Enhancing Semantic Interoperability in Precision Medicine: Converting OMOP CDM to Beacon v2 in the Spanish IMPaCT-Data Project

Abstract

Objective: To introduce novel methods to convert OMOP CDM data into GA4GH Beacon v2 format, enhancing semantic interoperability within Spain-s IMPaCT-Data program for personalized medicine. Materials and Methods: We utilized a file-based approach with the Convert-Pheno tool to transform OMOP CDM exports into Beacon v2 format. Additionally, we developed a direct connection from PostgreSQL OMOP CDM 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 nearly 100% data completeness. The direct connection approach improved data freshness and adaptability for dynamic environments. Discussion and Conclusion: This study introduces two methodologies for integrating OMOP CDM data with Beacon v2, offering performance optimization or real-time access. These methodologies can be adopted by other centers to enhance interoperability and collaboration in health data sharing.