OpenSkillIndex← back to search
claude-coderesearch

Claude-skill-registry BioMCP

name: biomcp-server

install
source · Clone the upstream repo
git clone https://github.com/majiayu000/claude-skill-registry
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/majiayu000/claude-skill-registry "$T" && mkdir -p ~/.claude/skills && cp -r "$T/skills/data/BioMCP" ~/.claude/skills/majiayu000-claude-skill-registry-biomcp && rm -rf "$T"
manifest: skills/data/BioMCP/SKILL.md
tags
#biomedical#api-integration#data-retrieval#research#genomics
source content

---name: biomcp-server description: Open source biomedical Model Context Protocol (MCP) toolkit for connecting LLMs to biomedical data sources (PubMed, ClinicalTrials, Genomics). license: MIT metadata: author: LobeHub / GenomOncology source: "https://lobehub.com/mcp/genomoncology-biomcp" version: "1.0.0" compatibility:

  • system: MCP-compliant Client (Claude Desktop, BioKernel) allowed-tools:
  • web_fetch

keywords:

  • biomcp
  • automation
  • biomedical measurable_outcome: execute task with >95% success rate. ---"

BioMCP Server

BioMCP is a standardized Model Context Protocol (MCP) server that provides AI agents with direct, structured access to essential biomedical databases and APIs. It acts as a bridge between the LLM and the vast world of biomedical data.

When to Use This Skill

  • Literature Search: When you need to search PubMed or PMC for recent papers.
  • Entity Normalization: When you need to map text to gene IDs, disease codes, or chemical IDs (using PubTator3).
  • Clinical Data: To search for active clinical trials.
  • Genomic Information: To look up variant information or gene summaries.

Core Capabilities

  1. PubMed/PMC Search: Execute complex queries against the NCBI literature databases.
  2. PubTator3 API: Annotate biomedical text with normalized entities (Genes, Diseases, Chemicals, Species).
  3. ClinicalTrials.gov: Search and retrieve clinical trial protocols.
  4. Genomic Variants: Retrieve information about specific genetic variants.

Workflow

  1. Connect: The agent connects to the running BioMCP server.
  2. Call Tool: The agent selects the appropriate tool (e.g., 
    search_pubmed
    , 
    annotate_text
    ).
  3. Process: The server executes the API call and returns structured JSON.
  4. Response: The agent uses the data to answer the user's query.

Example Usage

User: "Find recent clinical trials for CAR-T therapy in glioblastoma and list the key inclusion criteria."

Agent Action:

  1. Calls 
    biomcp_search_clinical_trials(query="CAR-T glioblastoma", status="Recruiting")
    .
  2. Parses the returned trial JSON.
  3. Extracts and summarizes the inclusion criteria.