Enhancing semantic interoperability in precision medicine: converting OMOP CDM to Beacon v2 in the Spanish IMPaCT-Data project

OBJECTIVE: To evaluate a file-based approach for converting OMOP CDM data into GA4GH Beacon v2 format and outline an alternative on-the-fly architecture for real-time access, with the aim of enhancing semantic interoperability within Spain's IMPaCT-Data program for personalized medicine. MATERIALS AND METHODS: We used the Convert-Pheno tool to transform OMOP CDM exports into Beacon v2 format using a file-based approach. In addition, we describe an architecture that connects PostgreSQL-based OMOP CDM instances directly to the Beacon v2 API, enabling real-time data access without intermediary text files. RESULTS: We successfully converted OMOP CDM datasets from three research centers (CNAG, IIS La Fe, and HMar) to Beacon v2 format with high data completeness (≥ 99.9% across most domains). DISCUSSION AND CONCLUSION: This study evaluates a file-based approach and describes an alternative on-the-fly architecture for integrating OMOP CDM data with Beacon v2. These approaches provide practical options for integrating OMOP CDM data with Beacon v2 in different deployment settings.