annotator.js's Introduction

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": ...}}