biomcp: Biomedical Model Context Protocol

by genomoncology · MCP Server · ★ 674

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How to install biomcp

uv tool install biomcp-cli

Taken from the project's README on GitHub. Check the security audit before running it.

Security audit verdict: SAFE · quality 70/100

None of the 42 rules matched — no credential harvesting, no data exfiltration, no curl-pipe-shell installer. Scanned against 42 published rules built on the SlowMist agent-security taxonomy, refreshed every 8 hours. Full audit →

The quality score combines nine heuristic checks of the repo and its README: completeness, clarity, specificity, examples, structure, agent readiness, step-by-step content, instruction quality and security notes. It rates how well the project explains itself to an agent, not the code.

aibioinformaticsclinical-trialsgenomicsllmmcpmcp-servermedicalmodel-context-protocolpubmed

Quick Facts

Stars674
Forks119
LanguageRust
CategoryMCP Server
LicenseMIT
Quality Score70/100
Open Issues1
Last Updated2026-11-05
Created2025-04-01
Platformsmcp, rust
Est. Tokens~23k

About biomcp

BioMCP BioMCP is a single-binary CLI and MCP server for querying biomedical databases. One command grammar, compact markdown output, 12 entities across 15+ data sources. Install PyPI tool install This installs the binary on your PATH.

Compatible Skills

These tools work well together with biomcp for enhanced workflows:

  • rust-sdk — semantic(0.25)+complementary+same_lang+similar_pop+shared_platform (54%)
  • BioClaw — semantic(0.36)+complementary+rare_topics+similar_pop (52%)

biomcp alternative? Top 6 similar tools

Looking for a biomcp alternative? If you're comparing biomcp with other mcp server tools, these 6 projects are the closest alternatives on Agent Skills Hub — ranked by topic overlap, star count, and community traction.

  • jadx-ai-mcp by zinja-coder · ⭐ 2.9k

    Plugin for JADX to integrate MCP server

  • mysql_mcp_server by designcomputer · ⭐ 1.4k

    A Model Context Protocol (MCP) server that enables secure interaction with MySQL databases

  • atlassian-mcp-server by atlassian · ⭐ 1.1k

    Official remote MCP server for Atlassian. Securely connect Jira, Confluence, Jira Service Management, Bitbucke

  • ScienceClaw by beita6969 · ⭐ 1.0k

    Verifiable program-level self-evolution for AI-for-Science agents: Skills and typed Operators grow from replay

  • pubmed-mcp-server by cyanheads · ⭐ 163

    Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. ST

  • arxiv-mcp-server by blazickjp · ⭐ 3.2k

    A local MCP server for agent literature work. Original-LaTeX section reads, BibTeX from arXiv metadata, and to

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How this security grade is produced

Grades come from a rule-based scan built on the SlowMist agent-security taxonomy: 42 published rules, covering credential harvesting, data exfiltration, curl | sh installers and more. It is a first-layer scan, not a manual audit — we say so rather than overstate it.

The scale of the problem is documented independently: Liu et al. (2026), in a study of 31,132 agent skills, report that 26.1% contain security vulnerabilities. Our own full-catalog census is published as a citable open dataset.

Sources & who's responsible:

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