", + "qualifier_value": "biolink:causes" + } + ], + "attributes": [ + { + "attribute_type_id": "biolink:publications", + "value": [ + "PMID:12481435", + "PMID:17999742", + "PMID:18794444", + "PMID:21376411", + "PMID:30671399", + "PMID:31576676", + "PMID:19956885", + "PMID:27370604", + "PMID:34359600" + ], + "value_type_id": "linkml:Uriorcurie" + }, + { + "attribute_type_id": "biolink:supporting_text", + "value": [ + "In signaling studies, addition of stem cell factor (SCF) induced phosphorylation of ERK and Akt by WTKit, and ERK, Akt and STAT3 by V560GKit, which were all blocked by Imatinib.", + "The protein tyrosine kinase inhibitor, imatinib (Gleevec), decreases the proliferation of non-parenchymal cells (NPC) in vitro and in vivo, with concomitant inhibition of Akt.", + "CONCLUSION: Our findings demonstrate that imatinib confers greater doxorubicin retention, presumably via inhibition of Akt, which regulates ABCG2 function.", + "PDGF-BB induced phosphorylation of Akt at 15 min, and Akt phosphorylation was inhibited by imatinib in IPAH-PASMCs.", + "Treatment of imatinib and GNF5 decreased Skp2 expression and Akt phosphorylation, and increased the expression of p27, p21, and active-caspases in SK-HEP1 cells.", + "LY294002 and imatinib were used to inhibit the activity of PI3K/Akt and platelet-derived growth factor receptor (PDGFR) beta.", + "Imatinib mesylate (STI571) enhances amrubicin-induced cytotoxic activity through inhibition of the phosphatidylinositol 3-kinase/Akt pathway in small cell lung cancer cells.", + "OBJECTIVE: To investigate whether the mechanism for the reversal of ABCG2 (also known as ABCP, MXR, and BCRP)-mediated drug resistance by imatinib mesylate (Gleevec, STI571; Novartis Pharmaceuticals Corp, East Hanover, New Jersey) is caused by the downregulation of Akt kinase.", + "EXPERIMENTAL DESIGN: Here, we performed in vitro and in vivo studies evaluating the novel combination of imatinib mesylate with the AKT inhibitor MK-2206 in GIST.", + "CONCLUSIONS: These studies provide strong preclinical justification for combining imatinib mesylate with an AKT inhibitor as a front-line therapy in GIST.", + "These studies provide strong rationale for further use of AKT inhibition in combination with IM in primary GIST; however, alternative agents will need to be tested in combination with AKT inhibition in the resistant setting." + ] + } + ], + "sources": [ + { + "resource_id": 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+ "PMID:15725473", + "PMID:15289315", + "PMID:17591808", + "PMID:16767900", + "PMID:20876428", + "PMID:14645423", + "PMID:18414381", + "PMID:17169414", + "PMID:22314612", + "PMID:15542802", + "PMID:15545668", + "PMID:24531699", + "PMID:23567324", + "PMID:25264277", + "PMID:24333732", + "PMID:12672043", + "PMID:18480468", + "PMID:17372901", + "PMID:18235442", + "PMID:15893416", + "PMID:15223958", + "PMID:16077968", + "PMID:18990444", + "PMID:22498828", + "PMID:22161019", + "PMID:16732863", + "PMID:30268485", + "PMID:18451237", + "PMID:20332468", + "PMID:15689683", + "PMID:17699867", + "PMID:17805064", + "PMID:25572173", + "PMID:16034302", + "PMID:21462307", + "PMID:26098203", + "PMID:21642685" + ], + "value_type_id": "linkml:Uriorcurie" + }, + { + "attribute_type_id": "biolink:supporting_text", + "value": [ + "Both PDGFRalpha and KIT receptors are targets of the tyrosine kinase inhibitor imatinib (Glivec) which has improved the treatment of advanced GISTs significantly.", + "Since pediatric GISTs are typically resistant to imatinib, we performed genotype analysis of the operative specimen that revealed KIT mutations associated with imatinib sensitivity and resistance.", + "Primary cultures of CD117(high) tumors were sensitive to imatinib (5 uM) in short term culture.", + "Gastrointestinal stromal tumors (GIST) are characterized by activating mutations of KIT or platelet-derived growth factor receptor alpha(PDGFRA), which can be therapeutically targeted by tyrosine kinase inhibitors (TKI) such as imatinib.", + "To determine the sensitivity of Kit mutants to Imatinib in the same cellular background, wild-type Kit (WTKit), V560GKit and D816VKit were expressed in FDC-P1 cells.", + "The clinical response to imatinib therapy correlates with the types of mutations of KIT and PDGFRA, and the determination of KIT and PDGFRA mutations is useful for predicting the effect of imatinib.", + "In vitro findings point out that L576P/KIT is constitutively activated, and shows poor imatinib sensitivity.", + "In parallel, the affinities of wild-type, L576P/KIT, and Delta559/KIT for imatinib were estimated by in silico studies.", + "Computer modeling proved that L576P/KIT is two times less sensitive than the wild-type counterpart and considerably less affine to imatinib than the sensitive Delta559/KIT.", + "To investigate the consequences of second-site Kit mutations on GIST development and imatinib sensitivity, we engineered a mouse model carrying in the endogenous Kit locus both the Kit(V558Delta) mutation found in a familial case of GIST and the Kit(T669I) (human KIT(T670I)) \"gatekeeper\" mutation found in imatinib-resistant GIST patients.", + "Molecular modeling studies found that the L576P mutation induces structural changes in KIT that reduce the affinity for imatinib (DeltaDeltaGbind = -2.52 kcal/mol) but not for dasatinib (DeltaDeltaGbind = +0.32 kcal/mol).", + "This case-study confirms the long-term efficacy and safety of imatinib in patients with SM lacking activating KIT mutations.", + "In particular, the mutation V560G in KIT increases its sensitivity to Imatinib, while the D816V in KIT, and D802V in CSF-1R, triggers resistance to the drug.", + "Further, we evaluated the sensitivity of the studied KIT receptors to Imatinib by measuring the inhibition of KIT phosphorylation.", + "p.(L576P) -KIT mutation in GIST: Favorable prognosis and sensitive to imatinib?", + "Mutation and expression of PDGFRA and KIT in malignant peripheral nerve sheath tumors, and its implications for imatinib sensitivity.", + "However, primary resistance to imatinib in GISTs with wild-type KIT and acquired resistance in GISTs with mutant KIT are becoming increasingly significant problems.", + "Similar to its ineffectiveness in wild-type GISTs, imatinib also failed to inhibit SCF-induced KIT activation in GISTs with mutant KIT.", + "Recombinant KIT with the second mutation was insensitive to 1 MUM but sensitive to 10 MUM imatinib.", + "This second mutation in KIT may play an important role in imatinib resistance in neoplastic mast cells.", + "Functionally, miR-125a-5p expression modulated imatinib sensitivity in GIST882 cells with a homozygous KIT mutation but not in GIST48 cells with double KIT mutations.", + "Residual and recurrent gastrointestinal stromal tumors with KIT mutations: findings at first follow-up CT after imatinib treatment.", + "PURPOSE: Gastrointestinal stromal tumors (GISTs) commonly harbor oncogenic mutations of the KIT or platelet-derived growth factor alpha (PDGFRA) kinases, which are targets for imatinib.", + "Imatinib mesylate is indicated for the treatment of patients with Kit (CD117)-positive unresectable and/or metastatic malignant gastrointestinal stromal tumors and patients with Philadelphia chromosome-positive chronic myeloid leukemia in blast crisis, accelerated phase, or in chronic phase after failure of interferon-alfa.", + "Imatinib mesylate in the treatment of Core Binding Factor leukemias with KIT mutations.", + "KIT expression is a key diagnostic feature of gastrointestinal stromal tumors (GISTs), and virtually all of the GISTs express oncogenic forms of the KIT or PDGFRA receptor tyrosine kinase proteins, which serve as therapeutic targets of imatinib mesylate (Gleevec; Novartis, Basel, Switzerland).", + "Most GISTs express constitutively activated mutant isoforms of KIT or kinase platelet-derived growth factor receptor alpha (PDGFRA) that are potential therapeutic targets for imatinib mesylate.", + "We conclude that the effect of IM should be assessed only in OM with positive immuno-histochemical c-kit (CD 117) expression.", + "Good clinical response to imatinib mesylate in atypical thymic carcinoid With KIT overexpression.", + "PURPOSE: Most gastrointestinal stromal tumors (GISTs) express constitutively activated mutant isoforms of KIT or kinase platelet-derived growth factor receptor alpha (PDGFRA) that are potential therapeutic targets for imatinib mesylate.", + "BACKGROUND AND PURPOSE: Effects of imatinib mesylate, a Kit receptor tyrosine kinase inhibitor, on spontaneous activity of interstitial cells of Cajal (ICC) and smooth muscles in the stomach were investigated.", + "This study investigated the consequences of KIT signaling on ovarian cancer cell proliferation and survival and evaluated the molecular basis of sensitivity to imatinib mesylate.", + "To investigate the pathophysiological function of KIT, the effects of KIT ligand, stem cell factor (SCF), and imatinib mesylate on cell proliferation were investigated using PrSC.", + "PURPOSE: KIT is a target for imatinib mesylate (Gleevec; Novartis Pharma, Basel, Switzerland).", + "PURPOSE: Mutated KIT and platelet-derived growth factor receptor alpha (PDGFRalpha) tyrosine kinases are the principal targets for imatinib mesylate in the treatment of gastrointestinal stromal tumors (GISTs).", + "The data presented centers on imatinib, vemurafenib, and most recently dabrafenib, targeting KIT and BRAF mutations and their outcomes in GIST and melanoma.", + "The relative affinities for ATP and Imatinib of each single (W557G, Y578C) and double (W557G/Y578C) mutant KITs were predicted by in silico studies (computer-based molecular simulations), and compared with those obtained for known Imatinib sensitive and resistant KIT mutants.", + "The effect of imatinib on CD117(high)/KIT+ tumors was determined on first passage cells; absolute cell counts and flow cytometry were readouts for drug sensitivity of cell subsets.", + "However, although neuroblastoma cells express c-Kit and PDGFR, the imatinib concentrations required to achieve significant growth inhibitory effects (>= 10 MUM) are substantially higher than those required for inhibition of ligand-induced phosphorylation of wild type c-Kit and PDGFR (<= 1 MUM), suggesting that additional mechanisms are responsible for the antitumor activity of imatinib on these cells.", + "Imatinib was confirmed to selectively target CD117(+) cells in vitro, and synergistically enhanced the anti-tumor effect of low dose cisplatin in vivo, which showed only modest effects when used as a single use.", + "To investigate the effect of Imatinib on various c-KIT mutations found in GISTs, we examined kinase activity of KIT, cell proliferation and tumorigenicity of transfectants with various c-KIT mutations.", + "In various types of activating mutant KIT, Imatinib could inhibit the constitutive activation of KIT signal transduction and cell proliferation both in vitro and in vivo although the effect of Imatinib on KIT(820Tyr) was weaker than that on KIT(del559-560) or KIT(642Glu).", + "We then checked the potential KIT dependence of ex vivo contractile activity of the uterus by combining genetic and pharmacological approaches, using the Kit W-v hypomorphic mutation, and imatinib as a KIT noncompetitive inhibitor.", + "However, compared to an imatinib-sensitive KIT mutant, dasatinib was potent at lower doses than imatinib in the KIT(L576P) mutant.", + "The tyrosine kinase inhibitor imatinib targets the human KIT receptor and the platelet-derived growth factor receptor-alpha.", + "Whether Imatinib, in combination with other agents, may play a role in the treatment of AML with more sensitive extracellular juxtamembrane KIT mutation remains to be determined.", + "Imatinib targets KIT and platelet-derived growth factor receptors (PDGFR) and is highly effective in the treatment of CML and GIST patients.", + "Notably, some KIT-negative GISTs contain imatinib-sensitive KIT or PDGFRA mutations; therefore, patients with KIT-negative GISTs should not, a priori, be denied imatinib therapy.", + "To investigate the effects of imatinib on various c-kit mutations found in GISTs, cell proliferation and apoptosis assays were performed in two GIST cell lines with different KIT mutations.", + "While no activity was seen in this phase II trial, the findings of the study do not rule out efficacy in subsets of AML with imatinib-sensitive Kit mutations.", + "Wide surgical excision of the tumor followed by adjuvant local radiotherapy were performed, and for the first time the use of imatinib was attempted, as neoplastic mast cells expressed the CD117 marker.", + "Imatinib is a powerful protein tyrosine kinase (PTK) inhibitor that specifically targets BCR-ABL, KIT, and PDGFR kinases, has become the current first-line therapy for all newly diagnosed chronic myeloid leukemia (CML).", + "Despite almost universal resistance to chemotherapy, a novel therapy, Imatinib, which targets the KIT receptor, has changed the natural history of this disease.", + "Amino acid sequence alignment confirmed homology to the imatinib-sensitive KIT N822 K activation loop mutation observed in GIST.", + "One patient with systemic mastocytosis and a partial response to therapy had a novel imatinib-sensitive KIT mutation (D816T).", + "We conducted a Phase II trial to evaluate the effectiveness of imatinib for patients with recurrent ESFT or DSRCT expressing KIT and/or PDGFRalpha.", + "Moreover, a unique therapeutic agent, imatinib, has been devised that specifically targets the aberrant KIT receptor and has demonstrated dramatic therapeutic efficacy in this otherwise resistant malignancy.", + "Comparison was made to imatinib-sensitive Ba/F3 KIT mutant cells as well as Ba/F3 cells expressing only secondary KIT mutations.", + "Imatinib targets KIT expression, providing rationale for studying its role in combination with chemotherapy in SCLC in a multicenter phase II trial.", + "Despite the clinical success of imatinib, which targets KIT, most patients with advanced GIST develop resistance and eventually die of the disease.", + "Results of ongoing pilot phase II studies may validate the efficacy of imatinib mesylate in malignant melanoma expressing KIT.", + "Imatinib mesylate, which targets KIT and PDGFRA, is effective in treating GISTs, but 90% of GIST patients become imatinib-resistant as a result of acquiring secondary KIT mutations.", + "Despite the successful clinical use of imatinib mesylate, a selective receptor tyrosine kinase (RTK) inhibitor that targets KIT, PDGFRA and BCR-ABL, we still do not have treatment for the long-term control of advanced GIST.", + "OBJECTIVE: To assess clinical effects of imatinib mesylate in patients with melanoma harboring KIT alterations." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-semmeddb" + ] + } + ] + }, + "cfdc99963cabc9f69ee654c9fa139124": { + "predicate": "biolink:interacts_with", + "subject": "PUBCHEM.COMPOUND:5291", + "object": "NCBIGene:5154", + "attributes": [ + { + "attribute_type_id": "biolink:publications", + "value": [ + "PMID:19096755", + "PMID:14645423", + "PMID:22718859", + "PMID:24132921", + "PMID:15928335", + "PMID:17087936" + ], + "value_type_id": "linkml:Uriorcurie" + }, + { + "attribute_type_id": "biolink:supporting_text", + "value": [ + "Despite patients with FIP1-like-1-platelet-derived growth factor alpha (FIP1L1-PDGFRA) associated HES (myeloid neoplasms associated with PDGFRA rearrangement) have been shown to respond to low-dose imatinib with a complete and durable hematological and cytogenetic remission, influences of imatinib on clinical manifestations related to hypereosinophilia heart involvement are variable.", + "All KIT mutant isoforms, but only a subset of PDGFRA mutant isoforms, were sensitive to imatinib, in vitro.", + "EXPERIMENTAL DESIGN: We conducted an international survey among GIST referral centers to collect clinical data on patients with advanced PDGFRA-mutant GISTs treated with imatinib for advanced disease.", + "CONCLUSIONS: This study is the largest reported to date on patients with advanced PDGFRA-mutant GISTs treated with imatinib.", + "Large-scale analysis of PDGFRA mutations in melanomas and evaluation of their sensitivity to tyrosine kinase inhibitors imatinib and crenolanib.", + "PDGFRA mutations in gastrointestinal stromal tumors: frequency, spectrum and in vitro sensitivity to imatinib.", + "Effects of PKC412, nilotinib, and imatinib against GIST-associated PDGFRA mutants with differential imatinib sensitivity." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-semmeddb" + ] + } + ] + }, + "4eef5fe4cbb29beba1d2b3527c188644": { + "predicate": "biolink:interacts_with", + "subject": "PUBCHEM.COMPOUND:5291", + "object": "NCBIGene:5243", + "attributes": [ + { + "attribute_type_id": "biolink:publications", + "value": [ + "PMID:24019750", + "PMID:18669873", + "PMID:22845311", + "PMID:27268766", + "PMID:22781602", + "PMID:17495881", + "PMID:16157201", + "PMID:21418741", + "PMID:27168851", + "PMID:35652931" + ], + "value_type_id": "linkml:Uriorcurie" + }, + { + "attribute_type_id": "biolink:supporting_text", + "value": [ + "It was found that dasatinib and the imatinib metabolite CGP74588 are effectively transported by ABCB1, while imatinib, nilotinib, and bosutinib are comparatively weaker ABCB1 substrates.", + "Both dasatinib and imatinib were transported from the basal to the apical layer, indicating that they were transported by ABCB1, which was confirmed using the ABCB1 inhibitor PSC833 (P = .001 and P < .001, respectively).", + "Imatinib and nilotinib appear to be transported by ABCB1 but do not interact strongly with ABCG2.", + "CONCLUSION: Imatinib, nilotinib and dasatinib are transported more efficiently by the ABCB1 variant (Asn400) compared with the wild-type (Ser400) protein.", + "OBJECTIVE: To determine plasma imatinib concentration, intracellular imatinib concentration, and hOCT1 and ABCB1 mRNA expression in bone marrow cells of CML patients to further evaluate the potential usefulness of these measures as markers of imatinib efficacy and their clinical relationships.", + "ABCB1 genotype was associated with steady-state CL/F due to an apparent genotype-specific influence of imatinib on elimination.", + "Reported data maintain that MDR1 expression would play an important role in Imatinib resistance when the disease is not fully controlled (e.g., progressive disease or during the first months of treatment).", + "Simultaneous targeting of P-gp and XIAP with siRNAs increases sensitivity of P-gp overexpressing CML cells to imatinib.", + "In conclusion, the concentration of IM in BMMCs may be regulated by the ABCB1 gene, and SNPs of the ABCB1 gene predict the therapeutic response to IM in patients with CML.", + "Only SNP rs1128503 of the ABCB1 gene had a small but insignificant effect on imatinib clearance, with a 25% reduction in clearance observed in patients carrying the polymorphism." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-semmeddb" + ] + } + ] + }, + "c053ece53503cbd222cefccad88d526e": { + "predicate": "biolink:interacts_with", + "subject": "PUBCHEM.COMPOUND:5291", + "object": "NCBIGene:4547", + "attributes": [ + { + "attribute_type_id": "biolink:publications", + "value": [ + "PMID:28661474", + "PMID:12094244", + "PMID:12743326", + "PMID:15703782", + "PMID:16757427", + "PMID:20596710", + "PMID:24753251", + "PMID:27666635", + "PMID:11680792", + "PMID:17043649", + "PMID:21586300", + "PMID:20337484", + "PMID:22592606", + "PMID:29925402", + "PMID:29554925", + "PMID:31071955", + "PMID:14744784", + "PMID:15052442", + "PMID:18525114", + "PMID:21330162", + "PMID:23434731", + "PMID:28533480", + "PMID:24969884", + "PMID:26316486", + "PMID:14635084" + ], + "value_type_id": "linkml:Uriorcurie" + }, + { + "attribute_type_id": "biolink:supporting_text", + "value": [ + "Moreover, we show that mutant p53 forms cytoplasmic complexes with c-Abl, thereby dictating the subcellular localization of c-Abl and the sensitivity of MDA-MB-231 cells to Imatinib.", + "Currently, patients with PDGFRB or ABL fusion genes are candidates for treatment with Imatinib (STI571), but it is likely that alternative strategies will be necessary for the treatment of most other patients.", + "Furthermore, the level of phosphorylated BCR/ABL protein was suppressed by imatinib treatment, suggesting that mechanisms independent of BCR/ABL signaling are involved in the imatinib resistance in KCL22/SR cells.", + "Chronic myeloid leukaemia with BCR-ABL fusion genes located to both chromosomes 9, cyclic leukocytosis and nodal T-lymphoblastic transformation--durable complete remission following imatinib therapy.", + "Several mechanisms of imatinib resistance have been identified, including BCR-ABL gene amplification that leads to overexpression of the BCR-ABL protein, point mutations in the BCR-ABL kinase domain that interfere with imatinib binding, and point mutations outside of the kinase domain that allosterically inhibit imatinib binding to BCR-ABL.", + "Here, we have studied the effects of Imatinib on human MA-11 breast carcinoma cells, expressing both c-abl and PDGFRbeta, in vitro and in mouse xenografts.", + "Tyrosine kinase inhibitors such as imatinib can effectively target the BCR-ABL oncoprotein in a majority of patients with chronic myeloid leukemia (CML).", + "The designed molecules contained two biologically active scaffolds: one was an imatinib derivative that binds to BCL-ABL and the other was a methyl bestatin that binds to cellular IAP 1 (cIAP1).", + "Imatinib also has substantial activity in Philadelphia chromosome-positive acute lymphoblastic leukaemia expressing the BCR-ABL fusion protein.", + "Imatinib targets the Bcr-Abl oncogene that causes chronic myelogenous leukemia (CML) in humans.", + "Imatinib targets PDGF, ABL-related gene, c-Abl, c-Kit and c-Fms receptors, many of which have multiple functions in the bone microenvironment.", + "Analysis of imatinib and sorafenib binding to p38alpha compared with c-Abl and b-Raf provides structural insights for understanding the selectivity of inhibitors targeting the DFG-out form of protein kinases.", + "Remarkably, the CML-iPSCs were resistant to imatinib although they consistently expressed BCR-ABL oncoprotein.", + "Imatinib was the first tyrosine kinase inhibitor to be discovered with high specificity for Bcr-Abl protein resulting from t(9, 22)-derived Philadelphia chromosome.", + "Induction of apoptosis in imatinib sensitive and resistant chronic myeloid leukemia cells by efficient disruption of bcr-abl oncogene with zinc finger nucleases.", + "Since imatinib (Glivec or Gleevec) has been used to target the BCR-ABL fusion protein, chronic myeloid leukemia (CML) has become a manageable chronic disease with long-term survival.", + "Imatinib mesylate (IM) binds to the BCR-ABL protein, inhibiting its kinase activity and effectively controlling diseases driven by this kinase.", + "The current success of molecular targeting therapy is shown by: imatinib mesylate (STI571, Gleevec), targeted to the Bcr/Abl fusion protein derived from a translocation between chromosomes 9 and 22 in chronic myelogenous leukemia; rituximab (Rituxan), a monoclonal antibody to CD20 used in non-Hodgkin's lymphoma; trastuzumab (Herceptin), a chimeric monoclonal antibody to HER-2 used in breast cancer; and gefinitib (ZD1839, Irresa), a tyrosine kinase inhibitor of the epidermal growth factor receptor used in non-small cell lung cancer.", + "These studies are of particular interest in light of recent evidence that chronic phase CML stem cells are not only innately resistant to imatinib mesylate and other drugs that target the BCR-ABL oncoprotein, but are also genetically unstable.", + "Imatinib mesylate is a tyrosine kinase inhibitor which targets Bcr-Abl-protein, c-Kit, and platelet-derived growth factor receptor.", + "Although the TK inhibitor imatinib mesylate, which targets the BCR-ABL protein, has been proven to be effective in controlling leukemic growth, imatinib resistance has been observed with disease relapse because of point mutations in the ABL gene that inhibit imatinib efficacy.", + "The development of Imatinib mesylate (IM), which targets the oncogenic BCR-ABL fusion protein, has greatly improved the outcome of Chronic Myeloid Leukemia (CML) patients.", + "Imatinib mesylate is a tyrosine kinase inhibitor that specifically targets the BCR-ABL protein and induces hematological remission in patients with chronic myeloid leukemia (CML).", + "Imatinib mesylate is a small-molecule tyrosine kinase inhibitor (TKi) designed to target c-ABL and BCR-ABL, approved for the treatment of chronic myeloid leukemia and gastrointestinal stromal tumors.", + "BACKGROUND: Imatinib mesylate is a tyrosine kinase inhibitor that targets the BCR-ABL protein in CML, c-kit (KIT) and platelet-derived growth factor receptors." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": 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"59fa656374debf31aecd4c9d4ccb6a2c": { + "predicate": "biolink:causes", + "subject": "NCBIGene:3497", + "object": "MONDO:0004979", + "attributes": [ + { + "attribute_type_id": "biolink:publications", + "value": [ + "PMID:24625841", + "PMID:8838111", + "PMID:8912771", + "PMID:2222192", + "PMID:1381575", + "PMID:2078298", + "PMID:2528947", + "PMID:2500384", + "PMID:3104640", + "PMID:6426351", + "PMID:11240941", + "PMID:11797935", + "PMID:11912176", + "PMID:18322200", + "PMID:17383539", + "PMID:18309276", + "PMID:17327992", + "PMID:23113020", + "PMID:15241350", + "PMID:25232422", + "PMID:30707957" + ], + "value_type_id": "linkml:Uriorcurie" + }, + { + "attribute_type_id": "biolink:supporting_text", + "value": [ + "IgE not only provides protective immunity against helminth parasites but can also mediate the type I hypersensitivity reactions that contribute to the pathogenesis of allergic diseases such as asthma, allergic rhinitis and atopic dermatitis.", + "On the basis of the progression of molecular biology, the genetic regulations of asthma are being examined extensively and, recently, the gene encoding a beta subunit of the high affinity receptor for IgE (Fc epsilon RI beta) and the gene encoding beta 2 adrenergic receptor (beta 2ADR) are considered to be responsible for asthma.", + "Nevertheless, the recent demonstration of increased numbers of cells expressing the high-affinity IgE receptor in bronchial biopsies from atopic and nonatopic asthmatic subjects, together with epidemiologic evidence indicating that serum IgE concentrations relate closely to asthma prevalence regardless of atopic status, suggests that IgE-mediated mechanisms may participate in the pathogenesis of both atopic and nonatopic asthma.", + "Anti IgE-induced asthma in guinea pigs; a new model for asthma.", + "Histamine release and morphological changes in basophilic granulocytes of atopic asthmatics induced by antigen, anti-IgE and Ca ionophore A 23187.", + "The late phase of asthma induced by an IgE--dependent mechanism is linked with a cellular activation (lymphocytes, eosinophils) and release of different mediators (Paf Acether, LTB4, ECFA, MBP, EcP) from those of the immediate phase.", + "These findings suggest that IgE production in the lung plays the main role in the pathogenesis of eosinophilic pneumonia and bronchial asthma.", + "Hypersensitivity Lung Disease (HLD) includes Hypersensitivity Pneumonitis (HP), IgE triggered asthma and Allergic Bronchopulmonary Aspergillosis (ABPA).", + "[Estimation of anti IgE-induced asthma in guinea pigs by the use of Mead's apparatus, and its application in the examination of disodium cromoglycate].", + "Following intravenous injection of these antisera into normal guinea pigs, anaphylaxis or asthma could be only provoked by anti IgE.", + "IgE regulation and roles in asthma pathogenesis.", + "Eosinophils and IgE molecules are considered the main factors inducing bronchial asthma.", + "From these findings we conclude that the human STAT6 gene is rather involved in the development of eosinophilia and changes in total IgE levels than contributing to the pathogenesis of asthma.", + "After induction of asthma, in contrast, MS animals exhibited proinflammatory effects in leukocyte subset composition including increased eosinophil numbers, whereas levels of IgE and the allergy-specific cytokine IL-13 were reduced compared with HA.", + "Anti-IgE has confirmed the roles of IgE in the pathogenesis of asthma and helped define the concept \"allergic asthma\" in clinical practice.", + "These findings suggest that LAB fermentation improves ID-mediated inhibition of IgE-induced allergic diseases such as rhinitis and asthma, and that ID works by inhibiting degranulation and NF-kB activation in mast cells and basophils.", + "This suggests that the antiallergic effects of licorice are mainly due to glycyrrhizin, 18beta-glycyrrhetinic acid, and liquiritigenin, which can relieve IgE-induced allergic diseases such as dermatitis and asthma.", + "BACKGROUND: IgE is an antibody class that regarded as an important factor in the pathogenesis of allergic diseases, asthma, immune responses to parasitic infection and it could be responsible for the late- phase allergic response.", + "Recently, we demonstrated, in a murine model of asthma with immunosuppressed mice reconstituted with antigen-specific IgE or IgG1 antibodies, that IgE, but not IgG1, participates in potentiation of airway inflammation and induction of airway hyperreactivity (AHR).", + "INF-gamma and IgE are major players in the pathogenesis of asthma in Arabic children.", + "In an anti-DNP-IgE-induced asthmatic model, inhaled MHF dose-dependently inhibited the increase in airway resistance after antigen challenge." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": 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article discusses the neuropeptides and NGF actions and mechanisms in the pathogenesis of asthma.", + "CONCLUSIONS: NGF can prime the functional redundancy of the adrenaline medullary chromaffin cells, which leads to the dysfunction of adrenaline release and hence the pathogenesis of asthma.", + "CONCLUSIONS: Our results present evidence that asthma during the pregnancy of rat dams promotes asthma susceptibility in their offspring, and that the transformation of AMCCs to neurons induced by NGF plays an important role in this process." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-semmeddb" + ] + } + ] + }, + "09b3a6d941c316c8806796456f399aff": { + "predicate": "biolink:causes", + "subject": "NCBIGene:90865", + "object": "MONDO:0004979", + "attributes": [ + { + "attribute_type_id": "biolink:publications", + "value": [ + "PMID:23380221", + "PMID:29453280", + "PMID:29593738", + "PMID:29728508", + "PMID:30506113", + "PMID:30242072", + "PMID:29977243", + "PMID:25523567" + ], + "value_type_id": "linkml:Uriorcurie" + }, + { + "attribute_type_id": "biolink:supporting_text", + "value": [ + "We propose that genetic variation associated with asthma at the IL33 and IL1RL1 loci can be dissected into independent signals with distinct functional consequences for this pathway that is central to asthma pathogenesis.", + "The data implicate TSLP and IL-33 in the pathogenesis of asthma that is characterized by persistent airway inflammation and impaired lung function despite intensive corticosteroid therapy, highlighting them as potential molecular targets.", + "In the IL-33-induced asthma model, coadministration of PGE2 or PGE1-alcohol resulted in diminished IL-5 and IL-13 production, reduced eosinophilia and alleviated lung pathology.", + "The importance of MyD88 in the IL-33/ST2 signaling transduction was demonstrated by the MyD88 knockout mice, which were protected from the IL-33-induced asthma.", + "MC-released preformed mediators including chymase, tryptase, and histamine and de novo synthesized mediators such as PGD2, LTC4, and LTE4 in addition of cytokines mainly TGFbeta1, TSLP, IL-33, IL-4, and IL-13 participate in pathogenesis of asthma.", + "IL-33 and cysteinyl leukotrienes (cysLTs) are key components of asthma pathogenesis, and both contribute to the initiation and maintenance of the type 2 inflammatory environment.", + "IL-33 is considered as one of the most critical molecules in asthma pathogenesis.", + "[Roles of CD4+CD25+Foxp3+ regulatory T cells and IL-33 in the pathogenesis of asthma in children]." + ] + } + ], + "sources": [ + { + "resource_id": 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rhinoconjunctivitis caused by IgE reactions in predisposed subjects.", + "BACKGROUND: A large body of evidence has demonstrated that treatment with omalizumab is clinically effective for the management of moderate to severe allergic asthma, emphasizing the importance of IgE in the pathogenesis of allergic asthma.", + "BACKGROUND: Allergic asthma is caused by allergen-specific IgE and T-helper cell (Th) type 2 responses towards airborne allergens." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-semmeddb" + ] + } + ] + }, + "8e00c6853143b538b62cdfa1e967d461": { + "predicate": "biolink:affects", + "subject": 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pharmacological studies of the IgE-dependent early asthmatic response.", + "An amount of IgE in these complexes has been increased in both atopic and infectious bronchial asthma.", + "We present the case of a 7-year-old IgE-dependent asthmatic child who, moments after ingesting several pomegranate seeds, showed a clinical condition of bronchospasm which responded to treatment with inhaled salbutamol.", + "Given the potent bronchoconstrictive activity of PAF-acether, its release from alveolar macrophages may provide an alternative explanation for non IgE-dependent asthmas and the implication of platelets in pulmonary diseases.", + "Analysis of complaints and anamnesis in asthmatics suggested by the authors facilitates recognizing forms of the disease at the very first consultation and allows to single out effectively subjects with IgE-dependent asthma.", + "On the other hand, allergic disease has gone through a major evolution of its own from a prehygiene state where there is minimal production of allergen-specific IgE, to the production of high-titer IgE, and then to the dramatic increase in asthma.", + "[Biological models of IgE-dependent bronchial asthma: methodology and prospects for application].", + "Allergen immunotherapy is effective in patients with IgE-dependent allergic rhinitis and asthma.", + "Sputum IgE was raised in asthmatics when compared to healthy subjects.", + "BACKGROUND: Epidemiological studies have indicated that anti-Ascaris IgE enhances asthma and allergies under specific conditions although the association between them is still controversial." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + 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hyperreactivity to histamine in an animal model of asthma, while anti-NGF treatment reduces airway hyperreactivity induced by ovalbumin topical challenge in the sensitized mouse.", + "In support of this, serum levels of NGF have been shown to be enhanced in asthmatics.", + "This study provides evidence that nerve growth factor is locally produced in the airways, and shows that this production is enhanced in asthmatics.", + "CONCLUSION: The expression of NGF in macrophages and lymphocytes in the airways is upregulated in asthma, which indicates a potential correlation between NGF and airway inflammation in asthma." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": 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dendritic cells (mDC) to produce Th1-like cytokines and chemokines necessary for asthma control.", + "These subsets of DCs induce different lineages of T cells, such as TH1, TH2, and TReg cells, including Th1Reg and Th2Reg cells, which regulate allergic diseases and asthma.", + "The aim of the present study was to evaluate the role of Th1- and Th2- related chemokines in the pathogenesis of asthma exacerbation.", + "These subsets induce different lineages of T cells such as Th1, Th2 and TReg cells, including Th1Reg and Th2Reg cells, which regulate allergic diseases and asthma.", + "Th2 cells are predominantly involved in mild asthma, whereas a mixture of Th1 and Th2 cells with neutrophilic inflammation, probably induced by Th17, affects more severe asthmatic disease." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + 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suggest that dsRNA challenges superimposed on allergic inflammation are suited for pharmacological studies of asthma exacerbations including the regulation of lung tissue TSLP, TNF-alpha, IFN-beta and IFN-lambda." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-semmeddb" + ] + } + ] + }, + "dc2fa916285c2a959ee41852fb004e7d": { + "predicate": "biolink:affects", + "subject": "NCBIGene:3497", + "object": "MONDO:0004979", + "attributes": [ + { + "attribute_type_id": "biolink:publications", + "value": [ + "PMID:16536012", + "PMID:16542358", + "PMID:24683397", + "PMID:24750112", + "PMID:9168851", + "PMID:68964", + 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"PMID:25521113", + "PMID:26031325", + "PMID:26695670", + "PMID:16650043", + "PMID:16253848", + "PMID:24800011", + "PMID:24290286", + "PMID:26442233", + "PMID:29714140", + "PMID:21083517", + "PMID:28427296", + "PMID:16522468", + "PMID:19130931", + "PMID:18440625", + "PMID:25585581", + "PMID:31520840", + "PMID:29233467", + "PMID:10855902", + "PMID:16249755", + "PMID:19962746" + ], + "value_type_id": "linkml:Uriorcurie" + }, + { + "attribute_type_id": "biolink:supporting_text", + "value": [ + "The main childhood asthma phenotypes are: transient infant wheezing, non atopic wheezing of the toddler and early school years, persistent IgE-mediated wheezing/asthma, late-onset childhood asthma.", + "Atopic dermatitis (AD) is a common, fluctuating skin disease that is often associated with atopic conditions such as asthma and IgE-mediated food allergy and whose skin lesions are characterized by a Th-2 cell-mediated response to environmental antigens.", + "Omalizumab is a monoclonal antibody against IgE, nowadays approved for the treatment of persistent severe (EU) or moderate-to severe (USA) IgE-mediated asthma but there is also some evidence (case reports and four published clinical trials) on the effectiveness of this medication in urticaria and angioedema.", + "Ag43/Fcepsilon3, as a protein vaccine, produced neutralizing autoantibodies to murine IgE, induced significant anti-asthma effects, and regulated IgE and T helper cytokines in a murine asthma model.", + "Distribution of IgE and IgG antibody levels against house dust mites in schoolchildren, and their relation with asthma.", + "Rheumatoid factor in high titer was found in one worker with IgE-mediated asthma and in two workers with asthma of late onset.", + "Just as asthmas and allergic rhinitis are prototypes of IgE-mediated respiratory disease, atopic dermatitis is the prototype allergic skin disease.", + "Non-IgE-Mediated Asthma after Zinc Exposure.", + "IgE dysregulation is a major pathogenic feature of atopic dermatitis and other IgE-mediated allergic diseases such as asthma and rhinitis.", + "Cutaneous tests are particularly helpful in IgE-mediated asthma in relation to the inhalation of animal or vegetable materials of glycoprotein origin.", + "Sensitization to TMA can take several forms--IgE-mediated asthma and rhinitis, a late reaction in the lung which resembles hypersensitivity pneumonitis and an irritated airways syndrome.", + "Seventeen workers had IgE-mediated asthma/rhinitis with a positive prick test to TM-HSA and IgE antibody of 0.8-57 ng of TM-HSA bound/ml.", + "Non-IgE-mediated asthma in children.", + "We established an experimental animal model for IgE-mediated asthma by the use of intravenous injection of rabbit anti guinea pig IgE in normal guinea pigs.", + "In a new classification by mechanism of onset, asthma was classified into three types according to the degree of participation of IgE-mediated reactions associated with specific IgE antibodies and serum