← Back to directory

BioMCP

Community

One binary. One grammar. Evidence from the biomedical sources you already trust.

GitHub source repository ↗

★ 608 Stars Category · Other Very popular Source revision c307ce928b29

75FMRS · B

Reliability

10/20

Security and permissions

16/20

Maintenance

18/20

Documentation

17/20

Setup experience

14/20

BioMCP provides a powerful unified CLI and MCP server for biomedical data search, with broad entity support and local analysis features. MIT-licensed, no telemetry, privacy-focused. Suitable for researchers and clinicians needing efficient access to trusted biomedical data.

Read the FMRS scoring method →

BioMCP is a CLI tool that provides a single command grammar to access ~30 trusted biomedical sources (PubMed, ClinVar, ClinicalTrials.gov, OncoKB, Reactome, and more). It is also an MCP (Model Context Protocol) server, making the same tools available to AI agents such as Claude Code, Codex, and Claude Desktop. BioMCP simplifies the biomedical data maze by letting one query reach 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 workflows for each source. It returns compact, evidence-oriented results across live public data plus local study analytics.

Tools

Search entities (articles, variants, trials, etc.) across multiple sources.

get

Fetch detailed information for a specific entity, with optional sections.

skill

List and install guided investigation workflows.

discover

Resolve concepts to aid entity selection.

enrich

Perform gene-set enrichment using g:Profiler.

batch

Parallel get calls for up to 10 focused entities.

study

Perform query, cohort, survival, comparison, and co-occurrence analysis on local cBioPortal-style datasets.

health

Check API connectivity and local resource readiness.

version

Show version and build info.

update

Self-update with checksum verification.

uninstall

Remove biomcp from ~/.local/bin.

Setup

Install: uv tool install biomcp-cli (or pip install biomcp-cli, or binary: curl -fsSL https://biomcp.org/install.sh | bash, or Homebrew: brew tap genomoncology/biomcp && brew install biomcp). 2. Verify: biomcp health --apis-only. 3. Configure MCP client: for Claude Desktop, use the JSON config; for Claude Code, use /plugin marketplace add genomoncology/biomcp and /plugin install biomcp@biomcp; for Codex, use codex mcp add biomcp -- biomcp serve. 4. (Optional) Install skills: biomcp skill install ~/.claude --force.

claude_desktop_config.json

{
  "mcpServers": {
    "biomcp": {
      "command": "biomcp",
      "args": ["serve"]
    }
  }
}

Generate and validate client config

Fit and risk

Best for

Biomedical researchers
Clinicians
AI agents that need efficient access to biomedical literature and data analysis

Not for

Users needing to write to upstream databases (read-only)
Users requiring direct access to closed datasets (e.g., COSMIC is not directly integrated)
Users expecting all advanced features without API keys

Required permissions

Requires internet access to query public biomedical APIs
Optional API keys (NCBI, Semantic Scholar, OpenFDA, etc.) to improve rate limits or unlock features
Local read/write access for skills, cache, and local study data (e.g., `~/.local/share/biomcp`)

Risks and side effects

Upstream API rate limits may affect performance
Some data sources (e.g., KEGG) have licensing terms that restrict non-academic use
Features requiring API keys (e.g., OncoKB) may be incomplete without them
Local binary installations need regular updates for compatibility

Troubleshooting

Check `biomcp health` to verify API connectivity
Ensure `biomcp` is on your PATH or use full path
If using Docker, ensure container port mappings are correct
For remote server, check `--allowed-hosts` restrictions
Refer to official docs <https://biomcp.org/> and GitHub Issues

Use cases

Get a low-noise overview of BRAF in melanoma (e.g., `biomcp search all --gene BRAF --disease melanoma`).

Retrieve ClinVar significance and population frequency for BRAF V600E (`biomcp get variant "BRAF V600E" clinvar population`).

Perform study-level analysis on local datasets, such as survival analysis (`biomcp study ...`).

Expand literature evidence map via article citations, references, and recommendations.

Supported clients

Claude DesktopFull support

Claude CodeFull support

CodexFull support

Other MCP stdio clientsFull support

Related MCP servers

Compare with other MCP servers