OMOP MCP Server
Model Context Protocol (MCP) server for mapping clinical terminology to Observational Medical Outcomes Partnership (OMOP) concepts using Large Language Models (LLMs).
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:
{
"mcpServers": {
"omop_mcp": {
"command": "uv",
"args": ["--directory", "<path-to-local-repo>", "run", "omop_mcp"]
}
}
}
Features
The OMOP MCP server provides the find_omop_concept tool for:
- Mapping clinical terminology to OMOP concepts
- Validating terminology mappings
- Searching OMOP vocabulary
- Converting between different clinical coding systems
Usage Example
-
It is recommended to specify the OMOP field and table name in the prompt for improved accuracy. Refer to omop_concept_id_fields.json for the list of OMOP fields and tables that store concept IDs.
-
You can specify preferred vocabularies for the mapping in order of priority (e.g., "SNOMED preferred" or "LOINC > SNOMED > RxNorm").
Prompt:
"Map Temperature Temporal Scanner - RR for measurement_concept_id in the measurement table."
Response:
CONCEPT_ID: 46235152
CODE: 75539-7
NAME: Body temperature - Temporal artery
CLASS: Clinical Observation
CONCEPT: Standard
VALIDITY: Valid
DOMAIN: Measurement
VOCAB: LOINC
URL: https://athena.ohdsi.org/search-terms/terms/46235152
REASON: This LOINC concept specifically represents body temperature measured at the temporal artery, which is what a temporal scanner measures. The "RR" in your source term likely refers to "Recovery Room" or another location/department indicator, but in OMOP, the location would typically be captured in a separate field rather than as part of the measurement concept itself.
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]
