name: biothings-api description: "Query gene, variant, and drug annotations via BioThings APIs" metadata: openclaw: emoji: "🧪" category: "domains" subcategory: "biomedical" keywords: ["gene annotation", "variant annotation", "drug data", "BioThings", "mygene", "myvariant", "bioinformatics"] source: "https://biothings.io"
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):
{
"_id": "1017",
"symbol": "CDK2",
"name": "cyclin dependent kinase 2",
"HGNC": "1771",
"MIM": "116953",
"AllianceGenome": "1771",
"taxid": 9606,
"type_of_gene": "protein-coding"
}
The full response includes accessions, Gene Ontology terms, pathway memberships (KEGG, Reactome, WikiPathways), protein domains (InterPro, Pfam), homology data, and genomic coordinates.
MyVariant.info — Variant Annotations
Search Variants
GET https://myvariant.info/v1/query?q={query}&size={n}
Query by rsID, HGVS notation (e.g., chr7:g.140453136A>T), gene symbol, or ClinVar significance. Returns aggregated annotations from 15+ sources.
curl -s "https://myvariant.info/v1/query?q=rs58991260&size=1"
Response (truncated):
{
"took": 20,
"total": 1,
"hits": [
{
"_id": "chr1:g.218631822G>A",
"_score": 21.382616,
"dbsnp": {
"rsid": "rs58991260",
"vartype": "snv",
"ref": "G",
"alt": "A",
"chrom": "1"
},
"cadd": {
"phred": 1.679,
"consequence": "INTERGENIC",
"chrom": 1,
"pos": 218631822
},
"gnomad_genome": {
"af": { "af": 0.0150338, "af_afr": 0.0528007, "af_eas": 0.0, "af_nfe": 0.00032417 },
"alt": "A",
"ref": "G"
}
}
]
}
Get Variant by HGVS ID
GET https://myvariant.info/v1/variant/{hgvs_id}
curl -s "https://myvariant.info/v1/variant/chr1:g.218631822G>A?fields=dbsnp,cadd,clinvar"
MyChem.info — Drug & Chemical Annotations
Search Drugs/Chemicals
GET https://mychem.info/v1/query?q={query}&size={n}
Query by drug name, NDC code, InChIKey, or active ingredient. Aggregates data from FDA NDC, DrugBank, ChEMBL, PubChem, SIDER, and more.
curl -s "https://mychem.info/v1/query?q=aspirin&size=1"
Response (truncated):
{
"took": 82,
"total": 248,
"hits": [
{
"_id": "0615-8613",
"_score": 13.657401,
"ndc": {
"substancename": "ASPIRIN",
"nonproprietaryname": "Aspirin",
"proprietaryname": "Adult Low Dose Aspirin",
"active_numerator_strength": "81",
"active_ingred_unit": "mg/1",
"dosageformname": "TABLET, DELAYED RELEASE",
"routename": "ORAL",
"producttypename": "HUMAN OTC DRUG",
"pharm_classes": [
"Cyclooxygenase Inhibitors [MoA]",
"Decreased Platelet Aggregation [PE]",
"Anti-Inflammatory Agents, Non-Steroidal [CS]",
"Nonsteroidal Anti-inflammatory Drug [EPC]",
"Platelet Aggregation Inhibitor [EPC]"
]
}
}
]
}
Get Chemical by ID
GET https://mychem.info/v1/chem/{id}
curl -s "https://mychem.info/v1/chem/CHEMBL25?fields=drugbank,chembl,pubchem"
Query Syntax (Shared Across All Three APIs)
All BioThings APIs share the same query engine. Key features:
| Feature | Syntax | Example |
|---|---|---|
| Field-specific | field:value | symbol:TP53 |
| Boolean | AND, OR, NOT | BRCA1 AND cancer |
| Wildcard | * | CDK* |
| Range | [min TO max] | exac.af:[0.01 TO 0.05] |
| Pagination | size, from | size=20&from=40 |
| Field selection | fields | fields=symbol,name,go |
| Sorting | sort | sort=_score:desc |
| Batch POST | POST with ids | Up to 1000 IDs per request |
Rate Limits
- GET requests: 3 per second sustained; bursts up to 10/s tolerated
- POST batch requests: 1 per second; up to 1000 IDs per batch
- No daily cap for reasonable academic usage
- Best practice: Add 350ms delays between sequential requests; use batch POST for bulk queries
- User-Agent header: Set a descriptive User-Agent for priority support from the BioThings team
Python Example: Cross-API Gene-Variant-Drug Lookup
import requests, time
MYGENE = "https://mygene.info/v3"
MYVARIANT = "https://myvariant.info/v1"
MYCHEM = "https://mychem.info/v1"
def search_gene(symbol):
resp = requests.get(f"{MYGENE}/query",
params={"q": f"symbol:{symbol}", "size": 1, "species": "human"})
resp.raise_for_status()
hits = resp.json().get("hits", [])
return hits[0] if hits else {}
def search_variants(gene_symbol, size=5):
resp = requests.get(f"{MYVARIANT}/query",
params={"q": f"clinvar.gene.symbol:{gene_symbol}",
"fields": "dbsnp.rsid,clinvar.rcv.clinical_significance,cadd.phred",
"size": size})
resp.raise_for_status()
return resp.json().get("hits", [])
def search_drug(name):
resp = requests.get(f"{MYCHEM}/query",
params={"q": name, "size": 1,
"fields": "ndc.substancename,ndc.pharm_classes"})
resp.raise_for_status()
hits = resp.json().get("hits", [])
return hits[0] if hits else {}
# Translational research pipeline: gene -> variants -> drug
gene = search_gene("BRCA1")
print(f"Gene: {gene.get('symbol')} (Entrez: {gene.get('entrezgene')})")
time.sleep(0.35)
variants = search_variants("BRCA1", size=3)
for v in variants:
rsid = v.get("dbsnp", {}).get("rsid", v.get("_id"))
print(f" Variant: {rsid} | CADD: {v.get('cadd', {}).get('phred', 'N/A')}")
time.sleep(0.35)
drug = search_drug("olaparib")
print(f" Drug: {drug.get('ndc', {}).get('substancename', 'N/A')}")
Academic Use Cases
- GWAS follow-up: Annotate thousands of significant SNPs with allele frequencies (gnomAD), functional predictions (CADD, SIFT, PolyPhen), and clinical significance (ClinVar) via MyVariant.info batch queries.
- Drug target mapping: Link gene symbols to pathway memberships (KEGG, Reactome) via MyGene.info, then find approved drugs targeting those pathways via MyChem.info.
- Pharmacogenomics: Cross-reference variant annotations with drug metabolism data to identify clinically actionable gene-drug interactions.
- Systematic reviews: Programmatically collect gene/variant metadata across large candidate lists to populate supplementary tables in genomics publications.
References
- BioThings API Hub: https://biothings.io
- MyGene.info Documentation: https://docs.mygene.info
- MyVariant.info Documentation: https://docs.myvariant.info
- MyChem.info Documentation: https://docs.mychem.info
- Publication: Xin J et al. Genome Biology 17:91 (2016). https://doi.org/10.1186/s13059-016-0953-9