@biothings-explorer/explain

2.1.0 • Public • Published

Build Status Coverage Status Documentation Version

Welcome to @biothings-explorer/explain 👋

A nodejs module to explain how two or more biomedical concepts are connected through shared intermediate nodes.

🏠 Homepage

Install

npm i @biothings-explorer/explain

Usage

  • Import and Initialize

    const explain = require("@biothings-explorer/explain")
    
    // a BTE representation of drug imatinib from biomedical_id_autocomplete nodejs package
    const INPUT1 = {
        "DRUGBANK": "DB00619",
        "CHEBI": "CHEBI:45783",
        "UMLS": "C0935989",
        "MESH": "D000068877",
        "name": "imatinib",
        "primary": {
            "identifier": "CHEBI",
            "cls": "ChemicalSubstance",
            "value": "CHEBI:45783"
        },
        "display": "CHEBI(CHEBI:45783) DRUGBANK(DB00619) name(imatinib)",
        "type": "ChemicalSubstance"
    }
    
    // a BTE representation of drug dasatinib from biomedical_id_autocomplete nodejs package
    const INPUT2 = {
        "CHEMBL.COMPOUND": "CHEMBL1421",
        "DRUGBANK": "DB01254",
        "PUBCHEM": 3062316,
        "CHEBI": "CHEBI:49375",
        "UMLS": "C1455147",
        "MESH": "D000069439",
        "UNII": "RBZ1571X5H",
        "name": "DASATINIB",
        "primary": {
            "identifier": "CHEBI",
            "cls": "ChemicalSubstance",
            "value": "CHEBI:49375"
        },
        "display": "CHEBI(CHEBI:49375) CHEMBL.COMPOUND(CHEMBL1421) DRUGBANK(DB01254) PUBCHEM(3062316) MESH(D000069439) UNII(RBZ1571X5H) UMLS(C1455147) name(DASATINIB)",
        "type": "ChemicalSubstance"
    }
    
    // a BTE representation of disease CML from biomedical_id_autocomplete nodejs package
    const OUTPUT = {
        "MONDO": "MONDO:0011996",
        "DOID": "DOID:8552",
        "UMLS": "C0023473",
        "name": "chronic myelogenous leukemia, BCR-ABL1 positive",
        "OMIM": "608232",
        "ORPHANET": "521",
        "primary": {
            "identifier": "MONDO",
            "cls": "Disease",
            "value": "MONDO:0011996"
        },
        "display": "MONDO(MONDO:0011996) DOID(DOID:8552) OMIM(608232) ORPHANET(521) UMLS(C0023473) name(chronic myelogenous leukemia, BCR-ABL1 positive)",
        "type": "Disease"
    }
  • Explain the connections between the inputs and outputs

    const ep = new explain();
    //find genes which connect both [Imatinib or DASATINIB] and CML Disease
    let res = await ep.query([INPUT1, INPUT2], [OUTPUT], ['Gene']);

Run tests

npm run test

Author

👤 Jiwen Xin

🤝 Contributing

Contributions, issues and feature requests are welcome!
Feel free to check issues page.

Show your support

Give a ⭐️ if this project helped you!

📝 License

Copyright © 2020 Jiwen Xin.
This project is ISC licensed.

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Install

npm i @biothings-explorer/explain

Weekly Downloads

3

Version

2.1.0

License

ISC

Unpacked Size

34.5 kB

Total Files

7

Last publish

Collaborators

  • ericz1803
  • kevinxin
  • marcocano
  • newgene