OMOP MCP Server
Model Context Protocol (MCP) server for mapping clinical terminology to Observational Medical Outcomes Partnership (OMOP) concepts using Large Language Models (LLMs). The vocabulary API is supported by OMOP HUB, and you can obtain an API key from omophub.com.
Demo Website
Overview
This server provides an agentic framework to standardize medical terms into the OMOP Common Data Model (CDM). It uses the OMOPHub API for vocabulary searching, concept suggestion, and terminology mapping.
Installation
Before configuring the MCP server, ensure you have:
uv installed on your system
- Install from: https://docs.astral.sh/uv/getting-started/installation/
Clone the repository
git clone https://github.com/OHNLP/omop_mcp.git cd omop_mcpSet up environment variables
Copy
.env.templateto.envand fill in your API credentials. You will need both an LLM provider key and an OMOPHUB_API_KEY (for vocabulary lookups).cp .env.template .env
Configuration for Claude Desktop
Add the following configuration to your claude_desktop_config.json file:
