OpenSkillIndex← back to search
openclawclaude-coderesearch

OpenClaw-Medical-Skills biomcp-server

<!--

install
source · Clone the upstream repo
git clone https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills "$T" && mkdir -p ~/.claude/skills && cp -r "$T/skills/biomcp-server" ~/.claude/skills/freedomintelligence-openclaw-medical-skills-biomcp-server && rm -rf "$T"
OpenClaw · Install into ~/.openclaw/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills "$T" && mkdir -p ~/.openclaw/skills && cp -r "$T/skills/biomcp-server" ~/.openclaw/skills/freedomintelligence-openclaw-medical-skills-biomcp-server && rm -rf "$T"
manifest: skills/biomcp-server/SKILL.md
tags
#biomedical-api#pubmed-query#clinical-trials#server-deployment#uv-pip#mcp-compliant
safety · automated scan (low risk)
This is a pattern-based risk scan, not a security review. Our crawler flagged:
  • pip install
Always read a skill's source content before installing. Patterns alone don't mean the skill is malicious — but they warrant attention.
source content
<!-- # 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. # # This code is proprietary and confidential. # Unauthorized copying of this file, via any medium is strictly prohibited. # # Provenance: Authenticated by MD BABU MIA -->

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 -->