@biothings-explorer/annotator

Welcome to @biothings-explorer/annotator 👋

A nodejs module to annotate biomedical entities in batch for BioThings Explorer

🏠 Homepage

Install

npm i @biothings-explorer/annotator

Usage

• Import and Initialize

  const annotate = require("@biothings-explorer/annotator")

• Annotate Gene IDs

  const gene_ids = {
    "NCBIGene:4888": {
        "db_ids": {
            "NCBIGene": [
                "4888"
            ],
            "HGNC": [
                "7959"
            ],
            "SYMBOL": [
                "NPY6R"
            ],
            "UMLS": [
                "C1417819"
            ]
        }
    },
    "NCBIGene:4597": {
        "db_ids": {
            "NCBIGene": [
                "4597"
            ],
            "ENSEMBL": [
                "ENSG00000167508"
            ],
            "HGNC": [
                "7529"
            ],
            "SYMBOL": [
                "MVD"
            ],
            "UMLS": [
                "C1417507"
            ]
          }
      }
  }
  let res = await annotate("Gene", gene_ids);
  console.log(res);
  // {"NCBIGene:4888": {"genomic_position": ..., "generif": ..., "biological_process": ...},"NCBIGene:4597": {"genomic_position": ..., "reactome": ..., "wikipathways": ...}}

• Annotate ChemicalSubstance IDs

  const chemical_ids = {
      "CHEBI:8863": {
          "id": {
              "label": "RILUZOLE",
              "identifier": "CHEBI:8863"
          },
          "db_ids": {
              "CHEBI": [
                  "CHEBI:8863"
              ],
              "CHEMBL.COMPOUND": [
                  "CHEMBL744"
              ]
          }
      },
      "CHEBI:133809": {
          "id": {
              "label": "ANISINDIONE",
              "identifier": "CHEBI:133809"
          },
          "db_ids": {
              "CHEBI": [
                  "CHEBI:133809"
              ],
              "CHEMBL.COMPOUND": [
                  "CHEMBL712"
              ]
          }
      }
  };
  let res = await annotate("ChemicalSubstance", chemical_ids);
  console.log(res);
  // {"CHEBI:133809": {"max_phase": ..., "molecular_weight": ..., "molecular_type": ...}, "CHEBI:8863": {"max_phase": ..., "enzymes": ..., "targets": ...}}

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

Give a ⭐️ if this project helped you!

📝 License

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