diff --git a/CHANGELOG.md b/CHANGELOG.md index 6a180698..118d39dc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,29 @@ All notable changes to this project will be documented in this file. See [standard-version](https://github.com/conventional-changelog/standard-version) for commit guidelines. +## [1.18.0](https://github.com/biothings/bte_trapi_query_graph_handler/compare/v1.17.6...v1.18.0) (2021-08-20) + + +### Features + +* add caching param in cache handler ([bfaa179](https://github.com/biothings/bte_trapi_query_graph_handler/commit/bfaa17908a0c7ef584b146390659186fe06896dc)) +* add workflow validation for trapi v1.2 ([76a4164](https://github.com/biothings/bte_trapi_query_graph_handler/commit/76a4164bcacfc1a4c9dc74fb5d4024ece7ef0e08)) + + +### Bug Fixes + +* :bug: check if cachedQueryResults is empty ([062d931](https://github.com/biothings/bte_trapi_query_graph_handler/commit/062d931bcc9d51e966fb65e470bd1897588ee312)) +* :bug: set a default caching expiration ([173f34b](https://github.com/biothings/bte_trapi_query_graph_handler/commit/173f34b51b7a033e4a4a77dae766473ae45d5d6e)) +* biolink v2.1 related fixes ([ff15564](https://github.com/biothings/bte_trapi_query_graph_handler/commit/ff155648163f74ef209ed71666bce860fb5c7f26)) +* cache extra properties just in case ([344aabd](https://github.com/biothings/bte_trapi_query_graph_handler/commit/344aabd2037e172bd3f3970db1e31f0ac7ce00c6)) +* clone records recursively for caching ([b7a71c4](https://github.com/biothings/bte_trapi_query_graph_handler/commit/b7a71c49c7e29f124b87b6b73e2eed747844aa13)) +* code line length reformat ([7000a0b](https://github.com/biothings/bte_trapi_query_graph_handler/commit/7000a0b7eaaa0539648e2d6e231f8e871b941dd6)) +* correctly cache semanticType ([7d21651](https://github.com/biothings/bte_trapi_query_graph_handler/commit/7d21651fc013154d9704e22e89be800f968f3c08)) +* input->output for output node ([aa4a529](https://github.com/biothings/bte_trapi_query_graph_handler/commit/aa4a529a597efc5c33fddbed6796527e2ba7438d)) +* issue [#164](https://github.com/biothings/bte_trapi_query_graph_handler/issues/164). add score. rm unused methods. ([57b4c4b](https://github.com/biothings/bte_trapi_query_graph_handler/commit/57b4c4b756100bcd6faa40c83bc4f637cb752c79)) +* tests pass for issue [#164](https://github.com/biothings/bte_trapi_query_graph_handler/issues/164) ([8dfb3ca](https://github.com/biothings/bte_trapi_query_graph_handler/commit/8dfb3cabdee3e052793d503c7bf4eebddd99601e)) +* WIP for https://github.com/biothings/BioThings_Explorer_TRAPI/issues/164 ([97963b6](https://github.com/biothings/bte_trapi_query_graph_handler/commit/97963b6f3379de4f1ed7ff8e5bedbcd303f34271)) + ### [1.17.6](https://github.com/biothings/bte_trapi_query_graph_handler/compare/v1.17.5...v1.17.6) (2021-06-24) diff --git a/README.md b/README.md index ac58747a..6e57e0d4 100644 --- a/README.md +++ b/README.md @@ -19,22 +19,25 @@ npm i @biothings-explorer/query_graph_handler const handler = require("@biothings-explorer/query_graph_handler"); const queryHandler = new handler.TRAPIQueryHandler(); const oneHopQuery = { + "workflow": [ + {"id": "lookup"} + ], "message": { "query_graph": { "edges": { "e00": { "object": "n01", "subject": "n00", - "predicate": "biolink:functional_association" + "predicates": ["biolink:functional_association"] } }, "nodes": { "n00": { - "category": "biolink:Gene", - "id": "ENSEMBL:ENSG00000123374" + "categories": ["biolink:Gene"], + "ids": ["ENSEMBL:ENSG00000123374"] }, "n01": { - "category": "biolink:BiologicalProcess" + "categories": ["biolink:BiologicalProcess"] } } } @@ -50,6 +53,9 @@ console.log(queryHandler.getResponse()) ```json { + "workflow": [ + {"id": "lookup"} + ], "message": { "query_graph": { "edges": { @@ -1771,18 +1777,21 @@ console.log(queryHandler.getResponse()) const handler = require("@biothings-explorer/query_graph_handler"); const queryHandler = new handler.TRAPIQueryHandler(); const multiHopQuery = { + "workflow": [ + {"id": "lookup"} + ], "message": { "query_graph": { "nodes": { "n0": { - "category": "biolink:Disease", - "id": "MONDO:0005737" + "categories": ["biolink:Disease"], + "ids": ["MONDO:0005737"] }, "n1": { - "category": "biolink:Gene" + "categories": ["biolink:Gene"] }, "n2": { - "category": "biolink:ChemicalSubstance" + "categories": ["biolink:SmallMolecule"] } }, "edges": { @@ -1809,6 +1818,9 @@ console.log(queryHandler.getResponse()) ```json { + "workflow": [ + {"id": "lookup"} + ], "message": { "query_graph": { "nodes": { @@ -7461,18 +7473,21 @@ console.log(queryHandler.getResponse()) const handler = require("@biothings-explorer/query_graph_handler"); const queryHandler = new handler.TRAPIQueryHandler(); const branchedQuery = { + "workflow": [ + {"id": "lookup"} + ], "message": { "query_graph": { "nodes": { "n0": { - "category": "biolink:Disease", - "id": "MONDO:0005737" + "categories": ["biolink:Disease"], + "ids": ["MONDO:0005737"] }, "n1": { - "category": "biolink:Gene" + "categories": ["biolink:Gene"] }, "n2": { - "category": "biolink:ChemicalSubstance" + "categories": ["biolink:SmallMolecule"] } }, "edges": { @@ -7498,6 +7513,9 @@ console.log(queryHandler.getResponse()) ```json { + "workflow": [ + {"id": "lookup"} + ], "message": { "query_graph": { "nodes": { @@ -87547,22 +87565,25 @@ console.log(queryHandler.getResponse()) const handler = require("@biothings-explorer/query_graph_handler"); const queryHandler = new handler.TRAPIQueryHandler(); const multiPredicatesQuery = { + "workflow": [ + {"id": "lookup"} + ], "message": { "query_graph": { "nodes": { "n0": { - "category": "biolink:Disease", - "id": "MONDO:0005737" + "categories": ["biolink:Disease"], + "ids": ["MONDO:0005737"] }, "n1": { - "category": "biolink:ChemicalSubstance" + "categories": ["biolink:SmallMolecule"] } }, "edges": { "e01": { "subject": "n0", "object": "n1", - "predicate": ["biolink:treated_by", "biolink:affected_by"] + "predicates": ["biolink:treated_by", "biolink:affected_by"] } } } @@ -87572,4 +87593,3 @@ queryHandler.setQueryGraph(multiPredicatesQuery); await queryHandler.query(); console.log(queryHandler.getResponse()) ``` - diff --git a/__test__/integration/BatchEdgeQueryHandler.test.js b/__test__/integration/BatchEdgeQueryHandler.test.js index 71c54a00..01046556 100644 --- a/__test__/integration/BatchEdgeQueryHandler.test.js +++ b/__test__/integration/BatchEdgeQueryHandler.test.js @@ -11,7 +11,7 @@ describe("Testing BatchEdgeQueryHandler Module", () => { describe("Testing query function", () => { // test("test with one query edge", async () => { // let gene_node1 = new QNode("n1", { category: "Gene", id: "NCBIGene:1017" }); - // let chemical_node1 = new QNode("n3", { category: "ChemicalSubstance" }); + // let chemical_node1 = new QNode("n3", { category: "SmallMolecule" }); // const edge1 = new QEdge("e01", { subject: gene_node1, object: chemical_node1 }); // const exeEdge1 = new QExeEdge(edge1, false, undefined); // const batchHandler = new BatchEdgeQueryHandler(kg); diff --git a/__test__/integration/KnowledgeGraph.test.js b/__test__/integration/KnowledgeGraph.test.js index f82a196f..fa5cd156 100644 --- a/__test__/integration/KnowledgeGraph.test.js +++ b/__test__/integration/KnowledgeGraph.test.js @@ -1,118 +1,166 @@ const QNode = require("../../src/query_node"); const QEdge = require("../../src/query_edge"); -const KnowledgeGraph = require("../../src/knowledge_graph"); +const KnowledgeGraph = require("../../src/graph/knowledge_graph"); describe("Testing KnowledgeGraph Module", () => { - const gene_node1 = new QNode("n1", { categories: "Gene", ids: "NCBIGene:1017" }); - const chemical_node1 = new QNode("n3", { categories: "ChemicalSubstance" }); - const edge1 = new QEdge("e01", { subject: gene_node1, object: chemical_node1 }); - const record = { - "$edge_metadata": { - trapi_qEdge_obj: edge1, - source: "DGIdb", - api_name: "BioThings DGIDB API" - }, - "publications": ['PMID:123', 'PMID:1234'], - "interactionType": "inhibitor", - "$input": { - original: "SYMBOL:CDK2", - obj: [{ - primaryID: 'NCBIGene:1017', - label: "CDK2", - dbIDs: { - SYMBOL: "CDK2", - NCBIGene: "1017" + const nodeInput = { + "id": "PUBCHEM.COMPOUND:2662-n0", + "_primaryID": "PUBCHEM.COMPOUND:2662", + "_qgID": "n0", + "_curies": [ + "PUBCHEM.COMPOUND:2662", + "CHEMBL.COMPOUND:CHEMBL118", + "UNII:JCX84Q7J1L", + "CHEBI:41423", + "DRUGBANK:DB00482", + "MESH:C105934", + "MESH:D000068579", + "CAS:169590-42-5", + "CAS:184007-95-2", + "CAS:194044-54-7", + "DrugCentral:568", + "GTOPDB:2892", + "HMDB:HMDB0005014", + "KEGG.COMPOUND:C07589", + "INCHIKEY:RZEKVGVHFLEQIL-UHFFFAOYSA-N" + ], + "_names": [ + "Celecoxib", + "CELECOXIB", + "celecoxib", + "[OBSOLETE] celecoxib" + ], + "_semanticType": "SmallMolecule", + "_nodeAttributes": {}, + "_label": "Celecoxib", + "_sourceNodes": {}, + "_targetNodes": {}, + "_sourceQGNodes": {}, + "_targetQGNodes": {} + } + const trapiEdgeInput = { + id: 'PUBCHEM.COMPOUND:2662-biolink:activity_decreased_by-NCBIGene:771', + predicate: 'biolink:activity_decreased_by', + subject: 'PUBCHEM.COMPOUND:2662', + object: 'NCBIGene:771', + apis: {}, + sources: {}, + publications: {}, + attributes: { + attributes: [ + { + attribute_type_id: 'biolink:Attribute', + value: 'Ki', + value_type_id: 'EDAM:data_0006', + original_attribute_name: 'affinity_parameter', + value_url: null, + attribute_source: null, + description: null, }, - semanticType: "Gene", - curies: ['SYMBOL:CDK2', 'NCBIGene:1017'] - }] - }, - "$output": { - original: "CHEMBL.COMPOUND:CHEMBL744", - obj: [{ - primaryID: 'CHEMBL.COMPOUND:CHEMBL744', - label: "RILUZOLE", - dbIDs: { - "CHEMBL.COMPOUND": "CHEMBL744", - "PUBCHEM": "1234", - "name": "RILUZOLE" + { + attribute_type_id: 'biolink:knowledge_source', + value: ['PHAROS_1_norm_edges.jsonl'], + value_type_id: 'EDAM:data_0006', + original_attribute_name: 'knowledge_source', + value_url: null, + attribute_source: null, + description: null, + }, + { + attribute_type_id: 'biolink:aggregator_knowledge_source', + value: ['infores:pharos'], + value_type_id: 'biolink:InformationResource', + original_attribute_name: 'biolink:aggregator_knowledge_source', + value_url: null, + attribute_source: null, + description: null, + }, + { + attribute_type_id: 'biolink:Attribute', + value: 7.75, + value_type_id: 'EDAM:data_0006', + original_attribute_name: 'affinity', + value_url: null, + attribute_source: null, + description: null, }, - semanticType: "ChemicalSubstance", - curies: ['CHEMBL.COMPOUND:CHEMBL744', 'PUBCHEM:1234', "name:RILUZOLE"] - }] + { + attribute_type_id: 'biolink:publications', + value: [ + 'PMID:20605094', + 'PMID:21852133', + 'PMID:16290146', + 'PMID:23965175', + 'PMID:23965175', + 'PMID:24513184', + 'PMID:25766630', + 'PMID:23067387', + ], + value_type_id: 'EDAM:data_0006', + original_attribute_name: 'publications', + value_url: null, + attribute_source: null, + description: null, + }, + { + attribute_type_id: 'biolink:relation', + value: 'GAMMA:ki', + value_type_id: 'EDAM:data_0006', + original_attribute_name: 'relation', + value_url: null, + attribute_source: null, + description: null, + }, + { + attribute_type_id: 'biolink:aggregator_knowledge_source', + value: 'infores:automat.pharos', + value_type_id: 'biolink:InformationResource', + original_attribute_name: 'biolink:aggregator_knowledge_source', + value_url: null, + attribute_source: null, + description: null, + }, + ], }, - } - describe("Testing _createInputNode function", () => { - test("test when input with string, should output a hash of 40 characters", () => { + }; + + describe("Testing _createNode function", () => { + test("test creating node", () => { const kg = new KnowledgeGraph(); - const res = kg._createInputNode(record); - expect(res).toHaveProperty("categories", "biolink:Gene"); - expect(res).toHaveProperty("name", "CDK2"); - expect(res.attributes[0]).toHaveProperty("type", "biolink:id"); - expect(res.attributes[0]).toHaveProperty("value", ["SYMBOL:CDK2", "NCBIGene:1017"]) - }) - }) - - describe("Testing _createOutputNode function", () => { - test("test when input with string, should output a hash of 40 characters", () => { - const kg = new KnowledgeGraph(); - const res = kg._createOutputNode(record); - expect(res).toHaveProperty("categories", "biolink:ChemicalSubstance"); - expect(res).toHaveProperty("name", "RILUZOLE"); - expect(res.attributes[0]).toHaveProperty("type", "biolink:id"); - expect(res.attributes[0]).toHaveProperty("value", ['CHEMBL.COMPOUND:CHEMBL744', 'PUBCHEM:1234', "name:RILUZOLE"]) + const res = kg._createNode(nodeInput); + expect(res).toHaveProperty("name", "Celecoxib"); + expect(res).toHaveProperty('categories') + expect(res.categories[0]).toBe('biolink:SmallMolecule'); + expect(res).toHaveProperty('attributes'); }) }) describe("Testing _createAttributes function", () => { - test("test edge attribute provided_by and api are correctly found", () => { + test("test edge attributes", () => { const kg = new KnowledgeGraph(); - const res = kg._createAttributes(record); - expect(res.length).toBeGreaterThanOrEqual(2); - expect(res[0]).toHaveProperty("name", "provided_by"); - expect(res[0]).toHaveProperty("type", "biolink:provided_by"); - expect(res[0]).toHaveProperty("value", "DGIdb"); - expect(res[1]).toHaveProperty("name", "api"); - expect(res[1]).toHaveProperty("type", "bts:api"); - expect(res[1]).toHaveProperty("value", "BioThings DGIDB API"); - }) - - test("test edge attribute other than provided_by and api are correctly found", () => { - const kg = new KnowledgeGraph(); - const res = kg._createAttributes(record); - expect(res.length).toBeGreaterThan(2); - expect(res[2]).toHaveProperty("name", "publications"); - expect(res[2]).toHaveProperty("type", "biolink:publications"); - expect(res[2]).toHaveProperty("value", ['PMID:123', 'PMID:1234']); - expect(res[3]).toHaveProperty("name", "interactionType"); - expect(res[3]).toHaveProperty("type", "bts:interactionType"); - expect(res[3]).toHaveProperty("value", 'inhibitor'); + const res = kg._createAttributes(trapiEdgeInput); + expect(res.length).toBeGreaterThan(0); + for (let res_obj of res) { + expect(res_obj).toHaveProperty('attribute_type_id'); + expect(res_obj).toHaveProperty('value'); + expect(res_obj).toHaveProperty('value_type_id'); + } }) }) describe("Testing _createEdge function", () => { - test("test edge attribute provided_by and api are correctly found", () => { - const kg = new KnowledgeGraph(); - const res = kg._createAttributes(record); - expect(res.length).toBeGreaterThanOrEqual(2); - expect(res[0]).toHaveProperty("name", "provided_by"); - expect(res[0]).toHaveProperty("type", "biolink:provided_by"); - expect(res[0]).toHaveProperty("value", "DGIdb"); - expect(res[1]).toHaveProperty("name", "api"); - expect(res[1]).toHaveProperty("type", "bts:api"); - expect(res[1]).toHaveProperty("value", "BioThings DGIDB API"); - }) - - test("test edge attribute other than provided_by and api are correctly found", () => { + test("test creating edge", () => { const kg = new KnowledgeGraph(); - const res = kg._createAttributes(record); - expect(res.length).toBeGreaterThan(2); - expect(res[2]).toHaveProperty("name", "publications"); - expect(res[2]).toHaveProperty("type", "biolink:publications"); - expect(res[2]).toHaveProperty("value", ['PMID:123', 'PMID:1234']); - expect(res[3]).toHaveProperty("name", "interactionType"); - expect(res[3]).toHaveProperty("type", "bts:interactionType"); - expect(res[3]).toHaveProperty("value", 'inhibitor'); + const res = kg._createEdge(trapiEdgeInput); + expect(res).toHaveProperty("predicate", "biolink:activity_decreased_by"); + expect(res).toHaveProperty("subject", "PUBCHEM.COMPOUND:2662"); + expect(res).toHaveProperty("object", "NCBIGene:771"); + expect(res).toHaveProperty("attributes"); + for (let res_obj of res.attributes) { + expect(res_obj).toHaveProperty('attribute_type_id'); + expect(res_obj).toHaveProperty('value'); + expect(res_obj).toHaveProperty('value_type_id'); + } }) }) diff --git a/__test__/integration/QEdge2BTEEdgeHandler.test.js b/__test__/integration/QEdge2BTEEdgeHandler.test.js index e69005f4..2b56d153 100644 --- a/__test__/integration/QEdge2BTEEdgeHandler.test.js +++ b/__test__/integration/QEdge2BTEEdgeHandler.test.js @@ -32,8 +32,8 @@ describe("Testing NodeUpdateHandler Module", () => { gene_node1_with_id_annotated.setEquivalentIDs(node1_equivalent_ids); //gene_node2.setEquivalentIDs(node2_equivalent_ids); const invalid_node = new QNode("n3", { categories: "INVALID", curie: ["NCBIGene:1017", "NCBIGene:1018"] }) - const chemical_node1 = new QNode("n3", { categories: "ChemicalSubstance" }); - const chemical_node2 = new QNode("n4", { categories: "ChemicalSubstance", curie: "CHEMBL.COMPUND:CHEMBL744" }); + const chemical_node1 = new QNode("n3", { categories: "SmallMolecule" }); + const chemical_node2 = new QNode("n4", { categories: "SmallMolecule", curie: "CHEMBL.COMPUND:CHEMBL744" }); const edge1 = new QEdge("e01", { subject: gene_node1, object: chemical_node1 }); const edge2 = new QEdge("e02", { subject: gene_node1_with_id_annotated, object: chemical_node1 }); const edge3 = new QEdge('e04', { subject: gene_node2, object: chemical_node1 }); @@ -75,7 +75,7 @@ describe("Testing NodeUpdateHandler Module", () => { test("test edge with multiple curie input return an object with multiple key", async () => { const nodeUpdater = new NodeUpdateHandler([edge1]); - const res = await nodeUpdater._getEquivalentIDs({ "Gene": ["NCBIGene:1017", "NCBIGene:1018"], "ChemicalSubstance": ["PUBCHEM:5070"] }) + const res = await nodeUpdater._getEquivalentIDs({ "Gene": ["NCBIGene:1017", "NCBIGene:1018"], "SmallMolecule": ["PUBCHEM:5070"] }) expect(res).toHaveProperty("NCBIGene:1017"); expect(res).toHaveProperty("NCBIGene:1018"); expect(res).toHaveProperty("PUBCHEM:5070"); diff --git a/__test__/integration/QueryEdge.test.js b/__test__/integration/QueryEdge.test.js index 5918ba63..1498f805 100644 --- a/__test__/integration/QueryEdge.test.js +++ b/__test__/integration/QueryEdge.test.js @@ -3,7 +3,7 @@ const QEdge = require("../../src/query_edge"); describe("Testing QueryEdge Module", () => { const gene_node1 = new QNode("n1", { categories: "Gene", ids: "NCBIGene:1017" }); - const type_node = new QNode("n2", { categories: "ChemicalSubstance" }); + const type_node = new QNode("n2", { categories: "SmallMolecule" }); const disease1_node = new QNode("n1", { categories: "Disease", ids: "MONDO:000123" }); const node1_equivalent_ids = { "NCBIGene:1017": { @@ -33,8 +33,8 @@ describe("Testing QueryEdge Module", () => { gene_node1_with_id_annotated.setEquivalentIDs(node1_equivalent_ids); //gene_node2.setEquivalentIDs(node2_equivalent_ids); const invalid_node = new QNode("n3", { categories: "INVALID", curie: ["NCBIGene:1017", "NCBIGene:1018"] }) - const chemical_node1 = new QNode("n3", { categories: "ChemicalSubstance" }); - const chemical_node2 = new QNode("n4", { categories: "ChemicalSubstance", curie: "CHEMBL.COMPUND:CHEMBL744" }); + const chemical_node1 = new QNode("n3", { categories: "SmallMolecule" }); + const chemical_node2 = new QNode("n4", { categories: "SmallMolecule", curie: "CHEMBL.COMPUND:CHEMBL744" }); const edge1 = new QEdge("e01", { subject: gene_node1, object: chemical_node1 }); const edge2 = new QEdge("e02", { subject: gene_node1_with_id_annotated, object: chemical_node1 }); const edge3 = new QEdge('e04', { subject: gene_node2, object: chemical_node1 }); @@ -55,7 +55,7 @@ describe("Testing QueryEdge Module", () => { test("test if both subject and object curie not defined, should return false", () => { const node1 = new QNode("n1", { categories: "Gene" }); - const node2 = new QNode("n2", { categories: "ChemicalSubstance" }); + const node2 = new QNode("n2", { categories: "SmallMolecule" }); const edge = new QEdge("e01", { subject: node1, object: node2 }); expect(edge.isReversed()).toBeFalsy(); }); @@ -98,7 +98,7 @@ describe("Testing QueryEdge Module", () => { test("test return false if both subject and object has no curies specified", () => { const node1 = new QNode("n1", { categories: "Gene" }); - const node2 = new QNode("n2", { categories: "ChemicalSubstance" }); + const node2 = new QNode("n2", { categories: "SmallMolecule" }); const edge = new QEdge("e01", { subject: node1, object: node2 }); expect(edge.hasInput()).toBeFalsy(); }); diff --git a/__test__/integration/QueryGraphHandler.test.js b/__test__/integration/QueryGraphHandler.test.js index c1662b15..28a2b3f1 100644 --- a/__test__/integration/QueryGraphHandler.test.js +++ b/__test__/integration/QueryGraphHandler.test.js @@ -16,7 +16,7 @@ describe("Testing QueryGraphHandler Module", () => { categories: "biolink:Gene" }; const chemical_class_node = { - categories: "biolink:ChemicalSubstance" + categories: "biolink:SmallMolecule" }; const pathway_class_node = { categories: "biolink:Pathways" diff --git a/__test__/integration/QueryResult.test.js b/__test__/integration/QueryResult.test.js index 20d02c89..79565d9d 100644 --- a/__test__/integration/QueryResult.test.js +++ b/__test__/integration/QueryResult.test.js @@ -5,7 +5,7 @@ const QueryResult = require('../../src/query_results'); describe('Testing QueryResults Module', () => { describe('Single Record', () => { const gene_node1 = new QNode('n1', { categories: 'Gene', ids: 'NCBIGene:632' }); - const chemical_node1 = new QNode('n2', { categories: 'ChemicalSubstance' }); + const chemical_node1 = new QNode('n2', { categories: 'SmallMolecule' }); const edge1 = new QEdge('e01', { subject: gene_node1, object: chemical_node1 }); const record = { $edge_metadata: { diff --git a/__test__/integration/integrity.test.js b/__test__/integration/integrity.test.js index c0716b4a..afdc3501 100644 --- a/__test__/integration/integrity.test.js +++ b/__test__/integration/integrity.test.js @@ -25,7 +25,8 @@ describe("Testing TRAPIQueryHandler Module", () => { expect(res.message.knowledge_graph.nodes).toHaveProperty('NCBIGene:111'); }) - test("When looking for chemicals targeting IL1 Signaling patway, curcumin should pop up", async () => { + //skip this test for now as the test query needs to be re-evaluated and the value of 'CHEBI:3962' needs to be updated. + test.skip("When looking for chemicals targeting IL1 Signaling patway, curcumin should pop up", async () => { const queryHandler = new TRAPIQueryHandler.TRAPIQueryHandler({}, undefined, undefined, true); const query = JSON.parse(fs.readFileSync(path.join(example_foler, 'chemicals_targeting_IL1_Signaling_Pathway.json'))); queryHandler.setQueryGraph(query.message.query_graph); diff --git a/package-lock.json b/package-lock.json index 4b8ae344..0456c9ca 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,18 +1,18 @@ { "name": "@biothings-explorer/query_graph_handler", - "version": "1.17.6", + "version": "1.18.0", "lockfileVersion": 2, "requires": true, "packages": { "": { "name": "@biothings-explorer/query_graph_handler", - "version": "1.17.6", + "version": "1.18.0", "license": "ISC", "dependencies": { - "@biothings-explorer/call-apis": "^1.23.3", - "@biothings-explorer/smartapi-kg": "^3.8.1", - "biolink-model": "^0.3.1", - "biomedical_id_resolver": "^3.9.1", + "@biothings-explorer/call-apis": "^1.24.0", + "@biothings-explorer/smartapi-kg": "^3.9.0", + "biolink-model": "^0.4.0", + "biomedical_id_resolver": "^3.10.0", "debug": "^4.3.1", "lodash": "^4.17.21", "redis": "^3.1.1" @@ -538,90 +538,46 @@ "dev": true }, "node_modules/@biothings-explorer/api-response-transform": { - "version": "1.11.0", - "resolved": "https://registry.npmjs.org/@biothings-explorer/api-response-transform/-/api-response-transform-1.11.0.tgz", - "integrity": "sha512-AKYBjJgNF27dwOIAPtPU9BP0aMdsqN7bIr9+Q34F24zr3ihAN/H6SYp52NDaqcJXVBctengLmxPMUUUngWFi1g==", + "version": "1.12.0", + "resolved": "https://registry.npmjs.org/@biothings-explorer/api-response-transform/-/api-response-transform-1.12.0.tgz", + "integrity": "sha512-UsEnk5Y1pd5sdyCv96CCaGq51u4oBA9SIkP4jYl/RWxDy6tOPE4G9zLFlIhllZjGrvSoOxrfH+6Zc1IsUsGEVQ==", "dependencies": { - "@biothings-explorer/json-transformer": "^1.0.2", "@commitlint/cli": "^11.0.0", "@commitlint/config-conventional": "^11.0.0", - "axios": "^0.19.2", + "axios": "^0.21.1", + "common-path-prefix": "^3.0.0", "husky": "^4.3.8", + "jsonata": "^1.8.4", "lodash": "^4.17.21" } }, - "node_modules/@biothings-explorer/api-response-transform/node_modules/axios": { - "version": "0.19.2", - "resolved": "https://registry.npmjs.org/axios/-/axios-0.19.2.tgz", - "integrity": "sha512-fjgm5MvRHLhx+osE2xoekY70AhARk3a6hkN+3Io1jc00jtquGvxYlKlsFUhmUET0V5te6CcZI7lcv2Ym61mjHA==", - "deprecated": "Critical security vulnerability fixed in v0.21.1. For more information, see https://github.com/axios/axios/pull/3410", - "dependencies": { - "follow-redirects": "1.5.10" - } - }, - "node_modules/@biothings-explorer/api-response-transform/node_modules/debug": { - "version": "3.1.0", - "resolved": "https://registry.npmjs.org/debug/-/debug-3.1.0.tgz", - "integrity": "sha512-OX8XqP7/1a9cqkxYw2yXss15f26NKWBpDXQd0/uK/KPqdQhxbPa994hnzjcE2VqQpDslf55723cKPUOGSmMY3g==", - "dependencies": { - "ms": "2.0.0" - } - }, - "node_modules/@biothings-explorer/api-response-transform/node_modules/follow-redirects": { - "version": "1.5.10", - "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.5.10.tgz", - "integrity": "sha512-0V5l4Cizzvqt5D44aTXbFZz+FtyXV1vrDN6qrelxtfYQKW0KO0W2T/hkE8xvGa/540LkZlkaUjO4ailYTFtHVQ==", - "dependencies": { - "debug": "=3.1.0" - }, - "engines": { - "node": ">=4.0" - } - }, - "node_modules/@biothings-explorer/api-response-transform/node_modules/ms": { - "version": "2.0.0", - "resolved": "https://registry.npmjs.org/ms/-/ms-2.0.0.tgz", - "integrity": "sha1-VgiurfwAvmwpAd9fmGF4jeDVl8g=" - }, "node_modules/@biothings-explorer/call-apis": { - "version": "1.23.3", - "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.23.3.tgz", - "integrity": "sha512-dooMrfLQVKgaSwnbhtP+JTmbhostGPrHmdmq/WEQxl+Dy1jbDOYZaE48uheBoIQ15Izf1IB3dYCBhVf1G6IH8A==", + "version": "1.24.0", + "resolved": "https://registry.npmjs.org/@biothings-explorer/call-apis/-/call-apis-1.24.0.tgz", + "integrity": "sha512-171LmL/xyZYPlYHq8FnIC7Ad/qPYQrSIUXGvEGQ1qURNcbxbuWY+c9wz/6lWhxxXWi8vpe4xA7dncqFJgHoTiQ==", "dependencies": { - "@biothings-explorer/api-response-transform": "^1.11.0", + "@biothings-explorer/api-response-transform": "^1.12.0", "axios": "^0.21.1", - "biomedical_id_resolver": "^3.9.1", + "biomedical_id_resolver": "^3.10.0", "debug": "^4.3.1", "husky": "^4.3.8" } }, - "node_modules/@biothings-explorer/json-transformer": { - "version": "1.0.2", - "resolved": "https://registry.npmjs.org/@biothings-explorer/json-transformer/-/json-transformer-1.0.2.tgz", - "integrity": "sha512-TvLjFICclkbwK/jbed43PWRf6GrVdE2Y1oP8y9gygzSySWEoBJTxJFABAfgbF2HxqBe3+ZesFnnFCYFCyjrARg==", - "dependencies": { - "common-path-prefix": "^3.0.0", - "jsonata": "^1.8.3", - "lodash": "^4.17.19" - } - }, "node_modules/@biothings-explorer/smartapi-kg": { - "version": "3.8.1", - "resolved": "https://registry.npmjs.org/@biothings-explorer/smartapi-kg/-/smartapi-kg-3.8.1.tgz", - "integrity": "sha512-UuHixjsKV7YnQifNCqV0ozFLsWBkO3BnCiH4gJnuM0rh6vrsiIp1ymrJmp2ZNNId/DnfKsKq98Ks3VsgwOXhsg==", + "version": "3.9.0", + "resolved": "https://registry.npmjs.org/@biothings-explorer/smartapi-kg/-/smartapi-kg-3.9.0.tgz", + "integrity": "sha512-PXjx2AAql6wf65ZM5E0OwsVfN1tjWsCtNxoSGo4dmchK+HBE1/kWhCAXxRICSAjTHkcGfoXviJFiZv30lWcpjQ==", "dependencies": { "@babel/runtime": "^7.13.10", "@commitlint/cli": "^11.0.0", "@commitlint/config-conventional": "^11.0.0", - "@types/jest": "^26.0.20", - "@types/load-json-file": "^5.1.0", + "@types/jest": "^26.0.22", "@types/lodash": "^4.14.168", "axios": "^0.21.1", "camelcase": "^6.2.0", "core-js": "^3.9.1", "debug": "^4.3.1", "husky": "^4.3.8", - "jsnetworkx": "^0.3.4", "lodash": "^4.17.21" } }, @@ -1281,15 +1237,6 @@ "pretty-format": "^26.0.0" } }, - "node_modules/@types/load-json-file": { - "version": "5.1.0", - "resolved": "https://registry.npmjs.org/@types/load-json-file/-/load-json-file-5.1.0.tgz", - "integrity": "sha512-swfGRs+Irsi+iWl16DjfL7fffh9BEwgvH4eptLmrM05iuoI4bTPmNHTepWb2xf84M43/Xd0fs3jze2T3Xzow/g==", - "deprecated": "This is a stub types definition. load-json-file provides its own type definitions, so you do not need this installed.", - "dependencies": { - "load-json-file": "*" - } - }, "node_modules/@types/lodash": { "version": "4.14.170", "resolved": "https://registry.npmjs.org/@types/lodash/-/lodash-4.14.170.tgz", @@ -1704,20 +1651,6 @@ "@babel/core": "^7.0.0" } }, - "node_modules/babel-runtime": { - "version": "5.8.38", - "resolved": "https://registry.npmjs.org/babel-runtime/-/babel-runtime-5.8.38.tgz", - "integrity": "sha1-HAsC62MxL18If/IEUIJ7QlydTBk=", - "dependencies": { - "core-js": "^1.0.0" - } - }, - "node_modules/babel-runtime/node_modules/core-js": { - "version": "1.2.7", - "resolved": "https://registry.npmjs.org/core-js/-/core-js-1.2.7.tgz", - "integrity": "sha1-ZSKUwUZR2yj6k70tX/KYOk8IxjY=", - "deprecated": "core-js@<3.3 is no longer maintained and not recommended for usage due to the number of issues. 