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. This server provides an agentic framework to standardize medical terms into the OMOP Common Data Model (CDM). It uses the OMOPHub API for vo
Add this skill
npx mdskills install OHNLP/omop-mcpWell-documented MCP server for medical terminology standardization with clear setup and useful capabilities
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.
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.
Before configuring the MCP server, ensure you have:
uv installed on your system
Clone the repository
git clone https://github.com/OHNLP/omop_mcp.git
cd omop_mcp
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
Add the following configuration to your claude_desktop_config.json file:
Location:
~/Library/Application\ Support/Claude/claude_desktop_config.json%APPDATA%/Claude/claude_desktop_config.jsonConfiguration:
Replace `` with the actual path to your cloned repository.
{
"mcpServers": {
"omop_mcp": {
"command": "uv",
"args": ["--directory", "", "run", "omop_mcp"]
}
}
}
The OMOP MCP server provides tools and resources for:
find_omop_concept.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
See CONTRIBUTING.md for guidelines to contribute to the project.
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
This project is licensed under the Apache License 2.0. See LICENSE file for details.
Contact: jaerongahn@gmail.com
Install via CLI
npx mdskills install OHNLP/omop-mcpOMOP MCP Server is a free, open-source AI agent skill. 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. This server provides an agentic framework to standardize medical terms into the OMOP Common Data Model (CDM). It uses the OMOPHub API for vo
Install OMOP MCP Server with a single command:
npx mdskills install OHNLP/omop-mcpThis downloads the skill files into your project and your AI agent picks them up automatically.
OMOP MCP Server works with Claude Code, Claude Desktop, Cursor, Vscode Copilot, Windsurf, Continue Dev, Gemini Cli, Amp, Roo Code, Goose. Skills use the open SKILL.md format which is compatible with any AI coding agent that reads markdown instructions.