Ensembl

What Ensembl MCP server does

The Ensembl MCP server exposes selected Ensembl REST API operations as MCP tools. It is intended for questions and workflows involving vertebrate genomes, gene annotations, nucleotide or protein sequences, comparative genomics, and genetic variation. Requests are sent to https://rest.ensembl.org through either the hosted Pipeworx gateway or the standalone package.

The available operations cover stable identifiers for genes, transcripts, exons, and translations; gene-symbol searches within a species; external cross-references; sequence retrieval; homology mappings; variation lookup; and variant consequence analysis with the Variant Effect Predictor.

How it works

A hosted MCP connection uses https://gateway.pipeworx.io/ensembl/mcp. The pack endpoint lists the Ensembl tools along with shared Pipeworx meta-tools. Those additional tools can route questions to other catalog sources, so the connection may report more tools than the Ensembl-specific list. The initialize response is the authoritative description of the connection's current scope.

The same gateway also offers a full endpoint at https://gateway.pipeworx.io/mcp. The pack endpoint lists Ensembl tools directly, while the full endpoint lists tools from all available packs directly. The ask_pipeworx tool can route a natural-language question from either endpoint.

Without an MCP client, individual tools can be called over HTTP. For local use, the npm package runs as a stdio MCP server and exposes only the Ensembl pack's tools, without gateway meta-tools or cross-catalog routing.

Setup and configuration

Add the hosted endpoint to an MCP client as a server URL:

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

The standalone configuration uses npx:

{
  "mcpServers": {
    "ensembl": {
      "command": "npx",
      "args": ["-y", "@pipeworx/mcp-ensembl"]
    }
  }
}

The package can also be started directly with npx -y @pipeworx/mcp-ensembl. The hosted service requires no account for its initial calls, and the standalone mode requires no Pipeworx account. No environment variables are documented.

Tools and capabilities

The Ensembl MCP server includes these operations:

• lookup(id, expand?) for stable Ensembl identifiers.
• lookup_symbol(species, symbol) for finding a gene by species and symbol.
• xrefs(species, symbol) and xref_symbol(species, symbol) for external references and symbol lookup.
• sequence(id, type?) for DNA, cDNA, CDS, or protein sequences.
• homology(species, symbol_or_id, target_species?) for cross-species homology mappings.
• variation(species, variant_id) for named variants such as rs56116432.
• vep(species, region, allele) for variant-effect analysis.

For direct HTTP use, the gateway exposes tool routes such as /v1/tools/ensembl_lookup and accepts JSON POST requests.

Limitations and notes

The hosted pack endpoint always includes shared Pipeworx meta-tools; it cannot be mounted with only the pack-specific schemas. Choose the full gateway if several pack endpoints would create unnecessary context overhead. The standalone server avoids those shared tools but also cannot use ask_pipeworx for routing outside Ensembl. The available data and behavior depend on the Ensembl REST API, and the gateway's reported tool scope can change over time.