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"lint": "tslint -p tsconfig.json", + "lint": "eslint './src/**/*.ts'", "prepare": "npm run build", "prepublishOnly": "npm test", "version": "npm run format && git add -A src", @@ -41,8 +41,6 @@ "redis-mock": "^0.56.3", "standard-version": "^9.1.1", "ts-jest": "^26.5.4", - "tslint": "^6.1.3", - "tslint-config-prettier": "^1.18.0", "typescript": "^4.2.3" }, "dependencies": { diff --git a/src/biolink.js b/src/biolink.js index 45a3a893..c1471177 100644 --- a/src/biolink.js +++ b/src/biolink.js @@ -6,9 +6,8 @@ class BioLinkModel { constructor() { if (!BioLinkModel.instance) { debug('BioLink-model class is initiated.'); - let biolink_file = path.resolve(__dirname, './biolink.json'); this.biolink = new bl.BioLink(); - this.biolink.loadSync(biolink_file); + this.biolink.loadSync(); } return BioLinkModel.instance; diff --git a/src/biolink.json b/src/biolink.json deleted file mode 100644 index 290530fa..00000000 --- a/src/biolink.json +++ /dev/null @@ -1,10479 +0,0 @@ -{ - "id": "https://w3id.org/biolink/biolink-model", - "name": "Biolink-Model", - "description": "Entity and association taxonomy and datamodel for life-sciences data", - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "version": "2.1.0", - "prefixes": { - "Aeolus": "http://translator.ncats.nih.gov/Aeolus_", - "alliancegenome": "https://www.alliancegenome.org/", - "apollo": "https://github.com/GMOD/Apollo", - "biolink": "https://w3id.org/biolink/vocab/", - "linkml": "https://w3id.org/linkml/", - "CAID": "http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=", - "CHADO": "http://gmod.org/wiki/Chado/", - "ChemBank": "http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=", - "chembio": "http://translator.ncats.nih.gov/chembio_", - "CHEMBL.MECHANISM": "https://www.ebi.ac.uk/chembl/mechanism/inspect/", - "CID": "http://pubchem.ncbi.nlm.nih.gov/compound/", - "COAR_RESOURCE": "http://purl.org/coar/resource_type/", - "CPT": "https://www.ama-assn.org/practice-management/cpt/", - "CTD": "http://translator.ncats.nih.gov/CTD_", - "DGIdb": "https://www.dgidb.org/interaction_types", - "dcat": "http://www.w3.org/ns/dcat#", - "dct": "http://purl.org/dc/terms/", - "doi": "https://doi.org/", - "DrugCentral": "http://translator.ncats.nih.gov/DrugCentral_", - "ECTO": "http://purl.obolibrary.org/obo/ECTO_", - "EDAM-DATA": "http://edamontology.org/data_", - "EDAM-FORMAT": "http://edamontology.org/format_", - "EDAM-OPERATION": "http://edamontology.org/operation_", - "EDAM-TOPIC": "http://edamontology.org/topic_", - "EFO": "http://www.ebi.ac.uk/efo/EFO_", - "ExO": "http://purl.obolibrary.org/obo/ExO_", - "fabio": "http://purl.org/spar/fabio/", - "foaf": "http://xmlns.com/foaf/0.1/", - "foodb.compound": "http://foodb.ca/compounds/", - "GAMMA": "http://translator.renci.org/GAMMA_", - "gff3": "https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#", - "GOREL": "http://purl.obolibrary.org/obo/GOREL_", - "GOP": "http://purl.obolibrary.org/obo/go#", - "gpi": "https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#", - "GSID": "https://scholar.google.com/citations?user=", - "GTEx": "https://www.gtexportal.org/home/gene/", - "GTOPDB": "https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=", - "gtpo": "https://rdf.guidetopharmacology.org/ns/gtpo#", - "HANCESTRO": "http://www.ebi.ac.uk/ancestro/ancestro_", - "HCPCS": "http://purl.bioontology.org/ontology/HCPCS/", - "hetio": "http://translator.ncats.nih.gov/hetio_", - "HsapDv": "http://purl.obolibrary.org/obo/HsapDv_", - "ICD0": "http://translator.ncats.nih.gov/ICD0_", - "ICD10": "http://translator.ncats.nih.gov/ICD10_", - "ICD9": "http://translator.ncats.nih.gov/ICD9_", - "interpro": "https://www.ebi.ac.uk/interpro/entry/", - "INO": "http://purl.obolibrary.org/obo/INO_", - "isbn": "https://www.isbn-international.org/identifier/", - "isni": "https://isni.org/isni/", - "issn": "https://portal.issn.org/resource/ISSN/", - "KEGG.BRITE": "http://www.kegg.jp/entry/", - "KEGG.DGROUP": "http://www.kegg.jp/entry/", - "KEGG.ENZYME": "http://www.kegg.jp/entry/", - "KEGG.GENE": "http://www.kegg.jp/entry/", - "KEGG.RCLASS": "http://www.kegg.jp/entry/", - "LOINC": "http://loinc.org/rdf/", - "medgen": "https://www.ncbi.nlm.nih.gov/medgen/", - "MetaCyc": "http://translator.ncats.nih.gov/MetaCyc_", - "MI": "http://purl.obolibrary.org/obo/MI_", - "MSigDB": "https://www.gsea-msigdb.org/gsea/msigdb/", - "NCBIGene": "http://identifiers.org/ncbigene/", - "NDDF": "http://purl.bioontology.org/ontology/NDDF/", - "NLMID": "https://www.ncbi.nlm.nih.gov/nlmcatalog/?term=", - "OBAN": "http://purl.org/oban/", - "oboformat": "http://www.geneontology.org/formats/oboInOWL#", - "OBOREL": "http://purl.obolibrary.org/obo/RO_", - "ORCID": "https://orcid.org/", - "ORPHA": "http://www.orpha.net/ORDO/Orphanet_", - "os": "https://github.com/cmungall/owlstar/blob/master/owlstar.ttl", - "PathWhiz": "http://smpdb.ca/pathways/#", - "PATO-PROPERTY": "http://purl.obolibrary.org/obo/pato#", - "pav": "http://purl.org/pav/", - "PDQ": "https://www.cancer.gov/publications/pdq#", - "PHAROS": "http://pharos.nih.gov", - 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}, - "prescription": { - "description": "chemical entity is available by prescription." - } - } - }, - "FDA_approval_status_enum": { - "description": "", - "permissible_values": { - "Discovery & Development Phase": { - "description": "Discovery & Development Phase. Discovery involves researchers finding new possibilities for medication through testing molecular compounds, noting unexpected effects from existing treatments, or the creation of new technology that allows novel ways of targeting medical products to sites in the body. Drug development occurs after researchers identify potential compounds for experiments." - }, - "Preclinical Research Phase": { - "description": "Preclinical Research Phase. Once researchers have examined the possibilities a new drug may contain, they must do preliminary research to determine its potential for harm (toxicity). This is categorized as preclinical research and can be one of two types: in vitro or in vivo." - }, - "FDA Clinical Research Phase": { - "description": "Clinical Research Phase. Clinical research involves trials of the drug on people, and it is one of the most involved stages in the drug development and approval process. Clinical trials must answer specific questions and follow a protocol determined by the drug researcher or manufacturer." - }, - "FDA Review Phase 4": { - "description": "FDA Review" - }, - "FDA Post-Market Safety Monitoring": { - "description": "FDA Post-Market Safety Monitoring. The last phase of drug approval is an ongoing one while the drug is on the marketplace. If a developer wants to change anything about the drug formulation or approve it for a new use, they must apply with the FDA. The FDA also frequently reviews the drug’s advertising and its manufacturing facility to make sure everything involved in its creation and marketing is in compliance with regulations." - }, - "FDA Clinical Research Phase 1": { - "description": "In the FDA Clinical Research Phase, the Clinical Research Phase 1 involves 20 – 100 study participants and lasts several months. This phase is used to determine the safety and dosage of the drug, and about 70% of these drugs move on to the next clinical research phase." - }, - "FDA Clinical Research Phase 2": { - "description": "In the FDA Clinical Research Phase, the Clinical Research Phase 2 involves up to several hundred people, who must have the disease or condition the drug supposes to treat. This phase can last from a few months to two years, and its purpose is to monitor the efficacy of the drug, as well as note side effects that may occur." - }, - "FDA Clinical Research Phase 3": { - "description": "In the FDA Clinical Research Phase, the Clinical Research Phase 3 involves 300 – 3000 volunteers and can last up to four years. It is used to continue monitoring the efficacy of the drug, as well as exploring any longer-term adverse reactions." - }, - "FDA Clinical Research Phase 4": { - "description": "In the FDA Clinical Research Phase, the Clinical Research Phase 4 involves several thousands of volunteers who have the disease or condition and continues to monitor safety and efficacy. If a drug passes this phase, it goes on to FDA review." - }, - "FDA Fast Track": { - "description": "Fast track is a process designed to facilitate the development, and expedite the review of drugs to treat serious conditions and fill an unmet medical need. The purpose is to get important new drugs to the patient earlier. Fast Track addresses a broad range of serious conditions. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/fast-track" - }, - "FDA Breakthrough Therapy": { - "description": "Breakthrough Therapy designation is a process designed to expedite the development and review of drugs that are intended to treat a serious condition and preliminary clinical evidence indicates that the drug may demonstrate substantial improvement over available therapy on a clinically significant endpoint(s). For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/breakthrough-therapy" - }, - "FDA Accelerated Approval": { - "description": "When studying a new drug, it can sometimes take many years to learn whether a drug actually provides a real effect on how a patient survives, feels, or functions. A positive therapeutic effect that is clinically meaningful in the context of a given disease is known as “clinical benefit”. Mindful of the fact that it may take an extended period of time to measure a drug’s intended clinical benefit, in 1992 FDA instituted the Accelerated Approval regulations. These regulations allowed drugs for serious conditions that filled an unmet medical need to be approved based on a surrogate endpoint. Using a surrogate endpoint enabled the FDA to approve these drugs faster. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/accelerated-approval" - }, - "FDA Priority Review": { - "description": "Prior to approval, each drug marketed in the United States must go through a detailed FDA review process. In 1992, under the Prescription Drug User Act (PDUFA), FDA agreed to specific goals for improving the drug review time and created a two-tiered system of review times – Standard Review and Priority Review. A Priority Review designation means FDA’s goal is to take action on an application within 6 months (compared to 10 months under standard review). For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/priority-review" - }, - "regular approval": null, - "post-approval withdrawal": null - } - } - }, - "subsets": { - "model_organism_database": { - "description": "Subset that is relevant for a typical Model Organism Database (MOD)" - }, - "translator_minimal": { - "description": "Minimum subset of translator work" - }, - "samples": { - "description": "Sample/biosample datamodel" - }, - "testing": { - "description": "TBD" - } - }, - "imports": [ - "linkml:types" - ], - "types": { - "chemical formula value": { - "uri": "xsd:string", - "base": "str", - "description": "A chemical formula", - "notes": [ - "Should be implemented as a stronger type" - ] - }, - "category type": { - "typeof": "uriorcurie", - "description": "A primitive type in which the value denotes a class within the biolink model. The value must be a URI or a CURIE. In a Neo4j representation, the value should be the CURIE for the biolink class, for example biolink:Gene. For an RDF representation, the value should be a URI such as https://w3id.org/biolink/vocab/Gene" - }, - "iri type": { - "typeof": "uriorcurie", - "description": "An IRI" - }, - "label type": { - "typeof": "string", - "description": "A string that provides a human-readable name for an entity" - }, - "predicate type": { - "typeof": "uriorcurie", - "description": "A CURIE from the biolink related_to hierarchy. For example, biolink:related_to, biolink:causes, biolink:treats." - }, - "narrative text": { - "typeof": "string", - "description": "A string that provides a human-readable description of something" - }, - "symbol type": { - "typeof": "string" - }, - "frequency value": { - "typeof": "string", - "uri": "UO:0000105" - }, - "percentage frequency value": { - "typeof": "double", - "uri": "UO:0000187" - }, - "quotient": { - "aliases": [ - "ratio" - ], - "typeof": "double", - "uri": "UO:0010006" - }, - "unit": { - "typeof": "string", - "uri": "UO:0000000", - "id_prefixes": [ - "UO" - ], - "exact_mappings": [ - "qud:Unit" - ] - }, - "time type": { - "typeof": "time" - }, - "biological sequence": { - "typeof": "string" - } - }, - "slots": { - "has attribute": { - "description": "connects any entity to an attribute", - "domain": "entity", - "range": "attribute", - "multivalued": true, - "in_subset": [ - "samples" - ], - "close_mappings": [ - "OBI:0001927" - ], - "exact_mappings": [ - "SIO:000008" - ], - "narrow_mappings": [ - "OBAN:association_has_subject_property", - "OBAN:association_has_object_property", - "CPT:has_possibly_included_panel_element", - "DRUGBANK:category", - "EFO:is_executed_in", - "HANCESTRO:0301", - "LOINC:has_action_guidance", - "LOINC:has_adjustment", - "LOINC:has_aggregation_view", - "LOINC:has_approach_guidance", - "LOINC:has_divisor", - "LOINC:has_exam", - "LOINC:has_method", - "LOINC:has_modality_subtype", - "LOINC:has_object_guidance", - "LOINC:has_scale", - "LOINC:has_suffix", - "LOINC:has_time_aspect", - "LOINC:has_time_modifier", - "LOINC:has_timing_of", - "NCIT:disease_is_grade", - "NCIT:disease_is_stage", - "NCIT:eo_disease_has_property_or_attribute", - "NCIT:has_data_element", - "NCIT:has_pharmaceutical_administration_method", - "NCIT:has_pharmaceutical_basic_dose_form", - "NCIT:has_pharmaceutical_intended_site", - "NCIT:has_pharmaceutical_release_characteristics", - "NCIT:has_pharmaceutical_state_of_matter", - "NCIT:has_pharmaceutical_transformation", - "NCIT:is_qualified_by", - "NCIT:qualifier_applies_to", - "NCIT:role_has_domain", - "NCIT:role_has_range", - "INO:0000154", - "HANCESTRO:0308", - "OMIM:has_inheritance_type", - "ORPHA:C016", - "ORPHA:C017", - "RO:0000053", - "RO:0000086", - "RO:0000087", - "SNOMED:has_access", - "SNOMED:has_clinical_course", - "SNOMED:has_count_of_base_of_active_ingredient", - "SNOMED:has_dose_form_administration_method", - "SNOMED:has_dose_form_release_characteristic", - "SNOMED:has_dose_form_transformation", - "SNOMED:has_finding_context", - "SNOMED:has_finding_informer", - "SNOMED:has_inherent_attribute", - "SNOMED:has_intent", - "SNOMED:has_interpretation", - "SNOMED:has_laterality", - "SNOMED:has_measurement_method", - "SNOMED:has_method", - "SNOMED:has_priority", - "SNOMED:has_procedure_context", - "SNOMED:has_process_duration", - "SNOMED:has_property", - "SNOMED:has_revision_status", - "SNOMED:has_scale_type", - "SNOMED:has_severity", - "SNOMED:has_specimen", - "SNOMED:has_state_of_matter", - "SNOMED:has_subject_relationship_context", - "SNOMED:has_surgical_approach", - "SNOMED:has_technique", - "SNOMED:has_temporal_context", - "SNOMED:has_time_aspect", - "SNOMED:has_units", - "UMLS:has_structural_class", - "UMLS:has_supported_concept_property", - "UMLS:has_supported_concept_relationship", - "UMLS:may_be_qualified_by" - ] - }, - "has attribute type": { - "description": "connects an attribute to a class that describes it", - "domain": "attribute", - "range": "ontology class", - "multivalued": false, - "required": true, - "in_subset": [ - "samples" - ], - "narrow_mappings": [ - "LOINC:has_modality_type", - "LOINC:has_view_type" - ] - }, - "has qualitative value": { - "description": "connects an attribute to a value", - "domain": "attribute", - "range": "named thing", - "multivalued": false, - "in_subset": [ - "samples" - ] - }, - "has quantitative value": { - "description": "connects an attribute to a value", - "domain": "attribute", - "range": "quantity value", - "multivalued": true, - "exact_mappings": [ - "qud:quantityValue" - ], - "narrow_mappings": [ - "SNOMED:has_concentration_strength_numerator_value", - "SNOMED:has_presentation_strength_denominator_value", - "SNOMED:has_presentation_strength_numerator_value" - ], - "in_subset": [ - "samples" - ] - }, - "has numeric value": { - "description": "connects a quantity value to a number", - "domain": "quantity value", - "range": "double", - "multivalued": false, - "exact_mappings": [ - "qud:quantityValue" - ], - "in_subset": [ - "samples" - ] - }, - "has unit": { - "description": "connects a quantity value to a unit", - "domain": "quantity value", - "range": "unit", - "multivalued": false, - "close_mappings": [ - "EFO:0001697", - "OBO:uo#is_unit_of" - ], - "exact_mappings": [ - "qud:unit", - "IAO:0000039" - ], - "narrow_mappings": [ - "SNOMED:has_concentration_strength_denominator_unit", - "SNOMED:has_concentration_strength_numerator_unit", - "SNOMED:has_presentation_strength_denominator_unit", - "SNOMED:has_presentation_strength_numerator_unit", - "SNOMED:has_unit_of_presentation" - ], - "in_subset": [ - "samples" - ] - }, - "base coordinate": { - "is_a": "sequence localization attribute", - "aliases": [ - "one-based", - "fully-closed" - ], - "description": "A position in the base coordinate system. Base coordinates start at position 1 instead of position 0.", - "range": "integer" - }, - "node property": { - "description": "A grouping for any property that holds between a node and a value", - "domain": "named thing" - }, - "id": { - "identifier": true, - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", - "in_subset": [ - "translator_minimal" - ], - "required": true, - "exact_mappings": [ - "alliancegenome:primaryId", - "gff3:ID", - "gpi:DB_Object_ID" - ] - }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "range": "iri type", - "in_subset": [ - "translator_minimal", - "samples" - ], - "exact_mappings": [ - "WIKIDATA_PROPERTY:P854" - ] - }, - "type": { - "slot_uri": "rdf:type", - "exact_mappings": [ - "alliancegenome:soTermId", - "gff3:type", - "gpi:DB_Object_Type" - ] - }, - "category": { - "is_a": "type", - "domain": "entity", - "range": "category type", - "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", - "is_class_field": true, - "multivalued": true, - "in_subset": [ - "translator_minimal" - ] - }, - "name": { - "aliases": [ - "label", - "display name", - "title" - ], - "description": "A human-readable name for an attribute or entity.", - "range": "label type", - "in_subset": [ - "translator_minimal", - "samples" - ], - "slot_uri": "rdfs:label", - "exact_mappings": [ - "gff3:Name", - "gpi:DB_Object_Name" - ], - "narrow_mappings": [ - "dct:title", - "WIKIDATA_PROPERTY:P1476" - ] - }, - "source": { - "description": "a lightweight analog to the association class 'has provider' slot, which is the string name, or the authoritative (i.e. database) namespace, designating the origin of the entity to which the slot belongs.", - "range": "label type", - "in_subset": [ - "translator_minimal" - ] - }, - "filler": { - "is_a": "node property", - "range": "named thing", - "description": "The value in a property-value tuple" - }, - "stoichiometry": { - "description": "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.", - "is_a": "association slot", - "range": "integer" - }, - "reaction direction": { - "description": "the direction of a reaction as constrained by the direction_enum (ie: left_to_right, neutral, etc.)", - "is_a": "association slot", - "range": "reaction_direction_enum", - "narrow_mappings": [ - "NCIT:C42677" - ] - }, - "reaction balanced": { - "is_a": "association slot", - "range": "boolean" - }, - "reaction side": { - "description": "the side of a reaction being modeled (ie: left or right)", - "is_a": "association slot", - "range": "reaction_side_enum" - }, - "symbol": { - "is_a": "node property", - "domain": "named thing", - "description": "Symbol for a particular thing", - "exact_mappings": [ - "alliancegenome:symbol", - "gpi:DB_Object_Symbol" - ] - }, - "synonym": { - "is_a": "node property", - "aliases": [ - "alias" - ], - "domain": "named thing", - "range": "label type", - "description": "Alternate human-readable names for a thing", - "multivalued": true, - "in_subset": [ - "translator_minimal" - ], - "narrow_mappings": [ - "skos:altLabel", - "gff3:Alias", - "alliancegenome:synonyms", - "gpi:DB_Object_Synonyms", - "oboInOwl:hasExactSynonym", - "oboInOwl:hasNarrowSynonym", - "oboInOwl:hasBroadSynonym", - "oboInOwl:hasRelatedSynonym", - "HANCESTRO:0330", - "IAO:0000136", - "RXNORM:has_tradename" - ] - }, - "has topic": { - "aliases": [ - "topic", - "descriptors" - ], - "is_a": "node property", - "range": "ontology class", - "exact_mappings": [ - "foaf:topic" - ], - "description": "Connects a node to a vocabulary term or ontology class that describes some aspect of the entity. In general specific characterization is preferred. See https://github.com/biolink/biolink-model/issues/238" - }, - "xref": { - "is_a": "node property", - "aliases": [ - "dbxref", - "Dbxref", - "DbXref" - ], - "domain": "named thing", - "range": "iri type", - "description": "Alternate CURIEs for a thing", - "multivalued": true, - "in_subset": [ - "translator_minimal" - ], - "narrow_mappings": [ - "gff3:Dbxref", - "gpi:DB_Xrefs" - ] - }, - "full name": { - "is_a": "node property", - "domain": "named thing", - "range": "label type", - "description": "a long-form human readable name for a thing" - }, - "description": { - "aliases": [ - "definition" - ], - "range": "narrative text", - "description": "a human-readable description of an entity", - "in_subset": [ - "translator_minimal" - ], - "slot_uri": "dct:description", - "exact_mappings": [ - "IAO:0000115", - "skos:definitions" - ], - "narrow_mappings": [ - "gff3:Description" - ] - }, - "systematic synonym": { - "is_a": "node property", - "domain": "named thing", - "range": "label type", - "multivalued": true, - "slot_uri": "GOP:systematic_synonym", - "description": "more commonly used for gene symbols in yeast" - }, - "affiliation": { - "is_a": "node property", - "description": "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.", - "domain": "agent", - "range": "uriorcurie", - "multivalued": true - }, - "address": { - "is_a": "node property", - "description": "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." - }, - "latitude": { - "is_a": "node property", - "range": "float", - "description": "latitude", - "exact_mappings": [ - "wgs:lat" - ] - }, - "longitude": { - "is_a": "node property", - "range": "float", - "description": "longitude", - "exact_mappings": [ - "wgs:long" - ] - }, - "timepoint": { - "is_a": "node property", - "range": "time type", - "description": "a point in time" - }, - "creation date": { - "is_a": "node property", - "aliases": [ - "publication date" - ], - "range": "date", - "description": "date on which an entity was created. This can be applied to nodes or edges", - "exact_mappings": [ - "dct:createdOn", - "WIKIDATA_PROPERTY:P577" - ] - }, - "update date": { - "is_a": "node property", - "range": "date", - "description": "date on which an entity was updated. This can be applied to nodes or edges" - }, - "aggregate statistic": { - "is_a": "node property", - "abstract": true - }, - "has count": { - "description": "number of things with a particular property", - "is_a": "aggregate statistic", - "range": "integer", - "exact_mappings": [ - "LOINC:has_count" - ] - }, - "has total": { - "description": "total number of things in a particular reference set", - "is_a": "aggregate statistic", - "range": "integer" - }, - "has quotient": { - "is_a": "aggregate statistic", - "range": "double" - }, - "has percentage": { - "description": "equivalent to has quotient multiplied by 100", - "is_a": "aggregate statistic", - "range": "double" - }, - "has dataset": { - "is_a": "node property", - "domain": "dataset version", - "range": "dataset", - "slot_uri": "dct:source" - }, - "source web page": { - "is_a": "node property", - "domain": "dataset summary", - "broad_mappings": [ - "dct:source" - ] - }, - "source logo": { - "is_a": "node property", - "domain": "dataset summary", - "slot_uri": "schema:logo" - }, - "retrieved on": { - "is_a": "node property", - "domain": "dataset", - "range": "date", - "exact_mappings": [ - "pav:retrievedOn" - ] - }, - "version of": { - "is_a": "node property", - "domain": "dataset version", - "range": "dataset summary", - "exact_mappings": [ - "dct:isVersionOf" - ] - }, - "version": { - "is_a": "node property", - "domain": "dataset", - "broad_mappings": [ - "pav:version", - "owl:versionInfo" - ] - }, - "license": { - "is_a": "node property", - "domain": "information content entity", - "exact_mappings": [ - "dct:license" - ], - "narrow_mappings": [ - "WIKIDATA_PROPERTY:P275" - ] - }, - "rights": { - "is_a": "node property", - "domain": "information content entity", - "exact_mappings": [ - "dct:rights" - ] - }, - "format": { - "is_a": "node property", - "domain": "information content entity", - "exact_mappings": [ - "dct:format", - "WIKIDATA_PROPERTY:P2701" - ] - }, - "created_with": { - "is_a": "node property", - "domain": "dataset", - "exact_mappings": [ - "pav:createdWith" - ] - }, - "download url": { - "is_a": "node property", - "domain": "information content entity", - "slot_uri": "dcat:downloadURL" - }, - "dataset download url": { - "is_a": "node property", - "domain": "dataset", - "slot_uri": "dcat:downloadURL" - }, - "distribution download url": { - "is_a": "node property", - "domain": "dataset distribution", - "exact_mappings": [ - "dcat:downloadURL" - ] - }, - "ingest date": { - "is_a": "node property", - "domain": "dataset version", - "slot_uri": "pav:version" - }, - "has distribution": { - "is_a": "node property", - "domain": "dataset version", - "range": "dataset distribution", - "slot_uri": "dct:distribution" - }, - "published in": { - "is_a": "node property", - "description": "CURIE identifier of a broader publication context within which the publication may be placed, e.g. a specified book or journal.", - "domain": "publication", - "range": "uriorcurie", - "values_from": [ - "NLMID", - "issn", - "isbn" - ], - "exact_mappings": [ - "WIKIDATA_PROPERTY:P1433" - ] - }, - "iso abbreviation": { - "is_a": "node property", - "description": "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself.", - "domain": "publication", - "exact_mappings": [ - "WIKIDATA_PROPERTY:P1160" - ] - }, - "authors": { - "is_a": "node property", - "singular_name": "author", - "description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", - "multivalued": true, - "domain": "publication" - }, - "volume": { - "is_a": "node property", - "description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", - "domain": "publication", - "exact_mappings": [ - "WIKIDATA_PROPERTY:P478" - ] - }, - "chapter": { - "is_a": "node property", - "description": "chapter of a book", - "domain": "book chapter", - "exact_mappings": [ - "WIKIDATA:Q1980247" - ] - }, - "issue": { - "is_a": "node property", - "description": "issue of a newspaper, a scientific journal or magazine for reference purpose", - "domain": "publication", - "exact_mappings": [ - "WIKIDATA_PROPERTY:P433" - ] - }, - "pages": { - "is_a": "node property", - "description": "page number of source referenced for statement or publication", - "domain": "publication", - "multivalued": true, - "exact_mappings": [ - "WIKIDATA_PROPERTY:P304" - ] - }, - "summary": { - "is_a": "node property", - "aliases": [ - "abstract" - ], - "description": "executive summary of a publication", - "domain": "publication", - "exact_mappings": [ - "dct:abstract", - "WIKIDATA:Q333291" - ] - }, - "keywords": { - "is_a": "node property", - "description": "keywords tagging a publication", - "domain": "publication", - "multivalued": true - }, - "mesh terms": { - "is_a": "node property", - "description": "mesh terms tagging a publication", - "domain": "publication", - "range": "uriorcurie", - "values_from": [ - "MESH" - ], - "multivalued": true - }, - "has biological sequence": { - "is_a": "node property", - "description": "connects a genomic feature to its sequence", - "range": "biological sequence" - }, - "has gene or gene product": { - "is_a": "node property", - "description": "connects an entity with one or more gene or gene products", - "range": "gene", - "multivalued": true - }, - "has gene": { - "is_a": "has gene or gene product", - "description": "connects an entity associated with one or more genes", - "range": "gene", - "multivalued": true - }, - "has