arXiv

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 (omapper)

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

   git clone https://github.com/OHNLP/omop_mcp.git
   cd omop_mcp
   

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).

   cp .env.template .env
   

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 <path-to-local-repo> with the actual path to your cloned repository.

{
  "mcpServers": {
    "omop_mcp": {
      "command": "uv",
      "args": ["--directory", "<path-to-local-repo>", "run", "omop_mcp"]
    }
  }
}

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:

Map `Temperature Temporal Scanner - RR` for `measurement_concept_id` in the `measurement` table.

Response Example:

CONCEPT_ID: 46235152
CODE: 75539-7
NAME: Body temperature - Temporal artery
CLASS: Clinical Observation
CONCEPT: Standard
VALIDITY: Valid
DOMAIN: Measurement
VOCAB: LOINC
REASON: This LOINC concept specifically represents body temperature measured at the temporal artery.
URL: https://athena.ohdsi.org/search-terms/terms/46235152

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:

An Agentic Model Context Protocol Framework for Medical Concept Standardization

License

This project is licensed under the Apache License 2.0. See LICENSE file for details.

Contact: [email protected]