Enhancing Semantic Interoperability in Precision Medicine: Converting OMOP CDM to Beacon v2 in the Spanish IMPaCT- Data Project
Rueda, M.; Ramirez-Anguita, J. M.; Lopez-Sanchez, V.; Aguilo-Castillo, S.; Gas Lopez, M. E.; Labarga, A.; Mayer, M. A.; Ripoll Esteve, J.; Gut, I. G.
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ObjectiveTo introduce novel methods to convert OMOP CDM data into GA4GH Beacon v2 format, enhancing semantic interoperability within Spains IMPaCT-Data program for personalized medicine. Materials and MethodsWe 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. ResultsWe 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 ConclusionThis 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.
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