@pipeworx/ensembl

Ensembl REST API MCP — vertebrate genomes, gene annotations, sequences, comparative genomics, variation. Keyless.

Part of Pipeworx — an MCP gateway connecting AI agents to 1394+ live data sources.

Tools

• lookup(id, expand?) — by stable id (gene/transcript/exon/translation)

• lookup_symbol(species, symbol) — gene by symbol within a species

• xrefs(species, symbol) — external cross-references for a gene symbol

• sequence(id, type?) — DNA / cDNA / CDS / protein sequence

• homology(species, symbol_or_id, target_species?) — homology mappings

• variation(species, variant_id) — variation by name (e.g. "rs56116432")

• vep(species, region, allele) — Variant Effect Predictor (region: "9:22125504-22125504:1")

• xref_symbol(species, symbol) — symbol lookup (alias for /xrefs/symbol)

Related MCP server: Ensembl MCP Server

Data source

https://rest.ensembl.org

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 1394+ 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

• Docs and guides

• pipeworx.io

License

MIT