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- Title
Ontologizing health systems data at scale: making translational discovery a reality.
- Authors
Callahan, Tiffany J.; Stefanski, Adrianne L.; Wyrwa, Jordan M.; Zeng, Chenjie; Ostropolets, Anna; Banda, Juan M.; Baumgartner Jr., William A.; Boyce, Richard D.; Casiraghi, Elena; Coleman, Ben D.; Collins, Janine H.; Deakyne Davies, Sara J.; Feinstein, James A.; Lin, Asiyah Y.; Martin, Blake; Matentzoglu, Nicolas A.; Meeker, Daniella; Reese, Justin; Sinclair, Jessica; Taneja, Sanya B.
- Abstract
Common data models solve many challenges of standardizing electronic health record (EHR) data but are unable to semantically integrate all of the resources needed for deep phenotyping. Open Biological and Biomedical Ontology (OBO) Foundry ontologies provide computable representations of biological knowledge and enable the integration of heterogeneous data. However, mapping EHR data to OBO ontologies requires significant manual curation and domain expertise. We introduce OMOP2OBO, an algorithm for mapping Observational Medical Outcomes Partnership (OMOP) vocabularies to OBO ontologies. Using OMOP2OBO, we produced mappings for 92,367 conditions, 8611 drug ingredients, and 10,673 measurement results, which covered 68–99% of concepts used in clinical practice when examined across 24 hospitals. When used to phenotype rare disease patients, the mappings helped systematically identify undiagnosed patients who might benefit from genetic testing. By aligning OMOP vocabularies to OBO ontologies our algorithm presents new opportunities to advance EHR-based deep phenotyping.
- Subjects
SEMANTICS; HOSPITALS; CLINICAL pathology; STATISTICS; INFERENTIAL statistics; MEDICAL information storage &; retrieval systems; RESEARCH evaluation; MANAGEMENT of medical records; IDENTIFICATION; METADATA; GENETIC testing; DISEASES; PATIENTS; CASE-control method; MANN Whitney U Test; COMPARATIVE studies; MEDICAL subject headings; VOCABULARY; DESCRIPTIVE statistics; DRUGS; CHI-squared test; ONTOLOGIES (Information retrieval); ELECTRONIC health records; MEDICAL practice; MEDICAL informatics; SYSTEMATIZED Nomenclature of Medicine; DATA analysis; DATA analysis software; ALGORITHMS; PHENOTYPES; RARE diseases; CONCEPTS
- Publication
NPJ Digital Medicine, 2023, Vol 6, Issue 1, p1
- ISSN
2398-6352
- Publication type
Article
- DOI
10.1038/s41746-023-00830-x