@biothings-explorer/query_graph_handler
Version:
A nodejs module to query TRAPI Query Graph
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Markdown
# BioThings Explorer TRAPI Query Graph Handler
A on-the-fly query engine for BioThings Explorer based on TRAPI Query Graph.
[](https://github.com/biothings/bte_trapi_query_graph_handler/actions/workflows/coverage.yml)
[](https://coveralls.io/github/biothings/bte_trapi_query_graph_handler?branch=main)
## Install
```bash
npm i @biothings-explorer/query_graph_handler
```
## Usage
### Making a single hop query
```javascript
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())
```
<details>
<summary> Example Result</summary>
```json
{
"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"
}
]
},
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