Your browser doesn't support javascript.
loading
Ontologizing health systems data at scale: making translational discovery a reality.
Callahan, Tiffany J; Stefanski, Adrianne L; Wyrwa, Jordan M; Zeng, Chenjie; Ostropolets, Anna; Banda, Juan M; Baumgartner, 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; Trinkley, Katy E; Vasilevsky, Nicole A; Williams, Andrew E; Zhang, Xingmin A; Denny, Joshua C; Ryan, Patrick B; Hripcsak, George; Bennett, Tellen D; Haendel, Melissa A; Robinson, Peter N; Hunter, Lawrence E; Kahn, Michael G.
Afiliación
  • Callahan TJ; Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA. tiffany.callahan@cuanschutz.edu.
  • Stefanski AL; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, 10032, USA. tiffany.callahan@cuanschutz.edu.
  • Wyrwa JM; Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
  • Zeng C; Department of Physical Medicine and Rehabilitation, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
  • Ostropolets A; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
  • Banda JM; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, 10032, USA.
  • Baumgartner WA; Department of Computer Science, Georgia State University, Atlanta, GA, 30303, USA.
  • Boyce RD; Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
  • Casiraghi E; Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA.
  • Coleman BD; Computer Science, Università degli Studi di Milano, Milan, Italy.
  • Collins JH; The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
  • Deakyne Davies SJ; The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
  • Feinstein JA; Department of Haematology, University of Cambridge, Cambridge, UK.
  • Lin AY; Department of Research Informatics & Data Science, Analytics Resource Center, Children's Hospital Colorado, Aurora, CO, 80045, USA.
  • Martin B; Adult and Child Center for Health Outcomes Research and Delivery Science (ACCORDS), University of Colorado Anschutz School of Medicine, Aurora, CO, 80045, USA.
  • Matentzoglu NA; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
  • Meeker D; Departments of Biomedical Informatics and Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
  • Reese J; Semanticly, Athens, Greece.
  • Sinclair J; Yale School of Medicine, New Haven, CT, 06510, USA.
  • Taneja SB; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
  • Trinkley KE; HealthLinc, Valparaiso, IN, 46383, USA.
  • Vasilevsky NA; Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
  • Williams AE; Department of Family Medicine, University of Colorado Anschutz School of Medicine, Aurora, CO, 80045, USA.
  • Zhang XA; Translational and Integrative Sciences Lab, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
  • Denny JC; Tufts Institute for Clinical Research and Health Policy Studies, Tufts University, Boston, MA, 02155, USA.
  • Ryan PB; The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
  • Hripcsak G; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
  • Bennett TD; Janssen Research and Development, Raritan, NJ, 08869, USA.
  • Haendel MA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, 10032, USA.
  • Robinson PN; Departments of Biomedical Informatics and Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
  • Hunter LE; Departments of Biomedical Informatics and Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
  • Kahn MG; The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
NPJ Digit Med ; 6(1): 89, 2023 May 19.
Article en En | MEDLINE | ID: mdl-37208468
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.
Texto completo
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Base de datos: MEDLINE Tipo de estudio: Guideline Idioma: En Revista: NPJ Digit Med Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Base de datos: MEDLINE Tipo de estudio: Guideline Idioma: En Revista: NPJ Digit Med Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos