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Biomart MCPServer

jzinno
GitHub
bioinformaticsdatabasessearch

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๐Ÿ’ก Description

A Model Context Protocol server that interacts with the Biomart database, enabling the model to search biological datasets, explore attributes and filters, retrieve biological data, and translate between various biological identifiers.

๐Ÿ“ JSON Entries

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

๐Ÿ› ๏ธ Tools

list_datasetslist_all_attributeslist_filterslist_common_attributesbatch_translateget_dataget_translationlist_marts

โšก Features

  • Marts and dataset discovery
  • Attribute and filter exploration
  • Data retrieval via Biomart queries
  • Identifier translation among various biological identifiers

๐Ÿ’ฌ Example Queries

  • List all available marts and datasets in Biomart.
  • Get common attributes for a specific dataset.
  • Translate gene symbols to Ensembl IDs.