BioThings Explorer TRAPI Query Graph Handler
A on-the-fly query engine for BioThings Explorer based on TRAPI Query Graph.
Install
npm i @biothings-explorer/query_graph_handlerUsage
Making a single hop query
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",
"predicates": ["biolink:functional_association"]
}
},
"nodes": {
"n00": {
"categories": ["biolink:Gene"],
"ids": ["ENSEMBL:ENSG00000123374"]
},
"n01": {
"categories": ["biolink:BiologicalProcess"]
}
}
}
}
};
queryHandler.setQueryGraph(OneHopQuery);
await queryHandler.query();
console.log(queryHandler.getResponse())Example Result
{
"workflow": [
{"id": "lookup"}
],
"message": {
"query_graph": {
"edges": {
"e00": {
"object": "n01",
"subject": "n00",
"predicate": "biolink:enables"
}
},
"nodes": {
"n00": {
"category": "biolink:Gene",
"id": "ENSEMBL:ENSG00000123374"
},
"n01": {
"category": "biolink:BiologicalProcess"
}
}
},
"knowledge_graph": {
"nodes": {
"NCBIGene:1017": {
"category": "biolink:Gene",
"name": "CDK2",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:1017",
"name:cyclin dependent kinase 2",
"SYMBOL:CDK2",
"UMLS:C1332733",
"UMLS:C0108855",
"HGNC:1771",
"UniProtKB:P24941",
"ENSEMBL:ENSG00000123374",
"OMIM:116953"
],
"type": "biolink:id"
}
]
},
"GO:0000082": {
"category": "biolink:BiologicalProcess",
"name": "G1/S transition of mitotic cell cycle",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:0000082",
"name:G1/S transition of mitotic cell cycle"
],
"type": "biolink:id"
}
]
},
"GO:0000086": {
"category": "biolink:BiologicalProcess",
"name": "G2/M transition of mitotic cell cycle",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:0000086",
"name:G2/M transition of mitotic cell cycle"
],
"type": "biolink:id"
}
]
},
"GO:0006260": {
"category": "biolink:BiologicalProcess",
"name": "DNA replication",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:0006260",
"name:DNA replication"
],
"type": "biolink:id"
}
]
},
"GO:0006281": {
"category": "biolink:BiologicalProcess",
"name": "DNA repair",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:0006281",
"name:DNA repair"
],
"type": "biolink:id"
}
]
},
"GO:0006468": {
"category": "biolink:BiologicalProcess",
"name": "protein phosphorylation",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:0006468",
"name:protein phosphorylation"
],
"type": "biolink:id"
}
]
},
"GO:0006977": {
"category": "biolink:BiologicalProcess",
"name": "DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:0006977",
"name:DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest"
],
"type": "biolink:id"
}
]
},
"GO:0007099": {
"category": "biolink:BiologicalProcess",
"name": "centriole replication",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:0007099",
"name:centriole replication"
],
"type": "biolink:id"
}
]
},
"GO:0007165": {
"category": "biolink:BiologicalProcess",
"name": "signal transduction",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:0007165",
"name:signal transduction"
],
"type": "biolink:id"
}
]
},
"GO:0007265": {
"category": "biolink:BiologicalProcess",
"name": "Ras protein signal transduction",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:0007265",
"name:Ras protein signal transduction"
],
"type": "biolink:id"
}
]
},
"GO:0008284": {
"category": "biolink:BiologicalProcess",
"name": "positive regulation of cell population proliferation",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:0008284",
"name:positive regulation of cell population proliferation"
],
"type": "biolink:id"
}
]
},
"GO:0010389": {
"category": "biolink:BiologicalProcess",
"name": "regulation of G2/M transition of mitotic cell cycle",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:0010389",
"name:regulation of G2/M transition of mitotic cell cycle"
],
"type": "biolink:id"
}
]
},
"GO:0010468": {
"category": "biolink:BiologicalProcess",
"name": "regulation of gene expression",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:0010468",
"name:regulation of gene expression"
],
"type": "biolink:id"
}
]
},
"GO:0016572": {
"category": "biolink:BiologicalProcess",
"name": "histone phosphorylation",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:0016572",
"name:histone phosphorylation"
],
"type": "biolink:id"
}
]
},
"GO:0018105": {
"category": "biolink:BiologicalProcess",
"name": "peptidyl-serine phosphorylation",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:0018105",
"name:peptidyl-serine phosphorylation"
],
"type": "biolink:id"
}
]
},
"GO:0031145": {
"category": "biolink:BiologicalProcess",
"name": "anaphase-promoting complex-dependent catabolic process",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:0031145",
"name:anaphase-promoting complex-dependent catabolic process"
],
"type": "biolink:id"
}
]
},
"GO:0031571": {
"category": "biolink:BiologicalProcess",
"name": "mitotic G1 DNA damage checkpoint",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:0031571",
"name:mitotic G1 DNA damage checkpoint"
],
"type": "biolink:id"
}
]
},
"GO:0051298": {
"category": "biolink:BiologicalProcess",
"name": "centrosome duplication",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:0051298",
"name:centrosome duplication"
],
"type": "biolink:id"
}
]
},
"GO:0051301": {
"category": "biolink:BiologicalProcess",
"name": "cell division",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:0051301",
"name:cell division"
],
"type": "biolink:id"
}
]
},
"GO:0051321": {
"category": "biolink:BiologicalProcess",
"name": "meiotic cell cycle",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:0051321",
"name:meiotic cell cycle"
],
"type": "biolink:id"
}
]
},
"GO:0060968": {
"category": "biolink:BiologicalProcess",
