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Gene Expression Omnibus (GEO) MCP

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A Model Context Protocol (MCP) server for accessing GEO (Gene Expression Omnibus) data through NCBI E-Utils API. The tool will enable you to search for GEO datasets, series, samples, platforms, and profiles for your LLM. Tested with Claude Desktop, chatGPT has no out of the box support for this tool yet. Claude will automatically use the tools if it fits the context.

By Matthias

Database Integration

Updated February 24, 2026

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Configuration

mcpServers:

{
  "geo-mcp": {
    "command": "/Users/youruser/miniforge3/bin/geo-mcp",
    "env": {
      "CONFIG_PATH": "/Users/youruser/.geo-mcp/config.json"
    }
  }
}

Installation

# Clone the repo (if not already) git clone https://github.com/MCPmed/GEOmcp cd GEO_MCP pip install -e .

Compatibility

claude

Details

Category: Database Integration

Status: active

Created: October 13, 2025

Last Updated: February 24, 2026