How do I install Ensembl?

Ensembl is a remote plugin. You do not need to install anything locally. Add the server URL to your AI app's MCP configuration and you are ready to go.

What AI apps work with Ensembl?

Ensembl uses the Model Context Protocol (MCP) and works with any MCP-compatible AI app, including Claude, ChatGPT / Codex, Gemini, Copilot, Cursor, and more.

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Ensembl MCP Server

by Pipeworx Io

Developer ToolsLow Risk10.0MCP RegistryRemote

Free

Server data from the Official MCP Registry

Ensembl REST — vertebrate genomes, sequences, comparative genomics, variation

About

Ensembl REST — vertebrate genomes, sequences, comparative genomics, variation

Remote endpoints: streamable-http: https://gateway.pipeworx.io/ensembl/mcp

Security Report

10.0

Low Risk10.0Low Risk

Valid MCP server (1 strong, 0 medium validity signals). No known CVEs in dependencies. Imported from the Official MCP Registry. Trust signals: trusted author (392/393 approved). 1 finding(s) downgraded by scanner intelligence.

18 tools verified · Open access · 1 issue found

Security scores are indicators to help you make informed decisions, not guarantees. Always review permissions before connecting any MCP server.

Permissions Required

This plugin requests these system permissions. Most are normal for its category.

file_system

Check that this permission is expected for this type of plugin.

HTTP Network Access

Connects to external APIs or services over the internet.

How to Connect

Remote Plugin

No local installation needed. Your AI client connects to the remote endpoint directly.

Add this to your MCP configuration to connect:

{
  "mcpServers": {
    "io-github-pipeworx-io-ensembl": {
      "url": "https://gateway.pipeworx.io/ensembl/mcp"
    }
  }
}

Documentation

View on GitHub

From the project's GitHub README.

mcp-ensembl

Ensembl REST — vertebrate genomes, sequences, comparative genomics, variation

Part of Pipeworx — an MCP gateway connecting AI agents to 250+ live data sources.

Tools

Tool	Description
`lookup`	Lookup by stable id (gene/transcript/exon/translation).
`lookup_symbol`	Gene by symbol within a species.
`xrefs`	External cross-references for a gene symbol.
`sequence`	Sequence by stable id.
`homology`	Homology mappings for a gene.
`variation`	Variation record by name.
`vep`	Variant Effect Predictor — region in "chrom:start-end:strand" form.

Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

{
  "mcpServers": {
    "ensembl": {
      "url": "https://gateway.pipeworx.io/ensembl/mcp"
    }
  }
}

Or connect to the full Pipeworx gateway for access to all 250+ data sources:

{
  "mcpServers": {
    "pipeworx": {
      "url": "https://gateway.pipeworx.io/mcp"
    }
  }
}

Using with ask_pipeworx

Instead of calling tools directly, you can ask questions in plain English:

ask_pipeworx({ question: "your question about Ensembl data" })

The gateway picks the right tool and fills the arguments automatically.

License

MIT

Reviews

No reviews yet

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Ensembl MCP Server

About

Security Report

Findings (1)

Permissions Required

How to Connect

Documentation

mcp-ensembl

Tools

Quick Start

Using with ask_pipeworx

More

License

Reviews

No reviews yet

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