"name": "regulation of gene silencing",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:0060968",
"name:regulation of gene silencing"
],
"type": "biolink:id"
}
]
},
"GO:0071732": {
"category": "biolink:BiologicalProcess",
"name": "cellular response to nitric oxide",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:0071732",
"name:cellular response to nitric oxide"
],
"type": "biolink:id"
}
]
},
"GO:1901796": {
"category": "biolink:BiologicalProcess",
"name": "regulation of signal transduction by p53 class mediator",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"GO:1901796",
"name:regulation of signal transduction by p53 class mediator"
],
"type": "biolink:id"
}
]
}
},
"edges": {
"NCBIGene:1017-GO:0000082-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:0000082",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "IBA",
"type": "bts:evidence"
},
{
"name": "term",
"value": "G1/S transition of mitotic cell cycle",
"type": "bts:term"
},
{
"name": "publications",
"value": [
"PMID:21873635"
],
"type": "biolink:publications"
}
]
},
"NCBIGene:1017-GO:0000086-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:0000086",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "NAS",
"type": "bts:evidence"
},
{
"name": "term",
"value": "G2/M transition of mitotic cell cycle",
"type": "bts:term"
},
{
"name": "publications",
"value": [
"PMID:1653904"
],
"type": "biolink:publications"
}
]
},
"NCBIGene:1017-GO:0006260-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:0006260",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "TAS",
"type": "bts:evidence"
},
{
"name": "term",
"value": "DNA replication",
"type": "bts:term"
},
{
"name": "publications",
"value": [
"PMID:19238148"
],
"type": "biolink:publications"
}
]
},
"NCBIGene:1017-GO:0006281-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:0006281",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "IEA",
"type": "bts:evidence"
},
{
"name": "term",
"value": "DNA repair",
"type": "bts:term"
}
]
},
"NCBIGene:1017-GO:0006468-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:0006468",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "IBA",
"type": "bts:evidence"
},
{
"name": "term",
"value": "protein phosphorylation",
"type": "bts:term"
},
{
"name": "publications",
"value": [
"PMID:21873635"
],
"type": "biolink:publications"
}
]
},
"NCBIGene:1017-GO:0006977-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:0006977",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "TAS",
"type": "bts:evidence"
},
{
"name": "term",
"value": "DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest",
"type": "bts:term"
}
]
},
"NCBIGene:1017-GO:0007099-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:0007099",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "IMP",
"type": "bts:evidence"
},
{
"name": "term",
"value": "centriole replication",
"type": "bts:term"
},
{
"name": "publications",
"value": [
"PMID:26297806"
],
"type": "biolink:publications"
}
]
},
"NCBIGene:1017-GO:0007165-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:0007165",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "IBA",
"type": "bts:evidence"
},
{
"name": "term",
"value": "signal transduction",
"type": "bts:term"
},
{
"name": "publications",
"value": [
"PMID:21873635"
],
"type": "biolink:publications"
}
]
},
"NCBIGene:1017-GO:0007265-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:0007265",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "IEP",
"type": "bts:evidence"
},
{
"name": "term",
"value": "Ras protein signal transduction",
"type": "bts:term"
},
{
"name": "publications",
"value": [
"PMID:9054499"
],
"type": "biolink:publications"
}
]
},
"NCBIGene:1017-GO:0008284-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:0008284",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "IBA",
"type": "bts:evidence"
},
{
"name": "term",
"value": "positive regulation of cell population proliferation",
"type": "bts:term"
},
{
"name": "publications",
"value": [
"PMID:21873635"
],
"type": "biolink:publications"
}
]
},
"NCBIGene:1017-GO:0010389-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:0010389",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "IBA",
"type": "bts:evidence"
},
{
"name": "term",
"value": "regulation of G2/M transition of mitotic cell cycle",
"type": "bts:term"
},
{
"name": "publications",
"value": [
"PMID:21873635"
],
"type": "biolink:publications"
}
]
},
"NCBIGene:1017-GO:0010468-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:0010468",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "IBA",
"type": "bts:evidence"
},
{
"name": "term",
"value": "regulation of gene expression",
"type": "bts:term"
},
{
"name": "publications",
"value": [
"PMID:21873635"
],
"type": "biolink:publications"
}
]
},
"NCBIGene:1017-GO:0016572-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:0016572",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "IDA",
"type": "bts:evidence"
},
{
"name": "term",
"value": "histone phosphorylation",
"type": "bts:term"
},
{
"name": "publications",
"value": [
"PMID:11746698"
],
"type": "biolink:publications"
}
]
},
"NCBIGene:1017-GO:0018105-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:0018105",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "IDA",
"type": "bts:evidence"
},
{
"name": "term",
"value": "peptidyl-serine phosphorylation",
"type": "bts:term"
},
{
"name": "publications",
"value": [
"PMID:23184662"
],
"type": "biolink:publications"
}
]
},
"NCBIGene:1017-GO:0031145-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:0031145",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "TAS",
"type": "bts:evidence"
},
{
"name": "term",
"value": "anaphase-promoting complex-dependent catabolic process",
"type": "bts:term"
}
]
},
"NCBIGene:1017-GO:0031571-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:0031571",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "TAS",
"type": "bts:evidence"
},
{
"name": "term",
"value": "mitotic G1 DNA damage checkpoint",
"type": "bts:term"
},
{
"name": "publications",
"value": [
"PMID:21319273"
],
"type": "biolink:publications"
}
]
},
"NCBIGene:1017-GO:0051298-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:0051298",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "TAS",
"type": "bts:evidence"
},
{
"name": "term",
"value": "centrosome duplication",
"type": "bts:term"
},
{
"name": "publications",
"value": [
"PMID:19238148"
],
"type": "biolink:publications"
}
]
},
"NCBIGene:1017-GO:0051301-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:0051301",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "IEA",
"type": "bts:evidence"
},
{
"name": "term",
"value": "cell division",
"type": "bts:term"
}
]
},
"NCBIGene:1017-GO:0051321-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:0051321",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "TAS",
"type": "bts:evidence"
},
{
"name": "term",
"value": "meiotic cell cycle",
"type": "bts:term"
},
{
"name": "publications",
"value": [
"PMID:19238148"
],
"type": "biolink:publications"
}
]
},
"NCBIGene:1017-GO:0060968-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:0060968",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "IDA",
"type": "bts:evidence"
},
{
"name": "term",
"value": "regulation of gene silencing",
"type": "bts:term"
},
{
"name": "publications",
"value": [
"PMID:20935635"
],
"type": "biolink:publications"
}
]
},
"NCBIGene:1017-GO:0071732-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:0071732",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "TAS",
"type": "bts:evidence"
},
{
"name": "term",
"value": "cellular response to nitric oxide",
"type": "bts:term"
},
{
"name": "publications",
"value": [
"PMID:20079829"
],
"type": "biolink:publications"
}
]
},
"NCBIGene:1017-GO:1901796-MyGene.info API-entrez": {
"predicate": "biolink:enables",
"subject": "NCBIGene:1017",
"object": "GO:1901796",
"attributes": [
{
"name": "provided_by",
"value": "entrez",
"type": "biolink:provided_by"
},
{
"name": "api",
"value": "MyGene.info API",
"type": "bts:api"
},
{
"name": "evidence",
"value": "TAS",
"type": "bts:evidence"
},
{
"name": "term",
"value": "regulation of signal transduction by p53 class mediator",
"type": "bts:term"
}
]
}
}
},
"results": [
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0000082"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0000082-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0000082"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0000082-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0000086"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0000086-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0000086"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0000086-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0006260"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0006260-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0006281"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0006281-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0006468"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0006468-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0006468"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0006468-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0006468"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0006468-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0006977"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0006977-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0007099"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0007099-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0007165"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0007165-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0007265"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0007265-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0008284"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0008284-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0008284"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0008284-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0010389"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0010389-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0010468"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0010468-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0016572"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0016572-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0018105"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0018105-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0031145"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0031145-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0031571"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0031571-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0051298"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0051298-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0051301"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0051301-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0051321"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0051321-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0060968"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0060968-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:0071732"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:0071732-MyGene.info API-entrez"
}
]
}
},
{
"node_bindings": {
"n00": [
{
"id": "NCBIGene:1017"
}
],
"n01": [
{
"id": "GO:1901796"
}
]
},
"edge_bindings": {
"e00": [
{
"id": "NCBIGene:1017-GO:1901796-MyGene.info API-entrez"
}
]
}
}
]
},
"logs": [
{
"timestamp": "2021-03-15T22:48:10.757Z",
"level": "DEBUG",
"message": "BTE identified 2 QNodes from your query graph",
"code": null
},
{
"timestamp": "2021-03-15T22:48:10.757Z",
"level": "DEBUG",
"message": "BTE identified 1 QEdges from your query graph",
"code": null
},
{
"timestamp": "2021-03-15T22:48:10.757Z",
"level": "DEBUG",
"message": "BTE identified your query graph as a 1-depth query graph",
"code": null
},
{
"timestamp": "2021-03-15T22:48:10.757Z",
"level": "DEBUG",
"message": "REDIS cache is not enabled.",
"code": null
},
{
"timestamp": "2021-03-15T22:48:10.797Z",
"level": "DEBUG",
"message": "BTE found 1 smartapi edges corresponding to e00. These smartaip edges comes from 1 unique APIs. They are MyGene.info API",
"code": null
},
{
"timestamp": "2021-03-15T22:48:10.808Z",
"level": "DEBUG",
"message": "BTE found 1 bte edges for this batch.",
"code": null
},
{
"timestamp": "2021-03-15T22:48:10.808Z",
"level": "DEBUG",
"message": "call-apis: Resolving ID feature is turned on",
"code": null
},
{
"timestamp": "2021-03-15T22:48:10.808Z",
"level": "DEBUG",
"message": "call-apis: Number of BTE Edges received is 1",
"code": null
},
{
"timestamp": "2021-03-15T22:48:10.828Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://mygene.info/v3/query\",\"params\":{\"fields\":\"go.BP\"},\"data\":\"q=1017&scopes=entrezgene\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:48:10.839Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 27 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:48:10.839Z",
"level": "DEBUG",
"message": "call-apis: Total number of results returned for this query is 27",
"code": null
},
{
"timestamp": "2021-03-15T22:48:10.857Z",
"level": "DEBUG",
"message": "call-apis: Query completes",
"code": null
}
]
}Making a multi hop query
const handler = require("@biothings-explorer/query_graph_handler");
const queryHandler = new handler.TRAPIQueryHandler();
const multiHopQuery = {
"workflow": [
{"id": "lookup"}
],
"message": {
"query_graph": {
"nodes": {
"n0": {
"categories": ["biolink:Disease"],
"ids": ["MONDO:0005737"]
},
"n1": {
"categories": ["biolink:Gene"]
},
"n2": {
"categories": ["biolink:SmallMolecule"]
}
},
"edges": {
"e01": {
"subject": "n0",
"object": "n1"
},
"e02": {
"subject": "n1",
"object": "n2"
}
}
}
}
}
queryHandler.setQueryGraph(multiHopQuery);
await queryHandler.query();
console.log(queryHandler.getResponse())Example Result
{
"workflow": [
{"id": "lookup"}
],
"message": {
"query_graph": {
"nodes": {
"n0": {
"category": "biolink:Disease",
"id": "MONDO:0005737"
},
"n1": {
"category": "biolink:Gene"
},
"n2": {
"category": "biolink:ChemicalSubstance"
}
},
"edges": {
"e01": {
"subject": "n0",
"object": "n1"
},
"e02": {
"subject": "n1",
"object": "n2"
}
}
},
"knowledge_graph": {
"nodes": {
"MONDO:0005737": {
"category": "biolink:Disease",
"name": "Ebola hemorrhagic fever",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"MONDO:0005737",
"DOID:4325",
"UMLS:C0282687",
"name:Ebola hemorrhagic fever",
"MESH:D019142",
"EFO:0007243",
"ORPHANET:319218",
"GARD:2035"
],
"type": "biolink:id"
}
]
},
"NCBIGene:116534309": {
"category": "biolink:Gene",
"name": "CD4",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:116534309",
"name:CD4 molecule",
"SYMBOL:CD4"
],
"type": "biolink:id"
}
]
},
"NCBIGene:539109": {
"category": "biolink:Gene",
"name": "MMP11",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:539109",
"name:matrix metallopeptidase 11",
"SYMBOL:MMP11",
"ENSEMBL:ENSBTAG00000006108"
],
"type": "biolink:id"
}
]
},
"NCBIGene:102448557": {
"category": "biolink:Gene",
"name": "GTPBP1",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:102448557",
"name:GTP binding protein 1",
"SYMBOL:GTPBP1",
"ENSEMBL:ENSPSIG00000004300"
],
"type": "biolink:id"
}
]
},
"NCBIGene:103074707": {
"category": "biolink:Gene",
"name": "CCL2",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:103074707",
"name:C-C motif chemokine ligand 2",
"SYMBOL:CCL2"
],
"type": "biolink:id"
}
]
},
"ENSEMBL:ENSSPUG00000015633": {
"category": "biolink:Gene",
"name": "MAPRE3",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"name:microtubule associated protein RP/EB family member 3",
"SYMBOL:MAPRE3",
"ENSEMBL:ENSSPUG00000015633"
],
"type": "biolink:id"
}
]
},
"NCBIGene:115865406": {
"category": "biolink:Gene",
"name": "BST2",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:115865406",
"name:bone marrow stromal cell antigen 2",
"SYMBOL:BST2"
],
"type": "biolink:id"
}
]
},
"NCBIGene:110132571": {
"category": "biolink:Gene",
"name": "IL1B",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:110132571",
"name:interleukin 1 beta",
"SYMBOL:IL1B"
],
"type": "biolink:id"
}
]
},
"NCBIGene:101571570": {
"category": "biolink:Gene",
"name": "Ifih1",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:101571570",
"name:interferon induced with helicase C domain 1",
"SYMBOL:Ifih1",
"ENSEMBL:ENSODEG00000013586"
],
"type": "biolink:id"
}
]
},
"ENSEMBL:ENSSMAG00000017984": {
"category": "biolink:Gene",
"name": "npc1",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"name:Niemann-Pick disease, type C1",
"SYMBOL:npc1",
"ENSEMBL:ENSSMAG00000017984"
],
"type": "biolink:id"
}
]
},
"NCBIGene:397686": {
"category": "biolink:Gene",
