BioMCP · Biomedical MCP Server

One command. 50+ biomedical databases. Genes, variants, drugs, trials, papers, pathways — all through a single MCP endpoint.

BioMCP is a production-grade MCP (Model Context Protocol) server that unifies PubMed, ClinicalTrials.gov, ClinVar, gnomAD, OncoKB, Reactome, KEGG, UniProt, PharmGKB, OpenFDA, GWAS Catalog, and 40+ other biomedical sources behind one consistent API.

Quickstart

# Option A: Pull from Docker Hub (recommended)
docker pull jackgucci/biomcp:latest
docker compose up -d

# Option B: Build from source
git clone https://github.com/gucci10248/JEFFREY.git && cd JEFFREY
cp .env.example .env
bash build.sh
docker compose up -d

# 4. Test
curl http://localhost:8080/health

Your MCP server is live at http://localhost:8080/mcp.

Related MCP server: PubMed Advanced MCP Server

Connecting MCP Clients

Claude Desktop

{
  "mcpServers": {
    "biomcp": {
      "type": "streamableHttp",
      "url": "http://localhost:8080/mcp"
    }
  }
}

Hermes Agent

# ~/.hermes/config.yaml
mcp:
  servers:
    biomcp:
      type: streamableHttp
      url: http://localhost:8080/mcp
      enabled: true

Any SSE-compatible client

SSE endpoint: http://localhost:8080/mcp

What You Can Query

Full command reference: docker exec biomcp biomcp list

Data Sources

PubMed · Europe PMC · PubTator3 · LitSense2 · ClinicalTrials.gov · ClinVar · gnomAD · OncoKB · OpenFDA · CDC VAERS · MyGene · MyVariant · MyChem · Enrichr · KEGG · Reactome · UniProt · PharmGKB · CPIC · DDInter · Monarch · GWAS Catalog · DisGeNET · AlphaGenome · EMA · WHO Prequalification · NCBI GTR · cBioPortal

Pricing

Deploy locally — all features available in the open-source release.

Security

• ✅ Read-only — no mutation of external data sources

• ✅ Non-root container — runs as unprivileged biomcp user

• ✅ Minimal attack surface — single static binary, no runtime dependencies

• ✅ Read-only root filesystem — docker compose enforces read_only: true

• ✅ No telemetry — zero outbound calls except to public biomedical APIs

• ✅ SHA256-verified — build.sh verifies binary checksum from GitHub Releases

Health & Monitoring

curl http://localhost:8080/health    # API connectivity status
curl http://localhost:8080/readyz    # 200 = ready to serve
curl http://localhost:8080/          # Welcome page

Requirements

• Docker 24+ & Docker Compose v2

• ~200MB disk (image + volumes)

• Outbound internet access to public biomedical APIs

License

Apache 2.0