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Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery.
Zhang, Xingmin Aaron; Yates, Amy; Vasilevsky, Nicole; Gourdine, J P; Callahan, Tiffany J; Carmody, Leigh C; Danis, Daniel; Joachimiak, Marcin P; Ravanmehr, Vida; Pfaff, Emily R; Champion, James; Robasky, Kimberly; Xu, Hao; Fecho, Karamarie; Walton, Nephi A; Zhu, Richard L; Ramsdill, Justin; Mungall, Christopher J; Köhler, Sebastian; Haendel, Melissa A; McDonald, Clement J; Vreeman, Daniel J; Peden, David B; Bennett, Tellen D; Feinstein, James A; Martin, Blake; Stefanski, Adrianne L; Hunter, Lawrence E; Chute, Christopher G; Robinson, Peter N.
Afiliación
  • Zhang XA; The Jackson Laboratory for Genomic Medicine, Farmington CT 06032, USA.
  • Yates A; Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR 97239, USA.
  • Vasilevsky N; Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR 97239, USA.
  • Gourdine JP; Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR 97239, USA.
  • Callahan TJ; Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR 97239, USA.
  • Carmody LC; Library, Oregon Health and Science University, Portland, OR 97239, USA.
  • Danis D; Computational Bioscience Program, Department of Pharmacology, University of Colorado Anschutz School of Medicine, Aurora, CO 80045, USA.
  • Joachimiak MP; The Jackson Laboratory for Genomic Medicine, Farmington CT 06032, USA.
  • Ravanmehr V; The Jackson Laboratory for Genomic Medicine, Farmington CT 06032, USA.
  • Pfaff ER; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Champion J; The Jackson Laboratory for Genomic Medicine, Farmington CT 06032, USA.
  • Robasky K; North Carolina Translational and Clinical Sciences Institute (NC TraCS), University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
  • Xu H; North Carolina Translational and Clinical Sciences Institute (NC TraCS), University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
  • Fecho K; North Carolina Translational and Clinical Sciences Institute (NC TraCS), University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
  • Walton NA; Genetics Department, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
  • Zhu RL; School of Information and Library Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
  • Ramsdill J; Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
  • Mungall CJ; Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
  • Köhler S; Genomic Medicine Institute, Geisinger Health System, Danville, PA 17822, USA.
  • Haendel MA; Institute for Clinical and Translational Research, Johns Hopkins University, Baltimore, MD 21202, USA.
  • McDonald CJ; Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR 97239, USA.
  • Vreeman DJ; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Peden DB; Charité Centrum für Therapieforschung, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany.
  • Bennett TD; Einstein Center Digital Future, Berlin 10117, Germany.
  • Feinstein JA; Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR 97239, USA.
  • Martin B; Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR 97239, USA.
  • Stefanski AL; Linus Pauling Institute and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA.
  • Hunter LE; Lister Hill National Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
  • Chute CG; Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
  • Robinson PN; Center for Biomedical Informatics, Regenstrief Institute, Inc., Indianapolis, IN 46202, USA.
NPJ Digit Med ; 22019.
Article en En | MEDLINE | ID: mdl-31119199
ABSTRACT
Electronic Health Record (EHR) systems typically define laboratory test results using the Laboratory Observation Identifier Names and Codes (LOINC) and can transmit them using Fast Healthcare Interoperability Resource (FHIR) standards. LOINC has not yet been semantically integrated with computational resources for phenotype analysis. Here, we provide a method for mapping LOINC-encoded laboratory test results transmitted in FHIR standards to Human Phenotype Ontology (HPO) terms. We annotated the medical implications of 2923 commonly used laboratory tests with HPO terms. Using these annotations, our software assesses laboratory test results and converts each result into an HPO term. We validated our approach with EHR data from 15,681 patients with respiratory complaints and identified known biomarkers for asthma. Finally, we provide a freely available SMART on FHIR application that can be used within EHR systems. Our approach allows readily available laboratory tests in EHR to be reused for deep phenotyping and exploits the hierarchical structure of HPO to integrate distinct tests that have comparable medical interpretations for association studies.
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Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Idioma: En Revista: NPJ Digit Med Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Idioma: En Revista: NPJ Digit Med Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos