Converting OMOP CDM to Phenopackets: A Model Alignment and Patient Data Representation Evaluation

Presentation Time: 09:45 AM - 10:00 AM

Abstract Keywords: Data Transformation/ETL, Interoperability and Health Information Exchange, Data Sharing, Controlled Terminologies, Ontologies, and Vocabularies
Primary Track: Foundations
Programmatic Theme: Clinical Informatics

The study developed a data transformation process from OMOP CDM to Phenopackets, an emerging data standard designed for multimodal patient data storage and exchange. We evaluated transformations using real-world data, and incorporated UMLS semantic type filtering to reconcile ambiguous model alignment. We further evaluated Phenopackets’ suitability in representing real-world clinical cases. The data model conversion bridges OMOP’s large-scale research capabilities with Phenopackets’ support for biomedical knowledge integration via ontologies and capacity for point-of-care deployment.

Speaker(s):
Kayla Schiffer-Kane, MA
Columbia University

Author(s):
Chunhua Weng, PhD - Columbia University; Cong Liu, PhD - Columbia University; Casey Ta - Columbia University Dept of Biomedical Informatics; Jordan Nestor, MD, MS - Columbia University; Tiffany Callahan, MPH, PhD - Columbia University Irving Medical Center;