--- name: biothings-api-627972b23d6c description: "Query gene, variant, and drug annotations via BioThings APIs" metadata: openclaw: emoji: "๐Ÿงช" 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** โ€” Gene annotations from NCBI Entrez, Ensembl, UniProt, GO, KEGG, Reactome, and 20+ sources. - **MyVariant.info** โ€” Variant annotations from dbSNP, ClinVar, gnomAD, CADD, COSMIC, and 15+ sources. - **MyChem.info** โ€” 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. ```bash # No API key needed โ€” just query directly curl "https://mygene.info/v3/query?q=BRCA1&size=1" ``` ## MyGene.info โ€” 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`. ```bash curl -s "https://mygene.info/v3/query?q=BRCA1&size=1" ``` Response: ```json { "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. ```bash # 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): ```json { "_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 โ€” 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. ```bash curl -s "https://myvariant.info/v1/query?q=rs58991260&size=1" ``` Response (truncated): ```json { "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} ``` ```bash curl -s "https://myvariant.info/v1/variant/chr1:g.218631822G>A?fields=dbsnp,cadd,clinvar" ``` ## MyChem.info โ€” 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. ```bash curl -s "https://mychem.info/v1/query?q=aspirin&size=1" ``` Response (truncated): ```json { "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} ``` ```bash 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 ```python 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 --- Source attribution: wentorai Original project: https://github.com/wentorai/research-plugins/blob/bf44b3cd617fa94c8a1b254c5d1987142ca3d631/skills/domains/biomedical/biothings-api/SKILL.md License: MIT License information: https://opensource.org/license/mit Original upstream instructions; downloaded from Mega AI Hub. ## Upstream license notice MIT License Copyright (c) 2026 Wentor AI Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # Mega AI Hub resource metadata Creator / publisher: wentorai Original project: https://github.com/wentorai/research-plugins/blob/bf44b3cd617fa94c8a1b254c5d1987142ca3d631/skills/domains/biomedical/biothings-api/SKILL.md Attribution basis: Source repository record Fields of work: Data & Analytics Roles: Data Scientist, Market Research Analyst Specialties: API Tools: Biothings Api Country applicability: Country not specified Classification basis: Source catalog labels Instruction SHA-256: cbf7452d04142ee929fd1a02016a74b4a36541dac908faf682950874b3038c92