LabKey’s MCP (Model Context Protocol) Service provides a standardized way for AI agents and external tools to securely interact with LabKey Server. The MCP Service defines how systems expose data, metadata, and actions in a structured, machine-readable form, making it possible for intelligent clients to discover datasets, run queries, and author reports.

MCP Service Set Up

Set up an MCP-driven development environment for working with LabKey Server.

Enable the MCP Server

• Go to Gear > Site > Admin Console.
• Click Experimental Features.
• Place a checkmark next to Enable MCP Service. (You do not need to press a confirmation button--simply adding the checkmark is sufficient to enable the service.)

Configure Your IDE

Install Claude Code

• Install the Claude Code plugin in your IDE (e.g., IntelliJ or VSCode).

brew install --cask claude-code

Windows: Download and run the installer: Claude Code Documentation

1.7 Configure the LabKey MCP Server

Create a file named .mcp.json in your project directory:

{
"mcpServers": {
"labkey": {
"type": "http",
"url": "https://nightly.labkey.com/mcp
",
"headers": {
"apikey": "YOUR_API_KEY_HERE"
}
}
}
}

Replace YOUR_API_KEY_HERE with your LabKey API key. Claude Code will automatically load this configuration when launched from this directory.