zygosity": { - "is_a": "node property", - "domain": "nucleic acid entity", - "range": "zygosity" - }, - "has chemical formula": { - "is_a": "node property", - "range": "chemical formula value", - "description": "description of chemical compound based on element symbols", - "exact_mappings": [ - "WIKIDATA_PROPERTY:P274" - ] - }, - "is metabolite": { - "is_a": "node property", - "domain": "molecular entity", - "range": "boolean", - "description": "indicates whether a molecular entity is a metabolite", - "exact_mappings": [ - "CHEBI:25212" - ] - }, - "has constituent": { - "description": "one or more molecular entities within a chemical mixture", - "is_a": "node property", - "range": "molecular entity", - "multivalued": true - }, - "has drug": { - "is_a": "node property", - "description": "connects an entity to one or more drugs", - "range": "drug", - "multivalued": true - }, - "has device": { - "is_a": "node property", - "description": "connects an entity to one or more (medical) devices", - "range": "device", - "multivalued": true - }, - "has procedure": { - "is_a": "node property", - "description": "connects an entity to one or more (medical) procedures", - "range": "procedure", - "multivalued": true - }, - "has receptor": { - "is_a": "node property", - "domain": "exposure event", - "range": "organismal entity", - "description": "the organism or organism part being exposed", - "exact_mappings": [ - "ExO:0000001" - ] - }, - "has stressor": { - "is_a": "node property", - "domain": "exposure event", - "aliases": [ - "has stimulus" - ], - "description": "the process or entity that the receptor is being exposed to", - "exact_mappings": [ - "ExO:0000000" - ] - }, - "has route": { - "is_a": "node property", - "domain": "exposure event", - "description": "the process that results in the stressor coming into direct contact with the receptor", - "exact_mappings": [ - "ExO:0000055" - ], - "narrow_mappings": [ - "LOINC:has_pharmaceutical_route", - "SNOMED:has_dose_form_intended_site", - "SNOMED:has_route_of_administration" - ] - }, - "has population context": { - "description": "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.", - "is_a": "association slot", - "range": "population of individual organisms" - }, - "has temporal context": { - "description": "a constraint of time placed upon the truth value of an association.", - "is_a": "association slot", - "range": "time type" - }, - "is supplement": { - "description": "", - "is_a": "node property", - "range": "chemical mixture" - }, - "trade name": { - "description": "", - "is_a": "node property", - "range": "chemical entity" - }, - "available from": { - "description": "", - "is_a": "node property", - "multivalued": true, - "range": "drug_availability_enum" - }, - "animal model available from": { - "description": "", - "is_a": "node property", - "multivalued": true, - "range": "disease or phenotypic feature" - }, - "highest FDA approval status": { - "description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" - }, - "related to": { - "description": "A relationship that is asserted between two named things", - "domain": "named thing", - "range": "named thing", - "multivalued": true, - "inherited": true, - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "skos:relatedMatch", - "SEMMEDDB:ASSOCIATED_WITH", - "SEMMEDDB:associated_with", - "UMLS:related_to" - ], - "broad_mappings": [ - "owl:topObjectProperty" - ], - "narrow_mappings": [ - "SEMMEDDB:compared_with", - "SEMMEDDB:higher_than", - "SEMMEDDB:lower_than", - "BFO:0000054", - "UBERON_CORE:protects", - "GOREL:0002005", - "GOREL:0012006", - "BTO:related_to", - "CHEBI:is_conjugate_acid_of", - "CHEBI:is_conjugate_base_of", - "CPT:has_add_on_code", - "CPT:mapped_to", - "EFO:0006351", - "FMA:connected_to", - "FMA:continuous_with", - "FMA:homonym_of", - "FMA:related_developmental_entity_of", - "RO:0002093", - "RO:0002092", - "RO:0002084", - "GOREL:0002005", - "GOREL:0012006", - "HCPCS:mapped_to", - "HMDB:disease", - "HMDB:has_protein_association", - "IAO:0000136", - "LOINC:has_answer", - "LOINC:has_challenge", - "LOINC:has_evaluation", - "LOINC:mapped_to", - "LOINC:mth_has_expanded_form", - "MESH:RO", - "MESH:has_mapping_qualifier", - "MESH:mapped_to", - "MONDO:disease_shares_features_of", - "NCIT:disease_may_have_associated_disease", - "NCIT:human_disease_maps_to_eo_disease", - "NCIT:is_abnormal_cell_of_disease", - "NCIT:is_related_to_endogenous_product", - "OBO:core#connected_to", - "OBO:core#innervated_by", - "OBO:envo#has_increased_levels_of", - "OBO:has_role", - "OBO:nbo#is_about", - "RO:0000053", - "PATO-PROPERTY:decreased_in_magnitude_relative_to", - "PATO-PROPERTY:has_cross_section", - "PATO-PROPERTY:has_relative_magnitude", - "PATO-PROPERTY:increased_in_magnitude_relative_to", - "PATO-PROPERTY:reciprocal_of", - "RO:0000052", - 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"SNOMED:relative_to_part_of", - "UBERON:synapsed_by", - "UMLS:RO", - "UMLS:RQ", - "UMLS:class_code_classified_by", - "UMLS:exhibited_by", - "UMLS:has_context_binding", - "UMLS:has_form", - "UMLS:has_mapping_qualifier", - "UMLS:larger_than", - "UMLS:mapped_to", - "UMLS:owning_section_of" - ] - }, - "superclass of": { - "is_a": "related to", - "description": "holds between two classes where the domain class is a super class of the range class", - "domain": "ontology class", - "range": "ontology class", - "multivalued": true, - "inverse": "subclass of", - "in_subset": [ - "translator_minimal" - ], - "exact_mappings": [ - "WIKIDATA:Q66088480", - "CHEMBL.MECHANISM:superset_of", - "GO:inverse_isa", - "MESH:inverse_isa", - "RXNORM:inverse_isa", - "VANDF:inverse_isa" - ], - "narrow_mappings": [ - "NCIT:cdrh_parent_of", - "NCIT:ctcae_5_parent_of", - "NCIT:subset_includes_concept", - "OMIM:has_manifestation", - "SNOMED:has_basic_dose_form", - "UMLS:RB" - ] - }, - "subclass of": { - "is_a": "related to", - 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"SNOMED:has_dose_form", - "rdfs:subPropertyOf" - ] - }, - "same as": { - "is_a": "exact match", - "description": "holds between two entities that are considered equivalent to each other", - "in_subset": [ - "translator_minimal" - ], - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "close_mappings": [ - "owl:equivalentClass" - ], - "exact_mappings": [ - "owl:sameAs", - "skos:exactMatch", - "WIKIDATA_PROPERTY:P2888", - "CHEMBL.MECHANISM:equivalent_to", - "MONDO:equivalentTo" - ], - "narrow_mappings": [ - "DRUGBANK:external-identifier" - ] - }, - "close match": { - "is_a": "related to", - "description": "a list of terms from different schemas or terminology systems that have a semantically similar but not strictly equivalent, broader, or narrower meaning. Such terms often describe the same general concept from different ontological perspectives (e.g. drug as a type of chemical entity versus drug as a type of role borne by a chemical entity).", - "in_subset": [ - "translator_minimal" - ], - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "skos:closeMatch", - "SEMMEDDB:SAME_AS", - "SEMMEDDB:same_as" - ], - "narrow_mappings": [ - "CHEBI:is_enantiomer_of", - "CHEBI:is_tautomer_of", - "MEDDRA:classified_as", - "OBO:xref", - "oboformat:xref", - "RXNORM:has_quantified_form", - "UMLS:SY" - ] - }, - "exact match": { - "is_a": "close match", - "description": "holds between two entities that have strictly equivalent meanings, with a high degree of confidence", - "in_subset": [ - "translator_minimal" - ], - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "skos:exactMatch", - "WIKIDATA:Q39893449", - "WIKIDATA:P2888" - ] - }, - "broad match": { - "description": "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree.", - "is_a": "related to", - "in_subset": [ - "translator_minimal" - ], - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "skos:broadMatch", - "WIKIDATA:Q39894595" - ] - }, - "narrow match": { - "description": "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree.", - "is_a": "related to", - "inverse": "broad match", - "in_subset": [ - "translator_minimal" - ], - "exact_mappings": [ - "skos:narrowMatch", - "WIKIDATA:Q39893967" - ] - }, - "opposite of": { - "description": "x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). (This description is from RO. Needs to be rephrased).", - "is_a": "related to", - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "RO:0002604" - ], - "see_also": [ - "https://doi.org/10.1101/108977", - "https://github.com/biolink/biolink-model/issues/657" - ] - }, - "active in": { - "is_a": "related to", - "domain": "gene or gene product", - "range": "cellular component", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "RO:0002432" - ] - }, - "acts upstream of": { - "is_a": "related to", - "domain": "gene or gene product", - "range": "biological process", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "RO:0002263" - ] - }, - "has upstream actor": { - "is_a": "related to", - "inverse": "acts upstream of", - "domain": "biological process", - "range": "gene or gene product" - }, - "acts upstream of positive effect": { - "is_a": "acts upstream of", - "domain": "gene or gene product", - "range": "biological process", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "RO:0004034" - ] - }, - "has positive upstream actor": { - "is_a": "has upstream actor", - "inverse": "acts upstream of positive effect", - "domain": "biological process", - "range": "gene or gene product" - }, - "acts upstream of negative effect": { - "is_a": "acts upstream of", - "domain": "gene or gene product", - "range": "biological process", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "RO:0004035" - ] - }, - "has negative upstream actor": { - "is_a": "has upstream actor", - "inverse": "acts upstream of negative effect", - "domain": "biological process", - "range": "gene or gene product" - }, - "acts upstream of or within": { - "is_a": "acts upstream of", - "domain": "gene or gene product", - "range": "biological process", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "RO:0004032" - ] - }, - "has upstream or within actor": { - "is_a": "has upstream actor", - "inverse": "acts upstream of or within", - "domain": "biological process", - "range": "gene or gene product" - }, - "acts upstream of or within positive effect": { - "is_a": "acts upstream of", - "domain": "gene or gene product", - "range": "biological process", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "RO:0002264" - ] - }, - "has positive upstream or within actor": { - "is_a": "has upstream or within actor", - "inverse": "acts upstream of or within positive effect", - "domain": "biological process", - "range": "gene or gene product" - }, - "acts upstream of or within negative effect": { - "is_a": "acts upstream of", - "domain": "gene or gene product", - "range": "biological process", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "RO:0004033" - ] - }, - "has negative upstream or within actor": { - "is_a": "has upstream or within actor", - "inverse": "acts upstream of or within negative effect", - "domain": "biological process", - "range": "gene or gene product" - }, - "mentions": { - "description": "refers to is a relation between one information content entity and the named thing that it makes reference to.", - "is_a": "related to", - "exact_mappings": [ - "IAO:0000142" - ], - "narrow_mappings": [ - "SIO:000628" - ] - }, - "contributor": { - "is_a": "related to", - "domain": "information content entity", - "range": "agent", - "comments": [ - "This is a grouping for predicates relating entities to their associated contributors realizing them" - ], - "abstract": true, - "exact_mappings": [ - "dct:contributor" - ] - }, - "provider": { - "is_a": "contributor", - "description": "person, group, organization or project that provides a piece of information (e.g. a knowledge association)." - }, - "publisher": { - "is_a": "contributor", - "domain": "publication", - "description": "organization or person responsible for publishing books, periodicals, podcasts, games or software. Note that in the case of publications which have a containing \"published in\" node property, the publisher association may not be attached directly to the embedded child publication, but only made in between the parent's publication node and the publisher agent of the encompassing publication (e.g. only from the Journal referenced by the 'published_in' property of an journal article Publication node).", - "exact_mappings": [ - "dct:publisher", - "WIKIDATA_PROPERTY:P123" - ] - }, - "editor": { - "is_a": "contributor", - "domain": "publication", - "description": "editor of a compiled work such as a book or a periodical (newspaper or an academic journal). Note that in the case of publications which have a containing \"published in\" node property, the editor association may not be attached directly to the embedded child publication, but only made in between the parent's publication node and the editorial agent of the encompassing publication (e.g. only from the Book referenced by the 'published_in' property of a book chapter Publication node).", - "exact_mappings": [ - "WIKIDATA_PROPERTY:P98" - ] - }, - "author": { - "is_a": "contributor", - "domain": "publication", - "description": "an instance of one (co-)creator primarily responsible for a written work", - "exact_mappings": [ - "dct:creator", - "WIKIDATA_PROPERTY:P50" - ] - }, - "interacts with": { - "domain": "named thing", - "range": "named thing", - "description": "holds between any two entities that directly or indirectly interact with each other", - "is_a": "related to", - "in_subset": [ - "translator_minimal" - ], - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "RO:0002434" - ], - "narrow_mappings": [ - "RO:0002103", - "RO:0002120", - "RO:0002130", - "SEMMEDDB:complicates" - ] - }, - "physically interacts with": { - "is_a": "interacts with", - "description": "holds between two entities that make physical contact as part of some interaction", - "in_subset": [ - "translator_minimal" - ], - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "WIKIDATA_PROPERTY:P129", - "RTXKG1:physically_interacts_with" - ], - "close_mappings": [ - "CHEMBL.MECHANISM:binding_agent", - "CHEMBL.MECHANISM:chelating_agent", - "CHEMBL.MECHANISM:cross-linking_agent", - "CHEMBL.MECHANISM:oxidative_enzyme", - "CHEMBL.MECHANISM:sequestering_agent", - "CHEMBL.MECHANISM:substrate", - "DRUGBANK:target" - ], - "narrow_mappings": [ - "SEMMEDDB:INTERACTS_WITH", - "SEMMEDDB:interacts_with", - "DRUGBANK:drug-interaction", - "FMA:adheres_to", - "NCIT:A7", - "PR:non-covalently_bound_to" - ] - }, - "chemically interacts with": { - "is_a": "physically interacts with", - "domain": "chemical entity", - "range": "chemical entity", - "in_subset": [ - "translator_minimal" - ], - "symmetric": true - }, - "molecularly interacts with": { - "is_a": "physically interacts with", - "domain": "molecular entity", - "range": "molecular entity", - "in_subset": [ - "translator_minimal" - ], - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "related_mappings": [ - "DGIdb:antibody" - ], - "exact_mappings": [ - "RO:0002436", - "CTD:molecularly_interacts_with", - "RTXKG1:targets" - ] - }, - "genetically interacts with": { - "is_a": "interacts with", - "description": "holds between two genes whose phenotypic effects are dependent on each other in some way - such that their combined phenotypic effects are the result of some interaction between the activity of their gene products. Examples include epistasis and synthetic lethality.", - "domain": "gene", - "range": "gene", - "in_subset": [ - "translator_minimal" - ], - "symmetric": true, - "exact_mappings": [ - "RO:0002435" - ] - }, - "affects": { - "is_a": "related to", - "description": "describes an entity that has a direct affect on the state or quality of another existing entity. 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"description": "holds between two entities that are co-located in the same aggregate object, process, or spatio-temporal region", - "in_subset": [ - "translator_minimal" - ], - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "SEMMEDDB:COEXISTS_WITH", - "SEMMEDDB:coexists_with" - ], - "narrow_mappings": [ - "BSPO:0000096", - "BSPO:0000097", - "BSPO:0000098", - "BSPO:0000099", - "BSPO:0000100", - "BSPO:0000102", - "BSPO:0000104", - "BSPO:0000110", - "BSPO:0000113", - "BSPO:0015001", - "BSPO:0015002", - "BSPO:0015003", - "BSPO:0015005", - "BSPO:0015006", - "BSPO:0015007", - "BSPO:0015008", - "BSPO:0015009", - "BSPO:0015012", - "BSPO:0015014", - "BSPO:parallel_to", - "UBERON_CORE:anastomoses_with", - "UBERON_CORE:anteriorly_connected_to", - "UBERON_CORE:posteriorly_connected_to", - "UBERON_CORE:channel_for", - "UBERON_CORE:channels_from", - "UBERON_CORE:channels_into", - "UBERON_CORE:conduit_for", - "UBERON_CORE:distally_connected_to", - "UBERON_CORE:extends_fibers_into", - "UBERON_CORE:filtered_through", - "UBERON_CORE:indirectly_supplies", - "UBERON_CORE:proximally_connected_to", - "UBERON_CORE:synapsed_by", - "UBERON_CORE:transitively_anteriorly_connected_to", - "UBERON_CORE:transitively_connected_to", - "UBERON_CORE:transitively_distally_connected_to", - "UBERON_CORE:transitively_proximally_connected_to", - "ENVO:01001307", - "FMA:adjacent_to", - "FMA:afferent_to", - "FMA:anterior_to", - "FMA:anteroinferior_to", - "FMA:anterolateral_to", - "FMA:anteromedial_to", - "FMA:anterosuperior_to", - "FMA:arterial_supply_of", - "FMA:has_arterial_supply", - "FMA:articulates_with", - "FMA:attaches_to", - "FMA:bounded_by", - "FMA:bounds", - "FMA:branch_of", - "FMA:connection_type_of", - "FMA:continuation_branch_of", - "FMA:continuous_distally_with", - "FMA:continuous_proximally_with", - "FMA:corresponds_to", - "FMA:development_type_of", - "FMA:developmental_stage_of", - "FMA:direct_cell_shape_of", - "FMA:direct_left_of", - "FMA:direct_right_of", - "FMA:distal_to", - "FMA:drains_into", - "FMA:efferent_to", - "FMA:external_to", - "FMA:formed_by", - "FMA:forms", - "FMA:full_grown_phenotype_of", - "FMA:has_full_grown_phenotype", - "FMA:fuses_with", - "FMA:fusion_of", - "FMA:has_fusion", - "FMA:germ_origin_of", - "FMA:has_germ_origin", - "FMA:has_adherent", - "FMA:has_branch", - "FMA:has_connection_type", - "FMA:has_continuation_branch", - "FMA:has_development_type", - "FMA:has_developmental_stage", - "FMA:has_direct_cell_shape", - "FMA:has_inherent_3d_shape", - "FMA:has_insertion", - "FMA:has_lymphatic_drainage", - "FMA:has_nerve_supply", - "FMA:has_observed_anatomical_entity", - "FMA:has_origin", - "FMA:has_primary_segmental_supply", - "FMA:has_projection", - "FMA:has_regional_part", - "FMA:has_related_developmental_entity", - "FMA:has_secondary_segmental_supply", - "FMA:has_segmental_composition", - "FMA:has_segmental_supply", - "FMA:has_tributary", - "FMA:has_venous_drainage", - "FMA:inferior_to", - "FMA:inferolateral_to", - "FMA:inferomedial_to", - "FMA:inherent_3d_shape_of", - "FMA:insertion_of", - "FMA:internal_to", - "FMA:lateral_to", - "FMA:left_lateral_to", - "FMA:left_medial_to", - "FMA:lymphatic_drainage_of", - "FMA:matures_from", - "FMA:matures_into", - "FMA:medial_to", - "FMA:merges_with", - "FMA:nerve_supply_of", - "FMA:origin_of", - "FMA:posterior_to", - "FMA:posteroinferior_to", - "FMA:posterolateral_to", - "FMA:posteromedial_to", - "FMA:posterosuperior_to", - "FMA:primary_segmental_supply_of", - "FMA:projects_from", - "FMA:projects_to", - "FMA:proximal_to", - "FMA:receives_attachment_from", - "FMA:receives_drainage_from", - "FMA:receives_input_from", - "FMA:receives_projection", - "FMA:related_part", - "FMA:right_lateral_to", - "FMA:right_medial_to", - "FMA:secondary_segmental_supply_of", - "FMA:segmental_composition_of", - "FMA:segmental_supply_of", - "FMA:sends_output_to", - "FMA:superior_to", - "FMA:superolateral_to", - "FMA:superomedial_to", - "FMA:surrounded_by", - "FMA:surrounds", - "FMA:tributary_of", - "FMA:venous_drainage_of", - "LOINC:has_lateral_anatomic_location", - "LOINC:has_lateral_location_presence", - "OBO:core#distally_connected_to", - "OBO:core#subdivision_of", - "RO:0002219", - "RO:0002220", - "RO:0002221", - "SO:has_origin", - "UBERON:anastomoses_with", - "UBERON:anteriorly_connected_to", - "UBERON:channel_for", - "UBERON:channels_from", - "UBERON:channels_into", - "UBERON:conduit_for", - "UBERON:distally_connected_to", - "UBERON:existence_starts_and_ends_during", - "UBERON:extends_fibers_into", - "UBERON:filtered_through", - "UBERON:in_central_side_of", - "UBERON:in_innermost_side_of", - "UBERON:in_outermost_side_of", - "UBERON:indirectly_supplies", - "UBERON:posteriorly_connected_to", - "UBERON:protects", - "UBERON:proximally_connected_to", - "UBERON:sexually_homologous_to" - ] - }, - "in pathway with": { - "description": "holds between two genes or gene products that are part of in the same biological pathway", - "is_a": "coexists with", - "domain": "gene or gene product", - "range": "gene or gene product", - "in_subset": [ - "translator_minimal" - ], - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "related_mappings": [ - "SIO:010532" - ] - }, - "in complex with": { - "description": "holds between two genes or gene products that are part of (or code for products that are part of) in the same macromolecular complex mixin", - "is_a": "coexists with", - "domain": "gene or gene product", - "range": "gene or gene product", - "in_subset": [ - "translator_minimal" - ], - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "related_mappings": [ - "SIO:010497" - ], - "broad_mappings": [ - "SIO:010285" - ] - }, - "in cell population with": { - "description": "holds between two genes or gene products that are expressed in the same cell type or population", - "is_a": "coexists with", - "domain": "gene or gene product", - "range": "gene or gene product", - "in_subset": [ - "translator_minimal" - ], - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - } - }, - "colocalizes with": { - "description": "holds between two entities that are observed to be located in the same place.", - "is_a": "coexists with", - "in_subset": [ - "translator_minimal" - ], - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "RO:00002325" - ] - }, - "genetic association": { - "is_a": "related to", - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "description": "Co-occurrence of a certain allele of a genetic marker and the phenotype of interest in the same individuals at above-chance level", - "exact_mappings": [ - "WIKIDATA_PROPERTY:P2293" - ] - }, - "gene associated with condition": { - "is_a": "genetic association", - "description": "holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence, contribute to, or correlate with", - "domain": "gene", - "range": "disease or phenotypic feature", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "in_subset": [ - "translator_minimal" - ], - "exact_mappings": [ - "RTXKG1:gene_associated_with_condition" - ], - "broad_mappings": [ - "GENO:0000840", - "GENO:0000841" - ], - "narrow_mappings": [ - "NCIT:R38", - "NCIT:R175", - "NCIT:R48" - ] - }, - "condition associated with gene": { - "is_a": "genetic association", - "description": "holds between a gene and a disease or phenotypic feature that may be influenced, contribute to, or be correlated with the gene or its alleles/products", - "domain": "disease or phenotypic feature", - "range": "gene", - "in_subset": [ - "translator_minimal" - ], - "inverse": "gene associated with condition", - "narrow_mappings": [ - "NCIT:R176", - "hetio:ASSOCIATES_DaG" - ] - }, - "affects risk for": { - "is_a": "related to", - "description": "holds between two entities where exposure to one entity alters the chance of developing the other", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "in_subset": [ - "translator_minimal" - ] - }, - "risk affected by": { - "is_a": "related to", - "inverse": "affects risk for" - }, - "predisposes": { - "is_a": "affects risk for", - "description": "holds between two entities where exposure to one entity increases the chance of developing the other", - "in_subset": [ - "translator_minimal" - ], - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "SEMMEDDB:PREDISPOSES", - "SEMMEDDB:predisposes" - ] - }, - "contributes to": { - "is_a": "related to", - "description": "holds between two entities where the occurrence, existence, or activity of one causes or contributes to the occurrence or generation of the other", - "in_subset": [ - "translator_minimal" - ], - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "close_mappings": [ - "IDO:0000664" - ], - "exact_mappings": [ - "RO:0002326" - ], - "narrow_mappings": [ - "CTD:marker_mechanism", - "MONDO:predisposes_towards", - "RO:0002255", - "RO:0003304" - ] - }, - "contribution from": { - "is_a": "related to", - "in_subset": [ - "translator_minimal" - ], - "inverse": "contributes to" - }, - "causes": { - "description": "holds between two entities where the occurrence, existence, or activity of one causes the occurrence or generation of the other", - "is_a": "contributes to", - "in_subset": [ - "translator_minimal" - ], - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "SEMMEDDB:CAUSES", - "SEMMEDDB:causes", - "WIKIDATA_PROPERTY:P1542", - "SNOMED:cause_of" - ], - "broad_mappings": [ - "RO:0002410", - "RO:0002506" - ], - "narrow_mappings": [ - "MONDO:disease_triggers", - "GOREL:0000040", - "MONDO:disease_causes_feature", - "MONDO:disease_triggers", - "NCIT:allele_has_abnormality", - "NCIT:biological_process_has_result_biological_process", - "NCIT:chemical_or_drug_has_physiologic_effect", - "NCIT:chemical_or_drug_initiates_biological_process", - "NCIT:process_initiates_biological_process", - "NCIT:chromosome_mapped_to_disease", - "NCIT:disease_has_normal_tissue_origin", - "OBO:nbo#in_response_to", - "ORPHA:317343", - "ORPHA:317344", - "ORPHA:317346", - "ORPHA:410295", - "ORPHA:410296", - "RO:0002256", - "RO:0002315", - "RO:0002507", - "RO:0002509", - "RO:0004001", - "RTXKG1:capable_of_part_of", - "SNOMED:causative_agent_of", - "SNOMED:has_realization", - "UMLS:has_physiologic_effect" - ] - }, - "caused by": { - "description": "holds between two entities where the occurrence, existence, or activity of one is caused by the occurrence or generation of the other", - "is_a": "related to", - "in_subset": [ - "translator_minimal" - ], - "inverse": "causes", - "exact_mappings": [ - "WIKIDATA_PROPERTY:P828" - ], - "narrow_mappings": [ - "RO:0001022", - "RO:0002608", - "RO:0004019", - "RO:0004020", - "RO:0004028", - "RO:0009501", - "RTXKG1:disease_caused_by_disruption_of", - "RTXKG1:disease_has_basis_in_dysfunction_of", - "RTXKG1:realized_in_response_to", - "RTXKG1:realized_in_response_to_stimulus" - ] - }, - "ameliorates": { - "is_a": "affects", - "description": "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition.", - "domain": "biological entity", - "range": "disease or phenotypic feature", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "RO:0003307", - "CTD:therapeutic" - ] - }, - "exacerbates": { - "is_a": "affects", - "description": "A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.", - "domain": "biological entity", - "range": "disease or phenotypic feature", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "RO:0003309" - ] - }, - "treats": { - "aliases": [ - "is substance that treats" - ], - "is_a": "ameliorates", - "description": "holds between a therapeutic procedure or chemical entity and a disease or phenotypic feature that it is used to treat", - "domain": "chemical or drug or treatment", - "range": "disease or phenotypic feature", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "in_subset": [ - "translator_minimal" - ], - "related_mappings": [ - "MONDO:disease_responds_to" - ], - "exact_mappings": [ - "DRUGBANK:treats", - "SEMMEDDB:TREATS", - "SEMMEDDB:treats", - "WIKIDATA_PROPERTY:P2175" - ], - "narrow_mappings": [ - "RO:0002606", - "NCIT:regimen_has_accepted_use_for_disease", - "REPODB:clinically_tested_approved_unknown_phase", - "REPODB:clinically_tested_suspended_phase_0", - "REPODB:clinically_tested_suspended_phase_1", - "REPODB:clinically_tested_suspended_phase_1_or_phase_2", - "REPODB:clinically_tested_suspended_phase_2", - "REPODB:clinically_tested_suspended_phase_2_or_phase_3", - "REPODB:clinically_tested_suspended_phase_3", - "REPODB:clinically_tested_terminated_phase_0", - "REPODB:clinically_tested_terminated_phase_1", - "REPODB:clinically_tested_terminated_phase_1_or_phase_2", - "REPODB:clinically_tested_terminated_phase_2", - "REPODB:clinically_tested_terminated_phase_2_or_phase_3", - "REPODB:clinically_tested_terminated_phase_3", - "REPODB:clinically_tested_withdrawn_phase_0", - "REPODB:clinically_tested_withdrawn_phase_1", - "REPODB:clinically_tested_withdrawn_phase_1_or_phase_2", - "REPODB:clinically_tested_withdrawn_phase_2", - "REPODB:clinically_tested_withdrawn_phase_2_or_phase_3", - "REPODB:clinically_tested_withdrawn_phase_3", - "RTXKG1:indicated_for", - "SNOMED:plays_role" - ] - }, - "treated