How do I install the Biomcp Server skill?

Run npx skillmds add majiayu000/biomcp-server in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Biomcp Server safe to use?

This skill has not completed SkillMD's automated safety review yet. Capability flags: makes network calls. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Biomcp Server?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Biomcp Server free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Biomcp Server?

majiayu000 (@majiayu000) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Biomcp Server by majiayu000 — Agent Skill

Name: Biomcp Server
Rating: 4.2 (5 reviews)
Author: majiayu000

File contents

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.

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

Frequently asked questions