Ensembl

Provides access to the Ensembl genomics REST API via MCP for gene, sequence, variant, and ontology data

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Language

6 months ago

First Indexed

3 months ago

Catalog Refreshed

Documentation & install

Readme and setup notes from the catalogue, plus a client-ready config you can copy for your MCP host.

Installation

Add the following to your MCP client configuration file.

Configuration

View docs

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

The Ensembl MCP Server gives you programmatic access to the Ensembl genomics REST API through the Model Context Protocol, letting you query genes, sequences, variants, cross-species data, phenotypes, and more from your preferred MCP client.

How to use

Connect to the Ensembl MCP Server from your MCP client to perform genomic data lookups, retrieve sequences, explore variants, and access regulatory and ontology data. You can add the server to your Claude Desktop setup for quick access, either by pointing to a built version of the MCP or by using the MCP package directly.

How to install

Prerequisites: you need Node.js installed on your system to build and run the MCP server.

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

If you prefer to start from source, clone the repository and build the project.

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

Configuration

Configure Claude Desktop to load the MCP by adding a new server entry that points to the built MCP index. This is a local stdio configuration using Node to run the built script.

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

Building

npm run build

Notes

The server depends on shared MCP tooling and SDK components. After building, you can run and test the MCP against your client to verify endpoints and data access. If you encounter issues, ensure your Node environment matches the project’s prerequisites and that the build step completes without errors.