levels of total IgE: asthma induced by definite IgE-mediated reaction (atopic asthma), possible IgE-mediated reactions (asthma), and asthma induced by non-IgE-mediated reaction (asthma syndrome).", + "It follows that the recognition of food dependent-IgE-mediated asthma is essentially limited to these cases characterized by food allergy with asthmatic expression.", + "A prospective study on non-IgE-mediated asthma in children.", + "Both subjects had rhinitis and asthma limited to the ragweed season, near normal out-of-season histamine PC20, and extreme IgE sensitivity to ragweed.", + "Allergen challenge is also used for diagnosis of specific IgE-mediated asthma and evaluation of the effect of immunotherapy.", + "Since IgE-mediated asthma is associated with bronchoconstriction, we asked whether EAA patients do in fact exhibit an obstructive component.", + "The bronchial provocation test was used as a reference of \"true\" IgE-mediated asthma.", + "This study demonstrated that LCL emanations are potent sensitizers and elicit IgE-mediated asthma.", + "A number of cytokines, including histamine-releasing factors (HRFs), have a role to play in IgE-mediated asthma.", + "IgE-mediated rhesus monkey asthma: natural history and individual animal variation.", + "Induction by aerosol allergen of sustained and nonspecific IgE-mediated airway hyperreactivity in the guinea pig.", + "An inhibitor of the lipoxygenase and cyclooxygenase pathways of arachidonic acid metabolism, BW755C, was evaluated with the rhesus monkey model of IgE-mediated asthma.", + "These data provide the first indication of a potential mechanism for MV-induced IgE up-regulation and suggest a model for a viral-induced exacerbation of IgE-mediated disorders such as asthma.", + "In order to maintain a colony of rhesus monkeys with IgE-mediated Ascaris asthma, we evaluated the response of four animals to infection with Ascaris suum ova.", + "There is an increased rate of IgE-mediated asthma among immigrant populations.", + "Studies of IgE-mediated asthma in rhesus monkeys have shown that the animals have individual characteristics analogous to the individuality of human asthmatic patients.", + "In the present study, IgE-mediated allergy for FA was rare in adult chronic asthmatics, and the FA-IgE titer did not seem parallel to severity or pathophysiological condition in bronchial asthma.", + "Effects of anti-IgE in asthmatic subjects.", + "In a group of adult normal rhesus monkeys and monkeys with IgE-mediated asthma observed over a period of 15 years, 2 of the latter group were found to have chronic, generalized pruritus and dermatitis.", + "The mechanisms of, and possible role of, both anti-IgE and anti-IL-5 treatment in asthma are discussed in this review article.", + "The concept that IgE plays a critical role in asthma pathogenesis has driven the development of IgE blockers, which are currently being introduced into clinical use.", + "The aim of the present study was to examine the effects of interleukin-5 (IL-5) inhalation on changes in the activity and number of circulating eosinophils, as well as concentrations of serum total IgE, in allergic asthmatics.", + "IgE-mediated allergic diseases, such as asthma and rhinitis seem to be increasing in industrialised societies.", + "IgE-mediated asthma and rhinitis I: a role of allergen exposure?", + "Several studies demonstrate that the use of powdered allergenic latex gloves leads to a significant aeroallergen load which is responsible for IgE-mediated rhinitis, bronchial asthma, and conjunctivitis in health care workers.", + "Asthma and other IgE-mediated atopic disorders are extremely common in the population, with a consistent, but rather small, genetic component (lambda 3-5) in the inheritance of the disease.", + "Treatment with either leukotriene receptor antagonists or anti-IgE also reduces the risks of asthma exacerbations, but the magnitude of the benefit compared with the combination of ICS and long-acting beta(2)-agonists is not yet known.", + "Response of older patients with IgE-mediated asthma to omalizumab: a pooled analysis.", + "This review synthesizes current understanding about the immunobiology of IgE-mediated asthma.", + "[Anti-IgE blocks central asthmatic mechanism].", + "Allergen immunotherapy (IT) has long-term efficacy in IgE-mediated allergic rhinitis and asthma.", + "IgE-mediated asthma associated with a unique allergen from Angelim pedra (Hymenolobium petraeum) wood.", + "These findings do not support NOS2 to be a major candidate gene for asthma or IgE-mediated allergic diseases in Chinese children.", + "Numerous studies demonstrate its efficacy in IgE-mediated asthma and particularly in mild-to-moderate asthma.", + "Few studies have evaluated the occurrence of immediate adverse reactions in allergic patients after an ultra-rush regimen of different commercial allergen extracts for sublingual immunotherapy (SLIT) Methods: 679 patients took part in trials of specific ultra-rush SLIT for the treatment of IgE-mediated rhinitis and/or IgE-mediated asthma.", + "Adenosine-activated mast cells induce IgE synthesis by B lymphocytes: an A2B-mediated process involving Th2 cytokines IL-4 and IL-13 with implications for asthma.", + "The efficacy of specific immunotherapy in allergic patients with IgE-mediated rhino-conjunctivitis, asthma and allergic reaction for stinging insects suggests the opportunity of improving technical procedures to minimize risk and optimise the safety of immunotherapy.", + "Monovalent targeting of the IgA Fc receptor (FcalphaRI or CD89) by anti-FcalphaRI Fab triggers potent inhibitory ITAM (ITAM(i)) signaling through the associated FcRgamma chain (FcalphaRI-FcRgamma ITAM(i)) that prevents IgG phagocytosis and IgE-mediated asthma.", + "We consider also the important implications that the existence of cytokinergic IgE may have for a fuller understanding of adaptive immunity and of the action of IgE in asthma and other diseases.", + "Subjects were followed for 6 months and performed monthly spirometry (pre- and postbronchodilator); Asthma Control Test (ACT) scoring; and measurements for fractional excretion of nitric oxide (NO), serum eosinophil count, leukocyte count, total IgE, specific IgE to Dermatophagoides pteronyssinus (Der p) and Dermatophagoides farinae (Der f), use of rescue albuterol, and dose of inhaled corticosteroid.", + "In the present study, the effects of nine phenolic compounds from GE on immediate-phase (IAR) and late-phase (LAR) asthmatic responses after aerosolized-ovalbumin (OA) challenge were evaluated by determining the specific airway resistance (sRaw) using a double-chambered plethysmograph in conscious guinea pigs with IgE-mediated asthma.", + "Changes of symptoms and other parameters were assessed, including the asthma control test (ACT) score, morning peak expiratory flow (PEF), peripheral eosinophil count, total serum IgE, and pulmonary function tests.", + "Knowledge of these and other functional properties of basophils may translate into the design of novel therapeutic strategies for Th2-IgE-mediated diseases, such as bronchial asthma.", + "Therapeutic neutralization of serum IgE in moderate-to-severe allergic asthmatics reduces the frequency of asthma exacerbations through a reduction in cell surface FcepsilonRI expression that results in decreased FcepsilonRI activation, leading to improved asthma control.", + "IgE plays a pivotal role in allergic reactions and asthma through its ability to bind to the mast cell FcR for IgE (FcepsilonRI).", + "The relevance of IgE in the pathogenesis of allergy: the effect of an anti-IgE drug in asthma and other diseases.", + "Recent evidence suggests that high titre IgE, particularly to dust mite, correlates to exacerbations of asthma related to rhinovirus infection.", + "IgE-mediated allergies, such as allergic rhinoconjunctivitis and asthma, have become highly prevalent, today affecting up to 30% of the population in industrialized countries.", + "Inhibitory effects of diterpene acids from root of Aralia cordata on IgE-mediated asthma in guinea pigs.", + "The effects of diterpene acids on asthma were evaluated by determining the specific airway resistance (sRaw) during the immediate asthmatic response (IAR) and the late-phase asthmatic response (LAR) in guinea pigs with IgE-mediated asthma.", + "These results suggested that C(7)-oxo radical of 7-oxo-sandaracopimaric acid was more active than the C(7)-hydroxy and hydrogen of the other compounds, and showed diterpene acids have anti-asthmatic effects, supporting the traditional application of this herb in treating IgE-mediated asthma.", + "IgE-mediated asthma: New revelations and future insights.", + "IgE-mediated allergies, in particular allergic rhinoconjunctivitis and asthma, have reached epidemic proportions, affecting about one-third of the population in developed countries.", + "They were compared depending on results of clinical history, and body mass index (BMI), aeroallergen sensitization, total serum IgE, eosinophil count, asthma control test, and asthma severity level.Ages at first asthma episode were 10.0 +/- 6.6 and 33.4 +/- 10.5 (p<0.001) in the <20 and >=20 group, respectively.", + "Although debate surrounding the mechanism or mechanisms governing this causal pathway remains intense, demonstration of the capacity of pretreatment with anti-IgE antibody to blunt seasonal virus-associated asthma exacerbations in children provides strong support for the underlying concept.", + "Timing is everything: Targeting IgE to reduce asthma exacerbation risk.", + "Monoclonal antibodies that target interleukin (IL)-5/IL-5Ralpha, IgE, and IL-4Ralpha have shown favorable results in clinical trials, including reductions in asthma exacerbations and other important clinical outcomes.", + "Thus, the question of whether or not isocyanate asthma is an IgE-mediated disease, has important implications for disease screening/surveillance, diagnosis, treatment and prevention.", + "Objective: We sought to explore the prevalence of atopic dermatitis (AD), asthma, allergic rhinitis (AR), IgE-mediated food allergies (FAs), and other immune-mediated food disorders requiring food avoidance in patients with PANS.", + "In conclusion, rabbit exposure may induce IgE-mediated bronchial asthma and/or rhinitis in domestic settings.", + "Cat allergen (Fel d 1) is a pervasive and common trigger of exacerbations in sensitized patients with IgE-mediated asthma.", + "Omalizumab improved asthma control by reducing exacerbations and decreasing symptoms in cat-allergic patients with moderate-to-severe persistent IgE-mediated asthma.", + "IgE plays a critical role in hypersensitivity reactions such as asthma and allergy as well as poorly defined roles in immunity to parasitic helminth infections.", + "Most of the IgE-mediated asthmatics had had symptoms for many years, while 70% of the non-IgE-mediated asthmatic farmers had no or only wheezing with colds 1982.", + "[Analysis of asthma control and quality of life in severe allergic asthmatics under treatment with anti-IgE, omalizumab].", + "As IgE is involved in allergic reactions, the production of Mycoplasma pneumoniae-specific IgE may have a role in exacerbation of bronchial asthma.", + "The association between tumor necrosis factor, HLA-DR alleles, and IgE-mediated asthma in Taiwanese adolescents.", + "The roles of HLA-DRB1 and TNF genotypes are unknown in Taiwanese adolescents with IgE-mediated asthma (I-asthma).", + "BACKGROUND: We report on IgE-mediated asthma, rhinoconjunctivitis, and contact urticaria to two Liliaceae plants, tulip and Easter lily (Lilium longiflorum), diagnosed in a floral shop worker.", + "These studies provided models for study of bioactive mediators and innovative pharmacologic therapies for IgE-mediated asthma.", + "Cytokine production from sputum cells after allergenic challenge in IgE-mediated asthma.", + "RECENT FINDINGS: In children, three asthma phenotypes are now well defined: transient infant wheezing, nonatopic wheezing of the toddler, and IgE-mediated wheezing/asthma.", + "SUMMARY: The classic phenotype of IgE-mediated asthma starting in childhood is now clearly defined.", + "CONCLUSIONS: Anti-IgE offers the potential not only to decrease asthma activity but also to reduce the risk of morbidity that can result from currently available treatment options.", + "Anti-IgE improved our patient's asthma and decreased the eosinophil blood count but did not worsen the outcome of CSS.", + "Polymorphisms in IL13, total IgE, eosinophilia, and asthma exacerbations in childhood.", + "BACKGROUND: Mast cells play a key role in asthma and recent evidence indicates that their ongoing activation in this disease is mediated, in part, via IgE in the absence of antigen.", + "IgE production in allergic asthmatic patients with different asthma control status.", + "OBJECTIVE: To determine the amount of total serum IgE among allergic asthmatic patients with various asthma controls.", + "METHODS: Children at least 6 years old with (n = 101) and without (n = 93) asthma and IgE-mediated cow's milk allergy, undergoing milk oral immunotherapy from April 2010 to December 2011, were compared.", + "The pulmonary function tests, sputum induction examination, measurement of IgM, IgG and IgE in serum, evaluation of asthma control were carried out for all the included patients.", + "The influences of SEA-IgE and SEB-IgE on asthma control have not been elucidated.", + "OBJECTIVE: To determine the relevance of SEA- and SEB-IgE in patients with adult asthma and to investigate the association of SEA-IgE, SEB-IgE, and asthma control, respectively.", + "CONCLUSIONS: This study demonstrates that emanations from LFB are sensitizers, which have the potential to elicit IgE-mediated asthma.", + "BACKGROUND: The value of cord blood IgE in predicting the development of asthma and other IgE-mediated allergic diseases is unclear.", + "METHODS: The study utilized cord blood obtained from a group of high risk infants who took part in a randomized controlled trial to assess the effectiveness of an intervention program in the primary prevention of asthma and other IgE-mediated allergic diseases.", + "Omalizumab has recently demonstrated clinical efficacy and safety in treating IgE-mediated asthma.", + "Are atopy and specific IgE to mites and molds important for adult asthma?", + "PURPOSE OF REVIEW: IgE-mediated allergies, such as allergic rhinoconjunctivitis and asthma, have become highly prevalent, today affecting up to 35% of the population in industrialized countries.", + "BACKGROUND: IgE and its high-affinity receptor Fc?RI play an important role in allergy and asthma.", + "Plasma total IgE, pulmonary function and Asthma Control Questionnaire were assessed.", + "This may be a potentially important mechanism that explains environmental allergen-induced exacerbation of IgE-mediated allergic diseases such as asthma.", + "None of the NPSR1 tagging SNPs was associated with asthma, IgE-mediated asthma, or sensitisation.", + "IgE levels towards Equ c 1 correlated with asthma control (r = -0.41, p = 0.04).", + "The differences in eCO levels among various asthmatic phenotypes and the correlations between eCO and other measured parameters (spirometric indices, Asthma Control Test score, exhaled nitric oxide, total IgE, blood eosinophils and marker of oxidative damage of proteins) were analysed.", + "Longitudinal increase in total IgE levels in patients with adult asthma: an association with poor asthma control.", + "Associations between longitudinal change in IgE and clinical characteristics including asthma control test (ACT) score, asthma control, pulmonary function test, and antigen specific IgE, were assessed.", + "CONCLUSIONS: These data suggest that a longitudinal increase in total IgE is associated with both poor asthma control and Aspergillus-specific IgE in patients with adult asthma.", + "These findings may pave the way toward the possible use of camel anti-huIgE HCAbs as blocking antibodies in the treatment of IgE-mediated allergy and asthma.", + "We examined for the first time PD-1.3 association with another inflammatory disease with strong immune component, IgE-mediated bronchial asthma, its severity and its biochemical markers (total serum IgE and IL-4).", + "RESULTS: We found a significant association of the PD-1.3 polymorphism with IgE-mediated bronchial asthma and total serum IgE level in the Russian population.", + "Exhaled breath FENO, blood eosinophils, skin prick test, total IgE, asthma control test (ACT), and FCER2 gene polymorphism were performed at inclusion.", + "A path analysis among sensitized children revealed that among all features of severe atopy, only excessive sIgE production early in life affected asthma risk.", + "The following factors were associated with this characteristic: patient age <50 years (OR 3.25; 95% CI: 1.33-7.94), a serum level of IgE >=300 UI/mL (OR 2.32; 95%CI: 1.14-4.75), and an Asthma Control Test (ACT) score <20 points (OR 3.10; 95%CI: 1.35-4.75); asthma with blood eosinophilia was also associated with a baseline FEV1/FVC <70% (OR 2.68; 95%CI: 1.28-5.59).", + "METHODS: The present study was thus conducted to determine the association of this polymorphism with the development of IgE-mediated asthma and other allergic diseases in the Czech population.", + "Results from clinical trials in adults, adolescents, and children with poorly controlled IgE-mediated asthma have shown that omalizumab improves symptom control and allows patients to be managed with lower doses of inhaled corticosteroids (ICS).", + "CONCLUSIONS: Anti-IgE therapy provides an effective and generally safe approach to the treatment of patients with IgE-mediated asthma who are not adequately controlled by conventional guideline-based medications.", + "Baseline: IgE, 332 +/- 243 KMU; total blood eosinophils, 304 +/- 266 cells/MUL; body mass index, 28 +/- 6; ACT, 16 to 19; and FEV(1), 2.5 +/- 0.7 L (86% +/- 20% predicted); exacerbation: FEV(1), 1.7 +/- 0.4 L (60% +/- 17%) (P < .001); recovery: FEV(1), 2.5 +/- 0.7 L (85% +/- 13%) (P < .001).", + "Baseline: IgE, 307 +/- 133 KMU; total blood eosinophils, 296 +/- 149 cells/MUL; body mass index, 28 +/- 6; ACT, 16 to 19; and FEV(1), 2.7 +/- 0.9 L (71% +/- 12% predicted); exacerbation: FEV(1), 1.7 +/- 0.6 L (54% +/- 19%) (P< .006); recovery: FEV(1), 2.7 +/- 0.9 L (70% +/- 14%) (P= .002).", + "On comparing group 1 versus group 2, there was no significant difference for baseline IgE, eosinophils, body mass index, and ACT and similar significant (<=.006) decrease from baseline in FEV(1) (L) during exacerbation and similar increase (<=.006) at recovery.", + "The IGHG2*n dose relationship to IgE sensitization and increased IgG2*n levels in IgE sensitized are risk markers for IgE-mediated asthma.", + "The opposite IGHG2*-n presents non-IgE-mediated asthma and IgG subclass deficiencies.", + "BACKGROUND: Local IgE production may play a role in asthma pathogenesis.", + "Urinary LTE4 levels as a diagnostic marker for IgE-mediated asthma in preschool children: a birth cohort study.", + "METHODS: The Comprehensive Early Childhood Allergy Questionnaire was designed for detecting AD, asthma, and IgE-mediated food allergies in children aged 1-5 years.", + "Serum IgE levels in the positive API group were significantly higher than in the negative API and control groups (P<0.01).", + "There was no interaction between the effects of maternal asthma and birth season on total IgE, as well as between the effects of maternal asthma and maternal vitamin supplements intake.", + "MATERIALS AND METHODS: A murine model of allergic airway inflammation was created in mice following allergen challenge using Af and IgE-mediated asthma.", + "CONCLUSION: Serum TIgE, IL-13 and eotaxin influence each other during exacerbation of bronchial asthma and influence the corresponding pathophysiologic changes.", + "CONCLUSION: We were unable to show a beneficial effect of 3 months of treatment with voriconazole in patients with moderate-to-severe asthma who were IgE sensitized to A fumigatus on either the rate of severe exacerbations, quality of life, or other markers of asthma control.", + "Atopic diseases (asthma, atopic dermatitis, and IgE-mediated food allergy) were assessed by questionnaire at age 1-5 years.", + "METHOD: Through the binding of serum free IgE, omalizumab impairs not only the effector phase of IgE-mediated asthma, but also affects the IgE biology and the related immune response, globally.", + "Omalizumab in the management of oral corticosteroid-dependent IGE-mediated asthma patients.", + "Demographic and functional characteristics, level of asthma control, fractional exhaled nitric oxide, blood and eosinophils and IgE level, induced sputum cell count, eosinophil cationic protein and Interleukin-13 in sputum supernatant were recorded.", + "We propose that diisocyanate-induced asthma is a non-IgE-mediated disease, at least in patients in whom specific IgE antibodies to diisocyanates are undetectable.", + "Reducing omalizumab doses below those in the dosing table cannot be recommended; the resulting increase in free IgE would cause a deterioration in asthma control.", + "We used family-based and population-based approaches to test for interactions between IL10 SNPs and dust mite allergen on serum IgE to dust mite in Costa Rica and on asthma exacerbations in Costa Rica and CAMP.", + "The additional drugs that can be used include tiotropium, omalizumab (for IgE-mediated asthma), and azithromycin (for non-eosinophilic asthma).", + "We further correlated rAsp-specific IgE levels in ABPA with asthma control, spirometry, imaging, and immunologic markers.", + "This study suggests that IgE may play a role in bronchial hyperreactivity associated to A. fumigatus exposure in mice.", + "METHODS: we examined the relationship of both IgE-mediated bronchial hyperresponsiveness and the cell content of bronchoalveolar lavage fluid with a family history of asthma in 263 patients with asthma classified according to age at onset.", + "In the airways, IgE plays an important role in bronchial hyperactivity, even in the absence of an allergen.", + "OBJECTIVE: We sought to investigate the effect of Ascaris infection on bronchial hyperreactivity, skin testing, and specific IgE levels." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-semmeddb" + ] + } + ] + }, + "1c9b623c164ef135f2f69418b438a6f6": { + "predicate": "biolink:affects", + "subject": "NCBIGene:90865", + "object": "MONDO:0004979", + "attributes": [ + { + "attribute_type_id": "biolink:publications", + "value": [ + "PMID:24904000", + "PMID:29728508", + "PMID:24636086", + "PMID:25746970", + "PMID:30316823", + "PMID:26119467", + "PMID:23810766", + "PMID:26879906", + "PMID:28682426", + "PMID:25350863" + ], + "value_type_id": "linkml:Uriorcurie" + }, + { + "attribute_type_id": "biolink:supporting_text", + "value": [ + "This review focuses on accumulating evidence in support of a role for epithelial cytokines, including IL-33, IL-25, and TSLP, as well as their targets, type 2 innate lymphoid cells (ILC2s), in the pathogenesis of virus-induced asthma exacerbations.", + "Small Molecule Mimetics of alpha-Helical Domain of IRAK2 Attenuate the Proinflammatory Effects of IL-33 in Asthma-like Mouse Models.", + "Alternaria-derived serine protease activity drives IL-33-mediated asthma exacerbations.", + "IL-33 is important in fungus-induced asthma exacerbations, but its role in fungal sensitization is unexplored.", + "OBJECTIVE: We hypothesized that IL-33 is necessary to drive asthma exacerbations.", + "CONCLUSIONS: Our study illustrates cell-type-specific regulation of the expression of asthma-related genes documenting SNPs in TSLP, GSDMB, IL33, HLA-DQB1, C11orf30, DEXI, CDHR3, and ZBTB10 affect asthma risk through cis-regulation of its gene expression.", + "RESULTS: Comparison of IL-25 and IL-33 pathway-deficient mice demonstrates that IL-33 signaling plays a more important in vivo role in airways hyperreactivity than IL-25.", + "We suggest that this model of asthma exacerbation involving dsRNA challenges given to mice with established HDM-induced asthma has translational value and suggest that it may be particularly suited for in vivo studies involving pharmacological effects on exacerbation-induced expression of major upstream TH2-cytokines; IL-33, TSLP and IL-25, as well as PRRs.", + "CONCLUSIONS: PM2.5 can enhance the Der p1 antigen-induced HBEC innate immune response through the expression of IL-25, IL-33 and TSLP, which may exacerbate the occurrence rate of bronchial asthma.", + "CONCLUSIONS: IL-33 and type 2 cytokines are induced during a rhinovirus-induced asthma exacerbation in vivo." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-semmeddb" + ] + } + ] + }, + "f3d09d865df27a0ff4ba6b1533f02178": { + "predicate": "biolink:affects", + "subject": "NCBIGene:3497", + "object": "MONDO:0004784", + "attributes": [ + { + "attribute_type_id": "biolink:publications", + "value": [ + "PMID:24885263", + "PMID:10525317", + "PMID:7888792", + "PMID:12759489", + "PMID:15172898", + "PMID:15133258", + "PMID:21880206", + "PMID:21212279", + "PMID:21146489", + "PMID:30191146", + "PMID:17482668", + "PMID:22139745", + "PMID:24412137", + "PMID:24886953", + "PMID:23521807", + "PMID:12197568" + ], + "value_type_id": "linkml:Uriorcurie" + }, + { + "attribute_type_id": "biolink:supporting_text", + "value": [ + "We also investigated the effect of allergic asthma and fenretinide treatment on markers of oxidative stress, levels of metabolites, IgE production, airway hyperresponsiveness, and histological changes.", + "On the other hand, IgE-mediated diseases such as allergic asthma and atopic dermatitis show a type 2 cytokine (amongst others IL-4 and IL-5) profile.", + "The same test was then applied to examine the platelets from patients with IgE-mediated allergic asthma before and after inhalation of the specific allergen (inhalative provocation test; a reduction of the FEV1 by > 15% was considered positive).", + "IgE plays a key role in allergic asthma.", + "IgE plays an important role in allergic asthma.", + "This study implies that the SCRT effect on CD4(+) T cells is a key pharmacologic point of effect for treating IgE-mediated allergic asthma.", + "IgE plays a central role in allergic asthma, and an anti-allergic effect of omalizumab has been confirmed in terms of its impact on Th2 cytokines.", + "Mast cells are critical effector cells in the pathophysiology of allergic asthma and other IgE-mediated diseases.", + "Anti-IgE therapeutics represent an efficient approach in the management of IgE-mediated allergic asthma.", + "Omalizumab, a monoclonal antibody against IgE, is an immunomodulatory biological agent, used as new drug in patients with confirmed IgE-mediated allergic asthma, only for patient's specific range of total IgE level.", + "BACKGROUND: Mast cells, IgE, and TNF, which have been implicated in human atopic asthma, contribute significantly to the allergic airway inflammation induced by ovalbumin (OVA) challenge in mice sensitized with OVA without alum.", + "PURPOSE OF REVIEW: IgE plays a pivotal role in allergic asthma especially in the acute response to antigen and in the propagation of airway inflammation.", + "OBJECTIVE: IgE-mediated allergic asthma phenotype appears to be heterogeneous.", + "PURPOSE OF REVIEW: The allergic march of childhood describes an association between atopic dermatitis, IgE-mediated food allergy, allergic asthma, and allergic rhinitis that begins with an atopic family history.", + "Atopic asthma is a typical IgE-mediated disease in which the enhanced production of IgE is driven by the activation of Th2 cells, which release a distinct pattern of cytokines, including interleukin 4 (IL4) and IL3, in response to specific antigen presentation.", + "RESULTS: IgE plays a key role in allergic diseases such as allergic asthma and allergic rhinitis." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-semmeddb" + ] + } + ] + }, + "8f7d46839f097283fc2c583218e774ae": { + "predicate": "biolink:affects", + "subject": "NCBIGene:3497", + "object": "MONDO:0022742", + "attributes": [ + { + "attribute_type_id": "biolink:publications", + "value": [ + "PMID:9284987", + "PMID:3392370", + "PMID:2376172", + "PMID:6630798", + "PMID:11422138", + "PMID:7076987", + "PMID:15373850", + "PMID:21747869", + "PMID:21738888", + "PMID:9396980", + "PMID:10321564", + "PMID:18716402", + "PMID:28439933", + "PMID:11152166" + ], + "value_type_id": "linkml:Uriorcurie" + }, + { + "attribute_type_id": "biolink:supporting_text", + "value": [ + "These results suggest that fish inhalation can elicit IgE-mediated occupational asthma.", + "Only one worker was identified with IgE-mediated occupational asthma exhibiting a positive prick test and elevated RAST to MDI-HSA of 25.5% bound.", + "We previously reported IgE-mediated occupational asthma among workers exposed to airborne egg protein at a plant that produces liquid and dried powdered egg products.", + "This study demonstrates that inhaled particulates from Tm exoskeletons are potent sensitizers and elicit IgE-mediated occupational asthma.", + "IgE-mediated occupational asthma induced by herbal medicine, Banha (Pinellia ternata).", + "This is the first report of a case of IgE-mediated occupational asthma involving the dried plant, baby's breath.", + "Occupational asthma and IgE-mediated contact dermatitis from sapele wood.", + "Exposure-response relationships have been demonstrated, and atopic workers directly handling fungal enzymes are at an increased risk for IgE-mediated disease and occupational asthma.", + "These findings suggest that the inhalation of the reactive dye Red-K can induce IgE-mediated occupational asthma and rhinitis in exposed workers.", + "CONCLUSIONS: We conclude that Passiflora and cascara sagrada are two new etiologic agents of IgE-mediated occupational asthma and rhinitis.", + "CONCLUSIONS: A case of IgE-mediated occupational asthma, rhinoconjunctivitis, and contact urticaria caused by L. longiflorum and tulip is presented.", + "IgE-mediated occupational asthma from epoxy resin.", + "CONCLUSIONS: This is the first study on a patient exposed to BADGE ER with IgE-mediated immediate OA, based on a positive inhalation challenge test.", + "Effect of anti-IgE in occupational asthma caused by exposure to low molecular weight agents.", + "BACKGROUND: The case of a restaurant seafood handler with IgE-mediated occupational asthma and contact urticaria to both shrimp and scallops is presented." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-semmeddb" + ] + } + ] + }, + "6e2a1033c4375b7600019a42f8037239": { + "predicate": "biolink:affects", + "subject": "NCBIGene:2697", + "object": "MONDO:0004979", + "attributes": [ + { + "attribute_type_id": "biolink:publications", + "value": [ + "PMID:32559685", + "PMID:32812836", + "PMID:32961469", + "PMID:34364825", + "PMID:34448255", + "PMID:34497674", + "PMID:35346926", + "PMID:35467328", + "PMID:36038131", + "PMID:36382233" + ], + "value_type_id": "linkml:Uriorcurie" + }, + { + "attribute_type_id": "biolink:supporting_text", + "value": [ + "Odds of asthma exacerbation were 11% higher on heavy precipitation vs. no precipitation days (95% CI: 1.02-1.21).", + "Similarly, those with poorer asthma control (baseline ACT scores <13) had greater odds of achieving improved asthma control (AOR 13.7, 95% CI 5.32-35.1, p < .0001).", + "We applied conditional logistic regression to estimate odds ratios (OR) and 95% confidence intervals (CI) for the association between the pollen level (vs. none detected) and odds of asthma exacerbation, adjusting for temperature, relative humidity, and holidays.", + "We found increased odds of asthma exacerbation among Philadelphia children in association with tree pollen, both for total tree pollen and most individual tree types.", + "Increased odds from total tree pollen were observed at the lowest levels studied (<=5 grains/m 3 , unlagged, OR = 1.06, 95% CI: 1.02, 1.10), and exhibited a positive exposure-response pattern of effect; tree pollen levels above 1000 grains/m 3 (unlagged) were associated with 64% increased odds of asthma exacerbation (95% CI: 1.45, 1.84).", + "Pollen from other weeds was associated with increased odds of asthma exacerbation, without a clear exposure-response pattern (2-day lag, significant increases ranging from 8% to 19%).", + "IPV was associated with increased odds of an asthma exacerbation (adjusted odds ratio [AOR] = 1.75, 95% confidence interval [CI] = 1.26-2.43), higher symptom burden (AOR = 2.33, 95% CI = 1.53-3.55), and lack of asthma control (AOR = 2.23, 95% CI = 1.22-4.09) when using composite measures for these outcomes.", + "GORD pediatric patients are at higher odds of asthma exacerbation than adults.", + "On multivariate logistic regression, being an urban dweller (AOR=3.70, p=0.025) and not applying proper inhalation technique (AOR=16.23, p=0.022) were increased the risk of suboptimal asthma control, while non-prescription anti-asthmatic drugs taking habit (AOR=0.25, p=0.010) reduces the odds of having suboptimal asthma control.", + "Being an urban dweller and not applying proper inhalation techniques were increased the likelihood of suboptimal asthma control, while non-prescription anti-asthmatic drugs taking habits had lower odds of suboptimal asthma control.", + "RESULTS: Among 41,276 children with asthma, Spanish-preferring Latine children had higher odds of clinic visits for asthma exacerbation than non-Hispanic White peers (OR = 1.10; 95% CI, 1.02-1.18).", + "Does Living near Trees and Other Vegetation Affect the Contemporaneous Odds of Asthma Exacerbation among Pediatric Asthma Patients?", + "Lower odds of asthma exacerbation were observed in association with greater levels of tree canopy near the home, but only for children who experienced multiple exacerbations in a year (OR = 0.94 per 10.2% greater tree canopy coverage, 95% CI = 0.90-0.99).", + "RESULTS: Participants using the RDS (n = 167) had an 85.3% probability of greater odds of clinically meaningful asthma control improvements than those using SoC (n = 166) after 3 months (mean odds ratio 1.33; 95% credible interval 0.813-2.050).", + "CONCLUSIONS: In this study, participants using the RDS had greater odds of clinically meaningful improvements in asthma control versus SoC after 3 months.", + "The odds for a second asthma exacerbation do not necessarily increase with increasing severity of an initial exacerbation." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-semmeddb" + ] + } + ] + }, + "e10a97404e9af41330e5a542603cc053": { + "predicate": "biolink:affects", + "subject": "NCBIGene:3596", + "object": "MONDO:0004979", + "attributes": [ + { + "attribute_type_id": "biolink:publications", + "value": [ + "PMID:17561245", + "PMID:16200868", + "PMID:19575932", + "PMID:31981729", + "PMID:32176091", + "PMID:33654596", + "PMID:33772732", + "PMID:34134447", + "PMID:34832562", + "PMID:34845137", + "PMID:35365694", + "PMID:35912902", + "PMID:36267097", + "PMID:36267519" + ], + "value_type_id": "linkml:Uriorcurie" + }, + { + "attribute_type_id": "biolink:supporting_text", + "value": [ + "The T allele of IL13 promoter SNP (rs1800925) was inversely associated with asthma exacerbations in Costa Rica (P = .069).", + "IL13 polymorphisms may also be associated with asthma exacerbations, and this effect may be dependent on medication use.", + "CONCLUSIONS: The - 1112 locus polymorphism of IL-13 gene promoter may be an important candidate gene for asthma Allele T is associated with asthma and increases the total plasma IgE level via enhanced (enhancing) IL-13 gene expression.", + "The IL-4 gene and IL-13 gene may be important candidate genes for asthma.", + "When we established an overall model that included interaction terms of cohort-by-other factors, there was a trend that comorbidity of allergic rhinitis affected the severity of asthma differently in the relapsed group compared to the other groups.", + "DISCUSSION: This study will provide correlation of NO2, SO2, PM10, and PM2.5 for AR in several aspects, including symptom score, drug score, quality of life score, asthma control score, side effects, and laboratory examination such as nasal function test, serum total immunoglobulin E, and nasal secretion smear.", + "Patients of AR were included and divided with the help of allergic rhinitis and its impact on asthma (ARIA) classification, into group A (cases), patients presenting with moderate to severe symptoms, and into group B (control), patients with mild symptoms, after treatment of AR.", + "As explorative endpoints, statistically significant reductions in AR and AA symptoms and medication use were seen along with improved asthma control after 1 year of treatment, implying that clinically meaningful changes were seen after 1 year of treatment with the SQ HDM SLIT-tablet.", + "The prevalence of AR, based on Allergic Rhinitis and Its Impact on Asthma (ARIA) classification (mild or moderate; intermittent or persistent) was calculated and the association of AR and CRS was evaluated using a multiple logistic regression model.", + "Moreover, AIT can control other allergic diseases complicated by asthma, such as allergic rhinitis, which also improves the control of asthma.", + "Here we specifically summarize the effects of environmental exposure on asthma, allergic rhinitis, and chronic rhinosinusitis.", + "Factors associated with asthma exacerbation were age of 3-5 years, exacerbation history before cohort entry date, allergic rhinitis, chronic sinusitis, otitis externa, blepharitis, upper respiratory infections, urticaria, LTRA prescription, were determined.", + "AR was classified according to Allergic Rhinitis and its Impact on Asthma.", + "AR was diagnosed according to Allergic Rhinitis and its Impact on Asthma (ARIA) guidelines and a positive SPT result.", + "Methods: Four hundred adults having allergic rhinitis and/or bronchial asthma, fulfilling the criteria as per Allergic Rhinitis and its Impact on Asthma (ARIA) guidelines, underwent skin prick test (SPT)." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-semmeddb" + ] + } + ] + }, + "a9e34f6a371d5b5090f48cdde9375b7e": { + "predicate": "biolink:affects", + "subject": "NCBIGene:920", + "object": "MONDO:0004979", + "attributes": [ + { + "attribute_type_id": "biolink:publications", + "value": [ + "PMID:11553626", + "PMID:17027299", + "PMID:22088452", + "PMID:24704667" + ], + "value_type_id": "linkml:Uriorcurie" + }, + { + "attribute_type_id": "biolink:supporting_text", + "value": [ + "Asthma pathophysiology is intimately regulated by CD4(+) Th2 lymphocytes and the cytokines interleukin (IL)-4 and IL-13.", + "T helper 1 (Th1) CD4(+) T cells protect against invasive A. fumigatus infections whereas Th2 CD4(+) T cells exacerbate asthma upon inhalation of A. fumigatus spores.", + "Other CD4(+) T cells subsets might play a role in asthma.", + "In asthma exacerbation group, the purified CD4(+)T cells and macrophages were co-cultured, and the changes of co-cultured cells with BSYQF treatment were further analyzed in vitro." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-semmeddb" + ] + } + ] + }, + "197b6d616af1db5a7934af549dab1274": { + "predicate": "biolink:affects", + "subject": "NCBIGene:3439", + "object": "MONDO:0004979", + "attributes": [ + { + "attribute_type_id": "biolink:publications", + "value": [ + "PMID:27836955", + "PMID:21646800", + "PMID:24283976", + "PMID:36045657" + ], + "value_type_id": "linkml:Uriorcurie" + }, + { + "attribute_type_id": "biolink:supporting_text", + "value": [ + "During asthma exacerbations associated with RV, asthmatic children can induce IFN-alpha secretion, indicating a hyperactive immune response to repeated respiratory virus infection.", + "RESULTS: The serum levels of ECP, IL-5, and IL-6 were significantly elevated in patients with rhinovirus-induced acute exacerbation of asthma compared with controls, while serum IL-1beta and IFN-gamma were significantly lower in patients with rhinovirus-induced acute exacerbation of asthma than in controls.", + "Our data suggest that dsRNA challenges superimposed on allergic inflammation are suited for pharmacological studies of asthma exacerbations including the regulation of lung tissue TSLP, TNF-alpha, IFN-beta and IFN-lambda.", + "Moreover, the percentages of eosinophils, neutrophils, lymphocytes, and the levels of inflammatory factors, IgE, ROS production, caspase 1, caspase 3, cleaved caspase 1/caspase 1, and cleaved caspase 3/caspase 3 increased in OVA + MDSC group, while the percentage of macrophages, IL-12, and IFN- gamma levels reduced, illustrating that MDSCs exacerbated asthma." