BioMCP (Typescript)

What it is

A biomedical MCP server that federates many upstream sources behind one set of tools — MyGene, MyVariant, MyChem, MyDisease, ClinVar, OpenTargets, OncoKB, DisGeNET, ClinicalTrials.gov, PubMed, EuropePMC and more. Searches fan out across backends and deduplicate, and a failed source degrades that section rather than the whole call.

What you get

• gene_search and gene_get — find a gene by symbol, name or keyword, and pull detail by section; smart mode resolves aliases such as HER2 to ERBB2
• gene_diseases, gene_drugs, gene_trials and gene_articles — the diseases associated with a gene, drugs targeting it, trials involving it, and the literature on it
• gene_enrich — pathway enrichment over a gene list
• variant_search, variant_get, variant_oncokb and variant_trials — search by rsid, HGVS or gene with clinical-significance and frequency filters, request extra sections on a hit, add OncoKB cancer annotations, and find trials for the variant
• drug_search, drug_get and drug_trials — drugs by name, mechanism or keyword, with regulatory, safety, target and indication sections
• disease_search, disease_get, disease_drugs and disease_trials — diseases by name or phenotype, with gene associations and phenotypes, plus their drugs and trials
• article_search and article_get — federated literature search across five backends with PMID, PMCID and DOI deduplication, and one article with open-access, annotation and citation sections
• trial_search and trial_get — clinical trials by condition, intervention or keyword, and one by NCT ID with eligibility, locations and outcomes
• pdb — search RCSB PDB structures, read entry metadata, and download mmCIF or PDB files
• discover and batch_get — resolve a free-text concept to entities, and fetch several entities in parallel

Requirements

Nothing for the default path: npx biomcp starts a zero-config stdio server on Node.js 22.13 or newer. Two tools need credentials — variant_oncokb requires ONCOKB_TOKEN, and gene_diseases uses DISGENET_API_KEY when present, falling back to OpenTargets associations without it. Other optional keys raise rate limits.

Setup effort

One command — npx biomcp

Tools you get

25 tools when we connected; the project documents 40. The patent, GEO, SRA, GenBank, GTEx and Ensembl tools are documented but were not listed, likely because the published 0.4.3 build predates the documentation. db_query, db_list_tables and db_describe_table register only when DB_TYPE is set.

Requires

npx on PATH

Where it runs

All 4 documented clients run the server on your machine.