OMOP MCP Server

Example Use Cases

• 1

  Map free-text or source clinical terms to OMOP concept IDs and receive concept metadata and justification.

• 2

  Validate or audit existing terminology mappings against OMOP vocabularies and flag non-standard or invalid mappings.

• 3

  Search OMOP vocabulary and convert between clinical coding systems (e.g., prioritize SNOMED, LOINC, RxNorm) for integration into ETL workflows.

Description

An open-source MCP server that uses large language models to map, validate, and search clinical terminology against the OMOP vocabulary. It provides a find_omop_concept tool to convert between coding systems (e.g., LOINC, SNOMED, RxNorm), validate mappings, and return concept metadata and rationale. Integrates with agents (e.g., Claude Desktop) and supports configuration for Azure/OpenAI; benefits include faster concept standardization and improved interoperability for clinical data pipelines.