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.

More

• All tools and guides
• pipeworx.io

License

MIT