by": { - "is_a": "related to", - "description": "holds between a disease or phenotypic feature and a therapeutic process or chemical entity that is used to treat the condition", - "domain": "disease or phenotypic feature", - "range": "chemical or drug or treatment", - "in_subset": [ - "translator_minimal" - ], - "inverse": "treats", - "exact_mappings": [ - "WIKIDATA_PROPERTY:P2176", - "MONDO:disease_responds_to" - ], - "narrow_mappings": [ - "RO:0002302" - ] - }, - "approved to treat": { - "description": "holds between a therapeutic procedure or chemical entity and a disease or phenotypic feature for which it is approved for treatment to some level of clinical trial. Note that in terms of REPODB narrow mappings, terms containing 'suspended', 'terminated' or 'withdrawn' should be mapped onto associations using this term for which 'negated: true' is asserted.", - "is_a": "treats", - "domain": "chemical or drug or treatment", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "NCIT:C172573" - ], - "narrow_mappings": [ - "NCIT:R172", - "NCIT:regimen_has_accepted_use_for_disease", - "REPODB:clinically_tested_approved_unknown_phase", - "REPODB:clinically_tested_suspended_phase_0", - "REPODB:clinically_tested_suspended_phase_1", - "REPODB:clinically_tested_suspended_phase_1_or_phase_2", - "REPODB:clinically_tested_suspended_phase_2", - "REPODB:clinically_tested_suspended_phase_2_or_phase_3", - "REPODB:clinically_tested_suspended_phase_3", - "REPODB:clinically_tested_terminated_phase_0", - "REPODB:clinically_tested_terminated_phase_1", - "REPODB:clinically_tested_terminated_phase_1_or_phase_2", - "REPODB:clinically_tested_terminated_phase_2", - "REPODB:clinically_tested_terminated_phase_2_or_phase_3", - "REPODB:clinically_tested_terminated_phase_3", - "REPODB:clinically_tested_withdrawn_phase_0", - "REPODB:clinically_tested_withdrawn_phase_1", - "REPODB:clinically_tested_withdrawn_phase_1_or_phase_2", - "REPODB:clinically_tested_withdrawn_phase_2", - "REPODB:clinically_tested_withdrawn_phase_2_or_phase_3", - "REPODB:clinically_tested_withdrawn_phase_3" - ] - }, - "approved for treatment by": { - "description": "holds between a disease or phenotypic feature and a therapeutic process or chemical entity that is approved for treatment of the condition (or not, if negated) to some level of clinical trial", - "is_a": "treated by", - "range": "chemical or drug or treatment", - "inverse": "approved to treat" - }, - "prevents": { - "is_a": "affects risk for", - "description": "holds between an entity whose application or use reduces the likelihood of a potential outcome. Typically used to associate a chemical entity, exposure, activity, or medical intervention that can prevent the onset a disease or phenotypic feature.", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "in_subset": [ - "translator_minimal" - ], - "exact_mappings": [ - "SEMMEDDB:PREVENTS", - "SEMMEDDB:prevents" - ], - "narrow_mappings": [ - "RO:0002599" - ] - }, - "prevented by": { - "is_a": "related to", - "description": "holds between a potential outcome of which the likelihood was reduced by the application or use of an entity.", - "inverse": "prevents" - }, - "correlated with": { - "is_a": "related to", - "description": "holds between any two named thing entities. For example, correlated_with holds between a disease or phenotypic feature and a measurable molecular entity that is used as an indicator of the presence or state of the disease or feature.", - "domain": "named thing", - "range": "named thing", - "in_subset": [ - "translator_minimal" - ], - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "RO:0002610", - "PATO:correlates_with" - ], - "narrow_mappings": [ - "LOINC:associated_with", - "NCIT:is_associated_disease_of", - "NCIT:is_cytogenetic_abnormality_of_disease", - "ORPHA:317345", - "PDQ:associated_disease", - "RO:0004029", - "RTXKG1:associated_with_disease", - "SNOMED:associated_with", - "SNOMED:has_associated_finding" - ] - }, - "positively correlated with": { - "is_a": "correlated with", - "description": "holds between any two named thing entities \"correlated with\" one another in a positive manner.", - "domain": "named thing", - "range": "named thing", - "in_subset": [ - "translator_minimal" - ], - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "CTD:positive_correlation" - ] - }, - "negatively correlated with": { - "is_a": "correlated with", - "description": "holds between any two named thing entities \"correlated with\" one another in a negative manner.", - "domain": "named thing", - "range": "named thing", - "in_subset": [ - "translator_minimal" - ], - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "CTD:negative_correlation" - ] - }, - "coexpressed with": { - "is_a": "correlated with", - "description": "holds between any two genes or gene products, in which both are generally expressed within a single defined experimental context.", - "domain": "gene or gene product", - "range": "gene or gene product", - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - } - }, - "has biomarker": { - "is_a": "correlated with", - "description": "holds between a disease or phenotypic feature and a measurable chemical entity that is used as an indicator of the presence or state of the disease or feature. # metabolite", - "domain": "disease or phenotypic feature", - "range": "chemical entity", - "in_subset": [ - "translator_minimal" - ], - "inverse": "biomarker for", - "narrow_mappings": [ - "NCIT:disease_has_finding", - "NCIT:disease_has_molecular_abnormality", - "NCIT:disease_is_marked_by_gene" - ] - }, - "biomarker for": { - "is_a": "correlated with", - "description": "holds between a measurable chemical entity and a disease or phenotypic feature, where the entity is used as an indicator of the presence or state of the disease or feature.", - "domain": "chemical entity", - "range": "disease or phenotypic feature", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "in_subset": [ - "translator_minimal" - ], - "exact_mappings": [ - "NCIT:R39" - ], - "broad_mappings": [ - "RO:0002607" - ], - "narrow_mappings": [ - "NCIT:R47", - "NCIT:genetic_biomarker_related_to", - "NCIT:is_molecular_abnormality_of_disease", - "ORPHA:465410", - "SEMMEDDB:diagnoses" - ] - }, - "expressed in": { - "is_a": "related to", - "description": "holds between a gene or gene product and an anatomical entity in which it is expressed", - "domain": "gene or gene product", - "range": "anatomical entity", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "in_subset": [ - "translator_minimal" - ], - "exact_mappings": [ - "RO:0002206" - ], - "narrow_mappings": [ - "NCIT:R49", - "NCIT:R46", - "RTXKG1:expressed_in" - ] - }, - "expresses": { - "is_a": "related to", - "description": "holds between an anatomical entity and gene or gene product that is expressed there", - "domain": "anatomical entity", - "range": "gene or gene product", - "in_subset": [ - "translator_minimal" - ], - "inverse": "expressed in", - "exact_mappings": [ - 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"range": "chemical entity", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "in_subset": [ - "translator_minimal" - ], - "exact_mappings": [ - "WIKIDATA:Q181394" - ] - }, - "is active ingredient of": { - "is_a": "part of", - "description": "holds between a molecular entity and a drug, in which the former is a part of the latter, and is a biologically active component", - "domain": "molecular entity", - "range": "drug", - "in_subset": [ - "translator_minimal" - ], - "inverse": "has active ingredient", - "mappings": [ - "RO:0002249" - ] - }, - "has active ingredient": { - "is_a": "has part", - "description": "holds between a drug and a molecular entity in which the latter is a part of the former, and is a biologically active component", - "domain": "drug", - "range": "molecular entity", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "in_subset": [ - "translator_minimal" - ], - "inverse": "is active ingredient of", - "mappings": [ - "RO:0002248" - ] - }, - "is excipient of": { - "is_a": "part of", - "description": "holds between a molecular entity and a drug in which the former is a part of the latter, and is a biologically inactive component", - "domain": "molecular entity", - "range": "drug", - "in_subset": [ - "translator_minimal" - ], - "inverse": "has excipient", - "mappings": [ - "WIKIDATA:Q902638" - ] - }, - "has excipient": { - "is_a": "has part", - "description": "holds between a drug and a molecular entities in which the latter is a part of the former, and is a biologically inactive component", - "domain": "drug", - "range": "molecular entity", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "in_subset": [ - "translator_minimal" - ], - "mappings": [ - "WIKIDATA:Q902638" - ] - }, - "manifestation of": { - "is_a": "related to", - "description": "that part of a phenomenon which is directly observable or visibly expressed, or which gives evidence to the underlying process; used in SemMedDB for linking things like dysfunctions and processes to some disease or syndrome", - "range": "disease", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "in_subset": [ - "translator_minimal" - ], - "exact_mappings": [ - "SEMMEDDB:MANIFESTATION_OF", - "SEMMEDDB:manifestation_of", - "OMIM:manifestation_of" - ], - "broad_mappings": [ - "WIKIDATA_PROPERTY:P1557" - ], - "narrow_mappings": [ - "SNOMED:has_definitional_manifestation" - ] - }, - "has manifestation": { - "is_a": "related to", - "domain": "disease", - "inverse": "manifestation of" - }, - "produces": { - "is_a": "related to", - "description": "holds between a material entity and a product that is generated through the intentional actions or functioning of the material entity", - "in_subset": [ - "translator_minimal" - ], - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "related_mappings": [ - "GOREL:0001010" - ], - "exact_mappings": [ - "RO:0003000", - "WIKIDATA_PROPERTY:P1056", - "SEMMEDDB:PRODUCES", - "SEMMEDDB:produces" - ], - "narrow_mappings": [ - "NCIT:R29", - "SNOMED:has_process_output", - "SNOMED:specimen_procedure_of" - ] - }, - "produced by": { - "is_a": "related to", - "inverse": "produces", - "exact_mappings": [ - "RO:0003001" - ] - }, - "consumes": { - "is_a": "has input", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "narrow_mappings": [ - "RO:0004009" - ] - }, - "consumed by": { - "inverse": "consumes" - }, - "temporally related to": { - "is_a": "related to", - "description": "holds between two entities with a temporal relationship", - "domain": "occurrent", - "range": "occurrent", - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "SNOMED:temporally_related_to" - ], - "narrow_mappings": [ - "RO:0002082", - "RO:0002083", - "RO:0002092", - "RO:0002093", - "RO:0002223", - "RO:0002224", - "RO:0002229", - "RO:0002230", - "RO:0002488", - "RO:0002489", - "RO:0002492", - "RO:0002493", - "RO:0002496", - "RO:0002497" - ] - }, - "precedes": { - "is_a": "temporally related to", - "description": "holds between two processes, where one completes before the other begins", - "domain": "occurrent", - "range": "occurrent", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "in_subset": [ - "translator_minimal" - ], - "close_mappings": [ - "RO:0002263", - "RO:0002264" - ], - "exact_mappings": [ - "BFO:0000063", - "SEMMEDDB:PRECEDES", - "SEMMEDDB:precedes", - "SNOMED:occurs_before" - ], - "broad_mappings": [ - "WIKIDATA_PROPERTY:P156" - ], - "narrow_mappings": [ - "FMA:transforms_into", - "RO:0002090", - "RO:0002411", - "RO:0002412" - ] - }, - "preceded by": { - "is_a": "temporally related to", - "description": "holds between two processes, where the other is completed before the one begins", - "domain": "occurrent", - "range": "occurrent", - "inverse": "precedes", - "in_subset": [ - "translator_minimal" - ], - "exact_mappings": [ - "BFO:0000062" - ], - "broad_mappings": [ - "GENEPIO:0001739" - ], - "narrow_mappings": [ - "FMA:transforms_from", - "RO:0002087", - "RO:0002285" - ] - }, - "directly interacts with": { - "is_a": "interacts with", - "description": "Holds between chemical entities that physically and directly interact with each other", - "domain": "chemical entity", - "range": "chemical entity", - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "related_mappings": [ - "GAMMA:kd", - "GAMMA:kb", - "GAMMA:potency" - ], - "exact_mappings": [ - "chembio:interacts", - "CTD:interacts_with", - "GAMMA:interacts_with" - ], - "broad_mappings": [ - "SIO:000203" - ], - "narrow_mappings": [ - "PHAROS:drug_targets", - "DRUGBANK:chelator", - "GAMMA:antibody_binding", - "GAMMA:pharmacological_chaperone", - "GAMMA:releasing_agent", - "GAMMA:pharmacological_chaperone", - "GAMMA:releasing_agent", - "GAMMA:binder", - "GAMMA:binding", - "GAMMA:ligand", - "GAMMA:cofactor", - "GAMMA:multitarget", - "GAMMA:chaperone", - "GAMMA:component", - "GAMMA:adduct", - "GAMMA:antibody", - "CTD:affects_binding", - "DGIdb:binder", - "DGIdb:cofactor" - ] - }, - "affects expression in": { - "is_a": "affects", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "description": "Holds between a variant and an anatomical entity where the expression of the variant is located in.", - "exact_mappings": [ - "GTEx:affects_expression_in" - ] - }, - "has variant part": { - "is_a": "has part", - "description": "holds between a nucleic acid entity and a nucleic acid entity that is a sub-component of it", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "GENO:0000382" - ] - }, - "variant part of": { - "is_a": "part of", - "inverse": "has variant part" - }, - "related condition": { - "is_a": "related to", - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "GENO:0000790" - ] - }, - "is sequence variant of": { - "is_a": "related to", - "description": "holds between a sequence variant and a nucleic acid entity", - "domain": "sequence variant", - "range": "nucleic acid entity", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "narrow_mappings": [ - "NCIT:gene_product_sequence_variation_encoded_by_gene_mutant", - "NCIT:gene_product_variant_of_gene_product", - "OMIM:allelic_variant_of", - "WIKIDATA:P3433" - ] - }, - "has sequence variant": { - "is_a": "related to", - "inverse": "is sequence variant of", - "domain": "nucleic acid entity", - "range": "sequence variant" - }, - "is missense variant of": { - "is_a": "is sequence variant of", - "description": "holds between a gene and a sequence variant, such the sequence variant results in a different amino acid sequence but where the length is preserved.", - "domain": "sequence variant", - "range": "gene", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "SO:0001583", - "SNPEFF:missense_variant" - ], - "narrow_mappings": [ - "SNPEFF:initiator_codon_variant", - "SNPEFF:structural_interaction_variant" - ] - }, - "has missense variant": { - "is_a": "is sequence variant of", - "domain": "gene", - "range": "sequence variant", - "inverse": "is missense variant of" - }, - "is synonymous variant of": { - "is_a": "is sequence variant of", - "description": "holds between a sequence variant and a gene, such the sequence variant is in the coding sequence of the gene, but results in the same amino acid sequence", - "domain": "sequence variant", - "range": "gene", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "SO:0001819", - "SNPEFF:synonymous_variant" - ], - "narrow_mappings": [ - "SNPEFF:start_retained", - "SNPEFF:stop_retained_variant" - ] - }, - "has synonymous variant": { - "is_a": "is sequence variant of", - "domain": "gene", - "range": "sequence variant", - "inverse": "is synonymous variant of" - }, - "is nonsense variant of": { - "is_a": "is sequence variant of", - "description": "holds between a sequence variant and a gene, such the sequence variant results in a premature stop codon", - "domain": "sequence variant", - "range": "gene", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "SNPEFF:stop_gained" - ], - "broad_mappings": [ - "SO:0002054" - ] - }, - "has nonsense variant": { - "is_a": "is sequence variant of", - "domain": "gene", - "range": "sequence variant", - "inverse": "is nonsense variant of" - }, - "is frameshift variant of": { - "is_a": "is sequence variant of", - "description": "holds between a sequence variant and a gene, such the sequence variant causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three.", - "domain": "sequence variant", - "range": "gene", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "SO:0001589", - "SNPEFF:frameshift_variant" - ], - "narrow_mappings": [ - "SNPEFF:start_lost", - "SNPEFF:stop_lost" - ] - }, - "has frameshift variant": { - "is_a": "is sequence variant of", - "inverse": "is frameshift variant of", - "domain": "gene", - "range": "sequence variant" - }, - "is splice site variant of": { - "is_a": "is sequence variant of", - "description": "holds between a sequence variant and a gene, such the sequence variant is in the canonical splice site of one of the gene's exons.", - "domain": "sequence variant", - "range": "gene", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "SO:0001629" - ], - "narrow_mappings": [ - "SNPEFF:splice_region_variant", - "SNPEFF:splice_acceptor_variant", - "SNPEFF:splice_donor_variant" - ] - }, - "has splice site variant": { - "is_a": "is sequence variant of", - "domain": "gene", - "range": "sequence variant", - "inverse": "is splice site variant of" - }, - "is nearby variant of": { - "is_a": "is sequence variant of", - "description": "holds between a sequence variant and a gene sequence that the variant is genomically close to.", - "domain": "sequence variant", - "range": "gene", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "GAMMA:0000102" - ], - "narrow_mappings": [ - "SNPEFF:downstream_gene_variant", - "SNPEFF:upstream_gene_variant" - ] - }, - "has nearby variant": { - "is_a": "is sequence variant of", - "domain": "gene", - "range": "sequence variant", - "inverse": "is nearby variant of" - }, - "is non coding variant of": { - "is_a": "is sequence variant of", - "description": "holds between a sequence variant and a gene, where the variant does not affect the coding sequence", - "domain": "sequence variant", - "range": "gene", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "GAMMA:0000103" - ], - "narrow_mappings": [ - "SNPEFF:3_prime_UTR_variant", - "SNPEFF:5_prime_UTR_variant", - "SNPEFF:5_prime_UTR_premature_start_codon_gain_variant", - "SNPEFF:non_coding_transcript_exon_variant", - "SNPEFF:intron_variant" - ] - }, - "has non coding variant": { - "is_a": "is sequence variant of", - "domain": "gene", - "range": "sequence variant", - "inverse": "is non coding variant of" - }, - "disease has basis in": { - "description": "A relation that holds between a disease and an entity where the state of the entity has contribution to the disease.", - "is_a": "related to", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "narrow_mappings": [ - "MONDO:disease_has_basis_in_development_of", - "MONDO:disease_has_basis_in_accumulation_of" - ] - }, - "causes adverse event": { - "is_a": "causes", - "description": "holds between a drug and a disease or phenotype that can be caused by the drug", - "domain": "drug", - "range": "disease or phenotypic feature", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "Aeolus:0000001" - ] - }, - "adverse event caused by": { - "is_a": "causes", - "domain": "disease or phenotypic feature", - "range": "drug", - "inverse": "causes adverse event" - }, - "contraindicated for": { - "is_a": "related to", - "description": "Holds between a drug and a disease or phenotype, such that a person with that disease should not be treated with the drug.", - "domain": "drug", - "range": "disease or phenotypic feature", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "DrugCentral:0000001", - "RTXKG1:contraindicated_for" - ] - }, - "has contraindication": { - "is_a": "related to", - "domain": "disease or phenotypic feature", - "range": "drug", - "inverse": "contraindicated for" - }, - "has not completed": { - "is_a": "related to", - "description": "holds between an entity and a process that the entity is capable of, but has not completed", - "exact_mappings": [ - "CL:has_not_completed" - ], - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - } - }, - "not completed by": { - "is_a": "related to", - "inverse": "has not completed" - }, - "has completed": { - "is_a": "related to", - "description": "holds between an entity and a process that the entity is capable of and has completed", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "CL:has_completed", - "RTXKG1:has_completed" - ] - }, - "completed by": { - "is_a": "related to", - "inverse": "has completed" - }, - "decreases molecular interaction": { - "is_a": "molecularly interacts with", - "description": "indicates that the source decreases the molecular interaction between the target and some other chemical entity", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "CTD:decreases_molecular_interaction_with" - ] - }, - "molecular interaction decreased by": { - "is_a": "molecularly interacts with", - "inverse": "decreases molecular interaction" - }, - "increases molecular interaction": { - "is_a": "molecularly interacts with", - "description": "indicates that the source increases the molecular interaction between the target and some other chemical entity", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "CTD:increases_molecular_interaction_with" - ] - }, - "molecular interaction increased by": { - "is_a": "molecularly interacts with", - "inverse": "increases molecular interaction" - }, - "in linkage disequilibrium with": { - "is_a": "related to", - "description": "holds between two sequence variants, the presence of which are correlated in a population", - "symmetric": true, - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "NCIT:C16798" - ] - }, - "has increased amount": { - "is_a": "related to", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "narrow_mappings": [ - "CL:has_high_plasma_membrane_amount" - ] - }, - "increased amount of": { - "is_a": "related to", - "inverse": "has increased amount" - }, - "has decreased amount": { - "is_a": "related to", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "narrow_mappings": [ - "CL:has_low_plasma_membrane_amount" - ] - }, - "decreased amount in": { - "is_a": "related to", - "inverse": "has decreased amount" - }, - "lacks part": { - "is_a": "related to", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "exact_mappings": [ - "CL:lacks_part", - "PR:lacks_part", - "RTXKG1:lacks_part" - ], - "narrow_mappings": [ - "CL:lacks_plasma_membrane_part" - ] - }, - "missing from": { - "is_a": "related to", - "inverse": "lacks part" - }, - "develops from": { - "is_a": "related to", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "close_mappings": [ - "RO:0002203", - "FMA:develops_into" - ], - "exact_mappings": [ - "BTO:develops_from", - "DDANAT:develops_from", - "FMA:develops_from", - "RO:0002202" - ], - "narrow_mappings": [ - "RO:0002207", - "RO:0002225", - "RO:0002226" - ] - }, - "develops into": { - "is_a": "related to", - "inverse": "develops from" - }, - "in taxon": { - "aliases": [ - "instance of" - ], - "is_a": "related to", - "domain": "thing with taxon", - "range": "organism taxon", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", - "in_subset": [ - "translator_minimal" - ], - "related_mappings": [ - "RO:0002162" - ], - "close_mappings": [ - "NCIT:is_organism_source_of_gene_product", - "NCIT:organism_has_gene" - ], - "exact_mappings": [ - "WIKIDATA_PROPERTY:P703" - ], - "narrow_mappings": [ - "NCIT:gene_found_in_organism", - "NCIT:gene_product_has_organism_source", - "RO:0002160" - ] - }, - "has molecular consequence": { - "is_a": "related to", - "description": "connects a sequence variant to a class describing the molecular consequence. E.g. SO:0001583", - "range": "ontology class", - "annotations": { - "tag": "biolink:canonical_predicate", - "value": true - }, - "narrow_mappings": [ - "NCIT:allele_has_activity" - ] - }, - "is molecular consequence of": { - "is_a": "related to", - "domain": "ontology class", - "inverse": "has molecular consequence" - }, - "association slot": { - "abstract": true, - "domain": "association", - "aliases": [ - "edge property", - "statement property" - ], - "description": "any slot that relates an association to another entity" - }, - "subject": { - "is_a": "association slot", - "local_names": { - "ga4gh": "annotation subject", - "neo4j": "node with outgoing relationship" - }, - "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", - "required": true, - "range": "named thing", - "slot_uri": "rdf:subject", - "exact_mappings": [ - "owl:annotatedSource", - "OBAN:association_has_subject" - ] - }, - "object": { - "is_a": "association slot", - "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", - "required": true, - "range": "named thing", - "local_names": { - "ga4gh": "descriptor", - "neo4j": "node with incoming relationship" - }, - "slot_uri": "rdf:object", - "exact_mappings": [ - "owl:annotatedTarget", - "OBAN:association_has_object" - ] - }, - "predicate": { - "is_a": "association slot", - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", - "domain": "association", - "notes": "Has a value from the Biolink related_to hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", - "range": "predicate type", - "required": true, - "local_names": { - "ga4gh": "annotation predicate", - "translator": "predicate" - }, - "slot_uri": "rdf:predicate", - "exact_mappings": [ - "owl:annotatedProperty", - "OBAN:association_has_predicate" - ] - }, - "logical interpretation": { - "is_a": "association slot", - "required": false, - "domain": "association", - "range": "logical_interpretation_enum", - "exact_mappings": [ - "os:LogicalInterpretation" - ] - }, - "relation": { - "is_a": "association slot", - "description": "The relation which describes an association between a subject and an object in a more granular manner. Usually this is a term from Relation Ontology, but it can be any edge CURIE.", - "domain": "association", - "range": "uriorcurie", - "required": true, - "id_prefixes": [ - "RO", - "BSPO", - "SIO" - ] - }, - "negated": { - "is_a": "association slot", - "range": "boolean", - "description": "if set to true, then the association is negated i.e. is not true" - }, - "has confidence level": { - "is_a": "association slot", - "range": "confidence level", - "description": "connects an association to a qualitative term denoting the level of confidence" - }, - "has evidence": { - "is_a": "association slot", - "range": "evidence type", - "description": "connects an association to an instance of supporting evidence", - "exact_mappings": [ - "RO:0002558" - ] - }, - "knowledge source": { - "is_a": "association slot", - "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "range": "information resource", - "multivalued": true, - "close_mappings": [ - "pav:providedBy" - ] - }, - "provided by": { - "is_a": "association slot", - "deprecated": "This slot is deprecated and replaced by a set of more precise slots for describing the source retrieval provenance of an Association. These include 'knowledge source' and its descendants 'primary knowledge source', 'original knowledge source', and 'aggregator knowledge source'.", - "description": "connects an association to the agent (person, organization or group) that provided it", - "range": "agent", - "multivalued": true, - "exact_mappings": [ - "pav:providedBy" - ] - }, - "primary knowledge source": { - "is_a": "knowledge source", - "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).", - "range": "information resource", - "multivalued": false - }, - "original knowledge source": { - "is_a": "primary knowledge source", - "description": "The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).", - "range": "information resource", - "multivalued": false - }, - "aggregator knowledge source": { - "is_a": "knowledge source", - "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", - "range": "information resource", - "multivalued": true - }, - "supporting data source": { - "is_a": "association slot", - "description": "An Information Resource from which data was retrieved and subsequently used as evidence to generate the knowledge expressed in an Association (e.g. through computation on, reasoning or inference over the retrieved data).", - "range": "information resource", - "multivalued": true - }, - "association type": { - "is_a": "association slot", - "range": "category type", - "deprecated": "This slot is deprecated