OMOP MCP

OMOP MCP

Map clinical terminology to OMOP concepts using LLMs for healthcare data standardization.

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Overview

OMOP MCP Server is a Model Context Protocol (MCP) server that maps clinical terminology to Observational Medical Outcomes Partnership (OMOP) concepts using Large Language Models (LLMs). It provides the find_omop_concept tool to map terms to OMOP concepts, validate terminology mappings, search the OMOP vocabulary, and convert between different clinical coding systems. This server supports prompting guidance to improve accuracy, such as specifying the target OMOP field and table name (e.g., measurement_concept_id in the measurement table) and prioritizing vocabularies (e.g., SNOMED preferred or LOINC > SNOMED > RxNorm). The OMOP concept data and fields can be explored through omop_concept_id_fields.json, which lists OMOP fields and tables that store concept IDs. Claude Desktop integration is supported via claude_desktop_config.json, enabling local workflow execution with a configured environment. Setup requires environment variables for API access (Azure OpenAI or OpenAI). The project emphasizes healthcare data standardization and interoperability, returning OMOP metadata such as CONCEPT_ID, CODE, NAME, CLASS, VOCAB, and related URLs for mapped concepts. The repository is Apache 2.0 licensed and designed for researchers and practitioners working with OMOP mappings.

Details

Owner
OHNLP
Language
Python
License
Other
Updated
2025-12-07

Features

Map clinical terminology to OMOP concepts

Uses the find_omop_concept tool to map terms to OMOP concepts and obtain related metadata.

Validate terminology mappings

Provides validation of mappings to ensure correctness and consistency.

Search OMOP vocabulary

Enables lookup and exploration of terms within the OMOP vocabulary.

Convert between clinical coding systems

Supports conversion between different coding systems as part of the mapping workflow.

Audience

DevelopersInstall, configure, and run the MCP server to map terminology to OMOP concepts for integration into healthcare data platforms.
Clinical informaticiansValidate and standardize terminology mappings against the OMOP vocabulary.
Healthcare data engineersIncorporate OMOP concept mappings into ETL pipelines and analytics workflows, and design prompts with vocabulary priorities.

Tags

OMOPMCPLLMclinical terminologyvocabulary mappinghealthcare standardizationconcept mappingOMOP vocabulary