Bio MCP Server

Access PubMed, ClinVar, and OncoKB data through a unified biomedical query grammar.

Data last scanned yesterday · Reviewed 3 weeks ago

486 tools★ 590RustMIT

Overview

BioMCP provides a single binary interface to interact with approximately 30 biomedical data sources, including PubMed, ClinicalTrials.gov, OncoKB, and Reactome. By using a consistent command grammar, it enables users to search for genes, variants, drugs, or diseases and pivot between different data contexts without needing to manage multiple API integrations or manual identifier reconciliation. Designed for clinicians and researchers, the server supports local study analytics through command-line tools that generate charts from cBioPortal-style datasets. It also includes advanced capabilities such as g:Profiler enrichment and citation mapping, allowing for the systematic exploration of literature and biological entities.

Our verdict

With a security score of 48/100, this tool is categorized as high risk. The security architecture, specifically the authentication and read-only mode, has not yet been editorially reviewed. Given that this is a community-maintained project and not provided by an official vendor, users should exercise caution when integrating it into sensitive research environments where data isolation is critical.

Unified access to 30 trusted biomedical sources
Zero direct dependencies reduces supply-chain surface area
Active development with daily commit frequency
Supports local analysis of cBioPortal-style datasets

Lacks external editorial or security review
Authentication and read-only mode capabilities remain unreviewed
Community-maintained rather than supported by an official vendor

Tools

Tool	Description	Risk
search	Search for entities like genes, variants, articles, trials, etc. across various biological data sources.	low
skill list	List available guided investigation workflows.	low
discover	Perform concept resolution for biological entities.	low
get	Retrieve focused details for a specific entity ID, with optional section filtering.	low
enrich	Perform gene-set enrichment analysis.	low
batch	Execute multiple focused get calls in parallel.	low

Compatibility

Client	Local	Docker	Remote	Read-only
ChatGPT
Claude Desktop
Cursor
VS Code
Windsurf

Frequently asked questions

›What is the correct PyPI package name for installation?

You must install biomcp-cli. The biomcp package on PyPI is unrelated to this project.

›Does the installer modify my shell startup files?

No, the installer does not edit your shell startup files. If the installation directory is not in your PATH, it simply prints the command needed to add it.

›Can I use BioMCP without a local installation?

Yes, you can use the Docker image ghcr.io/genomoncology/biomcp to run CLI checks or use the server via stdio.

›How do I configure BioMCP for use in Claude Desktop?

You can add it to your configuration file by setting the command to biomcp and the arguments to ["serve"] under the mcpServers key.

›Is it possible to run BioMCP as a remote server?

Yes, you can start a remote HTTP server by running the biomcp serve-http command, which allows remote clients to connect via http://127.0.0.1:8080/mcp.

›What is the purpose of the 'skill' commands?

The skill commands provide access to a catalog of worked examples and workflows, which can be installed into your agent directory to assist with guided investigations.