mcp-tx-tools

v1.1.0

Published

8 months ago

Tools for querying FHIR terminology from LLMs.

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johngrimes

FHIR LLM Model Context Protocol MCP

Terminology Tools

Tools for working with FHIR terminology services, including code lookup and validation.

Features

Code Lookup

Looks up clinical codes based on text descriptions using a FHIR terminology server, ensuring that codes are valid and compliant with value set bindings.

Configuration

Environment Variables

TX_SERVER: The base URL of the FHIR terminology server to use
- Default: https://tx.ontoserver.csiro.au/fhir
- Example: export TX_SERVER=http://your-terminology-server/fhir

Installation

Adding to Claude Desktop

To add this tool to your Claude Desktop configuration:

Open Claude Desktop and go to Settings > Developer Settings
Find your Claude desktop configuration file:
- macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
- Windows: %APPDATA%\Claude\claude_desktop_config.json
Add the following to your configuration file:

{
  "mcpServers": {
    "tx-tools": {
      "command": "npx",
      "args": ["-y", "mcp-tx-tools"]
    }
  }
}

If you already have other MCP servers configured, just add the "tx-tools" entry to the existing "mcpServers" object
Save the file and restart Claude Desktop
You should now see the Terminology Tools available in the tools menu (hammer icon)

Adding to Goose

To add this tool as a Command-Line Extension in Goose:

Run goose configure in your terminal.
Select Add Extension from the menu.
Choose Command-line Extension.
When prompted for "What would you like to call this extension?", you can enter a descriptive name, for example, "Terminology Tools".
For "What command should be run?", enter:
```
npx -y mcp-tx-tools
```
You can set a timeout (e.g., 300 seconds) or accept the default.
When prompted about environment variables, you can optionally add:
- TX_SERVER: to use a different FHIR terminology server

Goose will then confirm that the extension has been added. You can enable or disable it via goose configure > Toggle Extensions.

Usage

Starting the Server

CLI Mode (stdio)

bun run start-stdio

Web Server Mode (SSE)

bun run start-sse

This starts a server on port 3001 that can be accessed via Server-Sent Events (SSE).

Tool Documentation

lookup-code

Looks up a clinical code based on text description using a FHIR terminology server.

Parameters:

filter: Text to search for (e.g. "hypertension", "tracheotomy")
url: ValueSet URL to search within (e.g. "http://snomed.info/sct?fhir_vs")

Common ValueSet URLs:

http://snomed.info/sct?fhir_vs: All of SNOMED CT
http://loinc.org/vs: All of LOINC
http://snomed.info/sct?fhir_vs=isa/71388002: SNOMED CT procedures