Model Context Protocol (MCP) server for mapping clinical terminology to Observational Medical Outcomes Partnership (OMOP) concepts using Large Language Models (LLMs).

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 (only for API calls)

   Copy .env.template and configure your API credentials:

   cp .env.template .env

   Edit .env with API credentials:

   # Azure OpenAI Configuration
   AZURE_OPENAI_ENDPOINT=
   AZURE_OPENAI_API_KEY=
   AZURE_API_VERSION=
   MODEL_NAME=
   
   # OpenAI Configuration (alternative)
   OPENAI_API_KEY=

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"]
    }
  }
}

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

• 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.

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: [email protected]