"name": "IFNA1",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:397686",
"name:interferon, alpha 1",
"SYMBOL:IFNA1",
"ENSEMBL:ENSSSCG00000050619"
],
"type": "biolink:id"
}
]
},
"NCBIGene:102892030": {
"category": "biolink:Gene",
"name": "ALB",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:102892030",
"name:albumin",
"SYMBOL:ALB"
],
"type": "biolink:id"
}
]
},
"NCBIGene:104045425": {
"category": "biolink:Gene",
"name": "HDX",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:104045425",
"name:highly divergent homeobox",
"SYMBOL:HDX"
],
"type": "biolink:id"
}
]
},
"NCBIGene:110137949": {
"category": "biolink:Gene",
"name": "CXCL10",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:110137949",
"name:C-X-C motif chemokine ligand 10",
"SYMBOL:CXCL10"
],
"type": "biolink:id"
}
]
},
"NCBIGene:105822820": {
"category": "biolink:Gene",
"name": "CXCL8",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:105822820",
"name:C-X-C motif chemokine ligand 8",
"SYMBOL:CXCL8",
"ENSEMBL:ENSPCOG00000024593"
],
"type": "biolink:id"
}
]
},
"NCBIGene:116479423": {
"category": "biolink:Gene",
"name": "CLEC4M",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:116479423",
"name:C-type lectin domain family 4 member M",
"SYMBOL:CLEC4M"
],
"type": "biolink:id"
}
]
},
"NCBIGene:103814882": {
"category": "biolink:Gene",
"name": "F3",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:103814882",
"name:coagulation factor III, tissue factor",
"SYMBOL:F3",
"ENSEMBL:ENSSCAG00000012591"
],
"type": "biolink:id"
}
]
},
"NCBIGene:101142722": {
"category": "biolink:Gene",
"name": "KPNA1",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:101142722",
"name:karyopherin subunit alpha 1",
"SYMBOL:KPNA1"
],
"type": "biolink:id"
}
]
},
"NCBIGene:104673720": {
"category": "biolink:Gene",
"name": "CTSL",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:104673720",
"name:cathepsin L",
"SYMBOL:CTSL",
"ENSEMBL:ENSRROG00000038398"
],
"type": "biolink:id"
}
]
},
"NCBIGene:116543050": {
"category": "biolink:Gene",
"name": "CTSB",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:116543050",
"name:cathepsin B",
"SYMBOL:CTSB"
],
"type": "biolink:id"
}
]
},
"NCBIGene:29798": {
"category": "biolink:Gene",
"name": "C2orf27A",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:29798",
"name:chromosome 2 open reading frame 27A",
"SYMBOL:C2orf27A",
"UMLS:C2681192",
"HGNC:25077",
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{
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},
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]
},
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]
},
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"UMLS:C0021027",
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"logs": [
{
"timestamp": "2021-03-15T22:54:01.080Z",
"level": "DEBUG",
"message": "BTE identified 3 QNodes from your query graph",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.080Z",
"level": "DEBUG",
"message": "BTE identified 2 QEdges from your query graph",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.080Z",
"level": "DEBUG",
"message": "BTE identified your query graph as a 2-depth query graph",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.080Z",
"level": "DEBUG",
"message": "REDIS cache is not enabled.",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.160Z",
"level": "DEBUG",
"message": "BTE found 23 smartapi edges corresponding to e01. These smartaip edges comes from 7 unique APIs. They are MyDisease.info API,MGIgene2phenotype API,DISEASES API,SEMMED Disease API,Text Mining CO-OCCURRENCE API,TCGA Mutation Frequency KP API,BioLink API",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.297Z",
"level": "DEBUG",
"message": "BTE found 23 bte edges for this batch.",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.297Z",
"level": "DEBUG",
"message": "call-apis: Resolving ID feature is turned on",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.297Z",
"level": "DEBUG",
"message": "call-apis: Number of BTE Edges received is 23",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.321Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"http://mydisease.info/v1/query\",\"params\":{\"fields\":\"disgenet.genes_related_to_disease\"},\"data\":\"q=C0282687&scopes=mondo.xrefs.umls, disgenet.xrefs.umls\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.325Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.388Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/DISEASES/query\",\"params\":{\"fields\":\"DISEASES.associatedWith\"},\"data\":\"q=DOID:4325&scopes=DISEASES.doid\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.397Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 42 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.398Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/text_mining_co_occurrence_kp/query\",\"params\":{\"fields\":\"subject,association\",\"q\":\"object.MONDO:\\\"MONDO:0005737\\\" AND subject.type:Gene\",\"size\":1000},\"method\":\"get\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.398Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.398Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/mgigene2phenotype/query\",\"params\":{\"fields\":\"_id\",\"size\":\"300\"},\"data\":\"q=DOID:4325&scopes=mgi.associated_with_disease.doid\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.398Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.399Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/tcga_mut_freq_kp/query\",\"params\":{\"fields\":\"association.freq_by_sample,subject.SYMBOL\",\"q\":\"object.id:\\\"MONDO:0005737\\\" AND