Ensembl Mcp Server

# 🧬 Ensembl API MCP Server

[![smithery badge](https://smithery.ai/badge/@effieklimi/ensembl-mcp-server)](https://smithery.ai/server/@effieklimi/ensembl-mcp-server)

A full-featured Model Context Protocol (MCP) server that exposes Ensembl’s REST API. Built using the [TypeScript MCP SDK](https://github.com/modelcontextprotocol/typescript-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_](https://smithery.ai/server/@effieklimi/ensembl-mcp-server)
- [_Glama_](https://glama.ai/mcp/servers/@effieklimi/ensembl-mcp-server)

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## 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](https://smithery.ai/server/@effieklimi/ensembl-mcp-server). The most common platform options include:

```bash
# 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:**

   ```bash
   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:

   ```json
   {
     "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

### Developm

... [View full README on GitHub]