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

Autores de IIS La Fe

• Victoria López Sánchez

  Autor

• María Eugenia Gas López

  Autor

• Francisco Javier Ripoll Esteve

  Autor

Participantes ajenos a IIS La Fe

• Rueda M
• Ramírez-Anguita JM
• Aguiló-Castillo S
• Labarga A
• Mayer MÁ
• Gut IG

Grupos

• Unidad Mixta de Investigacion en TICs aplicadas a la reingeniería en procesos sociosanitarios (ERPSS)

Abstract

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.

© 2026. The Author(s).

Keywords

• Clinical data integration; Clinical data mapping; Electronic health records; FAIR data; GA4GH Beacon v2; Health data interoperability; OMOP Common Data Model (OMOP CDM); Open-source software; Precision medicine; Semantic interoperability