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Install with the open skills CLI (global, non-interactive — available in every Claude Code session):
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill "biomcp-server" -g -a claude-code -yOr manually — clone and copy the skill directory (SKILL.md + companion files):
git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills /tmp/OpenClaw-Medical-Skills && cp -r /tmp/OpenClaw-Medical-Skills/skills/biomcp-server ~/.claude/skills/biomcp-serverThis skill is a directory: SKILL.md is the entry point; the files below ship with it.
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# COPYRIGHT NOTICE
# This file is part of the "Universal Biomedical Skills" project.
# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>
# All Rights Reserved.
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# This code is proprietary and confidential.
# Unauthorized copying of this file, via any medium is strictly prohibited.
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---
name: biomcp-server
description: MCP bio bridge
keywords:
- MCP
- PubMed
- ClinicalTrials
- server
- uv
measurable_outcome: Stand up a working BioMCP endpoint (pip or uv) and return ≥1 PubMed + ≥1 ClinicalTrials.gov response to the client within 10 minutes.
license: MIT
metadata:
author: BioMCP Team
version: "1.0.0"
compatibility:
- system: MCP-compliant clients
allowed-tools:
- web_fetch
---
# 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 -->Operate the Antigravity CLI (agy): plugins, auth, sandbox.
Search arXiv papers by keyword, author, category, or ID.
Gateway to 400+ bioinformatics skills from bioSkills and ClawBio. Covers genomics, transcriptomics, single-cell, variant calling, pharmacogenomics, metagenomics, structural biology, and more. Fetches domain-specific reference material on demand.