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🧬 Ensembl API MCP Server

@effieklimi

Repository

About 🧬 Ensembl API MCP Server

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

#science#bioinformatics#biology#mcp#ai-agents#bioinformatics-tool#model-context-protocol#mcp-server

Basic information

Category

Developer Tools

License

MIT license

Runtime

node

Transports

stdio

Publisher

effieklimi

Config

Add this server to your MCP-compatible client using the configuration below.

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@smithery/cli@latest",
        "install",
        "@effieklimi/ensembl-mcp-server",
        "--client",
        "claude",
        "--key",
        "your-smithery-secret-key"
      ]
    }
  }
}

Tools

No tools detected

We auto-extract tools from the README. The maintainer can list them under a ## Tools heading to populate this section.

Overview

What is 🧬 Ensembl API MCP Server?

A full-featured Model Context Protocol (MCP) server that exposes Ensembl’s REST API through 10 biologically grouped tools. Built with the TypeScript MCP SDK, it offers comprehensive coverage of Ensembl endpoints (genes, variants, sequences, comparative genomics, and more) in a production‑ready, biologist‑friendly interface.

How to use 🧬 Ensembl API MCP Server?

Install via Smithery (e.g. npx -y @smithery/cli install @effieklimi/ensembl-mcp-server --client claude) or clone the repository, run npm install, then configure your MCP client (e.g. Claude Desktop) to point to the server’s start command. For development, use npm run dev for hot reload. No API key is required.

Key features of 🧬 Ensembl API MCP Server

  • 10 tools covering nearly the entire Ensembl REST API
  • Built‑in rate limiting to stay within Ensembl quotas
  • Support for every species available in Ensembl
  • Biologist‑friendly grouping by biological task
  • Production‑ready TypeScript with robust error handling
  • Cross‑references to external databases (UniProt, etc.)

Use cases of 🧬 Ensembl API MCP Server

  • Fetch gene details by ID or symbol across any species
  • Retrieve DNA, RNA, or protein sequences for genomic regions
  • Explore variants and their annotations (VEP, LD, phenotypes)
  • Map coordinates between genome, cDNA, CDS, and protein
  • Find orthologs, build gene trees, and pull comparative alignments

FAQ from 🧬 Ensembl API MCP Server

How is this different from calling the Ensembl REST API directly?

The server groups over 100 raw endpoints into 10 logical tools based on biological tasks, includes built‑in rate limiting, and handles error responses in a consistent way—making it easier for biologists and AI agents to query Ensembl.

What are the runtime dependencies?

Node.js and npm must be installed on the machine running the server. The server uses

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