association.freq_by_sample:>0.1\",\"size\":\"1000\",\"sort\":\"-association.freq_by_sample\"},\"method\":\"get\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.399Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.399Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmed/query\",\"params\":{\"fields\":\"caused_by\"},\"data\":\"q=C0282687&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.400Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 2 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.400Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmed/query\",\"params\":{\"fields\":\"affected_by\"},\"data\":\"q=C0282687&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.400Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 7 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.401Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmed/query\",\"params\":{\"fields\":\"affects\"},\"data\":\"q=C0282687&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.401Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.439Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/text_mining_co_occurrence_kp/query\",\"params\":{\"fields\":\"object,association\",\"q\":\"subject.MONDO:\\\"MONDO:0005737\\\" AND object.type:Gene\",\"size\":1000},\"method\":\"get\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.628Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.706Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://api.monarchinitiative.org/api/bioentity/disease/MONDO:0005737/genes\",\"params\":{\"direct\":true,\"rows\":200,\"unselect_evidence\":true},\"method\":\"get\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.707Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.709Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://api.monarchinitiative.org/api/bioentity/disease/MONDO:0005737/genes\",\"params\":{\"direct\":true,\"rows\":200,\"unselect_evidence\":true},\"method\":\"get\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.709Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.722Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmed/query\",\"params\":{\"fields\":\"derives_from\"},\"data\":\"q=C0282687&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.722Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.723Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmed/query\",\"params\":{\"fields\":\"disrupted_by\"},\"data\":\"q=C0282687&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.723Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 4 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.724Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmed/query\",\"params\":{\"fields\":\"coexists_with\"},\"data\":\"q=C0282687&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.724Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.736Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmed/query\",\"params\":{\"fields\":\"negatively_regulates\"},\"data\":\"q=C0282687&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.736Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.737Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmed/query\",\"params\":{\"fields\":\"negatively_regulated_by\"},\"data\":\"q=C0282687&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.737Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.737Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmed/query\",\"params\":{\"fields\":\"disrupts\"},\"data\":\"q=C0282687&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.737Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.749Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmed/query\",\"params\":{\"fields\":\"physically_interacts_with\"},\"data\":\"q=C0282687&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.749Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.750Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmed/query\",\"params\":{\"fields\":\"positively_regulates\"},\"data\":\"q=C0282687&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.750Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.750Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmed/query\",\"params\":{\"fields\":\"positively_regulated_by\"},\"data\":\"q=C0282687&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.750Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.762Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmed/query\",\"params\":{\"fields\":\"related_to\"},\"data\":\"q=C0282687&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.763Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 18 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.763Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmed/query\",\"params\":{\"fields\":\"prevented_by\"},\"data\":\"q=C0282687&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.763Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 1 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.764Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmed/query\",\"params\":{\"fields\":\"treated_by\"},\"data\":\"q=C0282687&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.765Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 14 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.765Z",
"level": "DEBUG",
"message": "call-apis: Total number of results returned for this query is 88",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.974Z",
"level": "DEBUG",
"message": "call-apis: Query completes",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.978Z",
"level": "DEBUG",
"message": "REDIS cache is not enabled.",
"code": null
},
{
"timestamp": "2021-03-15T22:54:01.997Z",
"level": "DEBUG",
