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.

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"
    }
  }
}

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.

MIT