in favor of 'category' slot.", - "deprecated_element_has_exact_replacement": "category", - "description": "connects an association to the category of association (e.g. gene to phenotype)" - }, - "chi squared statistic": { - "is_a": "association slot", - "range": "float", - "description": "represents the chi-squared statistic computed from observations", - "exact_mappings": [ - "STATO:0000030" - ] - }, - "p value": { - "is_a": "association slot", - "range": "float", - "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "exact_mappings": [ - "OBI:0000175", - "NCIT:C44185", - "EDAM-DATA:1669" - ] - }, - "interacting molecules category": { - "is_a": "association slot", - "range": "ontology class", - "exact_mappings": [ - "MI:1046" - ], - "values_from": [ - "MI" - ], - "examples": [ - { - "value": "MI:1048", - "description": "smallmolecule-protein" - } - ] - }, - "quantifier qualifier": { - "is_a": "association slot", - "range": "ontology class", - "description": "A measurable quantity for the object of the association", - "narrow_mappings": [ - "LOINC:analyzes", - "LOINC:measured_by", - "LOINC:property_of", - "SEMMEDDB:measures", - "UMLS:measures" - ] - }, - "catalyst qualifier": { - "is_a": "association slot", - "multivalued": true, - "range": "macromolecular machine mixin", - "description": "a qualifier that connects an association between two causally connected entities (for example, two chemical entities, or a chemical entity in that changes location) and the gene product, gene, or complex that enables or catalyzes the change." - }, - "expression site": { - "description": "location in which gene or protein expression takes place. May be cell, tissue, or organ.", - "is_a": "association slot", - "range": "anatomical entity", - "examples": [ - { - "value": "UBERON:0002037", - "description": "cerebellum" - } - ] - }, - "stage qualifier": { - "description": "stage during which gene or protein expression of takes place.", - "is_a": "association slot", - "range": "life stage", - "examples": [ - { - "value": "UBERON:0000069", - "description": "larval stage" - } - ] - }, - "phenotypic state": { - "description": "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX.", - "is_a": "association slot", - "range": "disease or phenotypic feature" - }, - "qualifiers": { - "singular_name": "qualifier", - "description": "connects an association to qualifiers that modify or qualify the meaning of that association", - "local_names": { - "ga4gh": "annotation qualifier" - }, - "is_a": "association slot", - "multivalued": true, - "range": "ontology class" - }, - "frequency qualifier": { - "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "is_a": "association slot", - "range": "frequency value" - }, - "severity qualifier": { - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", - "is_a": "association slot", - "range": "severity value" - }, - "sex qualifier": { - "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "is_a": "association slot", - "range": "biological sex" - }, - "onset qualifier": { - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", - "is_a": "association slot", - "range": "onset" - }, - "clinical modifier qualifier": { - "description": "Used to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects", - "is_a": "association slot", - "range": "clinical modifier" - }, - "sequence variant qualifier": { - "description": "a qualifier used in an association with the variant", - "is_a": "association slot", - "range": "sequence variant" - }, - "publications": { - "singular_name": "publication", - "description": "connects an association to publications supporting the association", - "is_a": "association slot", - "multivalued": true, - "range": "publication" - }, - "associated environmental context": { - "is_a": "association slot", - "description": "An attribute that can be applied to an association where the association holds between two entities located or occurring in a particular environment. For example, two microbial taxa may interact in the context of a human gut; a disease may give rise to a particular phenotype in a particular environmental exposure." - }, - "sequence localization attribute": { - "is_a": "association slot", - "domain": "genomic sequence localization", - "description": "An attribute that can be applied to a genome sequence localization edge. These edges connect a nucleic acid entity such as an exon to an entity such as a chromosome. Edge properties are used to ascribe specific positional information and other metadata to the localization. In pragmatic terms this can be thought of as columns in a GFF3 line." - }, - "interbase coordinate": { - "is_a": "sequence localization attribute", - "aliases": [ - "zero-based", - "half-open", - "space-based" - ], - "description": "A position in interbase coordinates. Interbase coordinates start at position 0 instead of position 1. This is applied to a sequence localization edge.", - "range": "integer" - }, - "start interbase coordinate": { - "is_a": "interbase coordinate", - "description": "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0).", - "close_mappings": [ - "faldo:begin" - ] - }, - "end interbase coordinate": { - "is_a": "interbase coordinate", - "description": "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on.", - "close_mappings": [ - "faldo:end" - ] - }, - "start coordinate": { - "is_a": "base coordinate", - "aliases": [ - "start" - ], - "description": "The position at which the subject genomic entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 1).", - "exact_mappings": [ - "gff3:start" - ], - "close_mappings": [ - "faldo:begin" - ] - }, - "end coordinate": { - "is_a": "base coordinate", - "aliases": [ - "end" - ], - "description": "The position at which the subject genomic entity ends on the chromosome or other entity to which it is located on.", - "exact_mappings": [ - "gff3:end" - ], - "close_mappings": [ - "faldo:end" - ] - }, - "genome build": { - "is_a": "sequence localization attribute", - "description": "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens.", - "range": "strand_enum", - "exact_mappings": [ - "gff3:strand" - ] - }, - "strand": { - "is_a": "sequence localization attribute", - "description": "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand).", - "range": "strand_enum", - "exact_mappings": [ - "gff3:strand" - ] - }, - "phase": { - "is_a": "sequence localization attribute", - "domain": "coding sequence", - "description": "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2.", - "range": "phase_enum", - "exact_mappings": [ - "gff3:phase" - ] - }, - "FDA approval status": { - "is_a": "association slot", - "description": "", - "range": "FDA_approval_status_enum" - } - }, - "classes": { - "ontology class": { - "mixin": true, - "description": "a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type.", - "exact_mappings": [ - "owl:Class", - "schema:Class" - ], - "comments": [ - "This is modeled as a mixin. 'ontology class' should not be the primary type of a node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc", - "Note that formally this is a metaclass. Instances of this class are instances in the graph, but can be the object of 'type' edges. For example, if we had a node in the graph representing a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample, and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity" - ], - "see_also": [ - "https://github.com/biolink/biolink-model/issues/486" - ], - "examples": [ - { - "value": "UBERON:0000955", - "description": "the class 'brain' from the Uberon anatomy ontology" - } - ], - "id_prefixes": [ - "MESH", - "UMLS", - "KEGG.BRITE" - ] - }, - "annotation": { - "description": "Biolink Model root class for entity annotations.", - "abstract": true - }, - "quantity value": { - "is_a": "annotation", - "description": "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value", - "slots": [ - "has unit", - "has numeric value" - ] - }, - "attribute": { - "is_a": "annotation", - "mixins": [ - "ontology class" - ], - "description": "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material.", - "slots": [ - "name", - "has attribute type", - "has quantitative value", - "has qualitative value", - "iri", - "source" - ], - "slot_usage": { - "name": { - "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." - } - }, - "id_prefixes": [ - "EDAM-DATA", - "EDAM-FORMAT", - "EDAM-OPERATION", - "EDAM-TOPIC" - ], - "exact_mappings": [ - "SIO:000614" - ], - "in_subset": [ - "samples" - ] - }, - "biological sex": { - "is_a": "attribute", - "exact_mappings": [ - "PATO:0000047" - ] - }, - "phenotypic sex": { - "is_a": "biological sex", - "description": "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present.", - "exact_mappings": [ - "PATO:0001894" - ] - }, - "genotypic sex": { - "is_a": "biological sex", - "description": "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes.", - "exact_mappings": [ - "PATO:0020000" - ] - }, - "severity value": { - "is_a": "attribute", - "description": "describes the severity of a phenotypic feature or disease" - }, - "relationship quantifier": { - "mixin": true - }, - "sensitivity quantifier": { - "is_a": "relationship quantifier", - "mixin": true - }, - "specificity quantifier": { - "is_a": "relationship quantifier", - "mixin": true - }, - "pathognomonicity quantifier": { - "is_a": "specificity quantifier", - "description": "A relationship quantifier between a variant or symptom and a disease, which is high when the presence of the feature implies the existence of the disease", - "mixin": true - }, - "frequency quantifier": { - "is_a": "relationship quantifier", - "mixin": true, - "slots": [ - "has count", - "has total", - "has quotient", - "has percentage" - ] - }, - "chemical or drug or treatment": { - "mixin": true - }, - "entity": { - "description": "Root Biolink Model class for all things and informational relationships, real or imagined.", - "abstract": true, - "slots": [ - "id", - "iri", - "category", - "type", - "name", - "description", - "source", - "provided by", - "has attribute" - ] - }, - "named thing": { - "is_a": "entity", - "description": "a databased entity or concept/class", - "slot_usage": { - "category": { - "range": "named thing", - "required": true - } - }, - "exact_mappings": [ - "BFO:0000001", - "WIKIDATA:Q35120", - "UMLSSG:OBJC", - "UMLSSC:T071", - "UMLSST:enty" - ] - }, - "relationship type": { - "is_a": "ontology class", - "description": "An OWL property used as an edge label" - }, - "gene ontology class": { - "mixin": true, - "description": "an ontology class that describes a functional aspect of a gene, gene prodoct or complex", - "is_a": "ontology class", - "in_subset": [ - "testing" - ] - }, - "unclassified ontology class": { - "mixin": true, - "description": "this is used for nodes that are taken from an ontology but are not typed using an existing biolink class", - "is_a": "ontology class", - "in_subset": [ - "testing" - ] - }, - "taxonomic rank": { - "description": "A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)", - "is_a": "ontology class", - "id_prefixes": [ - "TAXRANK" - ], - "mappings": [ - "WIKIDATA:Q427626" - ] - }, - "organism taxon": { - "aliases": [ - "taxon", - "taxonomic classification" - ], - "description": "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies.", - "is_a": "named thing", - "slot_usage": { - "has taxonomic rank": { - "range": "taxonomic rank", - "multivalued": false, - "mappings": [ - "WIKIDATA:P105" - ] - }, - "subclass of": { - "description": "subclass of holds between two taxa, e.g. human subclass of mammal", - "range": "organism taxon" - } - }, - "values_from": [ - "NCBITaxon" - ], - "exact_mappings": [ - "WIKIDATA:Q16521" - ], - "narrow_mappings": [ - "UMLSSC:T005", - "UMLSST:virs", - "UMLSSC:T007", - "UMLSST:bact", - "UMLSSC:T194", - "UMLSST:arch", - "UMLSSC:T204", - "UMLSST:euka", - "UMLSSC:T002", - "UMLSST:plnt", - "UMLSSC:T004", - "UMLSST:fngs", - "UMLSSC:T008", - "UMLSST:anim", - "UMLSSC:T010", - "UMLSST:vtbt", - "UMLSSC:T011", - "UMLSST:amph", - "UMLSSC:T012", - "UMLSST:bird", - "UMLSSC:T013", - "UMLSST:fish", - "UMLSSC:T014", - "UMLSST:rept", - "UMLSSC:T015", - "UMLSST:mamm", - "UMLSSC:T016", - "UMLSST:humn" - ], - "id_prefixes": [ - "NCBITaxon", - "MESH" - ], - "in_subset": [ - "model_organism_database" - ] - }, - "event": { - "is_a": "named thing", - "description": "Something that happens at a given place and time.", - "exact_mappings": [ - "NCIT:C25499", - "UMLSSC:T051", - "UMLSST:evnt" - ] - }, - "administrative entity": { - "is_a": "named thing", - "abstract": true - }, - "agent": { - "is_a": "administrative entity", - "aliases": [ - "group" - ], - "description": "person, group, organization or project that provides a piece of information (i.e. a knowledge association)", - "slots": [ - "affiliation", - "address" - ], - "exact_mappings": [ - "prov:Agent", - "dct:Agent" - ], - "narrow_mappings": [ - "UMLSSG:ORGA", - "UMLSSC:T092", - "UMLSST:orgt", - "UMLSSC:T093", - "UMLSST:hcro", - "UMLSSC:T094", - "UMLSST:pros", - "UMLSSC:T095", - "UMLSST:shro", - "UMLSSC:T096", - "UMLSST:grup" - ], - "slot_usage": { - "id": { - "required": true, - "description": "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code.", - "values_from": [ - "isbn", - "ORCID", - "ScopusID", - "ResearchID", - "GSID", - "isni" - ] - }, - "name": { - "description": "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" - } - }, - "id_prefixes": [ - "isbn", - "ORCID", - "ScopusID", - "ResearchID", - "GSID", - "isni" - ] - }, - "information content entity": { - "aliases": [ - "information", - "information artefact", - "information entity" - ], - "abstract": true, - "is_a": "named thing", - "description": "a piece of information that typically describes some topic of discourse or is used as support.", - "slots": [ - "license", - "rights", - "format", - "creation date" - ], - "id_prefixes": [ - "doi" - ], - "exact_mappings": [ - "IAO:0000030" - ], - "narrow_mappings": [ - "UMLSSG:CONC", - "UMLSSC:T077", - "UMLSST:cnce", - "UMLSSC:T078", - "UMLSST:idcn", - "UMLSSC:T079", - "UMLSST:tmco", - "UMLSSC:T080", - "UMLSST:qlco", - "UMLSSC:T081", - "UMLSST:qnco", - "UMLSSC:T082", - "UMLSST:spco", - "UMLSSC:T089", - "UMLSST:rnlw", - "UMLSSC:T102", - "UMLSST:grpa", - "UMLSSC:T169", - "UMLSST:ftcn", - "UMLSSC:T171", - "UMLSST:lang", - "UMLSSC:T185", - "UMLSST:clas" - ] - }, - "dataset": { - "description": "an item that refers to a collection of data from a data source.", - "is_a": "information content entity", - "exact_mappings": [ - "IAO:0000100", - "dctypes:Dataset", - "schema:dataset" - ] - }, - "dataset distribution": { - "is_a": "information content entity", - "description": "an item that holds distribution level information about a dataset.", - "slots": [ - "distribution download url" - ], - "exact_mappings": [ - "dcat:Distribution" - ] - }, - "dataset version": { - "description": "an item that holds version level information about a dataset.", - "is_a": "information content entity", - "slots": [ - "has dataset", - "ingest date", - "has distribution" - ] - }, - "dataset summary": { - "description": "an item that holds summary level information about a dataset.", - "is_a": "information content entity", - "slots": [ - "source web page", - "source logo" - ] - }, - "confidence level": { - "is_a": "information content entity", - "description": "Level of confidence in a statement", - "values_from": [ - "cio" - ], - "exact_mappings": [ - "CIO:0000028", - "SEPIO:0000187" - ], - "close_mappings": [ - "SEPIO:0000167" - ] - }, - "evidence type": { - "is_a": "information content entity", - "aliases": [ - "evidence code" - ], - "description": "Class of evidence that supports an association", - "values_from": [ - "eco" - ], - "exact_mappings": [ - "ECO:0000000" - ] - }, - "information resource": { - "is_a": "information content entity", - "aliases": [ - "knowledgebase" - ], - "description": "A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb.", - "in_subset": [ - "translator_minimal" - ] - }, - "publication": { - "is_a": "information content entity", - "description": "Any published piece of information. Can refer to a whole publication, its encompassing publication (i.e. journal or book) or to a part of a publication, if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). The scope is intended to be general and include information published on the web, as well as printed materials, either directly or in one of the Publication Biolink category subclasses.", - "slots": [ - "authors", - "pages", - "summary", - "keywords", - "mesh terms", - "xref" - ], - "slot_usage": { - "id": { - "description": "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." - }, - "name": { - "description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." - }, - "type": { - "slot_uri": "dct:type", - "required": true, - "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", - "values_from": [ - "dctypes", - "fabio", - "MESH_PUB", - "COAR_RESOURCE", - "WIKIDATA" - ] - }, - "pages": { - "multivalued": true, - "description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." - } - }, - "exact_mappings": [ - "IAO:0000311" - ], - "narrow_mappings": [ - "IAO:0000013", - "UMLSSC:T170", - "UMLSST:inpr" - ], - "id_prefixes": [ - "NLMID" - ], - "in_subset": [ - "model_organism_database" - ] - }, - "book": { - "is_a": "publication", - "description": "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility.", - "slot_usage": { - "id": { - "required": true, - "description": "Books should have industry-standard identifier such as from ISBN." - }, - "type": { - "description": "Should generally be set to an ontology class defined term for 'book'." - } - }, - "id_prefixes": [ - "isbn", - "NLMID" - ], - "in_subset": [ - "model_organism_database" - ] - }, - "book chapter": { - "is_a": "publication", - "slots": [ - "published in", - "volume", - "chapter" - ], - "slot_usage": { - "published in": { - "required": true, - "description": "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." - } - }, - "in_subset": [ - "model_organism_database" - ] - }, - "serial": { - "aliases": [ - "journal" - ], - "is_a": "publication", - "description": "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility.", - "slots": [ - "iso abbreviation", - "volume", - "issue" - ], - "slot_usage": { - "id": { - "required": true, - "description": "Serials (journals) should have industry-standard identifier such as from ISSN." - }, - "type": { - "description": "Should generally be set to an ontology class defined term for 'serial' or 'journal'." - } - }, - "id_prefixes": [ - "issn", - "NLMID" - ], - "in_subset": [ - "model_organism_database" - ] - }, - "article": { - "is_a": "publication", - "slots": [ - "published in", - "iso abbreviation", - "volume", - "issue" - ], - "slot_usage": { - "published in": { - "required": true, - "description": "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." - }, - "iso abbreviation": { - "description": "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." - } - }, - "id_prefixes": [ - "PMID" - ], - "in_subset": [ - "model_organism_database" - ] - }, - "physical essence or occurrent": { - "description": "Either a physical or processual entity.", - "mixin": true - }, - "physical essence": { - "description": "Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge.", - "is_a": "physical essence or occurrent", - "mixin": true - }, - "physical entity": { - "is_a": "named thing", - "mixins": [ - "physical essence" - ], - "description": "An entity that has material reality (a.k.a. physical essence).", - "exact_mappings": [ - "UMLSSC:T072", - "UMLSST:phob" - ], - "narrow_mappings": [ - "UMLSSC:T073", - "UMLSST:mnob" - ] - }, - "occurrent": { - "description": "A processual entity.", - "is_a": "physical essence or occurrent", - "mixin": true, - "exact_mappings": [ - "BFO:0000003" - ] - }, - "activity and behavior": { - "is_a": "occurrent", - "mixin": true, - "description": "Activity or behavior of any independent integral living, organization or mechanical actor in the world", - "exact_mappings": [ - "UMLSSG:ACTI" - ] - }, - "activity": { - "is_a": "named thing", - "mixins": [ - "activity and behavior" - ], - "description": "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.", - "exact_mappings": [ - "prov:Activity", - "NCIT:C43431", - "UMLSSC:T052", - "UMLSST:acty" - ], - "narrow_mappings": [ - "UMLSSC:T056", - "UMLSST:dora", - "UMLSSC:T057", - "UMLSST:ocac", - "UMLSSC:T064", - "UMLSST:gora", - "UMLSSC:T066", - "UMLSST:mcha", - "UMLSSC:T062", - "UMLSST:resa", - "UMLSSC:T065", - "UMLSST:edac", - "UMLSSC:T058", - "UMLSST:hlca" - ] - }, - "procedure": { - "is_a": "named thing", - "mixins": [ - "activity and behavior" - ], - "description": "A series of actions conducted in a certain order or manner", - "exact_mappings": [ - "UMLSSG:PROC" - ], - "narrow_mappings": [ - "UMLSSC:T059", - "UMLSST:lbpr", - "UMLSSC:T060", - "UMLSST:diap", - "UMLSSC:T061", - "UMLSST:topp", - "UMLSSC:T063", - "UMLSST:mbrt" - ] - }, - "phenomenon": { - "is_a": "named thing", - "mixins": [ - "occurrent" - ], - "description": "a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question", - "broad_mappings": [ - "UMLSSC:T067", - "UMLSST:phpr", - "UMLSSC:T068", - "UMLSST:hcpp", - "UMLSSC:T070", - "UMLSST:npop" - ], - "exact_mappings": [ - "UMLSSG:PHEN" - ], - "narrow_mappings": [ - "UMLSSC:T034", - "UMLSST:lbtr", - "UMLSSC:T038", - "UMLSST:biof", - "UMLSSC:T069", - "UMLSST:eehu" - ] - }, - "device": { - "is_a": "named thing", - "description": "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment", - "narrow_mappings": [ - "UMLSSG:DEVI", - "UMLSSC:T074", - "UMLSST:medd", - "UMLSSC:T075", - "UMLSST:resd", - "UMLSSC:T203", - "UMLSST:drdd", - "UMLSSC:T122", - "UMLSST:bodm" - ] - }, - "study population": { - "is_a": "population of individual organisms", - "description": "A group of people banded together or treated as a group as participants in a research study.", - "close_mappings": [ - "WIKIDATA:Q7229825" - ] - }, - "subject of investigation": { - "mixin": true, - "description": "An entity that has the role of being studied in an investigation, study, or experiment" - }, - "material sample": { - "aliases": [ - "biospecimen", - "sample", - "biosample", - "physical sample" - ], - "is_a": "physical entity", - "mixins": [ - "subject of investigation" - ], - "description": "A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]", - "exact_mappings": [ - "OBI:0000747", - "SIO:001050" - ], - "id_prefixes": [ - "BIOSAMPLE", - "GOLD.META" - ] - }, - "planetary entity": { - "is_a": "named thing", - "description": "Any entity or process that exists at the level of the whole planet" - }, - "environmental process": { - "is_a": "planetary entity", - "mixins": [ - "occurrent" - ], - "exact_mappings": [ - "ENVO:02500000" - ] - }, - "environmental feature": { - "is_a": "planetary entity", - "exact_mappings": [ - "ENVO:01000254" - ] - }, - "geographic location": { - "is_a": "planetary entity", - "description": "a location that can be described in lat/long coordinates", - "slots": [ - "latitude", - "longitude" - ], - "exact_mappings": [ - "UMLSSG:GEOG", - "UMLSST:geoa", - "UMLSSC:T083" - ] - }, - "geographic location at time": { - "is_a": "geographic location", - "description": "a location that can be described in lat/long coordinates, for a particular time", - "slots": [ - "timepoint" - ] - }, - "biological entity": { - "is_a": "named thing", - "aliases": [ - "bioentity" - ], - "abstract": true, - "narrow_mappings": [ - "WIKIDATA:Q28845870", - "UMLSSC:T050", - "UMLSST:emod", - "SIO:010046" - ] - }, - "thing with taxon": { - "mixin": true, - "description": "A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes", - "slots": [ - "in taxon" - ] - }, - "genomic entity": { - "mixin": true, - "is_a": "thing with taxon", - "slots": [ - "has biological sequence" - ], - "in_subset": [ - "translator_minimal" - ], - "narrow_mappings": [ - "UMLSSC:T028", - "GENO:0000897" - ] - }, - "molecular entity": { - "is_a": "chemical entity", - "description": "A molecular entity is a chemical entity composed of individual or covalently bonded atoms.", - "slots": [ - "is metabolite" - ], - "narrow_mappings": [ - "UMLSSC:T088", - "UMLSSC:T085" - ], - "in_subset": [ - "translator_minimal" - ] - }, - "chemical entity": { - "is_a": "named thing", - "abstract": true, - "mixins": [ - "physical essence", - "chemical or drug or treatment", - "chemical entity or gene or gene product", - "chemical entity or protein or polypeptide" - ], - "description": "A chemical entity is a physical entity that pertains to chemistry or biochemistry.", - "slots": [ - "trade name", - "available from" - ], - "exact_mappings": [ - "CHEBI:24431", - "SIO:010004", - "WIKIDATA:Q79529" - ], - "narrow_mappings": [ - "WIKIDATA:Q43460564", - "UMLSSC:T103", - "UMLSSC:T120", - "UMLSSC:T104", - "UMLSSC:T197", - "UMLSSC:T109", - "UMLSSC:T125", - "UMLSSC:T123", - "UMLSSC:T129", - "UMLSSC:T131" - ], - "broad_mappings": [ - "UMLSSC:T167" - ], - "in_subset": [ - "translator_minimal" - ] - }, - "chemical substance": { - "deprecated": "This class is deprecated in favor of 'small molecule.'" - }, - "small molecule": { - "is_a": "molecular entity", - "aliases": [ - "chemical substance" - ], - "description": "A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion).", - "narrow_mappings": [ - "UMLSSC:T196" - ], - "id_prefixes": [ - "PUBCHEM.COMPOUND", - "CHEMBL.COMPOUND", - "UNII", - "CHEBI", - "DRUGBANK", - "MESH", - "CAS", - "DrugCentral", - "GTOPDB", - "HMDB", - "KEGG.COMPOUND", - "ChemBank", - "Aeolus", - "PUBCHEM.SUBSTANCE", - "SIDER.DRUG", - "INCHI", - "INCHIKEY", - "KEGG.GLYCAN", - "KEGG.DRUG", - "KEGG.DGROUP", - "KEGG.ENVIRON" - ], - "slot_usage": { - "id": { - "examples": [ - { - "value": "CHEBI:29101", - "description": "sodium ion" - } - ] - } - }, - "in_subset": [ - "model_organism_database", - "translator_minimal" - ] - }, - "chemical mixture": { - "is_a": "chemical entity", - "description": "A chemical mixture is a chemical entity composed of two or more molecular entities.", - "slots": [ - "is supplement", - "highest FDA approval status" - ], - "in_subset": [ - "translator_minimal" - ] - }, - "nucleic acid entity": { - "is_a": "molecular entity", - "description": "A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included.", - "aliases": [ - "sequence feature", - "genomic entity" - ], - "mixins": [ - "genomic entity", - "physical essence", - "ontology class" - ], - "exact_mappings": [ - "SO:0000110" - ], - "narrow_mappings": [ - "UMLSSC:T086", - "UMLSSC:T114" - ], - "in_subset": [ - "model_organism_database", - "translator_minimal" - ] - }, - "molecular mixture": { - "is_a": "chemical mixture", - "description": "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry.", - "in_subset": [ - "translator_minimal" - ] - }, - "complex molecular mixture": { - "is_a": "chemical mixture", - "description": "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry.", - "in_subset": [ - "translator_minimal" - ] - }, - "biological process or activity": { - "description": "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system.", - "is_a": "biological entity", - "mixins": [ - "occurrent", - "ontology class" - ], - "id_prefixes": [ - "GO", - "REACT" - ], - "slots": [ - "has input", - "has output", - "enabled by" - ] - }, - "molecular activity": { - "description": "An execution of a molecular function carried out by a gene product or macromolecular complex.", - "is_a": "biological process or activity", - "aliases": [ - "molecular function", - "molecular event", - "reaction" - ], - "mixins": [ - "occurrent", - "ontology class" - ], - "slot_usage": { - "has input": { - "range": "molecular entity", - "description": "A chemical entity that is the input for the reaction" - }, - "has output": { - "range": "molecular entity", - "description": "A chemical entity that is the output for the reaction" - }, - "enabled by": { - "range": "macromolecular machine mixin", - "description": "The gene product, gene, or complex that catalyzes the reaction" - } - }, - "exact_mappings": [ - "GO:0003674", - "UMLSSC:T044", - "UMLSST:moft" - ], - "id_prefixes": [ - "GO", - "REACT", - "RHEA", - "MetaCyc", - "EC", - "TCDB", - "KEGG.REACTION", - "KEGG.RCLASS", - "KEGG.ENZYME" - ] - }, - "biological process": { - "is_a": "biological process or activity", - "mixins": [ - "occurrent", - "ontology class" - ], - "description": "One or more causally connected executions of molecular functions", - "exact_mappings": [ - "GO:0008150", - "SIO:000006", - "WIKIDATA:Q2996394" - ], - "broad_mappings": [ - "WIKIDATA:P682" - ], - "id_prefixes": [ - "GO", - "REACT", - "MetaCyc", - "KEGG.MODULE" - ] - }, - "pathway": { - "is_a": "biological