nci-gdc-mcp-server

NCI GDC MCP Server: Easy Access for Scientists

License and Citation

This project is available under the MIT License with an Academic Citation Requirement. This means you can freely use, modify, and distribute the code, but any academic or scientific publication that uses this software must provide appropriate attribution.

For academic/research use:

If you use this software in a research project that leads to a publication, presentation, or report, you must cite this work according to the format provided in .

For commercial/non-academic use:

Commercial and non-academic use follows the standard MIT License terms without the citation requirement.

By using this software, you agree to these terms. See for the complete license text.This server lets you explore and analyze data from the National Cancer Institute (NCI) Genomic Data Commons (GDC) using natural language tools like Claude Desktop or other Model Context Protocol (MCP) clients. You do not need to be a programmer to use it!

What is this?

• MCP Server: A bridge that lets you ask questions about cancer genomics data using AI tools.
• NCI GDC: A large database of cancer genomics data from the National Cancer Institute.
• Claude Desktop: An AI assistant you can run on your computer, which can connect to this server to answer your questions about GDC data.

How to Use This Server with Claude Desktop

1. Start the MCP Server

Ask your technical support or IT to start the server for you, or follow their instructions. By default, it will be available at:

http://localhost:8787/sse

2. Connect Claude Desktop to the Server

1. Open Claude Desktop.
2. Go to Settings > Developer > Edit Config.
3. Add this to your configuration (ask for help if you are unsure):

{
  "mcpServers": {
    "nci-gdc-local": {
      "command": "npx",
      "args": [
        "mcp-remote",
        "http://localhost:8787/sse"
      ]
    }
  }
}

4. Save and restart Claude Desktop.
5. In Claude, select the "nci-gdc-local" server from the MCP menu.

What Can I Do?

• Ask questions about cancer genomics data (e.g., "Show me all projects related to kidney cancer.")
• Explore available data types and fields (e.g., "What fields are available for cases?")
• Get summaries, counts, and more

If you are not sure what to ask, try:

• "List all available data types in the GDC."
• "How many cases are there for breast cancer?"
• "Show me the schema for the 'Project' type."

Need Help?

• If you have trouble connecting, ask your IT or technical support for help.
• For more information about the GDC, visit: https://gdc.cancer.gov/
• For more about Claude Desktop and MCP, see: https://modelcontextprotocol.io/quickstart/user

This server is designed to make cancer genomics data accessible to everyone. No programming required!