Ensembl MCP Server

Model Context Protocol (MCP) server providing access to the Ensembl genomics REST API.

Features

30+ tools for genomic data access:

• Gene lookup by symbol or ID
• Sequence retrieval
• Genetic variants
• Cross-species homology
• Phenotype data
• Regulatory features
• Ontology and taxonomy data

Full endpoint documentation available in ENDPOINTS.md.

Installation

From GitHub

npm install git+https://github.com/munch-group/ensembl-mcp.git
cd node_modules/ensembl-mcp
npm run build

From source

git clone https://github.com/munch-group/ensembl-mcp.git
cd ensembl-mcp
npm install
npm run build

Usage with Claude Desktop

# Using built version
claude mcp add ensembl node /path/to/ensembl-mcp/build/index.js

# Or from npm global install
claude mcp add ensembl npx -y ensembl-mcp

Configuration

Add to your Claude Desktop config:

{
  "mcpServers": {
    "ensembl": {
      "command": "node",
      "args": ["/path/to/ensembl-mcp/build/index.js"]
    }
  }
}

Building

npm run build

Dependencies

• @mcp/rest-utils - Shared REST utilities
• @modelcontextprotocol/sdk - MCP SDK
• zod - Schema validation

License

ISC