"message": "BTE found 20 smartapi edges corresponding to e02. These smartaip edges comes from 7 unique APIs. They are OpenTarget API,MyChem.info API,SEMMED Gene API,BioThings DGIdb API,Text Mining Targeted Association API,Text Mining CO-OCCURRENCE API,Drug Response KP API",
"code": null
},
{
"timestamp": "2021-03-15T22:54:02.041Z",
"level": "DEBUG",
"message": "BTE found 7 bte edges for this batch.",
"code": null
},
{
"timestamp": "2021-03-15T22:54:02.041Z",
"level": "DEBUG",
"message": "call-apis: Resolving ID feature is turned on",
"code": null
},
{
"timestamp": "2021-03-15T22:54:02.041Z",
"level": "DEBUG",
"message": "call-apis: Number of BTE Edges received is 7",
"code": null
},
{
"timestamp": "2021-03-15T22:54:02.102Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/text_mining_co_occurrence_kp/query\",\"params\":{\"fields\":\"subject,association\",\"q\":\"object.NCBIGene:\\\"116534309\\\" AND subject.type:ChemicalSubstance\",\"size\":1000},\"method\":\"get\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:02.102Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:02.103Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/text_mining_co_occurrence_kp/query\",\"params\":{\"fields\":\"object,association\",\"q\":\"subject.NCBIGene:\\\"116534309\\\" AND object.type:ChemicalSubstance\",\"size\":1000},\"method\":\"get\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:02.103Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:02.104Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/dgidb/query\",\"params\":{\"fields\":\"object.CHEMBL_COMPOUND,association.provided_by,association.pubmed\",\"size\":1000},\"data\":\"q=116534309&scopes=subject.NCBIGene\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:02.104Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:02.104Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/drug_response_kp/query\",\"params\":{\"fields\":\"association.context.disease.mondo,object.PUBCHEM,association.effect_size,association.pvalue\",\"q\":\"subject.NCBIGene:116534309 AND association.effect_size:<0 AND association.pvalue:<0.05\",\"size\":\"1000\",\"sort\":\"association.pvalue\"},\"method\":\"get\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:02.104Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:02.109Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://mychem.info/v1/query\",\"params\":{\"fields\":\"chembl.molecule_chembl_id\",\"size\":\"250\"},\"data\":\"q=CD4&scopes=drugcentral.bioactivity.uniprot.gene_symbol\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:02.109Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:02.110Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://mychem.info/v1/query\",\"params\":{\"fields\":\"drugbank.id\",\"size\":\"250\"},\"data\":\"q=CD4&scopes=drugbank.targets.gene_name\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:02.110Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 3 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:02.112Z",
"level": "DEBUG",
"message": "call-apis: Succesfully made the following query: {\"url\":\"https://mychem.info/v1/query\",\"params\":{\"fields\":\"drugbank.id\",\"size\":\"250\"},\"data\":\"q=CD4&scopes=drugbank.enzymes.gene_name\",\"method\":\"post\",\"timeout\":50000}",
"code": null
},
{
"timestamp": "2021-03-15T22:54:02.112Z",
"level": "DEBUG",
"message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
"code": null
},
{
"timestamp": "2021-03-15T22:54:02.112Z",
"level": "DEBUG",
"message": "call-apis: Total number of results returned for this query is 3",
"code": null
},
{
"timestamp": "2021-03-15T22:54:02.181Z",
"level": "DEBUG",
"message": "call-apis: Query completes",
"code": null
}
]
}Making a branched query
const handler = require("@biothings-explorer/query_graph_handler");
const queryHandler = new handler.TRAPIQueryHandler();
const branchedQuery = {
"workflow": [
{"id": "lookup"}
],
"message": {
"query_graph": {
"nodes": {
"n0": {
"categories": ["biolink:Disease"],
"ids": ["MONDO:0005737"]
},
"n1": {
"categories": ["biolink:Gene"]
},
"n2": {
"categories": ["biolink:SmallMolecule"]
}
},
"edges": {
"e01": {
"subject": "n0",
"object": "n1"
},
"e02": {
"subject": "n0",
"object": "n2"
}
}
}
}
}
queryHandler.setQueryGraph(branchedQuery);
await queryHandler.query();
console.log(queryHandler.getResponse())Example Result
{
"workflow": [
{"id": "lookup"}
],
"message": {
"query_graph": {
"nodes": {
"n0": {
"category": "biolink:Disease",
"id": "MONDO:0005737"
},
"n1": {
"category": "biolink:Gene"
},
"n2": {
"category": "biolink:ChemicalSubstance"
}
},
"edges": {
"e01": {
"subject": "n0",
"object": "n1"
},
"e02": {
"subject": "n0",
"object": "n2"
}
}
},
"knowledge_graph": {
"nodes": {
"MONDO:0005737": {
"category": "biolink:Disease",
"name": "Ebola hemorrhagic fever",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"MONDO:0005737",
"DOID:4325",
"UMLS:C0282687",
"name:Ebola hemorrhagic fever",
"MESH:D019142",
"EFO:0007243",
"ORPHANET:319218",
"GARD:2035"
],
"type": "biolink:id"
}
]
},
"NCBIGene:116534309": {
"category": "biolink:Gene",
"name": "CD4",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:116534309",
"name:CD4 molecule",
"SYMBOL:CD4"
],
"type": "biolink:id"
}
]
},
"NCBIGene:539109": {
"category": "biolink:Gene",
"name": "MMP11",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:539109",
"name:matrix metallopeptidase 11",
"SYMBOL:MMP11",
"ENSEMBL:ENSBTAG00000006108"
],
"type": "biolink:id"
}
]
},
"NCBIGene:102448557": {
"category": "biolink:Gene",
"name": "GTPBP1",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:102448557",
"name:GTP binding protein 1",
"SYMBOL:GTPBP1",
"ENSEMBL:ENSPSIG00000004300"
],