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-semmeddb" + ] + } + ] + }, + "fb8d8f98719dc9b8539eef7b87571e4c": { + "predicate": "biolink:causes", + "subject": "NCBIGene:3596", + "object": "MONDO:0004979", + "attributes": [ + { + "attribute_type_id": "biolink:publications", + "value": [ + "PMID:19772762", + "PMID:33743807", + "PMID:34920650", + "PMID:34942624", + "PMID:36524912" + ], + "value_type_id": "linkml:Uriorcurie" + }, + { + "attribute_type_id": "biolink:supporting_text", + "value": [ + "Interleukin (IL)-4 and IL-13 act on B cells and regulate the IgE production, and the single nucleotide polymorphisms (SNPs) in the IL-4 and IL-13 genes are implicated in the pathogenesis of asthma.", + "BACKGROUND: Allergic asthma is an inflammatory disease resulting from continued or intermittent allergen exposure, and allergic rhinitis can be trigger of asthma.", + "Allergy and allergic rhinitis (AR) are the main triggers of asthma.", + "Activating HMGB1/RAGE reversed the protective effect of miR-181a-5p overexpression on AR and induced the development of asthma.", + "The cooling agent, menthol, is also recognized as a trigger for asthma, AR and urticaria." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-semmeddb" + ] + } + ] + }, + "352078515e7586e8d63c9d8a6d55d5d5": { + "predicate": "biolink:causes", + "subject": "NCBIGene:920", + "object": "MONDO:0004979", + "attributes": [ + { + "attribute_type_id": "biolink:publications", + "value": [ + "PMID:25070841", + "PMID:10619862", + "PMID:20304475", + "PMID:18298910", + "PMID:17379071", + "PMID:16606533" + ], + "value_type_id": "linkml:Uriorcurie" + }, + { + "attribute_type_id": "biolink:supporting_text", + "value": [ + "Thus, GITR stimulation of nTregs and signaling through JNK2, but not JNK1, triggered the loss of regulatory function while concomitantly gaining pathogenic CD4(+) T effector cell function responsible for exacerbating asthma-like immunopathology.", + "CD4(+) T helper cells engineered to produce latent TGF-beta1 reverse allergen-induced airway hyperreactivity and inflammation.", + "Conventional MHC class II-restricted CD4(+) T cells are considered a key cell in asthma pathogenesis because they have a broad T-cell receptor repertoire, providing specificity and reactivity to diverse protein allergens.", + "BACKGROUND: CD4(+)CD25(+) regulatory T cells (Tregs) mediate immune suppression through cell-cell contact with surface molecules, particularly cytotoxic T lymphocyte-associated antigen 4 (CTLA-4), glucocorticoid-induced tumor necrosis factor receptor family-related protein (GITR), and transforming growth factor beta (TGF-beta), but little is known about the exact role of Tregs in the pathogenesis of asthma.", + "Adoptive transfer of sensitized alpha4(Delta/Delta) CD4(+) cells into challenged normal mice failed to induce asthma, whereas alpha4(+/+) CD4(+) cells were able to induce asthma in challenged alpha4(Delta/Delta) mice.", + "CONCLUSION: The decrease of CD4(+)CD25(+) regulatory T cells may be involved in the pathogenesis of asthma." + ] + } + ], + "sources": [ + { + "resource_id": "infores:semmeddb", + "resource_role": "primary_knowledge_source" + }, + { + "resource_id": "infores:biothings-semmeddb", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:semmeddb" + ] + }, + { + "resource_id": "infores:biothings-explorer", + "resource_role": "aggregator_knowledge_source", + "upstream_resource_ids": [ + "infores:biothings-semmeddb" + ] + } + ] + }, + "expanded-MONDO:0004765-subclass_of-MONDO:0004979": { + 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inferred from id.", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:38.546Z", + "level": "DEBUG", + "message": "BTE identified 3 qNodes from your query graph", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:38.556Z", + "level": "DEBUG", + "message": "BTE identified 3 qEdges from your query graph", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:38.561Z", + "level": "INFO", + "message": "Query proceeding in Inferred Mode.", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:38.774Z", + "level": "INFO", + "message": "Got 1 inferred query templates.", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:41.776Z", + "level": "INFO", + "message": "[Template-1]: Expanded ids for node creativeQuerySubject: (1 ids -> 1 ids)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:41.777Z", + "level": "INFO", + "message": "[Template-1]: Expanded ids for node creativeQueryObject: (1 ids -> 8 ids)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:41.777Z", + "level": "INFO", + "message": "[Template-1]: Added is_set:true to node creativeQueryObject", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:42.846Z", + "level": "WARNING", + "message": "[Template-1]: The following APIs were unavailable at the time of execution: Gene-List Network Enrichment Analysis, Service Provider TRAPI, Knowledge Collaboratory API", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:43.454Z", + "level": "DEBUG", + "message": "[Template-1]: BTE identified 3 qNodes from your query graph", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:43.457Z", + "level": "DEBUG", + "message": "[Template-1]: BTE identified 2 qEdges from your query graph", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:43.954Z", + "level": "DEBUG", + "message": "[Template-1]: Edge manager is managing 2 qEdges.", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:43.958Z", + "level": "DEBUG", + "message": "[Template-1]: Edge manager is sending next qEdge 'eA' for execution.", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:43.964Z", + "level": "INFO", + "message": "[Template-1]: Executing eA: creativeQuerySubject --> nA", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:44.335Z", + "level": "DEBUG", + "message": "[Template-1]: REDIS cache is not enabled.", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:44.340Z", + "level": "DEBUG", + "message": "[Template-1]: BTE is trying to find metaKG edges (smartAPI registry, x-bte annotation) connecting from MolecularEntity,SmallMolecule,NucleicAcidEntity,ChemicalMixture,MolecularMixture,Drug,ComplexMolecularMixture,ProcessedMaterial,Food,EnvironmentalFoodContaminant,FoodAdditive,ChemicalEntity to Gene with predicate regulates,affects_response_to,increases_response_to,decreases_response_to,disrupts,ameliorates_condition,exacerbates_condition,has_adverse_event,has_side_effect,affects,physically_interacts_with,directly_physically_interacts_with,binds,indirectly_physically_interacts_with,genetically_interacts_with,gene_fusion_with,genetic_neighborhood_of,interacts_with,associated_with_likelihood_of,associated_with_increased_likelihood_of,associated_with_decreased_likelihood_of,likelihood_associated_with,increased_likelihood_associated_with,decreased_likelihood_associated_with,associated_with_sensitivity_to,sensitivity_associated_with,associated_with_resistance_to,resistance_associated_with,genetic_association,genetically_associated_with,gene_associated_with_condition,condition_associated_with_gene,correlated_with,positively_correlated_with,negatively_correlated_with,occurs_together_in_literature_with,coexpressed_with,has_biomarker,biomarker_for,associated_with", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:44.719Z", + "level": "DEBUG", + "message": "[Template-1]: BTE found 104 metaKG edges corresponding to eA. These metaKG edges comes from 14 unique APIs. They are BioThings SEMMEDDB API,Biothings Therapeutic Target Database API,BioThings DGIdb API,BioThings PFOCR API,MyChem.info API,Multiomics BigGIM-DrugResponse KP API,BioThings BindingDB API,Text Mining Targeted Association API,Automat-hmdb(Trapi v1.4.0),Automat-pharos(Trapi v1.4.0),Automat-gtopdb(Trapi v1.4.0),Automat-icees-kg(Trapi v1.4.0),Automat-hetio(Trapi v1.4.0),Automat-ctd(Trapi v1.4.0)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:44.734Z", + "level": "DEBUG", + "message": "[Template-1]: BTE found 102 metaKG for this batch.", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:44.735Z", + "level": "DEBUG", + "message": "[Template-1]: Resolving ID feature is turned on", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:44.735Z", + "level": "DEBUG", + "message": "[Template-1]: call-apis: 102 planned queries for edge eA", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.272Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/ctd/1.4 (1 ID): MolecularMixture > affects > Gene (obtained 0 records, took 496ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.297Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/ctd/1.4 (1 ID): SmallMolecule > increases_response_to > Gene (obtained 0 records, took 539ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.333Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/ctd/1.4 (1 ID): SmallMolecule > affects > Gene (obtained 0 records, took 584ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.347Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/ctd/1.4 (1 ID): MolecularMixture > decreases_response_to > Gene (obtained 0 records, took 565ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.372Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/ctd/1.4 (1 ID): SmallMolecule > decreases_response_to > Gene (obtained 0 records, took 619ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.409Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/ctd/1.4 (1 ID): Drug > affects > Gene (obtained 0 records, took 622ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.433Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/ctd/1.4 (1 ID): MolecularMixture > increases_response_to > Gene (obtained 0 records, took 651ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.449Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/ctd/1.4 (1 ID): ComplexMolecularMixture > affects > Gene (obtained 0 records, took 652ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.466Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/ctd/1.4 (1 ID): ComplexMolecularMixture > decreases_response_to > Gene (obtained 0 records, took 661ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.514Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/ctd/1.4 (1 ID): ComplexMolecularMixture > increases_response_to > Gene (obtained 0 records, took 697ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.531Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/ctd/1.4 (1 ID): ChemicalEntity > affects > Gene (obtained 0 records, took 721ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.565Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/ctd/1.4 (1 ID): ChemicalEntity > decreases_response_to > Gene (obtained 0 records, took 742ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.573Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/ctd/1.4 (1 ID): ChemicalEntity > increases_response_to > Gene (obtained 0 records, took 746ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.628Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/hetio/1.4 (1 ID): MolecularMixture > directly_physically_interacts_with > Gene (obtained 0 records, took 785ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.712Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/hetio/1.4 (1 ID): SmallMolecule > regulates > Gene (obtained 14 records, took 873ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.780Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/hetio/1.4 (1 ID): MolecularMixture > regulates > Gene (obtained 0 records, took 503ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.792Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/icees-kg/1.4 (1 ID): SmallMolecule > negatively_correlated_with > Gene (obtained 0 records, took 418ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.801Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/icees-kg/1.4 (1 ID): SmallMolecule > correlated_with > Gene (obtained 0 records, took 449ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.847Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/hetio/1.4 (1 ID): SmallMolecule > directly_physically_interacts_with > Gene (obtained 37 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.888Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/icees-kg/1.4 (1 ID): Drug > negatively_correlated_with > Gene (obtained 0 records, took 434ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.916Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/icees-kg/1.4 (1 ID): Drug > correlated_with > Gene (obtained 0 records, took 478ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.931Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/icees-kg/1.4 (1 ID): SmallMolecule > positively_correlated_with > Gene (obtained 0 records, took 515ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.944Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/icees-kg/1.4 (1 ID): Drug > positively_correlated_with > Gene (obtained 0 records, took 476ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.962Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/hetio/1.4 (1 ID): ChemicalEntity > regulates > Gene (obtained 14 records, took 627ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.978Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/icees-kg/1.4 (1 ID): ChemicalEntity > correlated_with > Gene (obtained 0 records, took 445ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:45.996Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/icees-kg/1.4 (1 ID): ComplexMolecularMixture > correlated_with > Gene (obtained 0 records, took 478ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:46.021Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/hetio/1.4 (1 ID): ChemicalEntity > directly_physically_interacts_with > Gene (obtained 37 records, took 719ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:46.037Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/gtopdb/1.4 (1 ID): SmallMolecule > binds > Gene (obtained 0 records, took 461ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:46.093Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/gtopdb/1.4 (1 ID): SmallMolecule > affects > Gene (obtained 3 records, took 526ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:46.104Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/gtopdb/1.4 (1 ID): MolecularMixture > affects > Gene (obtained 0 records, took 461ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:46.117Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/gtopdb/1.4 (1 ID): ChemicalEntity > affects > Gene (obtained 3 records, took 402ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:46.217Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/gtopdb/1.4 (1 ID): ChemicalEntity > binds > Gene (obtained 0 records, took 436ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:46.319Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/pharos/1.4 (1 ID): SmallMolecule > affects > Gene (obtained 21 records, took 525ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:46.330Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/pharos/1.4 (1 ID): SmallMolecule > genetically_associated_with > Gene (obtained 0 records, took 481ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:46.346Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/pharos/1.4 (1 ID): MolecularMixture > affects > Gene (obtained 0 records, took 407ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:46.369Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/pharos/1.4 (1 ID): MolecularMixture > binds > Gene (obtained 0 records, took 423ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:46.384Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/pharos/1.4 (1 ID): MolecularMixture > genetically_associated_with > Gene (obtained 0 records, took 465ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:46.395Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/hmdb/1.4 (1 ID): ChemicalEntity > correlated_with > Gene (obtained 0 records, took 373ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:46.400Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/hmdb/1.4 (1 ID): SmallMolecule > correlated_with > Gene (obtained 0 records, took 403ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:46.408Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/pharos/1.4 (1 ID): SmallMolecule > binds > Gene (obtained 10 records, took 604ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:46.419Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/pharos/1.4 (1 ID): SmallMolecule > physically_interacts_with > Gene (obtained 0 records, took 520ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:46.489Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/pharos/1.4 (1 ID): ChemicalEntity > binds > Gene (obtained 10 records, took 509ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:46.511Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://automat.transltr.io/pharos/1.4 (1 ID): ChemicalEntity > affects > Gene (obtained 21 records, took 546ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:47.385Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://mychem.info/v1 (22 IDs): SmallMolecule > affects > Gene (obtained 0 records, took 340ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:47.753Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://mychem.info/v1 (22 IDs): SmallMolecule > affects > Gene (obtained 0 records, took 745ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:47.772Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/biggim_drugresponse_kp (2 IDs): SmallMolecule > resistance_associated_with > Gene (obtained 0 records, took 853ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:47.789Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://mychem.info/v1 (22 IDs): SmallMolecule > affects > Gene (obtained 0 records, took 550ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:47.802Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://mychem.info/v1 (22 IDs): SmallMolecule > affects > Gene (obtained 0 records, took 478ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:47.833Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://mychem.info/v1 (22 IDs): SmallMolecule > affects > Gene (obtained 0 records, took 864ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:47.862Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://mychem.info/v1 (22 IDs): SmallMolecule > affects > Gene (obtained 3 records, took 810ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:47.868Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/biggim_drugresponse_kp (2 IDs): SmallMolecule > sensitivity_associated_with > Gene (obtained 0 records, took 999ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:48.131Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/biggim_drugresponse_kp (2 IDs): SmallMolecule > physically_interacts_with > Gene (obtained 70 records, took 873ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:48.589Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://mychem.info/v1 (22 IDs): SmallMolecule > affects > Gene (obtained 0 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:48.601Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://mychem.info/v1 (22 IDs): SmallMolecule > physically_interacts_with > Gene (obtained 0 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:48.612Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://mychem.info/v1 (22 IDs): SmallMolecule > affects > Gene (obtained 0 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:48.618Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://mychem.info/v1 (22 