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bioRxiv · 10.1101/2025.07.15.664501

Mapping and Harmonization of CVX vaccine terms tothe Vaccine Ontology

Pan, Y.·Manuel, W.·Abeysinghe, R.·Zheng, J.·Davydov, A.·Yang, Q.·Lin, A. Y.·Cui, L.·He, Y.
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Abstract

BackgroundWith many vaccines developed and used, it is critical to standardize vaccine information. The OHDSI OMOP Common Data Model (CDM), widely used to support EHR data integration and analysis, leverages CVX, RxNorm, and RxNorm Extension codes to standardize vaccine-related records. However, these terminologies lack robust semantic relations, making the vaccine classification ineffective in OMOP CDM. To address this issue, our OHDSI Vaccine Vocabulary Working Group proposes to use the Vaccine Ontology (VO) to map these standards and build up its own semantic relations. As a first study of the work, we performed the mapping and alignment of the Vaccine Administered (CVX) codes with the VO using a combination of semi-automatic and manual mapping methods. ResultsA total of 273 CVX terms were first collected and classified. A high-level VO design pattern and an exact one-to-one mapping strategy were developed to guide the CVX-to-VO term mapping. To facilitate the manual mapping and harmonization process, we also developed and evaluated three semi-automated mapping approaches utilizing lexical and semantic information of vaccine concepts to map CVX to VO. These approaches suggested candidate VO mappings for CVX terms and also indicated CVX terms that were unmappable to VO and required new term additions to VO. The application of the best approach to the 2022-10-05 release of VO achieved an accuracy of 85.55% for its suggestions. The suggestions made by the semi-automated approaches were taken into account to further enhance the mappings, which led to our eventual mapping of all CVX terms to the latest version of VO. We innovatively proposed the inclusion of the passive vaccine branch in VO, which includes 24 immunoglobulins and antitoxins from CVX as passive vaccines. A specific CVX-VO OWL file was developed and added to the VO GitHub. Use case queries were developed to demonstrate its support for computer-assisted queries of vaccine groups based on CVX-VO hierarchies. ConclusionAll CVX terms were mapped to the VO using our combined semi-automatic and manual mapping methods. The mapped results enhanced semantic vaccine classification, providing a basis for further OMOP vaccine classification and EHR data analysis.

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Pan, Y., Manuel, W., Abeysinghe, R., Zheng, J., Davydov, A., Yang, Q., Lin, A. Y., Cui, L., He, Y.. 2025-07-18. Mapping and Harmonization of CVX vaccine terms tothe Vaccine Ontology. https://doi.org/10.1101/2025.07.15.664501

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