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

• Website: http://github.com/kevinxin90
• Github: @kevinxin90

🤝 Contributing

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

Show your support

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📝 License

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