Biomcp MCP Server

Connect Biomcp to Claude, Cursor or any other MCP client and it stops being a tab you switch to. One binary. One grammar. Evidence from the biomedical sources you already trust. The biomcp mcp server is what makes that connection.

What the server does

BioMCP is one CLI binary over a single command grammar that reaches ~30 trusted biomedical sources (PubMed, ClinVar, ClinicalTrials.gov, OncoKB, Reactome, and more). It is also an MCP (Model Context Protocol) server, so the same tools are available to AI agents such as Claude Code, Codex, and Claude Desktop.

• Search the literature: — search article fans out across PubTator3 and
• Pivot without rework: — move from a gene, variant, drug, disease, pathway,
• Choose a playbook: — biomcp skill list shows shipped worked examples
• Analyze studies locally: — study commands cover local query, cohort, survival,
• Follow the paper trail: — article citations, article references,
• Enrich and batch: — use biomcp enrich for top-level g:Profiler

Installation

Because this one is hosted, setup is mostly authentication — you point your client at the endpoint and approve access. Nothing runs on your machine, so there is no runtime to keep patched.

Available tools

The toolset is worth reading before you wire it up, because it tells you what the integration is really for:

• Homebrew — The separate genomoncology/homebrew-biomcp tap repository must exist before these commands can work

Credentials and setup notes

Configuration is passed through the environment: NCBI_API_KEY, S2_API_KEY, OPENFDA_API_KEY, NCI_API_KEY, ONCOKB_TOKEN, ALPHAGENOME_API_KEY, BIOMCP_STUDY_DIR, DISGENET_API_KEY. Treat anything key-shaped as a real credential — scope it to the minimum the server needs, and rotate it if it ever lands in a shared config.

Worth knowing first

• Your data travels to the provider's service, so the usual questions apply about what you send and what they retain.
• Missing credentials fail quietly in some clients — if no tools show up, check the environment block first.
• Keep per-call confirmation enabled while you learn its behaviour; it is the cheapest safeguard you have.

Where it fits

Among the developer tooling options, the useful question is rarely "what can it do" but "what does it cost you to run" — permissions, credentials, and how much of your context its toolset consumes. Biomcp's toolset — Homebrew — is a fair guide to whether it matches your workflow. It is maintained by genomoncology; worth a glance at recent repository activity before you build anything load-bearing on it.

SyncDev reviews every entry in this directory against the project's own documentation before publishing, and revisits them as servers change.