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