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Biomart MCP

jzinno/biomart-mcp

Model Context Protocol (MCP) is an open protocol that standardizes how applications provide context to LLMs developed by Anthropic. Here we use the MCP python-sdk to create a MCP server that interfaces with Biomart via the pybiomart package.

View on GitHub1

Install

npx -y @smithery/cli install @jzinno/biomart-mcp --client claude

Client configuration

{
  "mcpServers": {
    "Biomart": {
      "command": "uv",
      "args": [
        "run",
        "--with",
        "mcp[cli]",
        "--with",
        "pybiomart",
        "mcp",
        "run",
        "/your/path/to/biomart-mcp.py"
      ]
    }
  }
}
GitHub stars
1
Author
@jzinno
Category
Research & Data, Developer Tools
Updated
Oct 6, 2026

Features

  • Mart and Dataset Discovery: List available marts and datasets to explore the Biomart database structure

  • Attribute and Filter Exploration: View common or all available attributes and filters for specific datasets

  • Data Retrieval: Query Biomart with specific attributes and filters to get biological data

  • ID Translation: Convert between different biological identifiers (e.g., gene symbols to Ensembl IDs)

Details on this page are taken from the project's README. Open README

Supported clients

Clients mentioned in this server's README:

View all
Claude Desktop logo

Claude Desktop

Desktop · Freemium · Proprietary

Anthropic's official Claude AI desktop application. Supports MCP servers to extend functionality.

WindowsMacOS
Cursor logo

Cursor

Desktop · Freemium · Proprietary

The first agentic IDE. The Cursor editor truly merges how developers and AI work together, delivering a magical coding experience.

WindowsMacOSLinux

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