IDs): SmallMolecule > physically_interacts_with > Gene (obtained 0 records, took 982ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:49.999Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://mychem.info/v1 (2 IDs): SmallMolecule > interacts_with > Gene (obtained 0 records, took 2s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:50.029Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://mychem.info/v1 (2 IDs): SmallMolecule > interacts_with > Gene (obtained 5 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:50.033Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://mychem.info/v1 (22 IDs): SmallMolecule > affects > Gene (obtained 0 records, took 2s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:50.040Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://mychem.info/v1 (22 IDs): SmallMolecule > affects > Gene (obtained 1 record, took 2s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:50.275Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/dgidb (2 IDs): SmallMolecule > affects > Gene (obtained 0 records, took 2s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:50.302Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/dgidb (2 IDs): SmallMolecule > affects > Gene (obtained 12 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:50.317Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/dgidb (2 IDs): SmallMolecule > affects > Gene (obtained 0 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:50.322Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/dgidb (2 IDs): SmallMolecule > affects > Gene (obtained 0 records, took 2s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:50.935Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/bindingdb (2 IDs): SmallMolecule > physically_interacts_with > Gene (obtained 405 records, took 2s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:51.041Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/pfocr (2 IDs): SmallMolecule > occurs_together_in_literature_with > Gene (obtained 2138 records, took 2s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:51.047Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/dgidb (2 IDs): SmallMolecule > affects > Gene (obtained 0 records, took 2s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:51.052Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/dgidb (2 IDs): SmallMolecule > affects > Gene (obtained 0 records, took 2s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:51.060Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/dgidb (2 IDs): SmallMolecule > physically_interacts_with > Gene (obtained 0 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:51.139Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/dgidb (2 IDs): SmallMolecule > interacts_with > Gene (obtained 121 records, took 2s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:51.436Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/text_mining_targeted_association (1 ID): SmallMolecule > affects > Gene (obtained 351 records, took 2s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:51.764Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/dgidb (2 IDs): SmallMolecule > affects > Gene (obtained 0 records, took 2s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:51.776Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/dgidb (2 IDs): SmallMolecule > affects > Gene (obtained 0 records, took 2s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:51.782Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/dgidb (2 IDs): SmallMolecule > affects > Gene (obtained 0 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:51.922Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/dgidb (2 IDs): SmallMolecule > affects > Gene (obtained 0 records, took 2s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:52.418Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): SmallMolecule > affects > Gene (obtained 0 records, took 2s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:52.424Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): SmallMolecule > interacts_with > Gene (obtained 0 records, took 2s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:52.446Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/ttd (2 IDs): SmallMolecule > interacts_with > Gene (obtained 25 records, took 2s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:52.460Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/ttd (2 IDs): SmallMolecule > interacts_with > Gene (obtained 23 records, took 2s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:52.547Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): SmallMolecule > interacts_with > Gene (obtained 0 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:52.554Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): SmallMolecule > affects > Gene (obtained 0 records, took 1000ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:52.600Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): NucleicAcidEntity > affects > Gene (obtained 15 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:52.608Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): NucleicAcidEntity > interacts_with > Gene (obtained 6 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:52.616Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): NucleicAcidEntity > interacts_with > Gene (obtained 6 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:52.627Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): NucleicAcidEntity > interacts_with > Gene (obtained 7 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:52.655Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): NucleicAcidEntity > interacts_with > Gene (obtained 4 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:53.127Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/text_mining_targeted_association (1 ID): SmallMolecule > affects > Gene (obtained 668 records, took 3s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:53.951Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): SmallMolecule > interacts_with > Gene (obtained 4 records, took 578ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:53.962Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): NucleicAcidEntity > interacts_with > Gene (obtained 6 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:53.963Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): SmallMolecule > affects > Gene (obtained 0 records, took 966ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:53.965Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): SmallMolecule > affects > Gene (obtained 3 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:53.970Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): SmallMolecule > interacts_with > Gene (obtained 6 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:53.979Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): SmallMolecule > affects > Gene (obtained 9 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:53.980Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): SmallMolecule > affects > Gene (obtained 1 record, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:53.983Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): NucleicAcidEntity > interacts_with > Gene (obtained 7 records, took 2s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:53.998Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): SmallMolecule > affects > Gene (obtained 15 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:54.002Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): SmallMolecule > interacts_with > Gene (obtained 6 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:54.015Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): SmallMolecule > interacts_with > Gene (obtained 7 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:54.031Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): SmallMolecule > interacts_with > Gene (obtained 6 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:54.035Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): SmallMolecule > interacts_with > Gene (obtained 7 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:54.324Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): SmallMolecule > affects > Gene (obtained 52 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:54.847Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/semmeddb (22 IDs): NucleicAcidEntity > affects > Gene (obtained 52 records, took 3s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:50:54.847Z", + "level": "DEBUG", + "message": "[Template-1]: Total number of records returned for this qEdge is 4211", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:02.926Z", + "level": "DEBUG", + "message": "[Template-1]: call-apis: qEdge queries complete in 10s", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:04.112Z", + "level": "INFO", + "message": "[Template-1]: eA execution: 102 queries (102 success/0 fail) and (0) cached qEdges return (4211) records", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:04.605Z", + "level": "DEBUG", + "message": "[Template-1]: 'eA' kept (4211) / dropped (0) records.", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:04.855Z", + "level": "DEBUG", + "message": "[Template-1]: Next qEdge will pick lower entity value to use for query.", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:04.855Z", + "level": "DEBUG", + "message": "[Template-1]: Edge manager is sending next qEdge 'eB' for execution.", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:04.855Z", + "level": "INFO", + "message": "[Template-1]: Executing eB (reversed): nA <-- creativeQueryObject", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:05.178Z", + "level": "DEBUG", + "message": "[Template-1]: REDIS cache is not enabled.", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:05.179Z", + "level": "DEBUG", + "message": "[Template-1]: BTE is trying to find metaKG edges (smartAPI registry, x-bte annotation) connecting from Disease,PhenotypicFeature,BehavioralFeature,ClinicalFinding,DiseaseOrPhenotypicFeature to Gene,ProteinIsoform,Protein,MolecularEntity,SmallMolecule,NucleicAcidEntity,ChemicalMixture,MolecularMixture,Drug,ComplexMolecularMixture,ProcessedMaterial,Food,EnvironmentalFoodContaminant,FoodAdditive,ChemicalEntity with predicate condition_associated_with_gene,has_biomarker,response_affected_by,response_increased_by,response_decreased_by,regulated_by,disrupted_by,condition_ameliorated_by,condition_exacerbated_by,adverse_event_of,is_side_effect_of,affected_by,caused_by,contribution_from", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:05.320Z", + "level": "DEBUG", + "message": "[Template-1]: BTE found 199 metaKG edges corresponding to eB. These metaKG edges comes from 12 unique APIs. They are BioThings SEMMEDDB API,BioThings RARe-SOURCE API,BioThings IDISK API,MyVariant.info API,BioThings AGR API,BioThings DISEASES API,MyDisease.info API,MyChem.info API,Monarch API,Multiomics BigGIM-DrugResponse KP API,Text Mining Targeted Association API,BioThings HPO API", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:05.338Z", + "level": "DEBUG", + "message": "[Template-1]: BTE found 219 metaKG for this batch.", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:05.338Z", + "level": "DEBUG", + "message": "[Template-1]: Resolving ID feature is turned on", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:05.339Z", + "level": "DEBUG", + "message": "[Template-1]: call-apis: 219 planned queries for edge eB", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:06.676Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > condition_associated_with_gene > Gene (obtained 0 records, took 388ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:06.682Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > condition_associated_with_gene > Gene (obtained 0 records, took 884ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:06.690Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > condition_associated_with_gene > Gene (obtained 0 records, took 816ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:06.697Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > condition_associated_with_gene > Gene (obtained 0 records, took 756ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:06.701Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > condition_associated_with_gene > Gene (obtained 0 records, took 684ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:06.709Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > condition_associated_with_gene > Gene (obtained 0 records, took 606ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:06.721Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > condition_associated_with_gene > Gene (obtained 0 records, took 492ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:06.731Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/hpo (2 IDs): PhenotypicFeature > condition_associated_with_gene > Gene (obtained 151 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:06.741Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/biggim_drugresponse_kp (8 IDs): Disease > condition_associated_with_gene > Gene (obtained 0 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:06.746Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/biggim_drugresponse_kp (8 IDs): Disease > has_biomarker > Gene (obtained 0 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:06.754Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > contribution_from > Gene (obtained 0 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:06.761Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > contribution_from > Gene (obtained 0 records, took 997ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:06.767Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > condition_associated_with_gene > Gene (obtained 0 records, took 947ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:07.081Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/text_mining_targeted_association (2 IDs): PhenotypicFeature > contribution_from > SmallMolecule (obtained 74 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:07.334Z", + "level": "DEBUG", + "message": "[Template-1]: Successful POST https://biothings.ncats.io/text_mining_targeted_association (2 IDs): PhenotypicFeature > contribution_from > Gene (obtained 64 records, took 2s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:08.272Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > contribution_from > Gene (obtained 0 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:08.278Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > contribution_from > Gene (obtained 0 records, took 994ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:08.287Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > contribution_from > Gene (obtained 0 records, took 750ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:08.294Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > contribution_from > Gene (obtained 0 records, took 942ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:08.300Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > contribution_from > Gene (obtained 0 records, took 679ms)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:08.317Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > caused_by > Gene (obtained 0 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:08.323Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > caused_by > Gene (obtained 0 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:08.328Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > caused_by > Gene (obtained 0 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:08.334Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > caused_by > Gene (obtained 0 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:08.341Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > caused_by > Gene (obtained 0 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:08.346Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > contribution_from > Gene (obtained 0 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:08.405Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > caused_by > Gene (obtained 0 records, took 2s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:08.412Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > caused_by > Gene (obtained 0 records, took 1s)", + "code": null + }, + { + "timestamp": "2024-03-25T23:51:08.425Z", + "level": "DEBUG", + "message": "[Template-1]: Successful GET https://api-v3.monarchinitiative.org (1 ID): Disease > caused_by > Gene (obtained 0 records, took 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+ "resource_id": "infores:biothings-explorer", + "edge_bindings": { + "e2": [ + { + "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + } + ] + }, + "score": 0.06241874674751258 + }, + "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support627": { + "resource_id": "infores:biothings-explorer", + "edge_bindings": { + "e2": [ + { + "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + } + ] + }, + "score": 0.06241874674751258 + } + } +} \ No newline at end of file diff --git a/__test__/unittest/pathfinder.test.ts b/__test__/unittest/pathfinder.test.ts new file mode 100644 index 00000000..d3169e26 --- /dev/null +++ b/__test__/unittest/pathfinder.test.ts @@ -0,0 +1,75 @@ +import TRAPIQueryHandler, { TrapiQueryGraph, TrapiResponse } from '../../src/index'; +import path from 'path'; +import fs from 'fs'; +import _ from 'lodash'; +import Pathfinder from '../../src/inferred_mode/pathfinder'; + +const queryGraph1 = JSON.parse( + fs.readFileSync(path.resolve(__dirname, '../data/chemical_to_disease_pathfinder.json'), { encoding: 'utf8' }), +).message.query_graph as TrapiQueryGraph; + +const creativeResult1 = JSON.parse( + fs.readFileSync(path.resolve(__dirname, '../data/chemical_to_disease_pf_creative_result.json'), { encoding: 'utf8' }), +) as TrapiResponse; + + +describe('Test Pathfinder', () => { + test('Query Validation', () => { + const missingID = _.cloneDeep(queryGraph1); + missingID.nodes['n2'].ids = []; + + const queryGraphHandler = new TRAPIQueryHandler(); + queryGraphHandler.setQueryGraph(missingID); + expect(queryGraphHandler._queryIsPathfinder()).toBeFalsy(); + + const missingEdge = _.cloneDeep(queryGraph1); + delete missingEdge.edges.e1; + + queryGraphHandler.setQueryGraph(missingEdge); + expect(queryGraphHandler._queryIsPathfinder()).toBeFalsy(); + + const missingInferred = _.cloneDeep(queryGraph1); + delete missingInferred.edges.e1.knowledge_type; + + queryGraphHandler.setQueryGraph(missingInferred); + expect(queryGraphHandler._queryIsPathfinder()).toBeFalsy(); + + const swappedSubjObj = _.cloneDeep(queryGraph1); + const temp = swappedSubjObj.edges.e1.subject; + swappedSubjObj.edges.e1.subject = swappedSubjObj.edges.e1.object; + swappedSubjObj.edges.e1.object = temp; + + queryGraphHandler.setQueryGraph(swappedSubjObj); + const pfHandler1 = new Pathfinder([], swappedSubjObj, queryGraphHandler); + expect(queryGraphHandler._queryIsPathfinder()).toBeTruthy(); + expect(pfHandler1.extractData()).toBeTruthy(); // string = error + + queryGraphHandler.setQueryGraph(queryGraph1); + const pfHandler2 = new Pathfinder([], queryGraph1, queryGraphHandler); + expect(queryGraphHandler._queryIsPathfinder()).toBeTruthy(); + expect(pfHandler2.extractData()).toBeFalsy(); + }); + + test('extractData', () => { + const queryGraphHandler = new TRAPIQueryHandler(); + queryGraphHandler.setQueryGraph(queryGraph1); + const pfHandler = new Pathfinder([], queryGraph1, queryGraphHandler); + pfHandler.extractData(); + + expect(pfHandler.intermediateEdges[0][0]).toEqual('e0'); + expect(pfHandler.intermediateEdges[1][0]).toEqual('e1'); + expect(pfHandler.unpinnedNodeId).toEqual('un'); + expect(pfHandler.mainEdgeId).toEqual('e2'); + }); + + test('parse', () => { + const queryGraphHandler = new TRAPIQueryHandler(); + queryGraphHandler.setQueryGraph(queryGraph1); + const pfHandler = new Pathfinder([], queryGraph1, queryGraphHandler); + pfHandler.extractData(); + const pfResponse = pfHandler.parse(creativeResult1); + + expect(pfResponse.message.results.length).toEqual(500); + expect(Object.keys(pfResponse.message.auxiliary_graphs!).length).toEqual(2119); + }); +}); diff --git a/src/inferred_mode/pathfinder.ts b/src/inferred_mode/pathfinder.ts index 17a92a7c..a9745f8d 100644 --- a/src/inferred_mode/pathfinder.ts +++ b/src/inferred_mode/pathfinder.ts @@ -47,36 +47,24 @@ export default class PathfinderQueryHandler { } async query() { - [this.unpinnedNodeId, this.unpinnedNode] = Object.entries(this.queryGraph.nodes).find(([_, node]) => !node.ids); - // remove unpinned node & all edges involving unpinned node for now - delete this.queryGraph.nodes[this.unpinnedNodeId]; - this.intermediateEdges = Object.entries(this.queryGraph.edges).filter(([_, edge]) => edge.subject === this.unpinnedNodeId || edge.object === this.unpinnedNodeId); - [this.mainEdgeId, this.mainEdge] = Object.entries(this.queryGraph.edges).find(([_, edge]) => edge.subject !