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Biomcp server

Skill FridrichMethod/awesome-skills/skills/biomcp-server

MCP bio bridgeFrom its SKILL.md

Install
npx -y skills add FridrichMethod/awesome-skills --skill biomcp-server

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

2 things to look at

  • no licenseNo license file was found in the repository. Code published without one is not open source by default, so using it at work is a question for whoever answers licensing questions where you are.
  • 13 stars13 stars. Stars are a popularity signal and not a quality one, but at this level it is likely that nobody has read this closely except its author, and you would be relying on your own review.

What its file declares

Copied from the file, not written here

The file declares its own license as MIT. That is the author’s claim about this one file, and it is not the same thing as the license GitHub reports for the repository, which is listed with the other numbers below.

SKILL.md

2.3 KB, 463 tokens by cl100k_base, as published. Nobody here has run it

<!-- # COPYRIGHT NOTICE # This file is part of the "Universal Biomedical Skills" project. # Copyright (c) 2026 MD BABU MIA, PhD <[email protected]> # All Rights Reserved. # # This code is proprietary and confidential. # Unauthorized copying of this file, via any medium is strictly prohibited. # # Provenance: Authenticated by MD BABU MIA -->

BioMCP Server

Deploy and operate the BioMCP server so MCP-compatible clients (Claude Desktop, LobeChat, etc.) can query biomedical databases via a single standardized interface.

When to Use

  • Unified literature search (PubMed/PMC) inside MCP clients.
  • Entity normalization via PubTator3 or genomic variant lookups.
  • ClinicalTrials.gov queries without bespoke API wrappers.

Core Capabilities

  1. PubMed/PMC search: Execute complex literature queries.
  2. PubTator3 annotations: Map text to genes, diseases, chemicals, species.
  3. ClinicalTrials.gov: Retrieve trial metadata/protocols.
  4. Genomic variant lookups: Fetch variant/gene summaries from connected sources.

Deployment Workflow

  1. Install deps: cd repo && uv sync (preferred) or pip install ..
  2. Run server: python -m biomcp.server or make run; Docker Compose provided.
  3. Configure client: Add command/args snippet from README.md into MCP client config (Claude Desktop, BioKernel, etc.).
  4. Test tools: Invoke PubMed + ClinicalTrials + variant endpoints to ensure connectivity.
  5. Monitor: Capture logs, rate-limit statuses, and data-source versions for audit.

Guardrails

  • Keep API keys/env secrets outside the repo.
  • Respect upstream rate limits to avoid throttling or bans.
  • Document which data sources are enabled per deployment and update when they change.

References

  • Source repo + configuration examples in README.md, repo/docker-compose.yml, and repo/Makefile.
<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->

What ships with it: 338 files

8704.9 KB alongside SKILL.md, 216 of them executable

repo/

298 more files not listed here. See all 338 in the repository.

Keep looking

Skills are one crate of 325,949. Ordering is by how many stacks a row turns up in, so the top of any crate is what has actually been picked rather than what has the most stars.