OpenClaw · Skill

Biomcp Server

<! 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

Research & Tooling

vOfficial

Source & setup

This page is using a curated upstream skill source that is published as a reference page on Remote OpenClaw. Use the source repo for setup instructions and files.

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What this skill does

Typical use cases

Install this skill when you want a reusable OpenClaw workflow with clearer instructions than a one-off prompt.

Source instructions

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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.

This code is proprietary and confidential.

Unauthorized copying of this file, via any medium is strictly prohibited.

Provenance: Authenticated by MD BABU MIA

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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

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

Deployment Workflow

Install deps: cd repo && uv sync (preferred) or pip install ..
Run server: python -m biomcp.server or make run; Docker Compose provided.
Configure client: Add command/args snippet from README.md into MCP client config (Claude Desktop, BioKernel, etc.).
Test tools: Invoke PubMed + ClinicalTrials + variant endpoints to ensure connectivity.
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.

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