== this.unpinnedNodeId && edge.object !== this.unpinnedNodeId); + // add log for PF mode + this.logs.push(new LogEntry('INFO', null, 'Proceeding in Pathfinder mode.').getLog()); + debug('Proceeding in Pathfinder mode'); - // intermediateEdges should be in order of n0 -> un & un -> n1 - if (this.intermediateEdges[0][1].subject === this.unpinnedNodeId) { - let temp = this.intermediateEdges[0]; - this.intermediateEdges[0] = this.intermediateEdges[1]; - this.intermediateEdges[1] = temp; + const err = this.extractData(); + + if (typeof err === 'string') { + debug(err); + this.logs.push(new LogEntry('WARNING', null, err).getLog()); + return; } + // remove unpinned node & all edges involving unpinned node for now + delete this.queryGraph.nodes[this.unpinnedNodeId]; + // remove intermediates for creative execution this.intermediateEdges.forEach(([edgeId, _]) => delete this.queryGraph.edges[edgeId]); - if (Object.keys(this.queryGraph.edges).length !== 1) { - const message = 'Pathfinder Mode needs exactly one edge between nodes with IDs. Your query terminates.'; - debug(message); - this.logs.push(new LogEntry('WARNING', null, message).getLog()); - return; - } - - if (this.intermediateEdges[0][1].subject !== this.mainEdge.subject || this.intermediateEdges[1][1].object !== this.mainEdge.object || this.intermediateEdges[0][1].object !== this.unpinnedNodeId || this.intermediateEdges[1][1].subject !== this.unpinnedNodeId) { - const message = 'Intermediate edges for Pathfinder are incorrect. Your query terminates.'; - debug(message); - this.logs.push(new LogEntry('WARNING', null, message).getLog()); - return; - } - // run creative mode const inferredQueryHandler = new InferredQueryHandler( this.parent, @@ -103,6 +91,27 @@ export default class PathfinderQueryHandler { return creativeResponse; } + // extracts info from query into variables that are used by pathfinder + // returns string if an error occurred + extractData(): undefined | string { + [this.unpinnedNodeId, this.unpinnedNode] = Object.entries(this.queryGraph.nodes).find(([_, node]) => !node.ids); + + this.intermediateEdges = Object.entries(this.queryGraph.edges).filter(([_, edge]) => edge.subject === this.unpinnedNodeId || edge.object === this.unpinnedNodeId); + [this.mainEdgeId, this.mainEdge] = Object.entries(this.queryGraph.edges).find(([_, edge]) => edge.subject !== this.unpinnedNodeId && edge.object !== this.unpinnedNodeId); + + // intermediateEdges should be in order of n0 -> un & un -> n1 + if (this.intermediateEdges[0][1].subject === this.unpinnedNodeId) { + let temp = this.intermediateEdges[0]; + this.intermediateEdges[0] = this.intermediateEdges[1]; + this.intermediateEdges[1] = temp; + } + + if (this.intermediateEdges[0][1].subject !== this.mainEdge.subject || this.intermediateEdges[1][1].object !== this.mainEdge.object || this.intermediateEdges[0][1].object !== this.unpinnedNodeId || this.intermediateEdges[1][1].subject !== this.unpinnedNodeId) { + return 'Intermediate edges for Pathfinder are incorrect. Should follow pinned node -> unpinned node -> pinned node. Your query terminates.'; + } + } + + parse(creativeResponse: TrapiResponse) { const span = Telemetry.startSpan({ description: 'pathfinderParse' }); From a1619c3dde76fa2fe8d45ddc68a50fbcf17379e0 Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Tue, 2 Apr 2024 16:27:18 -0700 Subject: [PATCH 13/27] remove unnecessary types; creative mode bugfix --- src/inferred_mode/inferred_mode.ts | 5 ++--- src/inferred_mode/template_lookup.ts | 2 +- src/types.ts | 4 ---- 3 files changed, 3 insertions(+), 8 deletions(-) diff --git a/src/inferred_mode/inferred_mode.ts b/src/inferred_mode/inferred_mode.ts index 81ddc655..aca8b79f 100644 --- a/src/inferred_mode/inferred_mode.ts +++ b/src/inferred_mode/inferred_mode.ts @@ -16,8 +16,7 @@ import { TrapiQueryGraph, TrapiResponse, TrapiResult, - TrapiAnalysis, - CreativePathfinderResponse + TrapiAnalysis } from '../types'; const debug = Debug('bte:biothings-explorer-trapi:inferred-mode'); @@ -263,7 +262,7 @@ export default class InferredQueryHandler { combinedResponse: CombinedResponse, ): CombinedResponseReport { const span = Telemetry.startSpan({ description: 'creativeCombineResponse' }); - const newResponse: CreativePathfinderResponse = handler.getResponse(); + const newResponse = handler.getResponse(); const report: CombinedResponseReport = { querySuccess: 0, queryHadResults: false, diff --git a/src/inferred_mode/template_lookup.ts b/src/inferred_mode/template_lookup.ts index c525f6bb..83607a80 100644 --- a/src/inferred_mode/template_lookup.ts +++ b/src/inferred_mode/template_lookup.ts @@ -58,7 +58,7 @@ export async function getTemplates(lookups: TemplateLookup[], pathfinder = false const matchingTemplatePaths: string[] = templateGroups.reduce((matches: string[], group: TemplateGroup) => { const lookupMatch = lookups.some((lookup) => { return ( - group.pathfinder === pathfinder && + (!!group.pathfinder === pathfinder) && group.subject.includes(lookup.subject) && group.object.includes(lookup.object) && group.predicate.includes(lookup.predicate) && diff --git a/src/types.ts b/src/types.ts index a6fe069b..5e02e4ad 100644 --- a/src/types.ts +++ b/src/types.ts @@ -168,10 +168,6 @@ export interface TrapiResponse { logs: TrapiLog[]; } -export interface CreativePathfinderResponse extends TrapiResponse { - scores?: { [resID: string]: number }; -} - export type APIDefinition = { // Must have one of id or infores id?: string; // SmartAPI ID, takes priority over infores From 7ff4daaf62395603d4737a2049fb81fe9b9066ce Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Tue, 2 Apr 2024 16:27:43 -0700 Subject: [PATCH 14/27] use guard clauses for easier code readibility --- src/inferred_mode/pathfinder.ts | 177 +++++++++++++++++--------------- 1 file changed, 92 insertions(+), 85 deletions(-) diff --git a/src/inferred_mode/pathfinder.ts b/src/inferred_mode/pathfinder.ts index a9745f8d..262864e0 100644 --- a/src/inferred_mode/pathfinder.ts +++ b/src/inferred_mode/pathfinder.ts @@ -181,96 +181,103 @@ export default class PathfinderQueryHandler { const newAuxGraphs: AuxGraphObject = {}; while (stack.length !== 0) { const { node, path } = stack.pop()!; - if (node === kgDst) { - if (path.length > 2) { - // loop through all intermediate nodes - for (let i = 1; i < path.length - 1; i++) { - const intermediateNode = path[i]; - const firstEdges: string[] = []; - const secondEdges: string[] = []; - for (let j = 0; j < i; j++) { - for (let edge of dfsNodes[path[j]][path[j + 1]]) { - firstEdges.push(edge); - } - } - for (let j = i; j < path.length - 1; j++) { - for (let edge of dfsNodes[path[j]][path[j + 1]]) { - secondEdges.push(edge); - } - } - - if (!(`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}` in newResultObject)) { - newResultObject[`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}`] = { - node_bindings: { - [this.mainEdge.subject]: [{ id: kgSrc }], - [this.mainEdge.object]: [{ id: kgDst }], - [this.unpinnedNodeId]: [{ id: intermediateNode }] - }, - analyses: [{ - resource_id: "infores:biothings-explorer", - edge_bindings: { - [this.mainEdgeId]: [{ id: kgEdge }], - [this.intermediateEdges[0][0]]: [{ id: `pathfinder-${kgSrc}-${intermediateNode}` }], - [this.intermediateEdges[1][0]]: [{ id: `pathfinder-${intermediateNode}-${kgDst}` }], - }, - score: undefined - }], - }; - creativeResponse.message.knowledge_graph.edges[`pathfinder-${kgSrc}-${intermediateNode}`] = { - predicate: 'biolink:related_to', - subject: kgSrc, - object: intermediateNode, - sources: [ - { - resource_id: this.options.provenanceUsesServiceProvider - ? 'infores:service-provider-trapi' - : 'infores:biothings-explorer', - resource_role: 'primary_knowledge_source', - }, - ], - attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${kgSrc}-${intermediateNode}-support`] }], - }; - creativeResponse.message.knowledge_graph.edges[`pathfinder-${intermediateNode}-${kgDst}`] = { - predicate: 'biolink:related_to', - subject: intermediateNode, - object: kgDst, - sources: [ - { - resource_id: this.options.provenanceUsesServiceProvider - ? 'infores:service-provider-trapi' - : 'infores:biothings-explorer', - resource_role: 'primary_knowledge_source', - }, - ], - attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${intermediateNode}-${kgDst}-support`] }], - }; - newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`] = { edges: new Set(firstEdges) }; - newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`] = { edges: new Set(secondEdges) }; - - // calculate score - if (supportGraphsPerNode[intermediateNode]?.size > 0) { - let score: number | undefined = undefined; - for (const supportGraph of supportGraphsPerNode[intermediateNode]) { - score = scaled_sigmoid( - inverse_scaled_sigmoid(score ?? 0) + - inverse_scaled_sigmoid(this.originalAnalyses[supportGraph].score), - ); - } - newResultObject[`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}`].analyses[0].score = score; - } - - } else { - firstEdges.forEach(edge => newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`].edges.add(edge)); - secondEdges.forEach(edge => newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`].edges.add(edge)); - } - } - } - } else { + + // continue creating path if we haven't reached end yet + if (node !== kgDst) { for (const neighbor in dfsNodes[node]) { if (!path.includes(neighbor)) { stack.push({ node: neighbor, path: [...path, neighbor] }); } } + continue; + } + + // path to dest too short + if (path.length <= 2) { + continue; + } + + // loop through all intermediate nodes in path to dest + for (let i = 1; i < path.length - 1; i++) { + const intermediateNode = path[i]; + const firstEdges: string[] = []; + const secondEdges: string[] = []; + for (let j = 0; j < i; j++) { + for (let edge of dfsNodes[path[j]][path[j + 1]]) { + firstEdges.push(edge); + } + } + for (let j = i; j < path.length - 1; j++) { + for (let edge of dfsNodes[path[j]][path[j + 1]]) { + secondEdges.push(edge); + } + } + + if (`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}` in newResultObject) { + firstEdges.forEach(edge => newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`].edges.add(edge)); + secondEdges.forEach(edge => newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`].edges.add(edge)); + continue; + } + + // create new edges & aux graph + newResultObject[`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}`] = { + node_bindings: { + [this.mainEdge.subject]: [{ id: kgSrc }], + [this.mainEdge.object]: [{ id: kgDst }], + [this.unpinnedNodeId]: [{ id: intermediateNode }] + }, + analyses: [{ + resource_id: "infores:biothings-explorer", + edge_bindings: { + [this.mainEdgeId]: [{ id: kgEdge }], + [this.intermediateEdges[0][0]]: [{ id: `pathfinder-${kgSrc}-${intermediateNode}` }], + [this.intermediateEdges[1][0]]: [{ id: `pathfinder-${intermediateNode}-${kgDst}` }], + }, + score: undefined + }], + }; + creativeResponse.message.knowledge_graph.edges[`pathfinder-${kgSrc}-${intermediateNode}`] = { + predicate: 'biolink:related_to', + subject: kgSrc, + object: intermediateNode, + sources: [ + { + resource_id: this.options.provenanceUsesServiceProvider + ? 'infores:service-provider-trapi' + : 'infores:biothings-explorer', + resource_role: 'primary_knowledge_source', + }, + ], + attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${kgSrc}-${intermediateNode}-support`] }], + }; + creativeResponse.message.knowledge_graph.edges[`pathfinder-${intermediateNode}-${kgDst}`] = { + predicate: 'biolink:related_to', + subject: intermediateNode, + object: kgDst, + sources: [ + { + resource_id: this.options.provenanceUsesServiceProvider + ? 'infores:service-provider-trapi' + : 'infores:biothings-explorer', + resource_role: 'primary_knowledge_source', + }, + ], + attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${intermediateNode}-${kgDst}-support`] }], + }; + newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`] = { edges: new Set(firstEdges) }; + newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`] = { edges: new Set(secondEdges) }; + + // calculate score + if (supportGraphsPerNode[intermediateNode]?.size > 0) { + let score: number | undefined = undefined; + for (const supportGraph of supportGraphsPerNode[intermediateNode]) { + score = scaled_sigmoid( + inverse_scaled_sigmoid(score ?? 0) + + inverse_scaled_sigmoid(this.originalAnalyses[supportGraph].score), + ); + } + newResultObject[`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}`].analyses[0].score = score; + } } } From e4e1a3a145b1e8115973b9bf0e91c09f5454a328 Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Tue, 2 Apr 2024 16:47:38 -0700 Subject: [PATCH 15/27] variable names, cleaning up more loops --- src/inferred_mode/pathfinder.ts | 29 +++++++++++++---------------- 1 file changed, 13 insertions(+), 16 deletions(-) diff --git a/src/inferred_mode/pathfinder.ts b/src/inferred_mode/pathfinder.ts index 262864e0..b5f3a9b5 100644 --- a/src/inferred_mode/pathfinder.ts +++ b/src/inferred_mode/pathfinder.ts @@ -127,19 +127,20 @@ export default class PathfinderQueryHandler { const kgEdge = creativeResponse.message.results[0].analyses[0].edge_bindings[this.mainEdgeId][0].id; const kgSrc = creativeResponse.message.results[0].node_bindings[this.mainEdge.subject][0].id; const kgDst = creativeResponse.message.results[0].node_bindings[this.mainEdge.object][0].id; - const dfsNodes: DfsGraph = {}; + const dfsGraph: DfsGraph = {}; const supportGraphsPerNode: { [node: string]: Set } = {}; - for (const supportGraph of (creativeResponse.message.knowledge_graph.edges[kgEdge]?.attributes?.find(attr => attr.attribute_type_id === 'biolink:support_graphs')?.value ?? []) as string[]) { + const supportGraphs = (creativeResponse.message.knowledge_graph.edges[kgEdge]?.attributes?.find(attr => attr.attribute_type_id === 'biolink:support_graphs')?.value ?? []) as string[]; + for (const supportGraph of supportGraphs) { const auxGraph = (creativeResponse.message.auxiliary_graphs ?? {})[supportGraph]; for (const subEdge of auxGraph.edges) { const kgSubEdge = creativeResponse.message.knowledge_graph.edges[subEdge]; - if (!dfsNodes[kgSubEdge.subject]) { - dfsNodes[kgSubEdge.subject] = {}; + if (!dfsGraph[kgSubEdge.subject]) { + dfsGraph[kgSubEdge.subject] = {}; } - if (!dfsNodes[kgSubEdge.subject][kgSubEdge.object]) { - dfsNodes[kgSubEdge.subject][kgSubEdge.object] = []; + if (!dfsGraph[kgSubEdge.subject][kgSubEdge.object]) { + dfsGraph[kgSubEdge.subject][kgSubEdge.object] = []; } - dfsNodes[kgSubEdge.subject][kgSubEdge.object].push(subEdge); + dfsGraph[kgSubEdge.subject][kgSubEdge.object].push(subEdge); if (!supportGraphsPerNode[kgSubEdge.subject]) { supportGraphsPerNode[kgSubEdge.subject] = new Set(); @@ -152,7 +153,7 @@ export default class PathfinderQueryHandler { debug(message1); this.logs.push(new LogEntry('INFO', null, message1).getLog()); - const { results: newResultObject, graphs: newAuxGraphs } = this._searchForIntermediates(creativeResponse, dfsNodes, supportGraphsPerNode, kgSrc, kgDst, kgEdge); + const { results: newResultObject, graphs: newAuxGraphs } = this._searchForIntermediates(creativeResponse, dfsGraph, supportGraphsPerNode, kgSrc, kgDst, kgEdge); creativeResponse.message.results = Object.values(newResultObject).sort((a, b) => (b.analyses[0].score ?? 0) - (a.analyses[0].score ?? 0)).slice(0, this.CREATIVE_LIMIT); creativeResponse.description = `Query processed successfully, retrieved ${creativeResponse.message.results.length} results.` @@ -172,7 +173,7 @@ export default class PathfinderQueryHandler { return creativeResponse; } - _searchForIntermediates(creativeResponse: TrapiResponse, dfsNodes: DfsGraph, supportGraphsPerNode: { [node: string]: Set }, kgSrc: string, kgDst: string, kgEdge: string): ResultAuxObject { + _searchForIntermediates(creativeResponse: TrapiResponse, dfsGraph: DfsGraph, supportGraphsPerNode: { [node: string]: Set }, kgSrc: string, kgDst: string, kgEdge: string): ResultAuxObject { const span = Telemetry.startSpan({ description: 'pathfinderIntermediateSearch' }); // perform dfs @@ -184,7 +185,7 @@ export default class PathfinderQueryHandler { // continue creating path if we haven't reached end yet if (node !