@biothings-explorer/id_resolver

a nodejs package for resolving biomedical ids

Usage no npm install needed!

<script type="module">
  import biothingsExplorerIdResolver from 'https://cdn.skypack.dev/@biothings-explorer/id_resolver';
</script>

README

id_resolver.js

Coverage Status Build Status A nodejs package for resolving biomedical ids based on translator node normalization api. The package is built on top of the NCATS Translator Node Normalization API.

Install

$ npm install @biothings-explorer/id_resolver

Usage

const resolver = require('@biothings-explorer/id_resolver');

// resolve a list of gene ids
const ids = ['NCBIGene:1017', 'NCBIGene:1018', 'HGNC:1177'];

(async () => {
    console.log(await resolver.resolve(ids));
    //=> {'NCBIGene:1017': {...}, 'NCBIGene:1018': {...}, 'HGNC:1177': {...}}
})();

// resolve ids from different types
const ids = ['CHEMBL.COMPOUND:CHEMBL744', 'NCBIGene:1017', 'HP:0001166'];
(async () => {
    console.log(await resolver.resolve(ids);
    //=> {'CHEMBL.COMPOUND:CHEMBL744': {...}, 'NCBIGene:1017': {...}, 'HP:0001166': {...}}
})();

Available Semantic Types & prefixes

  • Gene

    • NCBIGene
    • ENSEMBL
    • HGNC
    • UniProtKB
    • IUPHAR

  • Pathway

    • SMPDB

  • ChemicalSubstance

    • PUBCHEM
    • INCHIKEY
    • CHEMBL.COMPOUND
    • CHEBI
    • DRUGBANK
    • HMDB
    • KEGG.COMPOUND
    • MESH
    • UNII
    • GTOPDB

  • Disease

    • UMLS
    • SNOMEDCT
    • MONDO
    • MESH
    • NCIT
    • HP
    • MEDDRA
    • EFO
    • DOID
    • ORPHANET
    • OMIM
    • ICD-10
    • MP
    • medgen
    • ICD-9

  • PhenotypicFeature

    • UMLS
    • SNOMEDCT
    • HP
    • MEDDRA
    • EFO
    • NCIT
    • MESH
    • MP

  • Cell

    • CL
    • UMLS
    • NCIT
    • MESH
    • UBERON
    • SNOMEDCT