A Novel Sentence Transformer-based Natural Language Processing Approach for Schema Mapping of Electronic Health Records to the OMOP Common Data Model

Abstract

AbstractMapping electronic health records (EHR) data to common data models (CDMs) enables the standardization of clinical records, enhancing interoperability and enabling large-scale, multi-centered clinical investigations. Using 2 large publicly available datasets, we developed transformer-based natural language processing models to map medication-related concepts from the EHR at a large and diverse healthcare system to standard concepts in OMOP CDM. We validated the model outputs against standard concepts manually mapped by clinicians. Our best model reached out-of-box accuracies of 96.5% in mapping the 200 most common drugs and 83.0% in mapping 200 random drugs in the EHR. For these tasks, this model outperformed a state-of-the-art large language model (SFR-Embedding-Mistral, 89.5% and 66.5% in accuracy for the two tasks), a widely-used software for schema mapping (Usagi, 90.0% and 70.0% in accuracy), and direct string match (7.5% and 7.5% accuracy). Transformer-based deep learning models outperform existing approaches in the standardized mapping of EHR elements and can facilitate an end-to-end automated EHR transformation pipeline.