== kgDst) { - for (const neighbor in dfsNodes[node]) { + for (const neighbor in dfsGraph[node]) { if (!path.includes(neighbor)) { stack.push({ node: neighbor, path: [...path, neighbor] }); } @@ -203,14 +204,10 @@ export default class PathfinderQueryHandler { const firstEdges: string[] = []; const secondEdges: string[] = []; for (let j = 0; j < i; j++) { - for (let edge of dfsNodes[path[j]][path[j + 1]]) { - firstEdges.push(edge); - } + firstEdges.push.apply(firstEdges, dfsGraph[path[j]][path[j+1]]); } for (let j = i; j < path.length - 1; j++) { - for (let edge of dfsNodes[path[j]][path[j + 1]]) { - secondEdges.push(edge); - } + secondEdges.push.apply(firstEdges, dfsGraph[path[j]][path[j+1]]); } if (`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}` in newResultObject) { From dd27a9d7b8ea281464cbd1aba7864f3389bafa77 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Tue, 2 Apr 2024 23:35:15 -0700 Subject: [PATCH 16/27] feat: add pathfinder templates for chem-gene --- data/templateGroups.json | 3 +- .../Pathfinder/pf-chem-gene-gene-gene.json | 45 +++++++++++++++++++ .../Pathfinder/pf-chem-gene-gene.json | 39 ++++++++++++++++ 3 files changed, 86 insertions(+), 1 deletion(-) create mode 100644 data/templates/Pathfinder/pf-chem-gene-gene-gene.json create mode 100644 data/templates/Pathfinder/pf-chem-gene-gene.json diff --git a/data/templateGroups.json b/data/templateGroups.json index afb5409c..ffdf1810 100644 --- a/data/templateGroups.json +++ b/data/templateGroups.json @@ -76,7 +76,8 @@ "predicate": ["related_to"], "object": ["Gene", "Protein"], "templates": [ - + "pf-chem-gene-gene.json", + "pf-chem-gene-gene-gene.json" ] }, { diff --git a/data/templates/Pathfinder/pf-chem-gene-gene-gene.json b/data/templates/Pathfinder/pf-chem-gene-gene-gene.json new file mode 100644 index 00000000..5103208c --- /dev/null +++ b/data/templates/Pathfinder/pf-chem-gene-gene-gene.json @@ -0,0 +1,45 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories":["biolink:ChemicalEntity"] + }, + "nA": { + "categories":["biolink:Gene", "biolink:Protein"] + }, + "nB": { + "categories":["biolink:Gene", "biolink:Protein"] + }, + "creativeQueryObject": { + "categories":["biolink:Gene", "biolink:Protein"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "nA", + "predicates": [ + "biolink:regulates", + "biolink:affects", + "biolink:interacts_with" + ] + }, + "eB": { + "subject": "nA", + "object": "nB", + "predicates": [ + "biolink:regulates" + ] + }, + "eC": { + "subject": "nB", + "object": "creativeQueryObject", + "predicates": [ + "biolink:regulates" + ] + } + } + } + } +} \ No newline at end of file diff --git a/data/templates/Pathfinder/pf-chem-gene-gene.json b/data/templates/Pathfinder/pf-chem-gene-gene.json new file mode 100644 index 00000000..9fe30f19 --- /dev/null +++ b/data/templates/Pathfinder/pf-chem-gene-gene.json @@ -0,0 +1,39 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories":["biolink:ChemicalEntity"] + }, + "nA": { + "categories":["biolink:Gene", "biolink:Protein"] + }, + "creativeQueryObject": { + "categories":["biolink:Gene", "biolink:Protein"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "nA", + "predicates": [ + "biolink:regulates", + "biolink:affects", + "biolink:interacts_with" + ] + }, + "eB": { + "subject": "nA", + "object": "creativeQueryObject", + "predicates": [ + "biolink:regulates", + "biolink:regulated_by", + "biolink:affects", + "biolink:affected_by", + "biolink:interacts_with" + ] + } + } + } + } +} \ No newline at end of file From c9c9e8c2cf687ace574cc574ef8a4ee0f9df742d Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Tue, 2 Apr 2024 23:59:42 -0700 Subject: [PATCH 17/27] chore: remove extra predicate from pathfinder template --- data/templates/Pathfinder/pf-drug-gene-disease.json | 1 - 1 file changed, 1 deletion(-) diff --git a/data/templates/Pathfinder/pf-drug-gene-disease.json b/data/templates/Pathfinder/pf-drug-gene-disease.json index e5032697..a56433c2 100644 --- a/data/templates/Pathfinder/pf-drug-gene-disease.json +++ b/data/templates/Pathfinder/pf-drug-gene-disease.json @@ -30,7 +30,6 @@ "biolink:gene_associated_with_condition", "biolink:biomarker_for", "biolink:affects", - "biolink:causes", "biolink:contributes_to" ] } From 6f84108f1d7d11bad6f727f5875276fe806c8235 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Wed, 3 Apr 2024 00:07:54 -0700 Subject: [PATCH 18/27] feat: add pathfinder templates for disease-disease --- data/templateGroups.json | 3 ++- .../Pathfinder/pf-disease-gene-disease.json | 27 +++++++++++++++++++ .../Pathfinder/pf-disease-seqvar-disease.json | 27 +++++++++++++++++++ 3 files changed, 56 insertions(+), 1 deletion(-) create mode 100644 data/templates/Pathfinder/pf-disease-gene-disease.json create mode 100644 data/templates/Pathfinder/pf-disease-seqvar-disease.json diff --git a/data/templateGroups.json b/data/templateGroups.json index ffdf1810..9afceb01 100644 --- a/data/templateGroups.json +++ b/data/templateGroups.json @@ -91,7 +91,8 @@ "DiseaseOrPhenotypicFeature" ], "templates": [ - + "pf-disease-seqvar-disease.json", + "pf-disease-gene-disease.json" ] }, { diff --git a/data/templates/Pathfinder/pf-disease-gene-disease.json b/data/templates/Pathfinder/pf-disease-gene-disease.json new file mode 100644 index 00000000..76c44b94 --- /dev/null +++ b/data/templates/Pathfinder/pf-disease-gene-disease.json @@ -0,0 +1,27 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories":["biolink:DiseaseOrPhenotypicFeature"] + }, + "nA": { + "categories":["biolink:Gene", "biolink:Protein"] + }, + "creativeQueryObject": { + "categories":["biolink:DiseaseOrPhenotypicFeature"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "nA" + }, + "eB": { + "subject": "nA", + "object": "creativeQueryObject" + } + } + } + } +} \ No newline at end of file diff --git a/data/templates/Pathfinder/pf-disease-seqvar-disease.json b/data/templates/Pathfinder/pf-disease-seqvar-disease.json new file mode 100644 index 00000000..08ebada4 --- /dev/null +++ b/data/templates/Pathfinder/pf-disease-seqvar-disease.json @@ -0,0 +1,27 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories":["biolink:DiseaseOrPhenotypicFeature"] + }, + "nA": { + "categories":["biolink:SequenceVariant"] + }, + "creativeQueryObject": { + "categories":["biolink:DiseaseOrPhenotypicFeature"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "nA" + }, + "eB": { + "subject": "nA", + "object": "creativeQueryObject" + } + } + } + } +} \ No newline at end of file From fd7bd75cadbf411b02b31fb298f10c245624ecae Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Wed, 3 Apr 2024 18:04:00 -0700 Subject: [PATCH 19/27] fix pathfinder improt --- src/inferred_mode/pathfinder.ts | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/inferred_mode/pathfinder.ts b/src/inferred_mode/pathfinder.ts index b5f3a9b5..89fcd140 100644 --- a/src/inferred_mode/pathfinder.ts +++ b/src/inferred_mode/pathfinder.ts @@ -1,8 +1,9 @@ -import TRAPIQueryHandler, { QueryHandlerOptions } from '../index'; +import TRAPIQueryHandler from '../index'; import { TrapiResponse, TrapiQEdge, TrapiResult, TrapiQueryGraph, TrapiQNode, TrapiAnalysis } from '../types'; import InferredQueryHandler from './inferred_mode'; import { scaled_sigmoid, inverse_scaled_sigmoid } from '../results_assembly/score'; import { LogEntry, StampedLog, Telemetry } from '@biothings-explorer/utils'; +import { QueryHandlerOptions } from '@biothings-explorer/types'; import Debug from 'debug'; const debug = Debug('bte:biothings-explorer-trapi:pathfinder'); From 080de45266082872582949cfc2c791911c1aac90 Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Thu, 4 Apr 2024 16:00:57 -0700 Subject: [PATCH 20/27] fix push call --- src/inferred_mode/pathfinder.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/inferred_mode/pathfinder.ts b/src/inferred_mode/pathfinder.ts index 89fcd140..6c427f1f 100644 --- a/src/inferred_mode/pathfinder.ts +++ b/src/inferred_mode/pathfinder.ts @@ -208,7 +208,7 @@ export default class PathfinderQueryHandler { firstEdges.push.apply(firstEdges, dfsGraph[path[j]][path[j+1]]); } for (let j = i; j < path.length - 1; j++) { - secondEdges.push.apply(firstEdges, dfsGraph[path[j]][path[j+1]]); + secondEdges.push.apply(secondEdges, dfsGraph[path[j]][path[j+1]]); } if (`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}` in newResultObject) { From 4a119a278b2d8b6c6fd1d0651ae259c0176274be Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Thu, 4 Apr 2024 17:29:40 -0700 Subject: [PATCH 21/27] implement pruning for pathfinder --- src/inferred_mode/pathfinder.ts | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/src/inferred_mode/pathfinder.ts b/src/inferred_mode/pathfinder.ts index 6c427f1f..07b10d9b 100644 --- a/src/inferred_mode/pathfinder.ts +++ b/src/inferred_mode/pathfinder.ts @@ -86,6 +86,9 @@ export default class PathfinderQueryHandler { this.parse(creativeResponse); + // prune KG + inferredQueryHandler.pruneKnowledgeGraph(creativeResponse); + // logs creativeResponse.logs = this.logs.map(log => log.toJSON()); @@ -159,11 +162,18 @@ export default class PathfinderQueryHandler { creativeResponse.message.results = Object.values(newResultObject).sort((a, b) => (b.analyses[0].score ?? 0) - (a.analyses[0].score ?? 0)).slice(0, this.CREATIVE_LIMIT); creativeResponse.description = `Query processed successfully, retrieved ${creativeResponse.message.results.length} results.` - const finalNewAuxGraphs: { [id: string]: { edges: string[] } } = newAuxGraphs as any; - for (const auxGraph in finalNewAuxGraphs) { - finalNewAuxGraphs[auxGraph].edges = Array.from(finalNewAuxGraphs[auxGraph].edges); + const finalNewAuxGraphs: { [id: string]: { edges: string[] } } = {}; + for (const res in creativeResponse.message.results) { + const edges = [...creativeResponse.message.results[res].analyses[0].edge_bindings[this.intermediateEdges[0][0]], ...creativeResponse.message.results[res].analyses[0].edge_bindings[this.intermediateEdges[1][0]]]; + for (const edge of edges) { + const auxGraph = creativeResponse.message.knowledge_graph.edges[edge.id].attributes.find(attr => attr.attribute_type_id === 'biolink:support_graphs')?.value[0]; + finalNewAuxGraphs[auxGraph] = { edges: Array.from(newAuxGraphs[auxGraph].edges) }; + } } + Object.assign(creativeResponse.message.auxiliary_graphs!, finalNewAuxGraphs); + // prune main aux graphs + creativeResponse.message.knowledge_graph.edges[kgEdge].attributes.find(attr => attr.attribute_type_id === 'biolink:support_graphs').value = Object.keys(finalNewAuxGraphs); const message2 = `[Pathfinder]: Pathfinder found ${creativeResponse.message.results.length} intermediate nodes and created ${Object.keys(finalNewAuxGraphs).length} support graphs.`; debug(message2); From fbd45582de873987cb069b3e18cb48652b000b95 Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Thu, 4 Apr 2024 17:57:03 -0700 Subject: [PATCH 22/27] fix aux graph for main edge --- src/inferred_mode/pathfinder.ts | 38 +++++++++++++++++++++++++-------- 1 file changed, 29 insertions(+), 9 deletions(-) diff --git a/src/inferred_mode/pathfinder.ts b/src/inferred_mode/pathfinder.ts index 07b10d9b..ae455a68 100644 --- a/src/inferred_mode/pathfinder.ts +++ b/src/inferred_mode/pathfinder.ts @@ -164,16 +164,15 @@ export default class PathfinderQueryHandler { const finalNewAuxGraphs: { [id: string]: { edges: string[] } } = {}; for (const res in creativeResponse.message.results) { - const edges = [...creativeResponse.message.results[res].analyses[0].edge_bindings[this.intermediateEdges[0][0]], ...creativeResponse.message.results[res].analyses[0].edge_bindings[this.intermediateEdges[1][0]]]; - for (const edge of edges) { - const auxGraph = creativeResponse.message.knowledge_graph.edges[edge.id].attributes.find(attr => attr.attribute_type_id === 'biolink:support_graphs')?.value[0]; - finalNewAuxGraphs[auxGraph] = { edges: Array.from(newAuxGraphs[auxGraph].edges) }; + for (const eb of Object.values(creativeResponse.message.results[res].analyses[0].edge_bindings)) { + for (const edge of eb) { + const auxGraph = creativeResponse.message.knowledge_graph.edges[edge.id].attributes.find(attr => attr.attribute_type_id === 'biolink:support_graphs')?.value[0]; + finalNewAuxGraphs[auxGraph] = { edges: Array.from(newAuxGraphs[auxGraph].edges) }; + } } } Object.assign(creativeResponse.message.auxiliary_graphs!, finalNewAuxGraphs); - // prune main aux graphs - creativeResponse.message.knowledge_graph.edges[kgEdge].attributes.find(attr => attr.attribute_type_id === 'biolink:support_graphs').value = Object.keys(finalNewAuxGraphs); const message2 = `[Pathfinder]: Pathfinder found ${creativeResponse.message.results.length} intermediate nodes and created ${Object.keys(finalNewAuxGraphs).length} support graphs.`; debug(message2); @@ -222,8 +221,14 @@ export default class PathfinderQueryHandler { } if (`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}` in newResultObject) { - firstEdges.forEach(edge => newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`].edges.add(edge)); - secondEdges.forEach(edge => newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`].edges.add(edge)); + firstEdges.forEach(edge => { + newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`].edges.add(edge); + newAuxGraphs[`pathfinder-${intermediateNode}-support`].edges.add(edge) + }); + secondEdges.forEach(edge => { + newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`].edges.add(edge); + newAuxGraphs[`pathfinder-${intermediateNode}-support`].edges.add(edge); + }); continue; } @@ -237,7 +242,7 @@ export default class PathfinderQueryHandler { analyses: [{ resource_id: "infores:biothings-explorer", edge_bindings: { - [this.mainEdgeId]: [{ id: kgEdge }], + [this.mainEdgeId]: [{ id: `pathfinder-${intermediateNode}` }], [this.intermediateEdges[0][0]]: [{ id: `pathfinder-${kgSrc}-${intermediateNode}` }], [this.intermediateEdges[1][0]]: [{ id: `pathfinder-${intermediateNode}-${kgDst}` }], }, @@ -272,8 +277,23 @@ export default class PathfinderQueryHandler { ], attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${intermediateNode}-${kgDst}-support`] }], }; + creativeResponse.message.knowledge_graph.edges[`pathfinder-${intermediateNode}`] = { + predicate: 'biolink:related_to', + subject: intermediateNode, + object: kgDst, + sources: [ + { + resource_id: this.options.provenanceUsesServiceProvider + ? 'infores:service-provider-trapi' + : 'infores:biothings-explorer', + resource_role: 'primary_knowledge_source', + }, + ], + attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${intermediateNode}-support`] }], + }; newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`] = { edges: new Set(firstEdges) }; newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`] = { edges: new Set(secondEdges) }; + newAuxGraphs[`pathfinder-${intermediateNode}-support`] = { edges: new Set([...firstEdges, ...secondEdges]) }; // calculate score if (supportGraphsPerNode[intermediateNode]?.size > 0) { From 2fc3fda0456c9a548cef90062222d3f7aa19d86a Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Thu, 4 Apr 2024 18:35:09 -0700 Subject: [PATCH 23/27] feat: add pathfinder gene-disease templates --- data/templateGroups.json | 3 +- .../Pathfinder/pf-gene-anything-disease.json | 27 +++++++++ .../Pathfinder/pf-gene-chem-gene-disease.json | 57 +++++++++++++++++++ 3 files changed, 86 insertions(+), 1 deletion(-) create mode 100644 data/templates/Pathfinder/pf-gene-anything-disease.json create mode 100644 data/templates/Pathfinder/pf-gene-chem-gene-disease.json diff --git a/data/templateGroups.json b/data/templateGroups.json index 9afceb01..4ff8b981 100644 --- a/data/templateGroups.json +++ b/data/templateGroups.json @@ -104,7 +104,8 @@ "DiseaseOrPhenotypicFeature" ], "templates": [ - + "pf-gene-anything-disease.json", + "pf-gene-chem-gene-disease.json" ] } ] diff --git a/data/templates/Pathfinder/pf-gene-anything-disease.json b/data/templates/Pathfinder/pf-gene-anything-disease.json new file mode 100644 index 00000000..d3d3bd6c --- /dev/null +++ b/data/templates/Pathfinder/pf-gene-anything-disease.json @@ -0,0 +1,27 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories":["biolink:Gene", "biolink:Protein"] + }, + "nA": { + "categories":["biolink:NamedThing"] + }, + "creativeQueryObject": { + "categories":["biolink:DiseaseOrPhenotypicFeature"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "nA" + }, + "eB": { + "subject": "nA", + "object": "creativeQueryObject" + } + } + } + } +} \ No newline at end of file diff --git a/data/templates/Pathfinder/pf-gene-chem-gene-disease.json b/data/templates/Pathfinder/pf-gene-chem-gene-disease.json new file mode 100644 index 00000000..3601b12f --- /dev/null +++ b/data/templates/Pathfinder/pf-gene-chem-gene-disease.json @@ -0,0 +1,57 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories":["biolink:Gene", "biolink:Protein"] + }, + "nA": { + "categories":["biolink:ChemicalEntity"] + }, + "nB": { + "categories":["biolink:Gene", "biolink:Protein"] + }, + "creativeQueryObject": { + "categories":["biolink:DiseaseOrPhenotypicFeature"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "nA", + "predicates": [ + "biolink:regulates", + "biolink:regulated_by", + "biolink:affects", + "biolink:affected_by", + "biolink:interacts_with", + "biolink:correlated_with" + ] + }, + "eB": { + "subject": "nA", + "object": "nB", + "predicates": [ + "biolink:regulates", + "biolink:regulated_by", + "biolink:affects", + "biolink:affected_by", + "biolink:interacts_with", + "biolink:correlated_with" + ] + }, + "eC": { + "subject": "nB", + "object": "creativeQueryObject", + "predicates": [ + "biolink:gene_associated_with_condition", + "biolink:affects", + "biolink:disrupts", + "biolink:contributes_to", + "biolink:biomarker_for" + ] + } + } + } + } +} \ No newline at end of file From be78fecf324013ab706c45f3cd6b8c8cfef1b430 Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Fri, 5 Apr 2024 19:10:57 -0700 Subject: [PATCH 24/27] fix node in PF edge --- src/inferred_mode/pathfinder.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/inferred_mode/pathfinder.ts b/src/inferred_mode/pathfinder.ts index ae455a68..889f099b 100644 --- a/src/inferred_mode/pathfinder.ts +++ b/src/inferred_mode/pathfinder.ts @@ -279,7 +279,7 @@ export default class PathfinderQueryHandler { }; creativeResponse.message.knowledge_graph.edges[`pathfinder-${intermediateNode}`] = { predicate: 'biolink:related_to', - subject: intermediateNode, + subject: kgSrc, object: kgDst, sources: [ { From 576721e6e20a027468d5ad760455332844f8c131 Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Fri, 5 Apr 2024 19:18:57 -0700 Subject: [PATCH 25/27] more pathfinder testing --- __test__/unittest/pathfinder.test.ts | 25 ++++++++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) diff --git a/__test__/unittest/pathfinder.test.ts b/__test__/unittest/pathfinder.test.ts index d3169e26..4cd9267f 100644 --- a/__test__/unittest/pathfinder.test.ts +++ b/__test__/unittest/pathfinder.test.ts @@ -70,6 +70,29 @@ describe('Test Pathfinder', () => { const pfResponse = pfHandler.parse(creativeResult1); expect(pfResponse.message.results.length).toEqual(500); - expect(Object.keys(pfResponse.message.auxiliary_graphs!).length).toEqual(2119); + expect(Object.keys(pfResponse.message.auxiliary_graphs!).length).toEqual(2363); + + const n0 = pfResponse.message.results[0].node_bindings['n0'][0].id; + const un = pfResponse.message.results[0].node_bindings['un'][0].id; + const n2 = pfResponse.message.results[0].node_bindings['n2'][0].id; + + const n0ToUn = pfResponse.message.results[0].analyses[0].edge_bindings['e0'][0].id; + const unToN2 = pfResponse.message.results[0].analyses[0].edge_bindings['e1'][0].id; + const n0ToN2 = pfResponse.message.results[0].analyses[0].edge_bindings['e2'][0].id; + + // check nodes on edges + expect(pfResponse.message.knowledge_graph.edges[n0ToUn].subject).toEqual(n0); + expect(pfResponse.message.knowledge_graph.edges[n0ToUn].object).toEqual(un); + expect(pfResponse.message.knowledge_graph.edges[unToN2].subject).toEqual(un); + expect(pfResponse.message.knowledge_graph.edges[unToN2].object).toEqual(n2); + expect(pfResponse.message.knowledge_graph.edges[n0ToN2].subject).toEqual(n0); + expect(pfResponse.message.knowledge_graph.edges[n0ToN2].object).toEqual(n2); + + // check that aux graphs are correct + const n0ToUnAux = pfResponse.message.knowledge_graph.edges[n0ToUn].attributes?.find(s => s.attribute_type_id === 'biolink:support_graphs')?.value as string; + const unToN2Aux = pfResponse.message.knowledge_graph.edges[unToN2].attributes?.find(s => s.attribute_type_id === 'biolink:support_graphs')?.value as string; + const n0ToN2Aux = pfResponse.message.knowledge_graph.edges[n0ToN2].attributes?.find(s => s.attribute_type_id === 'biolink:support_graphs')?.value as string; + + expect(pfResponse.message.auxiliary_graphs![n0ToN2Aux].edges.sort()).toEqual([...pfResponse.message.auxiliary_graphs![n0ToUnAux].edges, ...pfResponse.message.auxiliary_graphs![unToN2Aux].edges].sort()); }); }); From f861412af179564a72966024489dd82c477f0c25 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Wed, 10 Apr 2024 23:52:16 -0700 Subject: [PATCH 26/27] chore: fix error with missing pathfinder flag for one group --- data/templateGroups.json | 1 + 1 file changed, 1 insertion(+) diff --git a/data/templateGroups.json b/data/templateGroups.json index 4ff8b981..adc7591a 100644 --- a/data/templateGroups.json +++ b/data/templateGroups.json @@ -70,6 +70,7 @@ }, { "name": "Pathfinder: Chem-Gene", + "pathfinder": true, "subject": ["Drug", "SmallMolecule", "ChemicalEntity", "ComplexMolecularMixture", "MolecularMixture" ], From 82bd2d691f3997acab186cf384cc0618b3ec40f5 Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Tue, 16 Apr 2024 19:21:12 -0700 Subject: [PATCH 27/27] fix aux graph while loop --- src/inferred_mode/inferred_mode.ts | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/src/inferred_mode/inferred_mode.ts b/src/inferred_mode/inferred_mode.ts index dd5178a0..abcb0415 100644 --- a/src/inferred_mode/inferred_mode.ts +++ b/src/inferred_mode/inferred_mode.ts @@ -293,6 +293,7 @@ export default class InferredQueryHandler { // modified count used for pathfinder const pfIntermediateSet = new Set(); + let auxGraphSuffixes: {[inferredEdgeID: string]: number} = {}; // add results newResponse.message.results.forEach((result) => { const translatedResult: TrapiResult = { @@ -356,13 +357,9 @@ export default class InferredQueryHandler { attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [] }], }; } - let auxGraphSuffix = 0; - while ( - Object.keys(combinedResponse.message.auxiliary_graphs).includes(`${inferredEdgeID}-support${auxGraphSuffix}`) - ) { - auxGraphSuffix += 1; - } - const auxGraphID = `${inferredEdgeID}-support${auxGraphSuffix}`; + if (!auxGraphSuffixes[inferredEdgeID]) auxGraphSuffixes[inferredEdgeID] = 0; + const auxGraphID = `${inferredEdgeID}-support${auxGraphSuffixes[inferredEdgeID]}`; + auxGraphSuffixes[inferredEdgeID]++; (combinedResponse.message.knowledge_graph.edges[inferredEdgeID].attributes[0].value as string[]).push( auxGraphID, );