LabscoMCP early access ↗
genomoncologyMCP SERVER

BioMCP

One command grammar over roughly 30 biomedical sources — PubMed, ClinVar, ClinicalTrials.gov, OncoKB, Reactome and more — usable from the terminal or as an MCP server.

by genomoncology ↗Biomedical: Genomics & Clinical DataCommunity

LABSCO SUMMARY

One grammar instead of thirty search habits.

The pivots are what make it more than a federated search: from a variant to the trials that mention it, from a drug to its adverse events, from a paper to what cites it — without rebuilding the filters each time you cross a source boundary.

What it is

A single binary with one grammar that reaches the biomedical databases that normally each have their own API, identifiers and search habits. The same tools are available to an agent over MCP as to a person at a shell.

What you get

  • A grammar rather than a tool per source: search <entity> for discovery, get <entity> <id> [sections] for a detail card, <entity> <helper> <id> for cross-entity pivots, enrich for gene-set enrichment, batch for parallel gets, and search all for counts-first orientation across entities
  • Detail-card entities and the providers behind them: gene (MyGene.info, UniProt, Reactome, STRING, GTEx, Human Protein Atlas, DGIdb, ClinGen), variant (MyVariant.info, ClinVar, gnomAD v4, CIViC, OncoKB, cBioPortal, AlphaGenome), article, trial (ClinicalTrials.gov API v2 and NCI CTS), drug, disease, pathway, protein, diagnostic, adverse-event and pgx
  • Search-only surfaces for gwas via the GWAS Catalog and phenotype via Monarch Initiative HPO semantic similarity
  • Literature search that fans out across PubTator3 and Europe PMC, deduplicating PMID, PMCID and DOI identifiers, with an optional Semantic Scholar leg
  • Cross-entity pivots that avoid rebuilding filters — variant to trials or articles, drug to adverse events or trials, disease to trials, drugs or articles, gene to trials, drugs, articles or pathways, protein to structures, and article to citations, references, recommendations or entities
  • A paper trail from one known paper: citations, references, recommendations and extracted entities
  • Local study analytics for downloaded cBioPortal-style datasets — query, cohort, survival, comparison and co-occurrence, with terminal, SVG and PNG charts
  • biomcp skill list for shipped worked examples you can open as a workflow

Requirements

Install the CLI with uv tool install biomcp-cli, a one-line binary installer, Homebrew, Docker, or the PyPI package; the MCP server is the same package started with serve. Claude Code has a plugin, Claude Desktop an extension, and a remote HTTP server is available. Most commands work with no credentials at all. Optional keys raise limits or unlock enrichments: NCBI_API_KEY for PubTator, PubMed and PMC, S2_API_KEY for authenticated Semantic Scholar with a dedicated 1 req/sec quota instead of the shared 1 req/2sec pool, OPENFDA_API_KEY, NCI_API_KEY for NCI trial search, ONCOKB_TOKEN and ALPHAGENOME_API_KEY. References and recommendations can come back empty for paywalled papers because of publisher elision upstream.

Setup effort

One command — uv tool install biomcp-cli

See installation options