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Biomart MCP Server

[Model Context Protocol](https://modelcontextprotocol.io/introduction) (MCP) is an open protocol that standardizes how applications provide context

Local serverstdioPython

What is the Biomart MCP Server?

Biomart MCP connects Biomart MCP to AI assistants that speak the Model Context Protocol. 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.

What Biomart MCP does

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.

Key capabilities

  • 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)

Practical notes

  • Maintained by jzinno, written in Python.

More MCP options

Compare MCP servers by category, or browse hosted MCP servers if you prefer an endpoint over a local process.

Maintainer setup documentation.

How to install the Biomart MCP Server

{
  "mcpServers": {
    "Biomart": {
      "command": "uv",
      "args": [
        "run",
        "--with",
        "mcp[cli]",
        "--with",
        "pybiomart",
        "mcp",
        "run",
        "/your/path/to/biomart-mcp.py"
      ]
    }
  }
}

From the project documentation. Replace placeholders and example paths before connecting.

Example prompts to try

  • “Use Biomart MCP to Cursor.”
  • “Use Biomart MCP to Glama.”
  • “Use Biomart MCP to Development.”

Frequently asked questions

[Model Context Protocol](https://modelcontextprotocol.io/introduction) (MCP) is an open protocol that standardizes how applications provide context to LLMs Confirm the tools offered by your installed version in the connected client. Tool availability and permissions depend on the server and account configuration.

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