🧬 Ensembl API MCP Server

A full-featured Model Context Protocol (MCP) server that exposes Ensembl’s REST API. Built using the TypeScript MCP SDK

• Comprehensive coverage – 10 tools map to functional areas instead of 100 + individual endpoints, yet still expose nearly the whole API.
• Production-ready – TypeScript throughout, robust error handling, and a tidy API-client layer.
• Biologist-friendly – grouped by biological task (genes, variants, compara…), not by low-level REST paths.

Listed on:

• Smithery
• Glama

Use cases:

• 🧬 Gene information – fetch details by ID or symbol
• 🔍 Gene search – scan genes across any species
• 🧬 Sequence retrieval – pull DNA for any genomic region
• 🔬 Variant data – explore variants and their annotations
• 📊 Transcript info – inspect transcripts and isoforms
• 🌍 Multi-species – every species in Ensembl, right here
• 🔗 Cross-references – hop to external databases in one call
• ⚡ Rate-limited – built-in throttling keeps you within Ensembl limits

Installation

Choose your preferred installation method:

Option 1: Via Smithery

1. Visit Smithery - Ensembl MCP Server. The most common platform options include:

# claude code:
npx -y @smithery/cli@latest install @effieklimi/ensembl-mcp-server --client claude --key your-smithery-secret-key

# cursor:
npx -y @smithery/cli@latest install @effieklimi/ensembl-mcp-server --client cursor --key your-smithery-secret-key

# vscode:
npx -y @smithery/cli@latest install @effieklimi/ensembl-mcp-server --client vscode --key your-smithery-secret-key

# windsurf:
npx -y @smithery/cli@latest install @effieklimi/ensembl-mcp-server --client windsurf --key your-smithery-secret-key

Check the MCP's smithery link for additional platform options.

Option 2: Local Development Setup

For development or custom setups:

1. Clone and install dependencies:

   git clone https://github.com/effieklimi/ensembl-mcp-server.git
   cd ensembl-mcp-server
   npm install
   

2. Configure Claude Desktop manually:

   Edit your config file:

   • macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
   • Windows: %APPDATA%/Claude/claude_desktop_config.json

   Add this server configuration:

   {
     "mcpServers": {
       "ensembl": {
         "command": "npm",
         "args": ["run", "start"],
         "cwd": "/absolute/path/to/ensembl-mcp-server"
       }
     }
   }
   

3. Restart Claude Desktop - The Ensembl tools will appear in your available tools

Development Setup

# Development with hot reload
npm run dev

# Run tests
npm test

# Production build (optional)
npm run build
npm run start:prod

Contributing

We'd love your help! Here's how to get started:

Quick Contact

• Email the dev: effie@effie.bio

Development Workflow

1. Fork the repository
2. Clone your fork:

   git clone https://github.com/YOUR_USERNAME/ensembl-mcp-server.git
   cd ensembl-mcp-server
   

3. Install dependencies:

   npm install
   

4. Run tests to make sure everything works:

   npm test
   

5. Start development server:

   npm run dev
   

6. Make your changes and test thoroughly
7. Submit a pull request

Available Scripts

• npm run dev - Development with hot reload
• npm run start - Run the server
• npm test - Run all tests
• npm run build - Compile TypeScript (optional)
• npm run start:prod - Run compiled version

... View full README on GitHub