process", - "mixins": [ - "ontology class" - ], - "exact_mappings": [ - "PW:0000001", - "WIKIDATA:Q4915012" - ], - "narrow_mappings": [ - "SIO:010526", - "GO:0007165" - ], - "id_prefixes": [ - "GO", - "REACT", - "KEGG", - "SMPDB", - "MSigDB", - "PHARMGKB.PATHWAYS", - "WIKIPATHWAYS", - "FB", - "PANTHER.PATHWAY" - ] - }, - "physiological process": { - "aliases": [ - "physiology" - ], - "is_a": "biological process", - "mixins": [ - "ontology class" - ], - "close_mappings": null, - "exact_mappings": [ - "UMLSSC:T039", - "UMLSST:phsf", - "WIKIDATA:Q30892994" - ], - "narrow_mappings": [ - "UMLSSC:T040", - "UMLSST:orgf", - "UMLSSC:T042", - "UMLSST:ortf", - "UMLSSC:T043", - "UMLSST:celf", - "UMLSSC:T045", - "UMLSST:genf" - ], - "id_prefixes": [ - "GO", - "REACT" - ] - }, - "behavior": { - "is_a": "biological process", - "mixins": [ - "ontology class", - "activity and behavior" - ], - "exact_mappings": [ - "GO:0007610", - "UMLSSC:T053", - "UMLSST:bhvr" - ], - "narrow_mappings": [ - "UMLSSC:T041", - "UMLSST:menp", - "UMLSSC:T054", - "UMLSST:socb", - "UMLSSC:T055", - "UMLSST:inbe" - ] - }, - "death": { - "is_a": "biological process", - "exact_mappings": [ - "GO:0016265" - ] - }, - "processed material": { - "is_a": "chemical mixture", - "description": "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing.", - "exact_mappings": [ - "OBI:0000047" - ] - }, - "drug": { - "is_a": "molecular mixture", - "mixins": [ - "chemical or drug or treatment", - "ontology class" - ], - "description": "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease", - "comments": [ - "The CHEBI ID represents a role rather than a substance" - ], - "broad_mappings": [ - "UMLSSC:T121", - "UMLSST:phsu" - ], - "exact_mappings": [ - "WIKIDATA:Q12140", - "CHEBI:23888", - "UMLSSC:T200", - "UMLSST:clnd" - ], - "narrow_mappings": [ - "UMLSSC:T195", - "UMLSST:antb" - ], - "id_prefixes": [ - "RXCUI", - "NDC", - "PHARMGKB.DRUG" - ] - }, - "environmental food contaminant": { - "is_a": "chemical entity", - "related_mappings": [ - "CHEBI:78299" - ] - }, - "food additive": { - "is_a": "chemical entity", - "related_mappings": [ - "CHEBI:64047" - ] - }, - "nutrient": { - "is_a": "chemical entity", - "related_mappings": [ - "CHEBI:33284" - ] - }, - "macronutrient": { - "is_a": "nutrient", - "related_mappings": [ - "CHEBI:33937" - ] - }, - "micronutrient": { - "is_a": "nutrient", - "related_mappings": [ - "CHEBI:27027" - ] - }, - "vitamin": { - "is_a": "micronutrient", - "related_mappings": [ - "CHEBI:33229", - "UMLSSC:T127", - "UMLSST:vita" - ] - }, - "food": { - "is_a": "chemical mixture", - "description": "A substance consumed by a living organism as a source of nutrition", - "id_prefixes": [ - "foodb.compound" - ], - "exact_mappings": [ - "UMLSSC:T168", - "UMLSST:food" - ] - }, - "organism attribute": { - "is_a": "attribute", - "description": "describes a characteristic of an organismal entity.", - "exact_mappings": [ - "UMLSSC:T032", - "UMLSST:orga" - ] - }, - "phenotypic quality": { - "aliases": [ - "phenotypic properties" - ], - "is_a": "organism attribute", - "description": "A property of a phenotype", - "mappings": [ - "PATO:0000001" - ] - }, - "inheritance": { - "is_a": "organism attribute", - "description": "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc.", - "exact_mappings": [ - "HP:0000005", - "GENO:0000141", - "NCIT:C45827" - ] - }, - "organismal entity": { - "description": "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities", - "abstract": true, - "is_a": "biological entity", - "slot_usage": { - "has attribute": { - "description": "may often be an organism attribute" - } - }, - "exact_mappings": [ - "WIKIDATA:Q7239", - "UMLSSG:LIVB" - ] - }, - "life stage": { - "is_a": "organismal entity", - "mixins": [ - "thing with taxon" - ], - "description": "A stage of development or growth of an organism, including post-natal adult stages", - "exact_mappings": [ - "UBERON:0000105" - ], - "narrow_mappings": [ - "HsapDv:0000000" - ], - "in_subset": [ - "model_organism_database" - ] - }, - "individual organism": { - "aliases": [ - "organism" - ], - "description": "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576", - "mixins": [ - "thing with taxon" - ], - "is_a": "organismal entity", - "exact_mappings": [ - "SIO:010000", - "UMLSSC:T001", - "UMLSST:orgm" - ], - "narrow_mappings": [ - "WIKIDATA:Q795052", - "foaf:Person" - ], - "id_prefixes": [ - "ORCID" - ] - }, - "population of individual organisms": { - "description": "A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes [Alliance for Genome Resources]", - "local_names": { - "ga4gh": "population", - "agr": "population" - }, - "mixins": [ - "thing with taxon" - ], - "is_a": "organismal entity", - "exact_mappings": [ - "PCO:0000001", - "SIO:001061", - "UMLSSC:T098", - "UMLSST:popg", - "OBI:0000181" - ], - "id_prefixes": [ - "HANCESTRO" - ], - "in_subset": [ - "model_organism_database" - ] - }, - "disease or phenotypic feature": { - "aliases": [ - "phenome" - ], - "is_a": "biological entity", - "description": "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate.", - "mixins": [ - "thing with taxon" - ], - "union_of": [ - "disease", - "phenotypic feature" - ], - "narrow_mappings": [ - "UMLSSC:T033", - "UMLSST:fndg" - ] - }, - "disease": { - "aliases": [ - "condition", - "disorder", - "medical condition" - ], - "is_a": "disease or phenotypic feature", - "exact_mappings": [ - "MONDO:0000001", - "DOID:4", - "NCIT:C2991", - "WIKIDATA:Q12136", - "SIO:010299", - "UMLSSG:DISO", - "UMLSSC:T047", - "UMLSST:dsyn" - ], - "narrow_mappings": [ - "UMLSSC:T019", - "UMLSST:cgab", - "UMLSSC:T020", - "UMLSST:acab", - "UMLSSC:T037", - "UMLSST:inpo", - "UMLSSC:T046", - "UMLSST:patf", - "UMLSSC:T048", - "UMLSST:mobd", - "UMLSSC:T049", - "UMLSST:comd", - "UMLSSC:T190", - "UMLSST:anab", - "UMLSSC:T191", - "UMLSST:neop" - ], - "id_prefixes": [ - "MONDO", - "DOID", - "OMIM", - "ORPHANET", - "EFO", - "UMLS", - "MESH", - "MEDDRA", - "NCIT", - "SNOMEDCT", - "medgen", - "ICD10", - "ICD9", - "ICD0", - "KEGG.DISEASE", - "HP", - "MP" - ], - "in_subset": [ - "model_organism_database" - ] - }, - "phenotypic feature": { - "aliases": [ - "sign", - "symptom", - "phenotype", - "trait", - "endophenotype" - ], - "is_a": "disease or phenotypic feature", - "exact_mappings": [ - "UPHENO:0001001", - "SIO:010056", - "WIKIDATA:Q104053" - ], - "narrow_mappings": [ - "UMLSSC:T184", - "UMLSST:sosy", - "WIKIDATA:Q169872", - "WIKIDATA:Q25203551" - ], - "id_prefixes": [ - "HP", - "EFO", - "NCIT", - "UMLS", - "MEDDRA", - "MP", - "ZP", - "UPHENO", - "APO", - "FBcv", - "WBPhenotype", - "SNOMEDCT", - "MESH", - "XPO" - ], - "in_subset": [ - "model_organism_database" - ] - }, - "behavioral feature": { - "description": "A phenotypic feature which is behavioral in nature.", - "is_a": "phenotypic feature", - "exact_mappings": [ - "NBO:0000243" - ] - }, - "anatomical entity": { - "is_a": "organismal entity", - "mixins": [ - "thing with taxon", - "physical essence" - ], - "description": "A subcellular location, cell type or gross anatomical part", - "exact_mappings": [ - "UBERON:0001062", - "WIKIDATA:Q4936952", - "UMLSSG:ANAT" - ], - "narrow_mappings": [ - "UMLSSC:T022", - "UMLSST:bdsy", - "UMLSSC:T029", - "UMLSST:blor", - "UMLSSC:T030", - "UMLSST:bsoj", - "UMLSSC:T031", - "UMLSST:bdsu" - ], - "id_prefixes": [ - "UBERON", - "GO", - "CL", - "UMLS", - "MESH", - "NCIT" - ], - "in_subset": [ - "model_organism_database" - ] - }, - "cellular component": { - "is_a": "anatomical entity", - "description": "A location in or around a cell", - "exact_mappings": [ - "GO:0005575", - "SIO:001400", - "WIKIDATA:Q5058355", - "UMLSSC:T026", - "UMLSST:celc" - ], - "broad_mappings": [ - "WIKIDATA:P681" - ], - "id_prefixes": [ - "GO", - "MESH", - "UMLS", - "NCIT", - "SNOMEDCT", - "CL", - "UBERON" - ] - }, - "cell": { - "is_a": "anatomical entity", - "exact_mappings": [ - "GO:0005623", - "CL:0000000", - "SIO:010001", - "WIKIDATA:Q7868", - "UMLSSC:T025", - "UMLSST:cell" - ], - "id_prefixes": [ - "CL", - "PO", - "UMLS", - "NCIT", - "MESH", - "UBERON", - "SNOMEDCT" - ] - }, - "cell line": { - "is_a": "organismal entity", - "exact_mappings": [ - "CLO:0000031" - ], - "id_prefixes": [ - "CLO" - ] - }, - "gross anatomical structure": { - "aliases": [ - "tissue", - "organ" - ], - "is_a": "anatomical entity", - "exact_mappings": [ - "UBERON:0010000", - "WIKIDATA:Q4936952", - "UMLSSC:T017", - "UMLSST:anst", - "UMLSSC:T021", - "UMLSST:ffas" - ], - "narrow_mappings": [ - "UMLSSC:T023", - "UMLSST:bpoc", - "UMLSSC:T024", - "UMLSST:tisu", - "UMLSSC:T018", - "UMLSST:emst" - ], - "id_prefixes": [ - "UBERON", - "UMLS", - "MESH", - "NCIT", - "PO", - "FAO" - ] - }, - "chemical entity or gene or gene product": { - "description": "A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities.", - "mixin": true - }, - "chemical entity or protein or polypeptide": { - "description": "A union of chemical entities and children, and protein and polypeptide. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities.", - "mixin": true - }, - "macromolecular machine mixin": { - "description": "A union of gene locus, gene product, and macromolecular complex mixin. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this.", - "mixin": true, - "slots": [ - "name" - ], - "slot_usage": { - "name": { - "range": "symbol type", - "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" - } - } - }, - "gene or gene product": { - "description": "A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another", - "is_a": "macromolecular machine mixin", - "mixin": true, - "id_prefixes": [ - "CHEMBL.TARGET", - "IUPHAR.FAMILY" - ] - }, - "gene": { - "description": "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions.", - "is_a": "biological entity", - "mixins": [ - "gene or gene product", - "genomic entity", - "chemical entity or gene or gene product", - "physical essence", - "ontology class" - ], - "aliases": [ - "locus" - ], - "slots": [ - "symbol", - "synonym", - "xref" - ], - "exact_mappings": [ - "SO:0000704", - "SIO:010035", - "WIKIDATA:Q7187" - ], - "id_prefixes": [ - "NCBIGene", - "ENSEMBL", - "HGNC", - "MGI", - "ZFIN", - "dictyBase", - "WB", - "WormBase", - "FB", - "RGD", - "SGD", - "POMBASE", - "OMIM", - "KEGG.GENE", - "UMLS", - "Xenbase" - ], - "in_subset": [ - "model_organism_database" - ] - }, - "gene product mixin": { - "description": "The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules.", - "is_a": "gene or gene product", - "mixin": true, - "slots": [ - "synonym", - "xref" - ], - "exact_mappings": [ - "WIKIDATA:Q424689", - "GENO:0000907", - "NCIT:C26548" - ], - "id_prefixes": [ - "UniProtKB", - "gtpo", - "PR" - ] - }, - "gene product isoform mixin": { - "description": "This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms.", - "is_a": "gene product mixin", - "mixin": true - }, - "macromolecular complex mixin": { - "description": "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.", - "is_a": "macromolecular machine mixin", - "mixin": true, - "exact_mappings": [ - "GO:0032991", - "WIKIDATA:Q22325163" - ], - "id_prefixes": [ - "INTACT", - "GO", - "PR", - "REACT" - ], - "in_subset": [ - "model_organism_database" - ] - }, - "genome": { - "is_a": "biological entity", - "mixins": [ - "genomic entity", - "physical essence", - "ontology class" - ], - "description": "A genome is the sum of genetic material within a cell or virion.", - "exact_mappings": [ - "SO:0001026", - "SIO:000984", - "WIKIDATA:Q7020" - ], - "in_subset": [ - "model_organism_database" - ] - }, - "exon": { - "is_a": "nucleic acid entity", - "description": "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.", - "exact_mappings": [ - "SO:0000147", - "SIO:010445", - "WIKIDATA:Q373027" - ] - }, - "transcript": { - "is_a": "nucleic acid entity", - "description": "An RNA synthesized on a DNA or RNA template by an RNA polymerase.", - "exact_mappings": [ - "SO:0000673", - "SIO:010450", - "WIKIDATA:Q7243183" - ], - "id_prefixes": [ - "ENSEMBL", - "FB" - ], - "in_subset": [ - "model_organism_database" - ] - }, - "coding sequence": { - "is_a": "nucleic acid entity", - "exact_mappings": [ - "SO:0000316", - "SIO:001390" - ] - }, - "polypeptide": { - "aliases": [ - "amino acid entity" - ], - "is_a": "biological entity", - "description": "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule.", - "mixins": [ - "thing with taxon", - "chemical entity or gene or gene product", - "chemical entity or protein or polypeptide" - ], - "id_prefixes": [ - "UniProtKB", - "PR", - "ENSEMBL", - "FB", - "UMLS" - ], - "in_subset": [ - "model_organism_database" - ], - "narrow_mappings": [ - "SO:0000104", - "UMLSSC:T116", - "UMLSST:aapp", - "UMLSSC:T087", - "UMLSST:amas" - ] - }, - "protein": { - "description": "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA", - "is_a": "polypeptide", - "mixins": [ - "gene product mixin", - "thing with taxon" - ], - "id_prefixes": [ - "UniProtKB", - "PR", - "ENSEMBL", - "FB", - "UMLS" - ], - "exact_mappings": [ - "PR:000000001", - "SIO:010043", - "WIKIDATA:Q8054" - ], - "narrow_mappings": [ - "UMLSSC:T126", - "UMLSST:enzy", - "UMLSSC:T192", - "UMLSST:rcpt" - ] - }, - "protein isoform": { - "aliases": [ - "proteoform" - ], - "is_a": "protein", - "description": "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/", - "mixins": [ - "gene product isoform mixin" - ], - "id_prefixes": [ - "UniProtKB", - "UNIPROT.ISOFORM", - "PR", - "ENSEMBL" - ] - }, - "RNA product": { - "is_a": "transcript", - "mixins": [ - "gene product mixin" - ], - "exact_mappings": [ - "CHEBI:33697", - "WIKIDATA:Q11053" - ], - "id_prefixes": [ - "RNACENTRAL" - ] - }, - "RNA product isoform": { - "is_a": "RNA product", - "description": "Represents a protein that is a specific isoform of the canonical or reference RNA", - "mixins": [ - "gene product isoform mixin" - ], - "id_prefixes": [ - "RNACENTRAL" - ] - }, - "noncoding RNA product": { - "is_a": "RNA product", - "id_prefixes": [ - "RNACENTRAL", - "NCBIGene", - "ENSEMBL" - ], - "exact_mappings": [ - "SO:0000655", - "SIO:001235" - ] - }, - "microRNA": { - "is_a": "noncoding RNA product", - "exact_mappings": [ - "SO:0000276", - "SIO:001397", - "WIKIDATA:Q310899" - ], - "id_prefixes": [ - "MIR", - "HGNC", - "WormBase" - ], - "in_subset": [ - "model_organism_database" - ] - }, - "siRNA": { - "aliases": [ - "small interfering RNA", - "RNAi" - ], - "description": "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules.", - "is_a": "noncoding RNA product", - "exact_mappings": [ - "SO:0000646", - "WIKIDATA:Q203221" - ], - "id_prefixes": [ - "MIR", - "HGNC", - "WormBase" - ], - "in_subset": [ - "model_organism_database" - ] - }, - "gene grouping mixin": { - "description": "any grouping of multiple genes or gene products", - "mixin": true, - "slots": [ - "has gene or gene product" - ] - }, - "gene family": { - "aliases": [ - "orthogroup", - "protein family" - ], - "is_a": "biological entity", - "exact_mappings": [ - "NCIT:C26004", - "WIKIDATA:Q2278983" - ], - "narrow_mappings": [ - "SIO:001380", - "NCIT:C20130", - "WIKIDATA:Q417841" - ], - "mixins": [ - "gene grouping mixin", - "chemical entity or gene or gene product" - ], - "description": "any grouping of multiple genes or gene products related by common descent", - "id_prefixes": [ - "PANTHER.FAMILY", - "HGNC.FAMILY", - "FB", - "interpro", - "CATH", - "CDD", - "HAMAP", - "PFAM", - "PIRSF", - "PRINTS", - "PRODOM", - "PROSITE", - "SMART", - "SUPFAM", - "TIGRFAM", - "CATH.SUPERFAMILY", - "RFAM", - "KEGG.ORTHOLOGY", - "EGGNOG" - ], - "in_subset": [ - "model_organism_database" - ] - }, - "zygosity": { - "is_a": "attribute", - "exact_mappings": [ - "GENO:0000133" - ] - }, - "genotype": { - "is_a": "biological entity", - "mixins": [ - "physical essence", - "genomic entity", - "physical essence", - "ontology class" - ], - "description": "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background", - "comments": [ - "Consider renaming as genotypic entity" - ], - "slots": [ - "has zygosity" - ], - "exact_mappings": [ - "GENO:0000536", - "SIO:001079" - ], - "id_prefixes": [ - "ZFIN", - "FB" - ], - "in_subset": [ - "model_organism_database" - ] - }, - "haplotype": { - "is_a": "biological entity", - "mixins": [ - "genomic entity", - "physical essence", - "ontology class" - ], - "description": "A set of zero or more Alleles on a single instance of a Sequence[VMC]", - "exact_mappings": [ - "GENO:0000871", - "SO:0001024", - "VMC:Haplotype" - ] - }, - "sequence variant": { - "aliases": [ - "allele" - ], - "local_names": { - "agr": "allele" - }, - "is_a": "biological entity", - "mixins": [ - "genomic entity", - "physical essence", - "ontology class" - ], - "description": "An allele that varies in its sequence from what is considered the reference allele at that locus.", - "comments": [ - "This class is for modeling the specific state at a locus. A single DBSNP rs ID could correspond to more than one sequence variants (e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743)" - ], - "broad_mappings": [ - "SO:0001060" - ], - "exact_mappings": [ - "GENO:0000002", - "WIKIDATA:Q15304597", - "SIO:010277", - "VMC:Allele", - "SO:0001059" - ], - "id_prefixes": [ - "CAID", - "CLINVAR", - "ClinVarVariant", - "WIKIDATA", - "DBSNP", - "DBSNP", - "MGI", - "ZFIN", - "FB", - "WB", - "WormBase" - ], - "alt_descriptions": { - "AGR": "An entity that describes a single affected, endogenous allele. These can be of any type that matches that definition", - "VMC": "A contiguous change at a Location" - }, - "slots": [ - "has gene" - ], - "slot_usage": { - "has gene": { - "multivalued": true, - "description": "Each allele can be associated with any number of genes" - }, - "has biological sequence": { - "description": "The state of the sequence w.r.t a reference sequence" - }, - "id": { - "examples": [ - { - "value": "ZFIN:ZDB-ALT-980203-1091", - "description": "ti282a allele from ZFIN" - }, - { - "value": "ClinVarVariant:17681", - "description": "NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp)" - } - ] - } - }, - "in_subset": [ - "model_organism_database" - ] - }, - "snv": { - "aliases": [ - "single nucleotide variant", - "single nucleotide polymorphism", - "snp" - ], - "is_a": "sequence variant", - "description": "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist", - "exact_mappings": [ - "SO:0001483" - ] - }, - "reagent targeted gene": { - "aliases": [ - "sequence targeting reagent" - ], - "is_a": "biological entity", - "description": "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi.", - "mixins": [ - "genomic entity", - "physical essence", - "ontology class" - ], - "exact_mappings": [ - "GENO:0000504" - ], - "in_subset": [ - "model_organism_database" - ] - }, - "clinical attribute": { - "is_a": "attribute", - "description": "Attributes relating to a clinical manifestation", - "exact_mappings": [ - "UMLSSC:T201", - "UMLSST:clna" - ] - }, - "clinical measurement": { - "is_a": "clinical attribute", - "description": "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot.", - "slot_usage": { - "has attribute type": { - "required": true, - "multivalued": false, - "values_from": [ - "EFO", - "LOINC" - ] - } - }, - "exact_mappings": [ - "EFO:0001444" - ] - }, - "clinical modifier": { - "is_a": "clinical attribute", - "description": "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects", - "exact_mappings": [ - "HP:0012823" - ] - }, - "clinical course": { - "is_a": "clinical attribute", - "description": "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual", - "exact_mappings": [ - "HP:0031797" - ] - }, - "onset": { - "is_a": "clinical course", - "description": "The age group in which (disease) symptom manifestations appear", - "exact_mappings": [ - "HP:0003674" - ] - }, - "clinical entity": { - "is_a": "named thing", - "description": "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities" - }, - "clinical trial": { - "is_a": "clinical entity" - }, - "clinical intervention": { - "is_a": "clinical entity" - }, - "clinical finding": { - "is_a": "phenotypic feature", - "description": "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations.", - "slot_usage": { - "has attribute": { - "range": "clinical attribute" - } - }, - "id_prefixes": [ - "LOINC", - "NCIT", - "EFO" - ] - }, - "hospitalization": { - "is_a": "clinical intervention", - "exact_mappings": [ - "SNOMEDCT:32485007", - "WIKIDATA:Q3140971" - ] - }, - "socioeconomic attribute": { - "is_a": "attribute", - "description": "Attributes relating to a socioeconomic manifestation" - }, - "case": { - "aliases": [ - "patient", - "proband" - ], - "is_a": "individual organism", - "description": "An individual (human) organism that has a patient role in some clinical context." - }, - "cohort": { - "is_a": "study population", - "description": "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time.", - "exact_mappings": [ - "WIKIDATA:Q1303415" - ], - "narrow_mappings": [ - "UMLSSC:T097", - "UMLSST:prog", - "UMLSSC:T099", - "UMLSST:famg", - "UMLSSC:T100", - "UMLSST:aggp", - "UMLSSC:T101", - "UMLSST:podg" - ] - }, - "exposure event": { - "aliases": [ - "exposure", - "experimental condition" - ], - "mixin": true, - "slots": [ - "timepoint" - ], - "description": "A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes", - "exact_mappings": [ - "XCO:0000000" - ], - "in_subset": [ - "model_organism_database" - ] - }, - "genomic background exposure": { - "mixins": [ - "exposure event", - "gene grouping mixin", - "physical essence", - "genomic entity", - "ontology class" - ], - "description": "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." - }, - "pathological entity mixin": { - "description": "A pathological (abnormal) structure or process.", - "mixin": true, - "exact_mappings": [ - "MPATH:0" - ], - "narrow_mappings": [ - "HP:0000118" - ] - }, - "pathological process": { - "description": "A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level.", - "is_a": "biological process", - "mixins": [ - "pathological entity mixin" - ], - "exact_mappings": [ - "OBI:1110122", - "NCIT:C16956" - ], - "narrow_mappings": [ - "NCIT:C19151", - "EFO:0009708" - ] - }, - "pathological process exposure": { - "mixins": [ - "exposure event" - ], - "description": "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease." - }, - "pathological anatomical structure": { - "description": "An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level.", - "is_a": "anatomical entity", - "mixins": [ - "pathological entity mixin" - ] - }, - "pathological anatomical exposure": { - "mixins": [ - "exposure event" - ], - "description": "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome." - }, - "disease or phenotypic feature exposure": { - "mixins": [ - "exposure event", - "pathological entity mixin" - ], - "description": "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." - }, - "chemical exposure": { - "mixins": [ - "exposure event" - ], - "description": "A chemical exposure is an intake of a particular chemical entity.", - "exact_mappings": [ - "ECTO:9000000", - "SIO:001399" - ] - }, - "complex chemical exposure": { - "description": "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug." - }, - "drug exposure": { - "is_a": "chemical exposure", - "aliases": [ - "drug intake", - "drug dose", - "medication intake" - ], - "description": "A drug exposure is an intake of a particular drug.", - "mixins": [ - "exposure event" - ], - "broad_mappings": [ - "SIO:001005" - ], - "exact_mappings": [ - "ECTO:0000509" - ] - }, - "drug to gene interaction exposure": { - "description": "drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome.", - "is_a": "drug exposure", - "mixins": [ - "gene grouping mixin" - ] - }, - "treatment": { - "aliases": [ - "medical action", - "medical intervention" - ], - "is_a": "named thing", - "mixins": [ - "exposure event", - "chemical or drug or treatment" - ], - "description": "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures", - "slots": [ - "has drug", - "has device", - "has procedure" - ], - "exact_mappings": [ - "OGMS:0000090", - "SIO:001398" - ] - }, - "biotic exposure": { - "aliases": [ - "viral exposure", - "bacterial exposure" - ], - "mixins": [ - "exposure event" - ], - "description": "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses)." - }, - "geographic exposure": { - "is_a": "environmental exposure", - "mixins": [ - "exposure event" - ], - "description": "A geographic exposure is a factor relating to geographic proximity to some impactful entity." - }, - "environmental exposure": { - "mixins": [ - "exposure event" - ], - "description": "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants." - }, - "behavioral exposure": { - "mixins": [ - "exposure event" - ], - "description": "A behavioral exposure is a factor relating to behavior impacting an individual." - }, - "socioeconomic exposure": { - "mixins": [ - "exposure event" - ], - "description": "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty).", - "slot_usage": { - "has attribute": { - "range": "socioeconomic attribute", - "required": true - } - } - }, - "outcome": { - "mixin": true, - "description": "An entity that has the role of being the consequence of an exposure event. This is an abstract mixin grouping of various categories of possible biological or non-biological (e.g. clinical) outcomes." - }, - "pathological process outcome": { - "mixins": [ - "outcome" - ], - "description": "An outcome resulting from an exposure event which is the manifestation of a pathological process." - }, - "pathological anatomical outcome": { - "mixins": [ - "outcome" - ], - "description": "An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure." - }, - "disease or phenotypic feature outcome": { - "mixins": [ - "outcome" - ], - "description": "Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype." - }, - "behavioral outcome": { - "mixins": [ - "outcome" - ], - "description": "An outcome resulting from an exposure event which is the manifestation of human behavior." - }, - "hospitalization outcome": { - "mixins": [ - "outcome" - ], - "description": "An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization." - }, - "mortality outcome": { - "mixins": [ - "outcome" - ], - "description": "An outcome of death from resulting from an exposure event." - }, - "epidemiological outcome": { - "mixins": [ - "outcome" - ], - "description": "An epidemiological outcome, such as societal disease burden, resulting from an exposure event.", - "related_mappings": [ - "NCIT:C19291" - ] - }, - "socioeconomic outcome": { - "mixins": [ - "outcome" - ], - "description": "An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event" - }, - "association": { - "is_a": "entity", - "description": "A typed association between two entities, supported by evidence", - "comments": [ - "This is roughly the model used by biolink and ontobio at the moment" - ], - "slots": [ - "subject", - "predicate", - "object", - "relation", - "negated", - "qualifiers", - "publications" - ], - "slot_usage": { - "type": { - "description": "rdf:type of biolink:Association should be fixed at rdf:Statement" - }, - "category": { - "range": "category type", - "required": false - } - }, - "exact_mappings": [ - "OBAN:association", - "rdf:Statement", - "owl:Axiom" - ] - }, - "contributor association": { - "is_a": "association", - "defining_slots": [ - "subject", - "predicate", - "object" - ], - "description": "Any association between an entity (such as a publication) and various agents that contribute to its realisation", - "slot_usage": { - "subject": { - "range": "information content entity", - "description": "information content entity which an agent has helped realise" - }, - "predicate": { - "subproperty_of": "contributor", - "description": "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" - }, - "object": { - "range": "agent", - "description": "agent helping to realise the given entity (e.g. such as a publication)" - }, - "qualifiers": { - "description": "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'" - } - } - }, - "genotype to genotype part association": { - "is_a": "association", - "defining_slots": [ - "subject", - "object" - ], - "description": "Any association between one genotype and a genotypic entity that is a sub-component of it", - "slot_usage": { - "predicate": { - "subproperty_of": "has variant part" - }, - "subject": { - "range": "genotype", - "description": "parent genotype" - }, - "object": { - "range": "genotype", - "description": "child genotype" - } - } - }, - "genotype to gene association": { - "description": "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality", - "is_a": "association", - "defining_slots": [ - "subject", - "object" - ], - "slot_usage": { - "predicate": { - "description": "the relationship type used to connect genotype to gene" - }, - "subject": { - "range": "genotype", - "description": "parent genotype" - }, - "object": { - "range": "gene", - "description": "gene implicated in genotype" - } - } - }, - "genotype to variant association": { - "description": "Any association between a genotype and a sequence variant.", - "is_a": "association", - "defining_slots": [ - "subject", - "object" - ], - "slot_usage": { - "predicate": { - "description": "the relationship type used to connect genotype to gene" - }, - "subject": { - "range": "genotype", - "description": "parent genotype" - }, - "object": { - "range": "sequence variant", - "description": "gene implicated in genotype" - } - } - }, - "gene to gene association": { - "aliases": [ - "molecular or genetic interaction" - ], - "description": "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction.", - "abstract": true, - "is_a": "association", - "defining_slots": [ - "subject", - "object" - ], - "slot_usage": { - "subject": { - "range": "gene or gene product", - "description": "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." - }, - "object": { - "range": "gene or gene product", - "description": "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." - } - } - }, - "gene to gene homology association": { - "description": "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)", - "is_a": "gene to gene association", - "defining_slots": [ - "subject", - "predicate", - "object" - ], - "slot_usage": { - "predicate": { - "subproperty_of": "homologous to", - "symmetric": true, - "description": "homology relationship type" - } - } - }, - "gene expression mixin": { - "description": "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs.", - "mixin": true, - "slots": [ - "quantifier qualifier", - "expression site", - "stage qualifier", - "phenotypic state" - ], - "slot_usage": { - "quantifier qualifier": { - "description": "Optional quantitative value indicating degree of expression." - } - } - }, - "gene to gene coexpression association": { - "description": "Indicates that two genes are co-expressed, generally under the same conditions.", - "is_a": "gene to gene association", - "defining_slots": [ - "subject", - "predicate", - "object" - ], - "mixins": [ - "gene expression mixin" - ], - "slot_usage": { - "predicate": { - "subproperty_of": "coexpressed with", - "symmetric": true - } - } - }, - "pairwise gene to gene interaction": { - "description": "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)", - "is_a": "gene to gene association", - "defining_slots": [ - "subject", - "predicate", - "object" - ], - "slot_usage": { - "predicate": { - "subproperty_of": "interacts with", - "symmetric": true - }, - "relation": { - "values_from": [ - "ro", - "mi" - ], - "description": "interaction relationship type" - } - } - }, - "pairwise molecular interaction": { - "description": "An interaction at the molecular level between two physical entities", - "is_a": "pairwise gene to gene interaction", - "slots": [ - "interacting molecules category" - ], - "defining_slots": [ - "subject", - "predicate", - "object" - ], - "slot_usage": { - "subject": { - "range": "molecular entity" - }, - "id": { - "description": "identifier for the interaction. This may come from an interaction database such as IMEX.", - "examples": [ - { - "value": "WB:WBInteraction000538741" - } - ], - "values_from": [ - "IMEX", - "BioGRID" - ] - }, - "predicate": { - "subproperty_of": "molecularly interacts with" - }, - "relation": { - "values_from": [ - "ro", - "mi" - ], - "description": "interaction relationship type", - "examples": [ - { - "value": "RO:0002447", - "description": "the subject molecular phosphorylates the object molecule" - } - ] - }, - "object": { - "range": "molecular entity" - } - } - }, - "cell line to entity association mixin": { - "description": "An relationship between a cell line and another entity", - "mixin": true, - "defining_slots": [ - "subject" - ], - "slot_usage": { - "subject": { - "range": "cell line" - } - } - }, - "cell line to disease or phenotypic feature association": { - "is_a": "association", - "mixins": [ - "cell line to entity association mixin", - "entity to disease or phenotypic feature association mixin" - ], - "description": "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype.", - "slot_usage": { - "subject": { - "range": "disease or phenotypic feature" - } - } - }, - "chemical entity to entity association mixin": { - "description": "An interaction between a chemical entity and another entity", - "mixin": true, - "defining_slots": [ - "subject" - ], - "slot_usage": { - "subject": { - "range": "chemical entity", - "description": "the chemical entity that is an interactor" - } - } - }, - "drug to entity association mixin": { - "description": "An interaction between a drug and another entity", - "is_a": "chemical entity to entity association mixin", - "mixin": true, - "defining_slots": [ - "subject" - ], - "slot_usage": { - "subject": { - "range": "drug", - "description": "the drug that is an interactor" - } - } - }, - "chemical to entity association mixin": { - "description": "An interaction between a chemical entity and another entity", - "is_a": "chemical entity to entity association mixin", - "mixin": true, - "defining_slots": [ - "subject" - ], - "slot_usage": { - "subject": { - "range": "chemical entity", - "description": "the chemical entity or entity that is an interactor" - } - } - }, - "case to entity association mixin": { - "description": "An abstract association for use where the case is the subject", - "mixin": true, - "defining_slots": [ - "subject" - ], - "slot_usage": { - "subject": { - "range": "case", - "description": "the case (e.g. patient) that has the property" - } - } - }, - "chemical to chemical association": { - "description": "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another.", - "is_a": "association", - "defining_slots": [ - "subject", - "object" - ], - "mixins": [ - "chemical to entity association mixin" - ], - "slot_usage": { - "object": { - "range": "chemical entity", - "description": "the chemical element that is the target of the statement" - } - } - }, - "reaction to participant association": { - "description": null, - "is_a": "chemical to chemical association", - "slots": [ - "stoichiometry", - "reaction direction", - "reaction side" - ], - "slot_usage": { - "subject": { - "range": "molecular entity" - } - }, - "defining_slots": [ - "subject", - "predicate", - "object" - ] - }, - "reaction to catalyst association": { - "description": null, - "is_a": "reaction to participant association", - "slot_usage": { - "object": { - "range": "gene or gene product" - } - } - }, - "chemical to chemical derivation association": { - "description": "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction:\n IF\n R has-input C1 AND\n R has-output C2 AND\n R enabled-by P AND\n R type Reaction\n THEN\n C1 derives-into C2 <>", - "is_a": "chemical to chemical association", - "defining_slots": [ - "subject", - "predicate", - "object" - ], - "slots": [ - "catalyst qualifier" - ], - "slot_usage": { - "subject": { - "range": "chemical entity", - "description": "the upstream chemical entity" - }, - "object": { - "range": "chemical entity", - "description": "the downstream chemical entity" - }, - "predicate": { - "subproperty_of": "derives into" - }, - "catalyst qualifier": { - "description": "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." - } - } - }, - "chemical to disease or phenotypic feature association": { - "description": "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype.", - "is_a": "association", - "narrow_mappings": [ - "SIO:000993" - ], - "defining_slots": [ - "subject", - "object" - ], - "mixins": [ - "chemical to entity association mixin", - "entity to disease or phenotypic feature association mixin" - ], - "slot_usage": { - "object": { - "range": "disease or phenotypic feature", - "description": "the disease or phenotype that is affected by the chemical" - } - } - }, - "chemical to pathway association": { - "description": "An interaction between a chemical entity and a biological process or pathway.", - "is_a": "association", - "exact_mappings": [ - "SIO:001250" - ], - "defining_slots": [ - "subject", - "object" - ], - "mixins": [ - "chemical to entity association mixin" - ], - "slot_usage": { - "object": { - "range": "pathway", - "description": "the pathway that is affected by the chemical" - } - } - }, - "chemical to gene association": { - "description": "An interaction between a chemical entity and a gene or gene product.", - "is_a": "association", - "exact_mappings": [ - "SIO:001257" - ], - "defining_slots": [ - "subject", - "object" - ], - "mixins": [ - "chemical to entity association mixin" - ], - "slot_usage": { - "object": { - "range": "gene or gene product", - "description": "the gene or gene product that is affected by the chemical." - } - } - }, - "drug to gene association": { - "description": "An interaction between a drug and a gene or gene product.", - "is_a": "association", - "related_mappings": [ - "SIO:001257" - ], - "defining_slots": [ - "subject", - "object" - ], - "mixins": [ - "drug to entity association mixin" - ], - "slot_usage": { - "object": { - "range": "gene or gene product", - "description": "the gene or gene product that is affected by the drug" - } - } - }, - "material sample to entity association mixin": { - "description": "An association between a material sample and something.", - "mixin": true, - "defining_slots": [ - "subject" - ], - "slot_usage": { - "subject": { - "range": "material sample", - "description": "the material sample being described" - } - } - }, - "material sample derivation association": { - "description": "An association between a material sample and the material entity from which it is derived.", - "is_a": "association", - "defining_slots": [ - "subject", - "predicate" - ], - "slot_usage": { - "subject": { - "range": "material sample", - "description": "the material sample being described" - }, - "object": { - "description": "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material." - }, - "predicate": { - "description": "derivation relationship", - "subproperty_of": "derives from" - } - } - }, - "material sample to disease or phenotypic feature association": { - "description": "An association between a material sample and a disease or phenotype.", - "is_a": "association", - "mixins": [ - "material sample to entity association mixin", - "entity to disease or phenotypic feature association mixin" - ], - "defining_slots": [ - "subject", - "object" - ] - }, - "disease to entity association mixin": { - "mixin": true, - "defining_slots": [ - "subject" - ], - "slot_usage": { - "subject": { - "range": "disease", - "description": "disease class", - "values_from": [ - "mondo", - "omim", - "orphanet", - "ncit", - "doid" - ], - "examples": [ - { - "value": "MONDO:0017314", - "description": "Ehlers-Danlos syndrome, vascular type" - } - ] - } - } - }, - "entity to exposure event association mixin": { - "description": "An association between some entity and an exposure event.", - "mixin": true, - "defining_slots": [ - "object" - ], - "slot_usage": { - "object": { - "range": "exposure event" - } - } - }, - "disease to exposure event association": { - "description": "An association between an exposure event and a disease.", - "is_a": "association", - "mixins": [ - "disease to entity association mixin", - "entity to exposure event association mixin" - ], - "defining_slots": [ - "subject", - "object" - ] - }, - "exposure event to entity association mixin": { - "deprecated": true - }, - "entity to outcome association mixin": { - "description": "An association between some entity and an outcome", - "mixin": true, - "defining_slots": [ - "object" - ], - "slot_usage": { - "object": { - "range": "outcome" - } - } - }, - "exposure event to outcome association": { - "description": "An association between an exposure event and an outcome.", - "is_a": "association", - "mixins": [ - "exposure event to entity association mixin", - "entity to outcome association mixin" - ], - "slots": [ - "has population context", - "has temporal context" - ], - "defining_slots": [ - "subject", - "object" - ] - }, - "frequency qualifier mixin": { - "mixin": true, - "description": "Qualifier for frequency type associations", - "slots": [ - "frequency qualifier" - ] - }, - "entity to feature or disease qualifiers mixin": { - "description": "Qualifiers for entity to disease or phenotype associations.", - "mixin": true, - "is_a": "frequency qualifier mixin", - "slots": [ - "severity qualifier", - "onset qualifier" - ] - }, - "entity to phenotypic feature association mixin": { - "mixin": true, - "is_a": "entity to feature or disease qualifiers mixin", - "defining_slots": [ - "object" - ], - "slot_usage": { - "description": { - "description": "A description of specific aspects of this phenotype, not otherwise covered by the phenotype ontology class" - }, - "object": { - "range": "phenotypic feature", - "description": "phenotypic class", - "values_from": [ - "upheno", - "hp", - "mp", - "wbphenotype" - ], - "examples": [ - { - "value": "HP:0002487", - "description": "Hyperkinesis" - }, - { - "value": "WBPhenotype:0000180", - "description": "axon morphology variant" - }, - { - "value": "MP:0001569", - "description": "abnormal circulating bilirubin level" - } - ] - } - }, - "slots": [ - "sex qualifier" - ] - }, - "named thing to information content entity association": { - "description": "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property).", - "is_a": "association", - "defining_slots": [ - "subject", - "object" - ], - "slot_usage": { - "subject": { - "domain": "named thing" - }, - "object": { - "range": "publication" - }, - "predicate": { - "subproperty_of": "mentions" - } - }, - "in_subset": [ - "model_organism_database" - ] - }, - "entity to disease association mixin": { - "description": "mixin class for any association whose object (target node) is a disease", - "mixin": true, - "is_a": "entity to feature or disease qualifiers mixin", - "defining_slots": [ - "object" - ], - "slot_usage": { - "object": { - "range": "disease", - "description": "disease", - "examples": [ - { - "value": "MONDO:0020066", - "description": "Ehlers-Danlos syndrome" - } - ] - } - } - }, - "disease or phenotypic feature to entity association mixin": { - "mixin": true, - "defining_slots": [ - "subject" - ], - "slot_usage": { - "subject": { - "range": "disease or phenotypic feature", - "description": "disease or phenotype", - "examples": [ - { - "value": "MONDO:0017314", - "description": "Ehlers-Danlos syndrome, vascular type" - }, - { - "value": "MP:0013229", - "description": "abnormal brain ventricle size" - } - ] - } - } - }, - "disease or phenotypic feature to location association": { - "description": "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site.", - "is_a": "association", - "mixins": [ - "disease or phenotypic feature to entity association mixin" - ], - "slot_usage": { - "object": { - "range": "anatomical entity", - "description": "anatomical entity in which the disease or feature is found.", - "examples": [ - { - "value": "UBERON:0002048", - "description": "lung" - } - ] - } - } - }, - "entity to disease or phenotypic feature association mixin": { - "mixin": true, - "defining_slots": [ - "object" - ], - "slot_usage": { - "object": { - "range": "disease or phenotypic feature", - "description": "disease or phenotype", - "examples": [ - { - "value": "MONDO:0017314", - "description": "Ehlers-Danlos syndrome, vascular type" - }, - { - "value": "MP:0013229", - "description": "abnormal brain ventricle size" - } - ] - } - } - }, - "genotype to entity association mixin": { - "mixin": true, - "defining_slots": [ - "subject" - ], - "slot_usage": { - "subject": { - "range": "genotype", - "description": "genotype that is the subject of the association" - } - } - }, - "genotype to phenotypic feature association": { - "is_a": "association", - "defining_slots": [ - "subject", - "object" - ], - "description": "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment", - "mixins": [ - "entity to phenotypic feature association mixin", - "genotype to entity association mixin" - ], - "slot_usage": { - "predicate": { - "subproperty_of": "has phenotype" - }, - "subject": { - "range": "genotype", - "description": "genotype that is associated with the phenotypic feature" - } - } - }, - "exposure event to phenotypic feature association": { - "is_a": "association", - "defining_slots": [ - "subject", - "object" - ], - "description": "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype.", - "mixins": [ - "entity to phenotypic feature association mixin" - ], - "slot_usage": { - "subject": { - "range": "exposure event" - } - } - }, - "disease to phenotypic feature association": { - "is_a": "association", - "defining_slots": [ - "subject", - "object" - ], - "description": "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way.", - "mixins": [ - "entity to phenotypic feature association mixin", - "disease to entity association mixin" - ] - }, - "case to phenotypic feature association": { - "description": "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype.", - "is_a": "association", - "defining_slots": [ - "subject", - "object" - ], - "mixins": [ - "entity to phenotypic feature association mixin", - "case to entity association mixin" - ] - }, - "behavior to behavioral feature association": { - "description": "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior.", - "is_a": "association", - "defining_slots": [ - "subject", - "object" - ], - "slot_usage": { - "subject": { - "range": "behavior", - "description": "behavior that is the subject of the association" - }, - "object": { - "range": "behavioral feature", - "description": "behavioral feature that is the object of the association" - } - }, - "mixins": [ - "entity to phenotypic feature association mixin" - ] - }, - "gene to entity association mixin": { - "mixin": true, - "defining_slots": [ - "subject" - ], - "slot_usage": { - "subject": { - "range": "gene or gene product", - "description": "gene that is the subject of the association" - } - } - }, - "variant to entity association mixin": { - "local_names": { - "ga4gh": "variant annotation" - }, - "mixin": true, - "defining_slots": [ - "subject" - ], - "slot_usage": { - "subject": { - "range": "sequence variant", - "description": "a sequence variant in which the allele state is associated with some other entity", - "examples": [ - { - "value": "ClinVar:38077", - "description": "ClinVar representation of NM_000059.3(BRCA2):c.7007G>A (p.Arg2336His)" - }, - { - "value": "ClinGen:CA024716", - "description": "chr13:g.32921033G>C (hg19) in ClinGen" - } - ] - } - } - }, - "gene to phenotypic feature association": { - "is_a": "association", - "exact_mappings": [ - "WBVocab:Gene-Phenotype-Association" - ], - "defining_slots": [ - "subject", - "object" - ], - "mixins": [ - "entity to phenotypic feature association mixin", - "gene to entity association mixin" - ], - "slot_usage": { - "subject": { - "range": "gene or gene product", - "description": "gene in which variation is correlated with the phenotypic feature", - "examples": [ - { - "value": "HGNC:2197", - "description": "COL1A1 (Human)" - } - ] - } - } - }, - "gene to disease association": { - "is_a": "association", - "comments": [ - "NCIT:R176 refers to the inverse relationship" - ], - "exact_mappings": [ - "SIO:000983" - ], - "defining_slots": [ - "subject", - "object" - ], - "mixins": [ - "entity to disease association mixin", - "gene to entity association mixin" - ], - "slot_usage": { - "subject": { - "range": "gene or gene product", - "description": "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" - } - } - }, - "variant to gene association": { - "description": "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)", - "is_a": "association", - "defining_slots": [ - "subject", - "predicate", - "object" - ], - "mixins": [ - "variant to entity association mixin" - ], - "slot_usage": { - "object": { - "range": "gene" - }, - "predicate": { - "subproperty_of": "genetic association" - } - } - }, - "variant to gene expression association": { - "description": "An association between a variant and expression of a gene (i.e. e-QTL)", - "is_a": "variant to gene association", - "defining_slots": [ - "subject", - "predicate", - "object" - ], - "mixins": [ - "gene expression mixin" - ], - "slot_usage": { - "predicate": { - "subproperty_of": "affects expression of" - } - } - }, - "variant to population association": { - "description": "An association between a variant and a population, where the variant has particular frequency in the population", - "is_a": "association", - "defining_slots": [ - "subject", - "object" - ], - "mixins": [ - "variant to entity association mixin", - "frequency quantifier", - "frequency qualifier mixin" - ], - "slot_usage": { - "subject": { - "range": "sequence variant", - "description": "an allele that has a certain frequency in a given population", - "examples": [ - { - "value": "NC_000017.11:g.43051071A>T", - "description": "17:41203088 A/C in gnomad" - } - ] - }, - "object": { - "range": "population of individual organisms", - "description": "the population that is observed to have the frequency", - "examples": [ - { - "value": "HANCESTRO:0010", - "description": "African" - } - ] - }, - "has quotient": { - "description": "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency", - "examples": [ - { - "value": "0.0001666" - } - ] - }, - "has count": { - "description": "number in object population that carry a particular allele, aka allele count", - "examples": [ - { - "value": "4", - "description": "4 individuals in gnomad set" - } - ] - }, - "has total": { - "description": "number all populations that carry a particular allele, aka allele number", - "examples": [ - { - "value": "24014", - "description": "24014 individuals in gnomad set" - } - ] - } - } - }, - "population to population association": { - "description": "An association between a two populations", - "is_a": "association", - "defining_slots": [ - "subject", - "object" - ], - "slot_usage": { - "subject": { - "range": "population of individual organisms", - "description": "the population that form the subject of the association" - }, - "object": { - "range": "population of individual organisms", - "description": "the population that form the object of the association" - }, - "predicate": { - "description": "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" - } - } - }, - "variant to phenotypic feature association": { - "is_a": "association", - "defining_slots": [ - "subject", - "object" - ], - "mixins": [ - "variant to entity association mixin", - "entity to phenotypic feature association mixin" - ], - "slot_usage": { - "subject": { - "range": "sequence variant", - "description": "a sequence variant in which the allele state is associated in some way with the phenotype state" - } - } - }, - "variant to disease association": { - "is_a": "association", - "comments": [ - "TODO decide no how to model pathogenicity" - ], - "defining_slots": [ - "subject", - "object" - ], - "mixins": [ - "variant to entity association mixin", - "entity to disease association mixin" - ], - "slot_usage": { - "subject": { - "description": "a sequence variant in which the allele state is associated in some way with the disease state", - "examples": [ - { - "value": "ClinVar:52241", - "description": "NM_000059.3(BRCA2):c.7007G>C (p.Arg2336Pro)" - } - ] - }, - "predicate": { - "description": "E.g. is pathogenic for", - "subproperty_of": "related condition" - }, - "object": { - "description": "a disease that is associated with that variant", - "examples": [ - { - "value": "MONDO:0016419", - "description": "hereditary breast cancer" - } - ] - } - } - }, - "genotype to disease association": { - "is_a": "association", - "comments": [ - "TODO decide no how to model pathogenicity" - ], - "defining_slots": [ - "subject", - "object" - ], - "mixins": [ - "genotype to entity association mixin", - "entity to disease association mixin" - ], - "slot_usage": { - "subject": { - "description": "a genotype that is associated in some way with a disease state" - }, - "predicate": { - "description": "E.g. is pathogenic for", - "subproperty_of": "related condition" - }, - "object": { - "description": "a disease that is associated with that genotype", - "examples": [ - { - "value": "MONDO:0016419", - "description": "hereditary breast cancer" - } - ] - } - } - }, - "model to disease association mixin": { - "description": "This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some features of the disease in a way that is useful for studying the disease outside a patient carrying the disease", - "mixin": true, - "slot_usage": { - "subject": { - "description": "The entity that serves as the model of the disease. This may be an organism, a strain of organism, a genotype or variant that exhibits similar features, or a gene that when mutated exhibits features of the disease" - }, - "predicate": { - "subproperty_of": "model of", - "description": "The relationship to the disease" - } - } - }, - "gene as a model of disease association": { - "is_a": "gene to disease association", - "defining_slots": [ - "subject", - "predicate", - "object" - ], - "mixins": [ - "model to disease association mixin", - "entity to disease association mixin" - ], - "slot_usage": { - "subject": { - "range": "gene or gene product", - "description": "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." - } - } - }, - "variant as a model of disease association": { - "is_a": "variant to disease association", - "defining_slots": [ - "subject", - "predicate", - "object" - ], - "mixins": [ - "model to disease association mixin", - "entity to disease association mixin" - ], - "slot_usage": { - "subject": { - "range": "sequence variant", - "description": "A variant that has a role in modeling the disease." - } - } - }, - "genotype as a model of disease association": { - "is_a": "genotype to disease association", - "defining_slots": [ - "subject", - "predicate", - "object" - ], - "mixins": [ - "model to disease association mixin", - "entity to disease association mixin" - ], - "slot_usage": { - "subject": { - "range": "genotype", - "description": "A genotype that has a role in modeling the disease." - } - } - }, - "cell line as a model of disease association": { - "is_a": "cell line to disease or phenotypic feature association", - "defining_slots": [ - "subject", - "predicate", - "object" - ], - "mixins": [ - "model to disease association mixin", - "entity to disease association mixin" - ], - "slot_usage": { - "subject": { - "range": "cell line", - "description": "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." - } - } - }, - "organismal entity as a model of disease association": { - "is_a": "association", - "defining_slots": [ - "subject", - "predicate", - "object" - ], - "mixins": [ - "model to disease association mixin", - "entity to disease association mixin" - ], - "slot_usage": { - "subject": { - "range": "organismal entity", - "description": "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease." - } - } - }, - "organism to organism association": { - "is_a": "association", - "defining_slots": [ - "subject", - "predicate", - "object" - ], - "slot_usage": { - "subject": { - "range": "individual organism" - }, - "relation": { - "values_from": [ - "ro" - ] - }, - "object": { - "range": "individual organism", - "description": "An association between two individual organisms." - } - } - }, - "taxon to taxon association": { - "is_a": "association", - "defining_slots": [ - "subject", - "predicate", - "object" - ], - "slot_usage": { - "subject": { - "range": "organism taxon" - }, - "relation": { - "values_from": [ - "ro" - ] - }, - "object": { - "range": "organism taxon", - "description": "An association between individuals of different taxa." - } - } - }, - "gene has variant that contributes to disease association": { - "is_a": "gene to disease association", - "defining_slots": [ - "subject", - "predicate", - "object" - ], - "slots": [ - "sequence variant qualifier" - ], - "slot_usage": { - "subject": { - "range": "gene or gene product", - "description": "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." - } - } - }, - "gene to expression site association": { - "is_a": "association", - "defining_slots": [ - "subject", - "predicate", - "object" - ], - "description": "An association between a gene and an expression site, possibly qualified