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

Mapping 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. ### Competing Interest Statement Dr. Khera is an Associate Editor of JAMA. He also receives research support, through Yale, from Bristol-Myers Squibb, Novo Nordisk, and BridgeBio. He is a coinventor of U.S. Pending Patent Applications 63/562,335, 63/177,117, 63/428,569, 63/346,610, 63/484,426, 63/508,315, and 63/606,203. He is a co-founder of Ensight-AI, Inc. and Evidence2Health, health platforms to improve cardiovascular diagnosis and evidence-based cardiovascular care. ### Funding Statement Dr. Khera was supported by the National Heart, Lung, and Blood Institute of the National Institutes of Health (under awards R01HL167858 and K23HL153775) and the Doris Duke Charitable Foundation (under award 2022060). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The Yale institutional review board reviewed the study, approved the study protocol, and waived the need for informed consent, as the study represents a secondary analysis of existing data. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes The model was evaluated on protected health information, which cannot be shared publicly to protect patient confidentiality. The OMOP dictionaries used to train the model are available at: https://athena.ohdsi.org/vocabulary/list