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Development of a Coronavirus Disease 2019 (COVID-19) Application Ontology for the Accrual to Clinical Trials (ACT) network.
Visweswaran, Shyam; Samayamuthu, Malarkodi J; Morris, Michele; Weber, Griffin M; MacFadden, Douglas; Trevvett, Philip; Klann, Jeffrey G; Gainer, Vivian S; Benoit, Barbara; Murphy, Shawn N; Patel, Lav; Mirkovic, Nebojsa; Borovskiy, Yuliya; Johnson, Robert D; Wyatt, Matthew C; Wang, Amy Y; Follett, Robert W; Chau, Ngan; Zhu, Wenhong; Abajian, Mark; Chuang, Amy; Bahroos, Neil; Reeder, Phillip; Xie, Donglu; Cai, Jennifer; Sendro, Elaina R; Toto, Robert D; Firestein, Gary S; Nadler, Lee M; Reis, Steven E.
  • Visweswaran S; Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
  • Samayamuthu MJ; Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
  • Morris M; Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
  • Weber GM; Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
  • MacFadden D; Department of Biomedical Informatics, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.
  • Trevvett P; The Harvard Clinical and Translational Science Center, Harvard Medical School, Boston, Massachusetts, USA.
  • Klann JG; The Harvard Clinical and Translational Science Center, Harvard Medical School, Boston, Massachusetts, USA.
  • Gainer VS; Laboratory of Computer Science, Department of Medicine, Mass General Brigham, Boston, Massachusetts, USA.
  • Benoit B; Research Information Science and Computing, Partners Healthcare, Boston, Massachusetts, USA.
  • Murphy SN; Research Information Science and Computing, Partners Healthcare, Boston, Massachusetts, USA.
  • Patel L; Research Information Science and Computing, Partners Healthcare, Boston, Massachusetts, USA.
  • Mirkovic N; Department of Neurology, Mass General Brigham, Harvard Medical School, Boston, Massachusetts, USA.
  • Borovskiy Y; Center for Medical Informatics and Enterprise Analytics, University of Kansas Medical Center, Kansas City, Kansas, USA.
  • Johnson RD; Data Analytics Center, University of Pennsylvania Health System, Philadelphia, Pennsylvania, USA.
  • Wyatt MC; Data Analytics Center, University of Pennsylvania Health System, Philadelphia, Pennsylvania, USA.
  • Wang AY; Center for Clinical and Translational Science, The University of Alabama at Birmingham, Birmingham, Alabama, USA.
  • Follett RW; Center for Clinical and Translational Science, The University of Alabama at Birmingham, Birmingham, Alabama, USA.
  • Chau N; Departments of Medicine and Family and Community Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, USA.
  • Zhu W; Clinical and Translational Institute, University of California at Los Angeles, Los Angeles, California, USA.
  • Abajian M; Clinical and Translational Institute, University of California at Los Angeles, Los Angeles, California, USA.
  • Chuang A; Altman Clinical Translational Research Institute, University of California at San Diego, La Jolla, California, USA.
  • Bahroos N; Southern California Clinical and Translational Institute, University of Southern California, Los Angeles, California, USA.
  • Reeder P; Southern California Clinical and Translational Institute, University of Southern California, Los Angeles, California, USA.
  • Xie D; Southern California Clinical and Translational Institute, University of Southern California, Los Angeles, California, USA.
  • Cai J; University of Texas Southwestern Medical Center, Dallas, Texas, USA.
  • Sendro ER; Academic Information Systems-Information Resources, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
  • Toto RD; University of Texas Southwestern Medical Center, Dallas, Texas, USA.
  • Firestein GS; The Chartis Group, Chicago, Illinois, USA and Center for Translational Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
  • Nadler LM; Center for Medical Informatics and Enterprise Analytics, University of Kansas Medical Center, Kansas City, Kansas, USA.
  • Reis SE; Altman Clinical Translational Research Institute, University of California at San Diego, La Jolla, California, USA.
JAMIA Open ; 4(2): ooab036, 2021 Apr.
Article in English | MEDLINE | ID: covidwho-1266122
ABSTRACT
Clinical data networks that leverage large volumes of data in electronic health records (EHRs) are significant resources for research on coronavirus disease 2019 (COVID-19). Data harmonization is a key challenge in seamless use of multisite EHRs for COVID-19 research. We developed a COVID-19 application ontology in the national Accrual to Clinical Trials (ACT) network that enables harmonization of data elements that are critical to COVID-19 research. The ontology contains over 50 000 concepts in the domains of diagnosis, procedures, medications, and laboratory tests. In particular, it has computational phenotypes to characterize the course of illness and outcomes, derived terms, and harmonized value sets for severe acute respiratory syndrome coronavirus 2 laboratory tests. The ontology was deployed and validated on the ACT COVID-19 network that consists of 9 academic health centers with data on 14.5M patients. This ontology, which is freely available to the entire research community on GitHub at https//github.com/shyamvis/ACT-COVID-Ontology, will be useful for harmonizing EHRs for COVID-19 research beyond the ACT network.
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Full text: Available Collection: International databases Database: MEDLINE Language: English Journal: JAMIA Open Year: 2021 Document Type: Article Affiliation country: Jamiaopen

Full text: Available Collection: International databases Database: MEDLINE Language: English Journal: JAMIA Open Year: 2021 Document Type: Article Affiliation country: Jamiaopen