biothings-api

BioThings API Suite

Overview

BioThings is a family of high-performance biomedical annotation APIs developed at the Scripps Research Institute. The suite provides unified, up-to-date access to gene, variant, and chemical/drug annotations aggregated from dozens of authoritative sources. Three primary services cover the core entities in translational research:

• MyGene.info — Gene annotations from NCBI Entrez, Ensembl, UniProt, GO, KEGG, Reactome, and 20+ sources.
• MyVariant.info — Variant annotations from dbSNP, ClinVar, gnomAD, CADD, COSMIC, and 15+ sources.
• MyChem.info — Drug and chemical annotations from NDC, DrugBank, ChEMBL, FDA, PubChem, and 10+ sources.

All three share identical query syntax, require no authentication, and return JSON. Free for academic and commercial use.

Authentication

No authentication or API keys are required. All endpoints are open-access.

# No API key needed — just query directly
curl "https://mygene.info/v3/query?q=BRCA1&size=1"

MyGene.info — Gene Annotations

Search Genes

GET https://mygene.info/v3/query?q={query}&size={n}

Query by gene symbol, name, Entrez ID, Ensembl ID, or keyword. Supports boolean operators (AND, OR, NOT) and field-specific queries like symbol:CDK2.

curl -s "https://mygene.info/v3/query?q=BRCA1&size=1"

Response:

{
  "took": 178,
  "total": 13223,
  "hits": [
    {
      "_id": "672",
      "_score": 145.6796,
      "entrezgene": "672",
      "name": "BRCA1 DNA repair associated",
      "symbol": "BRCA1",
      "taxid": 9606
    }
  ]
}

Get Gene by ID

GET https://mygene.info/v3/gene/{entrez_id}

Returns comprehensive annotations for a single gene. Use the fields parameter to select specific data sources.

# Full annotation (large response)
curl -s "https://mygene.info/v3/gene/1017"

# Selective fields
curl -s "https://mygene.info/v3/gene/1017?fields=symbol,name,summary,genomic_pos,go"

Response (key fields for CDK2, Entrez ID 1017):