"type": "biolink:id"
}
]
},
"NCBIGene:103074707": {
"category": "biolink:Gene",
"name": "CCL2",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:103074707",
"name:C-C motif chemokine ligand 2",
"SYMBOL:CCL2"
],
"type": "biolink:id"
}
]
},
"ENSEMBL:ENSSPUG00000015633": {
"category": "biolink:Gene",
"name": "MAPRE3",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"name:microtubule associated protein RP/EB family member 3",
"SYMBOL:MAPRE3",
"ENSEMBL:ENSSPUG00000015633"
],
"type": "biolink:id"
}
]
},
"NCBIGene:115865406": {
"category": "biolink:Gene",
"name": "BST2",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:115865406",
"name:bone marrow stromal cell antigen 2",
"SYMBOL:BST2"
],
"type": "biolink:id"
}
]
},
"NCBIGene:110132571": {
"category": "biolink:Gene",
"name": "IL1B",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:110132571",
"name:interleukin 1 beta",
"SYMBOL:IL1B"
],
"type": "biolink:id"
}
]
},
"NCBIGene:101571570": {
"category": "biolink:Gene",
"name": "Ifih1",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:101571570",
"name:interferon induced with helicase C domain 1",
"SYMBOL:Ifih1",
"ENSEMBL:ENSODEG00000013586"
],
"type": "biolink:id"
}
]
},
"ENSEMBL:ENSSMAG00000017984": {
"category": "biolink:Gene",
"name": "npc1",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"name:Niemann-Pick disease, type C1",
"SYMBOL:npc1",
"ENSEMBL:ENSSMAG00000017984"
],
"type": "biolink:id"
}
]
},
"NCBIGene:397686": {
"category": "biolink:Gene",
"name": "IFNA1",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:397686",
"name:interferon, alpha 1",
"SYMBOL:IFNA1",
"ENSEMBL:ENSSSCG00000050619"
],
"type": "biolink:id"
}
]
},
"NCBIGene:102892030": {
"category": "biolink:Gene",
"name": "ALB",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:102892030",
"name:albumin",
"SYMBOL:ALB"
],
"type": "biolink:id"
}
]
},
"NCBIGene:104045425": {
"category": "biolink:Gene",
"name": "HDX",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:104045425",
"name:highly divergent homeobox",
"SYMBOL:HDX"
],
"type": "biolink:id"
}
]
},
"NCBIGene:110137949": {
"category": "biolink:Gene",
"name": "CXCL10",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:110137949",
"name:C-X-C motif chemokine ligand 10",
"SYMBOL:CXCL10"
],
"type": "biolink:id"
}
]
},
"NCBIGene:105822820": {
"category": "biolink:Gene",
"name": "CXCL8",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:105822820",
"name:C-X-C motif chemokine ligand 8",
"SYMBOL:CXCL8",
"ENSEMBL:ENSPCOG00000024593"
],
"type": "biolink:id"
}
]
},
"NCBIGene:116479423": {
"category": "biolink:Gene",
"name": "CLEC4M",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:116479423",
"name:C-type lectin domain family 4 member M",
"SYMBOL:CLEC4M"
],
"type": "biolink:id"
}
]
},
"NCBIGene:103814882": {
"category": "biolink:Gene",
"name": "F3",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:103814882",
"name:coagulation factor III, tissue factor",
"SYMBOL:F3",
"ENSEMBL:ENSSCAG00000012591"
],
"type": "biolink:id"
}
]
},
"NCBIGene:101142722": {
"category": "biolink:Gene",
"name": "KPNA1",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:101142722",
"name:karyopherin subunit alpha 1",
"SYMBOL:KPNA1"
],
"type": "biolink:id"
}
]
},
"NCBIGene:104673720": {
"category": "biolink:Gene",
"name": "CTSL",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:104673720",
"name:cathepsin L",
"SYMBOL:CTSL",
"ENSEMBL:ENSRROG00000038398"
],
"type": "biolink:id"
}
]
},
"NCBIGene:116543050": {
"category": "biolink:Gene",
"name": "CTSB",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:116543050",
"name:cathepsin B",
"SYMBOL:CTSB"
],
"type": "biolink:id"
}
]
},
"NCBIGene:29798": {
"category": "biolink:Gene",
"name": "C2orf27A",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:29798",
"name:chromosome 2 open reading frame 27A",
"SYMBOL:C2orf27A",
"UMLS:C2681192",
"HGNC:25077",
"UniProtKB:P0DPF5"
],
"type": "biolink:id"
}
]
},
"NCBIGene:118012204": {
"category": "biolink:Gene",
"name": "STAT1",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:118012204",
"name:signal transducer and activator of transcription 1",
"SYMBOL:STAT1"
],
"type": "biolink:id"
}
]
},
"NCBIGene:101937382": {
"category": "biolink:Gene",
"name": "KPNA5",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:101937382",
"name:karyopherin subunit alpha 5",
"SYMBOL:KPNA5"
],
"type": "biolink:id"
}
]
},
"ENSEMBL:ENSNVIG00000024389": {
"category": "biolink:Gene",
"name": "IFIT2",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"name:interferon induced protein with tetratricopeptide repeats 2",
"SYMBOL:IFIT2",
"ENSEMBL:ENSNVIG00000024389"
],
"type": "biolink:id"
}
]
},
"NCBIGene:104395366": {
"category": "biolink:Gene",
"name": "THBD",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:104395366",
"name:thrombomodulin",
"SYMBOL:THBD"
],
"type": "biolink:id"
}
]
},
"NCBIGene:100731608": {
"category": "biolink:Gene",
"name": "Isg15",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:100731608",
"name:ISG15 ubiquitin like modifier",
"SYMBOL:Isg15"
],
"type": "biolink:id"
}
]
},
"NCBIGene:108529797": {
"category": "biolink:Gene",
"name": "DDX58",
"attributes": [
{
"name": "equivalent_identifiers",
"value": [
"NCBIGene:108529797",
"name:DExD/H-box helicase 58",
"SYMBOL:DDX58",
"ENSEMBL:ENSRBIG00000040257"
],
"type": "biolink:id"
}
]
},
"NCBIGene:106971145": {
"category": "biolink:Gene",
"name": "IFNB1",
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},
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},
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]
},
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