Development of a Coronavirus Disease 2019 (COVID-19) Application Ontology for the Accrual to Clinical Trials (ACT) network

Shyam Visweswaran^{1

2}, Malarkodi J Samayamuthu¹, Michele Morris¹, Griffin M Weber³, Douglas MacFadden⁴, Philip Trevvett⁴, Jeffrey G Klann⁵, Vivian S Gainer⁶, Barbara Benoit⁶, Shawn N Murphy^{6

7}, Lav Patel⁸, Nebojsa Mirkovic⁹, Yuliya Borovskiy⁹, Robert D Johnson¹⁰, Matthew C Wyatt¹⁰, Amy Y Wang¹¹, Robert W Follett¹², Ngan Chau¹², Wenhong Zhu¹³, Mark Abajian¹⁴, Amy Chuang¹⁴, Neil Bahroos¹⁴, Phillip Reeder¹⁵, Donglu Xie¹⁶, Jennifer Cai¹⁵, Elaina R Sendro¹⁷, Robert D Toto⁸, Gary S Firestein¹³, Lee M Nadler⁴, Steven E Reis²

Affiliations

¹ Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
² Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
³ Department of Biomedical Informatics, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.
⁴ The Harvard Clinical and Translational Science Center, Harvard Medical School, Boston, Massachusetts, USA.
⁵ Laboratory of Computer Science, Department of Medicine, Mass General Brigham, Boston, Massachusetts, USA.
⁶ Research Information Science and Computing, Partners Healthcare, Boston, Massachusetts, USA.
⁷ Department of Neurology, Mass General Brigham, Harvard Medical School, Boston, Massachusetts, USA.
⁸ Center for Medical Informatics and Enterprise Analytics, University of Kansas Medical Center, Kansas City, Kansas, USA.
⁹ Data Analytics Center, University of Pennsylvania Health System, Philadelphia, Pennsylvania, USA.
¹⁰ Center for Clinical and Translational Science, The University of Alabama at Birmingham, Birmingham, Alabama, USA.
¹¹ Departments of Medicine and Family and Community Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, USA.
¹² Clinical and Translational Institute, University of California at Los Angeles, Los Angeles, California, USA.
¹³ Altman Clinical Translational Research Institute, University of California at San Diego, La Jolla, California, USA.
¹⁴ Southern California Clinical and Translational Institute, University of Southern California, Los Angeles, California, USA.
¹⁵ University of Texas Southwestern Medical Center, Dallas, Texas, USA.
¹⁶ Academic Information Systems-Information Resources, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
¹⁷ The Chartis Group, Chicago, Illinois, USA and Center for Translational Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA.

PMID: 34113801
PMCID: PMC8083220
DOI: 10.1093/jamiaopen/ooab036

Development of a Coronavirus Disease 2019 (COVID-19) Application Ontology for the Accrual to Clinical Trials (ACT) network

Shyam Visweswaran et al. JAMIA Open. 2021.

. 2021 Apr 19;4(2):ooab036.

doi: 10.1093/jamiaopen/ooab036. eCollection 2021 Apr.

Authors

Affiliations

¹ Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
² Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
³ Department of Biomedical Informatics, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.
⁴ The Harvard Clinical and Translational Science Center, Harvard Medical School, Boston, Massachusetts, USA.
⁵ Laboratory of Computer Science, Department of Medicine, Mass General Brigham, Boston, Massachusetts, USA.
⁶ Research Information Science and Computing, Partners Healthcare, Boston, Massachusetts, USA.
⁷ Department of Neurology, Mass General Brigham, Harvard Medical School, Boston, Massachusetts, USA.
⁸ Center for Medical Informatics and Enterprise Analytics, University of Kansas Medical Center, Kansas City, Kansas, USA.
⁹ Data Analytics Center, University of Pennsylvania Health System, Philadelphia, Pennsylvania, USA.
¹⁰ Center for Clinical and Translational Science, The University of Alabama at Birmingham, Birmingham, Alabama, USA.
¹¹ Departments of Medicine and Family and Community Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, USA.
¹² Clinical and Translational Institute, University of California at Los Angeles, Los Angeles, California, USA.
¹³ Altman Clinical Translational Research Institute, University of California at San Diego, La Jolla, California, USA.
¹⁴ Southern California Clinical and Translational Institute, University of Southern California, Los Angeles, California, USA.
¹⁵ University of Texas Southwestern Medical Center, Dallas, Texas, USA.
¹⁶ Academic Information Systems-Information Resources, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
¹⁷ The Chartis Group, Chicago, Illinois, USA and Center for Translational Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA.

PMID: 34113801
PMCID: PMC8083220
DOI: 10.1093/jamiaopen/ooab036

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.

Keywords: COVID-19; clinical data network; electronic health records; ontology.

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Figures

**Figure 1.**
Screenshot of ACT COVID-19 ontology with illustrative examples of computable phenotype, derived term, existing terms, harmonized value set, and emerging terms. In the screenshot, only terms are displayed for easy comprehension; however, codes can also be displayed. ACT: Accrual to Clinical Trials; COVID-19: coronavirus disease 2019.

See this image and copyright information in PMC

Update of

Development of a COVID-19 Application Ontology for the ACT Network.
Visweswaran S, Samayamuthu MJ, Morris M, Weber GM, MacFadden D, Trevvett P, Klann JG, Gainer V, Benoit B, Murphy SN, Patel L, Mirkovic N, Borovskiy Y, Johnson RD, Wyatt MC, Wang AY, Follett RW, Chau N, Zhu W, Abajian M, Chuang A, Bahroos N, Reeder P, Xie D, Cai J, Sendro ER, Toto RD, Firestein GS, Nadler LM, Reis SE. Visweswaran S, et al. medRxiv [Preprint]. 2021 Apr 14:2021.03.15.21253596. doi: 10.1101/2021.03.15.21253596. medRxiv. 2021. Update in: JAMIA Open. 2021 Apr 19;4(2):ooab036. doi: 10.1093/jamiaopen/ooab036. PMID: 33791734 Free PMC article. Updated. Preprint.

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Development of a Coronavirus Disease 2019 (COVID-19) Application Ontology for the Accrual to Clinical Trials (ACT) network

Affiliations

Development of a Coronavirus Disease 2019 (COVID-19) Application Ontology for the Accrual to Clinical Trials (ACT) network

Authors

Affiliations

Abstract

Figures

Update of

References

Grants and funding

LinkOut - more resources

Full Text Sources