id_resolver.js

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