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

Area of Science:

• Bioinformatics
• Health Informatics
• Genomic Data Standards

Background:

• The IMPaCT-Data program requires semantic interoperability for personalized medicine.
• Standardizing data formats like OMOP CDM and GA4GH Beacon v2 is crucial for data sharing and analysis.
• Existing methods for data conversion may not support real-time access needs.

Purpose of the Study:

• To assess a file-based method for converting OMOP CDM to GA4GH Beacon v2.
• To propose an on-the-fly architecture for real-time OMOP CDM data access via Beacon v2.
• To improve semantic interoperability within Spain's IMPaCT-Data program.

Main Methods:

• Utilized the Convert-Pheno tool for file-based OMOP CDM to Beacon v2 conversion.
• Developed and described an architecture connecting PostgreSQL OMOP CDM instances directly to the Beacon v2 API.
• Tested conversion with datasets from three Spanish research centers.

Main Results:

• Successful conversion of OMOP CDM datasets to Beacon v2 format.
• Achieved high data completeness (≥99.9%) across most data domains.
• Demonstrated feasibility of both file-based and real-time access architectures.

Conclusions:

• The file-based approach and on-the-fly architecture offer practical solutions for integrating OMOP CDM with Beacon v2.
• These methods enhance data accessibility and interoperability for personalized medicine research.
• The study provides adaptable strategies for diverse deployment scenarios in data integration.