biomedical_id_resolver

biomedical_id_resolver.js

js library for resolving biological ids to their equivalent ids in batch

Install

$ npm i biomedical_id_resolver

Usage

const resolve = require('biomedical_id_resolver');

// input should be an object, with semantic type as the key, and array of CURIEs as value
let input = {
    "Gene": ["NCBIGene:1017", "NCBIGene:1018", "HGNC:1177"],
    "ChemicalSubstance": ["CHEBI:15377"],
    "Disease": ["MONDO:0004976"],
    "Cell": ["CL:0002372"]
  };

(async () => {
	console.log(await resolve(input);
	//=> {'NCBIGene:1017': {...}, 'NCBIGene:1018': {...}, 'HGNC:1177': {...}, 'CHEBI:15377': {...}, 'MONDO:0004976': {...}, 'CL:0002372': {...}}
})();

Output Schema

• Output is a javascript Object

• The root keys are CURIES (e.g. NCBIGene:1017) which are passed in as input

• The values represents resolved identifiers

• Each CURIE will have 4 required fields

  • id: the primary id (selected based on the ranking described in the next section) and label

  • curies: an array, each element represents a resolved id in CURIE format

  • type: the semantic type of the identifier

  • db_ids: original ids from source database, could be curies or non-curies.

• if an ID can not be resolved using the package, it will have an additional field called "flag", with value equal to "failed"

• Example Output

{
  "NCBIGene:1017": {
    "id": {
      "label": "cyclin dependent kinase 2",
      "identifier": "NCBIGene:1017"
    },
    "db_ids": {
      "NCBIGene": [
        "1017"
      ],
      "ENSEMBL": [
        "ENSG00000123374"
      ],
      "HGNC": [
        "1771"
      ],
      "SYMBOL": [
        "CDK2"
      ],
      "UMLS": [
        "C1332733",
        "C0108855"
      ],
      "name": [
        "cyclin dependent kinase 2"
      ]
    },
    "type": "Gene",
    "curies": [
      "NCBIGene:1017",
      "ENSEMBL:ENSG00000123374",
      "HGNC:1771",
      "SYMBOL:CDK2",
      "UMLS:C1332733",
      "UMLS:C0108855"
    ]
  }
}

Available Semantic Types & prefixes

Gene ID resolution is done through MyGene.info API

• Gene
  1. NCBIGene
  2. ENSEMBL
  3. HGNC
  4. SYMBOL
  5. OMIM
  6. UniProtKB
  7. UMLS
  8. name

Variant ID resolution is done through MyVariant.info API

• SequenceVariant
  1. HGVS
  2. DBSNP
  3. MYVARIANT_HG19
  4. ClinVar

ChemicalSubstance ID resolution is done through MyChem.info API

• ChemicalSubstance
  1. CHEBI
  2. CHEMBL.COMPOUND
  3. DRUGBANK
  4. PUBCHEM
  5. MESH
  6. INCHI
  7. INCHIKEY
  8. UNII
  9. KEGG
  10. UMLS
  11. name
  12. id

Disease ID Resolution is done through MyDisease.info API

• Disease

  1. MONDO
  2. DOID
  3. OMIM
  4. ORPHANET
  5. EFO
  6. UMLS
  7. MESH
  8. name

Pathway ID Resolution is done through biothings.ncats.io/geneset API

• Pathway
  1. Reactome
  2. KEGG
  3. PHARMGKB
  4. WIKIPATHWAYS
  5. name

MolecularActivity ID Resolution is done through BioThings Gene Ontology Molecular Activity API

• MolecularActivity
  1. GO
  2. MetaCyc
  3. RHEA
  4. KEGG.REACTION
  5. Reactome

CellularComponent ID Resolution is done through BioThings Gene Ontology Cellular Component API

• CellularComponent
  1. GO
  2. MESH
  3. UMLS
  4. NCIT
  5. SNOMEDCT
  6. UBERON
  7. CL
  8. name

BiologicalProcess ID Resolution is done through BioThings Gene Ontology Biological Process API

• BiologicalProcess

  1. GO
  2. MetaCyc
  3. Reactome
  4. name

AnatomicalEntity ID Resolution is done through BioThings UBERON API

• AnatomicalEntity
  1. UBERON
  2. UMLS
  3. NCIT
  4. MESH
  5. name

PhenotypicFeature ID Resolution is done through BioThings HPO API

• PhenotypicFeature
  1. UMLS
  2. SNOMEDCT
  3. HP
  4. MEDDRA
  5. EFO
  6. NCIT
  7. MESH
  8. MP
  9. name

Cell ID Resolution is done through nodenormalization API

• Cell
  1. CL
  2. UMLS
  3. NCIT
  4. MESH
  5. UBERON
  6. SNOMEDCT
  7. name

Development

1. Install Node 12 or later. You can use the package manager of your choice. Tests need to pass in Node 12 and 14.
2. Clone this repository.
3. Run npm ci to install the dependencies.
4. scripts are stored in /src folder
5. Add test to /__tests__ folder
6. run npm run release to bump version and generte change log
7. run npx depcheck to check for unused packages in package.json

CHANGELOG

See CHANGELOG.md

Changelog

2.1.0 (2021-01-29)

Features

• :sparkles: add debug if api query fails (86e691f)
• :sparkles: Have ValidBioEntity and InValidBioEntity derive from abstract class BioEntity (352d2a1)
• :sparkles: integrate npm debug module for debugging (2b1cc72)

Refactor

• :fire: remove empty constructor for IDResolver (94c0718)
• :fire: remove unused functions (51b7605)
• :recycle: fix linting error (3696995)
• :recycle: fix typescript linting error (f55ac5a)
• :recycle: fix typescript linting errors (22a54b4)
• :recycle: import debug the correct way in TypeScript (1d25ac3)
• :recycle: import debug the correct way in TypeScript (c50f763)