OHNLP/omop_mcp

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:
1. **uv** installed on your system
- Install from: https://docs.astral.sh/uv/getting-started/installation/
2. Clone the repository
3. Set up environment variables
Copy .env.template to .env and fill in your API credentials. You will need both an LLM provider key and an **OMOPHUB_API_KEY** (for vocabulary lookups).
Configuration for Claude Desktop
Add the following configuration to your claude_desktop_config.json file:
**Location:**
- MacOS: ~/Library/Application\ Support/Claude/claude_desktop_config.json
- Windows: %APPDATA%/Claude/claude_desktop_config.json
**Configuration:**
Replace with the actual path to your cloned repository.
Features
The OMOP MCP server provides tools and resources for:
- **Mapping clinical terminology**: Intelligent mapping of free-text terms to standardized OMOP concepts.
- **Vocabulary Search**: Direct access to OMOP vocabulary via find_omop_concept.
- **Batch Processing**: Tool for mapping multiple concepts from a CSV file.
- **Preferred Vocabularies**: Automatic domain-specific vocabulary prioritization (e.g., LOINC for measurements, SNOMED for conditions).
- **Live Documentation**: Resource access to live OMOP CDM documentation.
Usage Example
The agent is most effective when you provide context such as the OMOP table or field name.
**Prompt:**
**Response Example:**
Contributing
See CONTRIBUTING.md for guidelines to contribute to the project.
Citation Policy
If you use this software, please cite the pre-print at arXiv (cs.AI) below: