ensembl-mcp-server

effieklimi/ensembl-mcp-server

3.4

If you are the rightful owner of ensembl-mcp-server and would like to certify it and/or have it hosted online, please leave a comment on the right or send an email to henry@mcphub.com.

The Ensembl API MCP Server is a comprehensive Model Context Protocol server that provides access to Ensembl's REST API, designed for biologists and developers.

The Ensembl API MCP Server is a robust and full-featured Model Context Protocol (MCP) server that offers extensive access to Ensembl’s REST API. Built using the TypeScript MCP SDK, this server is designed to be both biologist-friendly and production-ready. It simplifies the interaction with Ensembl's vast biological data by grouping endpoints into functional areas rather than individual paths, making it easier for users to access gene, variant, and comparative genomics data. The server is structured to handle requests efficiently, with built-in rate limiting to ensure compliance with Ensembl's usage policies. It supports a wide range of biological tasks, from gene information retrieval to cross-referencing external databases, and is compatible with multiple platforms, including Smithery, Glama, and local development environments.

Features

  • Comprehensive coverage with 10 tools mapping to functional areas.
  • Production-ready with TypeScript, robust error handling, and a tidy API-client layer.
  • Biologist-friendly grouping by biological task rather than low-level REST paths.
  • Built-in rate limiting to adhere to Ensembl's usage policies.
  • Multi-platform support including Smithery, Glama, and local development setups.

Usages

smithery with claude

bash
npx -y @smithery/cli@latest install @effieklimi/ensembl-mcp-server --client claude --key your-smithery-secret-key

smithery with cursor

bash
npx -y @smithery/cli@latest install @effieklimi/ensembl-mcp-server --client cursor --key your-smithery-secret-key

smithery with vscode

bash
npx -y @smithery/cli@latest install @effieklimi/ensembl-mcp-server --client vscode --key your-smithery-secret-key

smithery with windsurf

bash
npx -y @smithery/cli@latest install @effieklimi/ensembl-mcp-server --client windsurf --key your-smithery-secret-key

local development with claude

{
  "mcpServers": {
    "ensembl": {
      "command": "npm",
      "args": ["run", "start"],
      "cwd": "/absolute/path/to/ensembl-mcp-server"
    }
  }
}

Tools

  1. ensembl_feature_overlap

    Find genes, transcripts, or regulatory elements that overlap a region or another feature.

  2. ensembl_regulatory

    Regulatory features, binding matrices and related annotations.

  3. ensembl_protein_features

    Protein-level domains and functional sites.

  4. ensembl_meta

    Server metadata, species lists, release info, and diagnostics.

  5. ensembl_lookup

    Translate IDs ↔ symbols, pull xrefs, recode variants.

  6. ensembl_sequence

    Retrieve DNA, RNA or protein sequences.

  7. ensembl_mapping

    Coordinate conversion (genome ↔ cDNA/CDS/protein) and assembly lift-over.

  8. ensembl_compara

    Comparative genomics—homology, gene trees, alignments.

  9. ensembl_variation

    Variant lookup, VEP consequences, LD, phenotype mapping.

  10. ensembl_ontotax

    Ontology term search and NCBI taxonomy traversal.