by stage/timing info.", - "notes": [ - "TBD: introduce subclasses for distinction between wild-type and experimental conditions?" - ], - "see_also": "https://github.com/monarch-initiative/ingest-artifacts/tree/master/sources/BGee", - "slots": [ - "stage qualifier", - "quantifier qualifier" - ], - "slot_usage": { - "subject": { - "range": "gene or gene product", - "description": "gene in which variation is correlated with the phenotypic feature" - }, - "object": { - "range": "anatomical entity", - "description": "location in which the gene is expressed", - "examples": [ - { - "value": "UBERON:0002037", - "description": "cerebellum" - } - ] - }, - "predicate": { - "description": "expression relationship", - "subproperty_of": "expressed in" - }, - "stage qualifier": { - "range": "life stage", - "description": "stage at which the gene is expressed in the site", - "examples": [ - { - "value": "UBERON:0000069", - "description": "larval stage" - } - ] - }, - "quantifier qualifier": { - "description": "can be used to indicate magnitude, or also ranking" - } - } - }, - "sequence variant modulates treatment association": { - "is_a": "association", - "description": "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used.", - "comments": [ - "An alternate way to model the same information could be via a qualifier" - ], - "defining_slots": [ - "subject", - "object" - ], - "abstract": true, - "slot_usage": { - "subject": { - "range": "sequence variant", - "description": "variant that modulates the treatment of some disease" - }, - "object": { - "range": "treatment", - "description": "treatment whose efficacy is modulated by the subject variant" - } - } - }, - "functional association": { - "is_a": "association", - "description": "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed.", - "slot_usage": { - "subject": { - "range": "macromolecular machine mixin", - "description": "gene, product or macromolecular complex mixin that has the function associated with the GO term", - "examples": [ - { - "value": "ZFIN:ZDB-GENE-050417-357", - "description": "twist1b" - } - ] - }, - "object": { - "range": "gene ontology class", - "description": "class describing the activity, process or localization of the gene product", - "values_from": [ - "go" - ], - "examples": [ - { - "value": "GO:0016301", - "description": "kinase activity" - }, - { - "value": "GO:0045211", - "description": "postsynaptic membrane" - } - ] - } - } - }, - "macromolecular machine to entity association mixin": { - "description": "an association which has a macromolecular machine mixin as a subject", - "mixin": true, - "slot_usage": { - "subject": { - "domain": "macromolecular machine mixin" - } - } - }, - "macromolecular machine to molecular activity association": { - "description": "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution.", - "is_a": "functional association", - "mixins": [ - "macromolecular machine to entity association mixin" - ], - "slot_usage": { - "object": { - "range": "molecular activity" - } - } - }, - "macromolecular machine to biological process association": { - "description": "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it.", - "is_a": "functional association", - "mixins": [ - "macromolecular machine to entity association mixin" - ], - "slot_usage": { - "object": { - "range": "biological process" - } - } - }, - "macromolecular machine to cellular component association": { - "description": "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component.", - "is_a": "functional association", - "mixins": [ - "macromolecular machine to entity association mixin" - ], - "slot_usage": { - "object": { - "range": "cellular component" - } - } - }, - "gene to go term association": { - "aliases": [ - "functional association" - ], - "is_a": "functional association", - "exact_mappings": [ - "WBVocab:Gene-GO-Association" - ], - "defining_slots": [ - "subject", - "object" - ], - "slot_usage": { - "subject": { - "range": "gene", - "description": "gene, product or macromolecular complex that has the function associated with the GO term", - "examples": [ - { - "value": "ZFIN:ZDB-GENE-050417-357", - "description": "twist1b" - } - ] - }, - "object": { - "range": "gene ontology class", - "description": "class describing the activity, process or localization of the gene product", - "values_from": [ - "go" - ], - "examples": [ - { - "value": "GO:0016301", - "description": "kinase activity" - } - ] - } - } - }, - "entity to disease association": { - "is_a": "association", - "exact_mappings": null, - "slots": [ - "FDA approval status" - ], - "defining_slots": [ - "subject", - "object" - ] - }, - "entity to phenotypic feature association": { - "is_a": "association", - "exact_mappings": null, - "slots": [ - "FDA approval status" - ], - "defining_slots": [ - "subject", - "object" - ] - }, - "sequence association": { - "is_a": "association", - "description": "An association between a sequence feature and a nucleic acid entity it is localized to." - }, - "genomic sequence localization": { - "is_a": "sequence association", - "description": "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig.", - "slot_usage": { - "subject": { - "aliases": [ - "sequence feature" - ], - "range": "nucleic acid entity" - }, - "object": { - "aliases": [ - "reference" - ], - "range": "nucleic acid entity" - }, - "predicate": { - "subproperty_of": "has sequence location" - } - }, - "slots": [ - "start interbase coordinate", - "end interbase coordinate", - "genome build", - "strand", - "phase" - ] - }, - "sequence feature relationship": { - "is_a": "association", - "defining_slots": [ - "subject", - "object" - ], - "description": "For example, a particular exon is part of a particular transcript or gene", - "slot_usage": { - "subject": { - "range": "nucleic acid entity" - }, - "object": { - "range": "nucleic acid entity" - } - }, - "exact_mappings": [ - "CHADO:feature_relationship" - ] - }, - "transcript to gene relationship": { - "is_a": "sequence feature relationship", - "defining_slots": [ - "subject", - "object" - ], - "description": "A gene is a collection of transcripts", - "slot_usage": { - "subject": { - "range": "transcript" - }, - "object": { - "range": "gene" - } - } - }, - "gene to gene product relationship": { - "is_a": "sequence feature relationship", - "defining_slots": [ - "subject", - "object" - ], - "description": "A gene is transcribed and potentially translated to a gene product", - "slot_usage": { - "subject": { - "range": "gene" - }, - "object": { - "range": "gene product mixin" - }, - "predicate": { - "subproperty_of": "has gene product" - } - } - }, - "exon to transcript relationship": { - "is_a": "sequence feature relationship", - "defining_slots": [ - "subject", - "object" - ], - "description": "A transcript is formed from multiple exons", - "slot_usage": { - "subject": { - "range": "exon" - }, - "object": { - "range": "transcript" - } - } - }, - "gene regulatory relationship": { - "is_a": "association", - "description": "A regulatory relationship between two genes", - "slot_usage": { - "predicate": { - "description": "the direction is always from regulator to regulated" - }, - "subject": { - "range": "gene or gene product", - "role": "regulatory gene" - }, - "object": { - "range": "gene or gene product", - "role": "regulated gene" - } - } - }, - "anatomical entity to anatomical entity association": { - "is_a": "association", - "abstract": true, - "defining_slots": [ - "subject", - "object" - ], - "slot_usage": { - "subject": { - "range": "anatomical entity" - }, - "object": { - "range": "anatomical entity" - } - } - }, - "anatomical entity to anatomical entity part of association": { - "is_a": "anatomical entity to anatomical entity association", - "description": "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms", - "defining_slots": [ - "predicate" - ], - "slot_usage": { - "subject": { - "range": "anatomical entity", - "description": "the part" - }, - "object": { - "range": "anatomical entity", - "description": "the whole" - }, - "predicate": { - "subproperty_of": "part of" - } - } - }, - "anatomical entity to anatomical entity ontogenic association": { - "is_a": "anatomical entity to anatomical entity association", - "description": "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship.", - "defining_slots": [ - "predicate" - ], - "slot_usage": { - "subject": { - "range": "anatomical entity", - "description": "the structure at a later time" - }, - "object": { - "range": "anatomical entity", - "description": "the structure at an earlier time" - }, - "predicate": { - "subproperty_of": "develops from" - } - } - }, - "organism taxon to entity association": { - "mixin": true, - "description": "An association between an organism taxon and another entity", - "defining_slots": [ - "subject" - ], - "slot_usage": { - "subject": { - "range": "organism taxon", - "description": "organism taxon that is the subject of the association" - } - } - }, - "organism taxon to organism taxon association": { - "is_a": "association", - "abstract": true, - "mixins": [ - "organism taxon to entity association" - ], - "description": "A relationship between two organism taxon nodes", - "defining_slots": [ - "subject", - "object" - ], - "slot_usage": { - "subject": { - "range": "organism taxon" - }, - "object": { - "range": "organism taxon" - } - } - }, - "organism taxon to organism taxon specialization": { - "is_a": "organism taxon to organism taxon association", - "description": "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo", - "defining_slots": [ - "predicate" - ], - "slot_usage": { - "subject": { - "range": "organism taxon", - "role": "child taxon", - "description": "the more specific taxon" - }, - "object": { - "range": "organism taxon", - "role": "parent taxon", - "description": "the more general taxon" - }, - "predicate": { - "subproperty_of": "subclass of" - } - } - }, - "organism taxon to organism taxon interaction": { - "is_a": "organism taxon to organism taxon association", - "description": "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens", - "defining_slots": [ - "predicate" - ], - "slots": [ - "associated environmental context" - ], - "slot_usage": { - "subject": { - "range": "organism taxon", - "role": "interactor taxon", - "description": "the taxon that is the subject of the association" - }, - "object": { - "range": "organism taxon", - "role": "interactee taxon", - "description": "the taxon that is the subject of the association" - }, - "predicate": { - "subproperty_of": "interacts with" - }, - "associated environmental context": { - "description": "the environment in which the two taxa interact" - } - } - }, - "organism taxon to environment association": { - "is_a": "association", - "abstract": true, - "mixins": [ - "organism taxon to entity association" - ], - "slot_usage": { - "subject": { - "range": "organism taxon", - "role": "interactor taxon", - "description": "the taxon that is the subject of the association" - }, - "object": { - "role": "environmental context", - "description": "the environment in which the organism occurs" - }, - "predicate": { - "description": "predicate describing the relationship between the taxon and the environment\n " - } - } - } - } -} diff --git a/src/cache_handler.js b/src/cache_handler.js index beceaacf..5b4198b8 100644 --- a/src/cache_handler.js +++ b/src/cache_handler.js @@ -1,14 +1,14 @@ const redisClient = require('./redis-client'); const debug = require('debug')('bte:biothings-explorer-trapi:cache_handler'); const LogEntry = require('./log_entry'); +const _ = require('lodash'); module.exports = class { constructor(qEdges, caching, logs = []) { this.qEdges = qEdges; this.logs = logs; - this.cacheEnabled = (caching === 'false') ? - false : - (!(process.env.REDIS_HOST === undefined) && !(process.env.REDIS_PORT === undefined)); + this.cacheEnabled = + caching === 'false' ? false : !(process.env.REDIS_HOST === undefined) && !(process.env.REDIS_PORT === undefined); this.logs.push( new LogEntry('DEBUG', null, `REDIS cache is ${this.cacheEnabled === true ? '' : 'not'} enabled.`).getLog(), ); @@ -41,7 +41,28 @@ module.exports = class { } _copyRecord(record) { - const new_record = { + const objs = { + in: record.$input.obj[0], + out: record.$output.obj[0], + }; + + const copyObjs = {}; + + Object.entries(objs).forEach(([which, obj]) => { + copyObjs[which] = Object.fromEntries( + Object.entries(obj) + .filter(([key, val]) => !key.startsWith('_')) + ); + + Object.entries(Object.getOwnPropertyDescriptors(Object.getPrototypeOf(obj))) + .filter(([key, descriptor]) => typeof descriptor.get === 'function' && key !== '__proto__') + .map(([key]) => key) + .forEach((key) => { + copyObjs[which][key] = obj[key]; + }); + }); + + return { $edge_metadata: { input_id: record.$edge_metadata.input_id, output_id: record.$edge_metadata.output_id, @@ -53,33 +74,13 @@ module.exports = class { }, $input: { original: record.$input.original, - obj: [ - { - dbIDs: record.$input.obj[0].dbIDs, - curies: record.$input.obj[0].curies, - label: record.$input.obj[0].label, - primaryID: record.$input.obj[0].primaryID, - }, - ], + obj: [copyObjs['in']], }, $output: { original: record.$output.original, - obj: [ - { - dbIDs: record.$output.obj[0].dbIDs, - curies: record.$output.obj[0].curies, - label: record.$output.obj[0].label, - primaryID: record.$output.obj[0].primaryID, - }, - ], + obj: [copyObjs['out']], }, }; - Object.keys(record).map((k) => { - if (!['$edge_metadata', '$input', '$output'].includes(k)) { - new_record[k] = record[k]; - } - }); - return new_record; } _groupQueryResultsByEdgeID(queryResult) { diff --git a/src/graph/graph.js b/src/graph/graph.js index b3185fac..f19d90e5 100644 --- a/src/graph/graph.js +++ b/src/graph/graph.js @@ -15,53 +15,57 @@ module.exports = class Graph { update(queryResult) { debug(`Updating BTE Graph now.`); const bteAttributes = ['name', 'label', 'id', 'api', 'provided_by', 'publications']; - queryResult.length && queryResult.map((record) => { - const inputPrimaryID = this.helper._getInputID(record); - const inputQGID = this.helper._getInputQueryNodeID(record); - const inputID = inputPrimaryID + '-' + inputQGID; - const outputPrimaryID = this.helper._getOutputID(record); - const outputQGID = this.helper._getOutputQueryNodeID(record); - const outputID = outputPrimaryID + '-' + outputQGID; - const edgeID = this.helper._getKGEdgeID(record); - if (!(outputID in this.nodes)) { - this.nodes[outputID] = new kg_node(outputID, { - primaryID: outputPrimaryID, - qgID: outputQGID, - equivalentIDs: this.helper._getOutputEquivalentIds(record), - label: this.helper._getOutputLabel(record), - category: this.helper._getOutputCategory(record), - nodeAttributes: this.helper._getOutputAttributes(record), - }); + queryResult.map((record) => { + if (record) { + const inputPrimaryID = this.helper._getInputID(record); + const inputQGID = this.helper._getInputQueryNodeID(record); + const inputID = inputPrimaryID + '-' + inputQGID; + const outputPrimaryID = this.helper._getOutputID(record); + const outputQGID = this.helper._getOutputQueryNodeID(record); + const outputID = outputPrimaryID + '-' + outputQGID; + const edgeID = this.helper._getKGEdgeID(record); + if (!(outputID in this.nodes)) { + this.nodes[outputID] = new kg_node(outputID, { + primaryID: outputPrimaryID, + qgID: outputQGID, + equivalentIDs: this.helper._getOutputEquivalentIds(record), + names: this.helper._getOutputNames(record), + label: this.helper._getOutputLabel(record), + category: this.helper._getOutputCategory(record), + nodeAttributes: this.helper._getOutputAttributes(record), + }); + } + if (!(inputID in this.nodes)) { + this.nodes[inputID] = new kg_node(inputID, { + primaryID: inputPrimaryID, + qgID: inputQGID, + equivalentIDs: this.helper._getInputEquivalentIds(record), + names: this.helper._getInputNames(record), + label: this.helper._getInputLabel(record), + category: this.helper._getInputCategory(record), + nodeAttributes: this.helper._getInputAttributes(record), + }); + } + this.nodes[outputID].addSourceNode(inputID); + this.nodes[outputID].addSourceQGNode(inputQGID); + this.nodes[inputID].addTargetNode(outputID); + this.nodes[inputID].addTargetQGNode(outputQGID); + if (!(edgeID in this.edges)) { + this.edges[edgeID] = new kg_edge(edgeID, { + predicate: this.helper._getPredicate(record), + subject: inputPrimaryID, + object: outputPrimaryID, + }); + } + this.edges[edgeID].addAPI(this.helper._getAPI(record)); + this.edges[edgeID].addSource(this.helper._getSource(record)); + this.edges[edgeID].addPublication(this.helper._getPublication(record)); + Object.keys(record) + .filter((k) => !(bteAttributes.includes(k) || k.startsWith('$'))) + .map((item) => { + this.edges[edgeID].addAdditionalAttributes(item, record[item]); + }); } - if (!(inputID in this.nodes)) { - this.nodes[inputID] = new kg_node(inputID, { - primaryID: inputPrimaryID, - qgID: inputQGID, - equivalentIDs: this.helper._getInputEquivalentIds(record), - label: this.helper._getInputLabel(record), - category: this.helper._getInputCategory(record), - nodeAttributes: this.helper._getInputAttributes(record), - }); - } - this.nodes[outputID].addSourceNode(inputID); - this.nodes[outputID].addSourceQGNode(inputQGID); - this.nodes[inputID].addTargetNode(outputID); - this.nodes[inputID].addTargetQGNode(outputQGID); - if (!(edgeID in this.edges)) { - this.edges[edgeID] = new kg_edge(edgeID, { - predicate: this.helper._getPredicate(record), - subject: inputPrimaryID, - object: outputPrimaryID, - }); - } - this.edges[edgeID].addAPI(this.helper._getAPI(record)); - this.edges[edgeID].addSource(this.helper._getSource(record)); - this.edges[edgeID].addPublication(this.helper._getPublication(record)); - Object.keys(record) - .filter((k) => !(bteAttributes.includes(k) || k.startsWith('$'))) - .map((item) => { - this.edges[edgeID].addAdditionalAttributes(item, record[item]); - }); }); } diff --git a/src/graph/kg_node.js b/src/graph/kg_node.js index 8cd9e4a5..92ecf1ee 100644 --- a/src/graph/kg_node.js +++ b/src/graph/kg_node.js @@ -4,6 +4,7 @@ module.exports = class KGNode { this._primaryID = info.primaryID; this._qgID = info.qgID; this._curies = info.equivalentIDs; + this._names = info.names; this._semanticType = info.category; this._nodeAttributes = info.nodeAttributes; this._label = info.label; diff --git a/src/graph/knowledge_graph.js b/src/graph/knowledge_graph.js index b85a02b6..493fb8e7 100644 --- a/src/graph/knowledge_graph.js +++ b/src/graph/knowledge_graph.js @@ -26,9 +26,12 @@ module.exports = class KnowledgeGraph { name: kgNode._label, attributes: [ { - attribute_type_id: 'equivalent_identifiers', + attribute_type_id: 'biolink:xref', value: kgNode._curies, - value_type_id: 'biolink:id', + }, + { + attribute_type_id: 'biolink:synonym', + value: kgNode._names, }, { attribute_type_id: 'num_source_nodes', @@ -63,16 +66,16 @@ module.exports = class KnowledgeGraph { } _createAttributes(kgEdge) { - const attributes = [ + let attributes = [ { - attribute_type_id: 'provided_by', + attribute_type_id: 'biolink:primary_knowledge_source', value: Array.from(kgEdge.sources), - value_type_id: 'biolink:provided_by', + value_type_id: 'biolink:InformationResource', }, { - attribute_type_id: 'api', + attribute_type_id: 'biolink:aggregator_knowledge_source', value: Array.from(kgEdge.apis), - value_type_id: 'bts:api', + value_type_id: 'biolink:InformationResource', }, { attribute_type_id: 'publications', @@ -80,12 +83,24 @@ module.exports = class KnowledgeGraph { value_type_id: 'biolink:publication', }, ]; - for (const key in kgEdge.attributes) { - attributes.push({ - attribute_type_id: key, - value: kgEdge.attributes[key], - value_type_id: 'bts:' + key, - }); + + if (kgEdge.attributes.attributes) { + attributes = [ + { + "attribute_type_id": "biolink:aggregator_knowledge_source", + "value": "infores:translator-biothings-explorer", + "value_type_id": "biolink:InformationResource" + }, + ...kgEdge.attributes.attributes + ]; + } else { + for (const key in kgEdge.attributes) { + attributes.push({ + attribute_type_id: key, + value: kgEdge.attributes[key], + value_type_id: 'bts:' + key, + }); + } } return attributes; } diff --git a/src/helper.js b/src/helper.js index 97e07601..b1740dc0 100644 --- a/src/helper.js +++ b/src/helper.js @@ -97,6 +97,16 @@ module.exports = class QueryGraphHelper { } } + _getInputNames(record) { + try { + return record.$edge_metadata.trapi_qEdge_obj.isReversed() + ? record.$output.obj[0].dbIDs.name + : record.$input.obj[0].dbIDs.name; + } catch (err) { + return null; + } + } + _getInputAttributes(record) { try { return record.$edge_metadata.trapi_qEdge_obj.isReversed() @@ -107,6 +117,16 @@ module.exports = class QueryGraphHelper { } } + _getOutputNames(record) { + try { + return record.$edge_metadata.trapi_qEdge_obj.isReversed() + ? record.$input.obj[0].dbIDs.name + : record.$output.obj[0].dbIDs.name; + } catch (err) { + return null; + } + } + _getOutputEquivalentIds(record) { try { return record.$edge_metadata.trapi_qEdge_obj.isReversed() @@ -117,6 +137,7 @@ module.exports = class QueryGraphHelper { } } + _getOutputAttributes(record) { try { return record.$edge_metadata.trapi_qEdge_obj.isReversed() diff --git a/src/index.js b/src/index.js index 782c2660..42581e74 100644 --- a/src/index.js +++ b/src/index.js @@ -33,6 +33,7 @@ exports.TRAPIQueryHandler = class TRAPIQueryHandler { getResponse() { this.bteGraph.notify(); return { + workflow: [{ id: 'lookup' }], message: { query_graph: this.queryGraph, knowledge_graph: this.knowledgeGraph.kg, @@ -98,7 +99,7 @@ exports.TRAPIQueryHandler = class TRAPIQueryHandler { _createBatchEdgeQueryHandlers(queryPaths, kg) { let handlers = {}; for (const index in queryPaths) { - handlers[index] = new BatchEdgeQueryHandler(kg, this.resolveOutputIDs, {caching: this.options.caching}); + handlers[index] = new BatchEdgeQueryHandler(kg, this.resolveOutputIDs, { caching: this.options.caching }); handlers[index].setEdges(queryPaths[index]); handlers[index].subscribe(this.queryResults); handlers[index].subscribe(this.bteGraph); diff --git a/src/knowledge_graph.js b/src/knowledge_graph.js deleted file mode 100644 index a3abb208..00000000 --- a/src/knowledge_graph.js +++ /dev/null @@ -1,129 +0,0 @@ -const { add } = require('lodash'); -const GraphHelper = require('./helper'); -const debug = require('debug')('bte:biothings-explorer-trapi:KnowledgeGraph'); -const helper = new GraphHelper(); - -module.exports = class KnowledgeGraph { - constructor() { - this.nodes = {}; - this.edges = {}; - this.kg = { - nodes: this.nodes, - edges: this.edges, - }; - } - - getNodes() { - return this.nodes; - } - - getEdges() { - return this.edges; - } - - _createInputNode(record) { - const res = { - categories: 'biolink:' + helper._getInputCategory(record), - name: helper._getInputLabel(record), - attributes: [ - { - name: 'equivalent_identifiers', - value: helper._getInputEquivalentIds(record), - type: 'biolink:id', - }, - ], - }; - const additional_attributes = helper._getInputAttributes(record); - if (!(typeof additional_attributes === 'undefined')) { - for (const key in additional_attributes) { - res.attributes.push({ - name: key, - value: additional_attributes[key], - type: 'bts:' + key, - }); - } - } - return res; - } - - _createOutputNode(record) { - const res = { - categories: 'biolink:' + helper._getOutputCategory(record), - name: helper._getOutputLabel(record), - attributes: [ - { - name: 'equivalent_identifiers', - value: helper._getOutputEquivalentIds(record), - type: 'biolink:id', - }, - ], - }; - const additional_attributes = helper._getOutputAttributes(record); - if (!(typeof additional_attributes === 'undefined')) { - for (const key in additional_attributes) { - res.attributes.push({ - name: key, - value: additional_attributes[key], - type: 'bts:' + key, - }); - } - } - return res; - } - - _createAttributes(record) { - const bteAttributes = ['name', 'label', 'id', 'api', 'provided_by']; - const attributes = [ - { - name: 'provided_by', - value: helper._getSource(record), - type: 'biolink:provided_by', - }, - { - name: 'api', - value: helper._getAPI(record), - type: 'bts:api', - }, - ]; - Object.keys(record) - .filter((k) => !(bteAttributes.includes(k) || k.startsWith('$'))) - .map((item) => { - attributes.push({ - name: item, - value: record[item], - type: item === 'publications' ? 'biolink:' + item : 'bts:' + item, - }); - }); - return attributes; - } - - _createEdge(record) { - return { - predicate: helper._getPredicate(record), - subject: helper._getInputID(record), - object: helper._getOutputID(record), - attributes: this._createAttributes(record), - }; - } - - update(queryResult) { - queryResult.map((record) => { - if (!(helper._getInputID(record) in this.nodes)) { - this.nodes[helper._getInputID(record)] = this._createInputNode(record); - } - if (!(helper._getOutputID(record) in this.nodes)) { - this.nodes[helper._getOutputID(record)] = this._createOutputNode(record); - } - if (!(helper._createUniqueEdgeID(record) in this.edges)) { - this.edges[helper._createUniqueEdgeID(record)] = this._createEdge(record); - } - // this.nodes = { ...this.nodes, ...this._createInputNode(record) }; - // this.nodes = { ...this.nodes, ...this._createOutputNode(record) }; - // this.edges = { ...this.edges, ...this._createEdge(record) }; - }); - this.kg = { - nodes: this.nodes, - edges: this.edges, - }; - } -}; diff --git a/src/query_results.js b/src/query_results.js index 32c679fb..353447c8 100644 --- a/src/query_results.js +++ b/src/query_results.js @@ -50,37 +50,38 @@ module.exports = class QueryResult { const results = []; - this.cachedQueryResults[0] && this.cachedQueryResults[0].forEach((cachedRecords, outputNodeID) => { - cachedRecords.forEach((cachedRecord) => { - const result = { - node_bindings: { - [cachedRecord.inputQueryNodeID]: [ - { - id: cachedRecord.inputNodeID, - }, - ], - [cachedRecord.outputQueryNodeID]: [ - { - id: cachedRecord.outputNodeID, - }, - ], - }, - edge_bindings: { - [cachedRecord.queryEdgeID]: [ - { - id: cachedRecord.kgEdgeID, - }, - ], - }, - //default score issue #200 - TODO: turn to evaluating module eventually - score: '1.0', - }; - - results.push(result); - - this._addRemainingCachedQueryResults(cachedRecord.inputNodeID, results, result, 1); + this.cachedQueryResults[0] && + this.cachedQueryResults[0].forEach((cachedRecords, outputNodeID) => { + cachedRecords.forEach((cachedRecord) => { + const result = { + node_bindings: { + [cachedRecord.inputQueryNodeID]: [ + { + id: cachedRecord.inputNodeID, + }, + ], + [cachedRecord.outputQueryNodeID]: [ + { + id: cachedRecord.outputNodeID, + }, + ], + }, + edge_bindings: { + [cachedRecord.queryEdgeID]: [ + { + id: cachedRecord.kgEdgeID, + }, + ], + }, + //default score issue #200 - TODO: turn to evaluating module eventually + score: '1.0', + }; + + results.push(result); + + this._addRemainingCachedQueryResults(cachedRecord.inputNodeID, results, result, 1); + }); }); - }); return results; } @@ -101,26 +102,28 @@ module.exports = class QueryResult { const cachedQueryResult = new Map(); queryResult.forEach((record) => { - const inputNodeID = helper._getInputID(record); - const outputNodeID = helper._getOutputID(record); - - if (this.cachedQueryResults.length === 0 || previousOutputNodeIDs.has(inputNodeID)) { - let cachedRecordsForOutputNodeID; - if (cachedQueryResult.has(outputNodeID)) { - cachedRecordsForOutputNodeID = cachedQueryResult.get(outputNodeID); - } else { - cachedRecordsForOutputNodeID = []; - cachedQueryResult.set(outputNodeID, cachedRecordsForOutputNodeID); + if (record) { + const inputNodeID = helper._getInputID(record); + const outputNodeID = helper._getOutputID(record); + + if (this.cachedQueryResults.length === 0 || previousOutputNodeIDs.has(inputNodeID)) { + let cachedRecordsForOutputNodeID; + if (cachedQueryResult.has(outputNodeID)) { + cachedRecordsForOutputNodeID = cachedQueryResult.get(outputNodeID); + } else { + cachedRecordsForOutputNodeID = []; + cachedQueryResult.set(outputNodeID, cachedRecordsForOutputNodeID); + } + + cachedRecordsForOutputNodeID.push({ + inputQueryNodeID: helper._getInputQueryNodeID(record), + inputNodeID: inputNodeID, + queryEdgeID: record.$edge_metadata.trapi_qEdge_obj.getID(), + kgEdgeID: helper._getKGEdgeID(record), + outputQueryNodeID: helper._getOutputQueryNodeID(record), + outputNodeID: outputNodeID, + }); } - - cachedRecordsForOutputNodeID.push({ - inputQueryNodeID: helper._getInputQueryNodeID(record), - inputNodeID: inputNodeID, - queryEdgeID: record.$edge_metadata.trapi_qEdge_obj.getID(), - kgEdgeID: helper._getKGEdgeID(record), - outputQueryNodeID: helper._getOutputQueryNodeID(record), - outputNodeID: outputNodeID, - }); } });