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 <slug> 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:

uv tool install biomcp-cli
biomcp health --apis-only
biomcp skill list
biomcp list gene
biomcp search all --gene BRAF --disease melanoma  # unified cross-entity discovery
biomcp get gene BRAF pathways hpa

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

curl -fsSL https://biomcp.org/install.sh | bash

PyPI tool install

uv tool install biomcp-cli
# or: pip install biomcp-cli

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.