---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.