genomoncology/biomcp

One binary. One grammar. Evidence from the biomedical sources you already trust.
Data terms
BioMCP retrieves data from upstream biomedical sources. Those sources' terms govern how you use the data they return: some restrict commercial or clinical use. Check each source's terms and obtain any licence you need before relying on the data. See Source Licensing and Terms for the per-source breakdown.
What is BioMCP?
BioMCP is one CLI binary over a single command grammar that reaches 70 trusted
biomedical sources directly (PubMed, ClinVar, ClinicalTrials.gov, OncoKB,
Reactome, and more; ten further sources arrive inside another source's
answer). 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.
BioMCP cuts through the usual biomedical data maze: one query reaches the
sources that normally live behind different APIs, identifiers, and search
habits. Researchers, clinicians, and agents use the same command grammar to
search, focus, and pivot without rebuilding the workflow for each source. You
get compact, evidence-oriented results across live public data plus local study analytics.
Features
- **Search the literature:** search article fans out across PubTator3 and
Europe PMC, deduplicates PMID/PMCID/DOI identifiers, and can add a Semantic
Scholar leg when your filters support it.
- **Pivot without rework:** move from a gene, variant, drug, disease, pathway,
protein, or article straight into the next built-in view instead of
rebuilding filters by hand.
- **Choose a playbook:** biomcp skill list shows shipped worked examples
so you can open the matching biomcp skill workflow.
- **Analyze studies locally:** study commands cover local query, cohort, survival,
compare, and co-occurrence workflows with native terminal, SVG, and PNG
charts for downloaded cBioPortal-style datasets.
- **Follow the paper trail:** article citations, article references,
article recommendations, and article entities turn one known paper into a
broader evidence map.
- **Enrich and batch:** use biomcp enrich for top-level g:Profiler
enrichment and biomcp batch for up to 10 focused get calls in one
command.
Quick start
First useful query in under 30 seconds:
Watch the introduction
A project using BioMCP won St. Jude's KIDS BioHackathon in 2025. The talk that
followed is a one-hour introduction to BioMCP, recorded October 24, 2025.
Watch on YouTube ·
Read the write-up ·
Full transcript
Installation
Binary install
PyPI tool install
> **PyPI package warning:** install biomcp-cli, not biomcp. The biomcp
> PyPI package is unrelated to this project.
MCP Registry ownership marker: mcp-name: io.github.genomoncology/biomcp.
This installs the biomcp binary in ~/.local/bin. If that directory is not
already on PATH, the installer prints one command to add it; it never edits
your shell startup files.
Homebrew
The separate genomoncology/homebrew-biomcp tap repository must exist before these commands can work.
Docker
Use the GHCR image for quick CLI checks or stdio MCP clients without a local install.
Claude Code plugin
Install the biomcp binary first, then add the hosted plugin marketplace and
install the BioMCP plugin in Claude Code:
The plugin wires Claude Code to the local stdio MCP server with biomcp serve.
For guided BioMCP workflows, also install the skill assets below.
Codex MCP server
Install the biomcp binary first, then register the same stdio MCP server with
Codex:
Claude Desktop extension (.mcpb)
Install BioMCP from the Anthropic Directory in Claude Desktop when that path is
available for your environment. For local/manual setups, use the JSON MCP
config below.
Install skills
Install guided investigation workflows into your agent directory:
MCP clients
Remote HTTP server
For shared or remote deployments:
Remote clients connect to http://127.0.0.1:8080/mcp. Probe routes are
GET /health, GET /readyz, and GET /.
Runnable demo:
See Remote HTTP Server for
the newcomer guide.