BioMCP: Biomedical Model Context Protocol

What is BioMCP?

BioMCP is a command-line and MCP server tool that unifies search and retrieval across dozens of biomedical sources (PubTator3, Europe PMC, ClinVar, UniProt, etc.) behind a single grammar. It is designed for researchers, clinicians, and AI agents who need compact, evidence-oriented results without rebuilding workflows for each source.

How to use BioMCP?

Install the biomcp binary via the install script or uv tool install biomcp-cli, then run biomcp serve to start the MCP stdio server. Use commands such as search, get, suggest, enrich, batch, or study directly in the terminal, or register the server with Claude Desktop, Claude Code, or Codex. Optional API keys improve rate limits and unlock additional data.

Key features of BioMCP

• Search literature across PubTator3, Europe PMC, and Semantic Scholar
• Pivot between genes, variants, drugs, diseases, and more
• Route questions to shipped worked examples with suggest
• Analyze local study datasets with native terminal charts
• Follow paper trails with citations, references, and recommendations
• Enrich gene sets via g:Profiler and batch multiple focused queries

Use cases of BioMCP

• Literature discovery: search articles by gene and disease filters
• Variant interpretation: get ClinVar, gnomAD, and OncoKB data for a variant
• Drug interaction scanning: query drugs and their adverse events or approvals
• Gene-set enrichment: run enrichment analysis on a list of genes
• Cross-entity pivoting: move from a disease to its known drugs, trials, or articles

FAQ from BioMCP

What biomedical sources does BioMCP query?

BioMCP queries over 40 upstream providers including PubTator3, Europe PMC, MyGene.info, UniProt, ClinVar, ClinicalTrials.gov, OpenFDA, MyDisease.info, Reactome, and many more, depending on the entity and command.

Do I need API keys to use BioMCP?

Most commands work without credentials. Optional keys such as NCBI_API_KEY, S2_API_KEY, OPENFDA_API_KEY, and ONCOKB_TOKEN improve rate limits or unlock additional data sections (e.g., Semantic Scholar TLDRs, OncoKB variant evidence).

How do I pivot between different entities?

Use built-in cross-entity helpers like biomcp variant trials "BRAF V600E" or biomcp disease drugs melanoma. These commands pivot from one entity to related entities without rebuilding filters.

What transport protocols does BioMCP support?

BioMCP supports stdio (local MCP server) and HTTP (remote server via biomcp serve-http). The HTTP server exposes health probes and a Streamable HTTP MCP endpoint.

Are there any known limitations in data coverage?

References and recommendations for articles can be empty for paywalled papers because of publisher elision in Semantic Scholar upstream coverage. Additionally, some detail sections (e.g., diagnostics, funding) remain opt‑in and are not included in the all shortcut.