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. 2021 Jul;68(4):1753-1760.
doi: 10.1111/tbed.13892. Epub 2021 Jan 29.

Interoperable medical data: The missing link for understanding COVID-19

Denis C Bauer  1   2 , Alejandro Metke-Jimenez  3 , Sebastian Maurer-Stroh  4   5   6   7 , Suma Tiruvayipati  7   8   9 , Laurence O W Wilson  1 , Yatish Jain  1 , Amandine Perrin  10   11   12 , Kate Ebrill  3 , David P Hansen  3 , Seshadri S Vasan  13   14
Affiliations

Interoperable medical data: The missing link for understanding COVID-19

Denis C Bauer et al. Transbound Emerg Dis. 2021 Jul.

Abstract

Being able to link clinical outcomes to SARS-CoV-2 virus strains is a critical component of understanding COVID-19. Here, we discuss how current processes hamper sustainable data collection to enable meaningful analysis and insights. Following the 'Fast Healthcare Interoperable Resource' (FHIR) implementation guide, we introduce an ontology-based standard questionnaire to overcome these shortcomings and describe patient 'journeys' in coordination with the World Health Organization's recommendations. We identify steps in the clinical health data acquisition cycle and workflows that likely have the biggest impact in the data-driven understanding of this virus. Specifically, we recommend detailed symptoms and medical history using the FHIR standards. We have taken the first steps towards this by making patient status mandatory in GISAID ('Global Initiative on Sharing All Influenza Data'), immediately resulting in a measurable increase in the fraction of cases with useful patient information. The main remaining limitation is the lack of controlled vocabulary or a medical ontology.

Keywords: COVID-19; GISAID; SARS-CoV-2; genome sequence; ontology; patient information.

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Conflict of interest statement

The authors declare that there are no competing interests.

Figures

Figure 1
Figure 1
Word cloud of GISAID 'patient status' entries, where word size represents number of entries with this term (log10‐transformed and pseudocounts to also visualize low frequency). (a) snapshot from 15 May 2020, (b) snapshot from 1 October 2020, after 'unknown' was made the default status when no status is provided. Actual counts are in Table S1; typographical and other errors faithfully reproduced, though now corrected in GISAID [Colour figure can be viewed at wileyonlinelibrary.com]
Figure 2
Figure 2
Example of a hierarchical terminology relationship [Colour figure can be viewed at wileyonlinelibrary.com]
Figure 3
Figure 3
Minimal common outcome measure as compiled by WHO. Figure reproduced from WHO Working Group on the Clinical Characterisation & Management of COVID‐ infection,  [Colour figure can be viewed at wileyonlinelibrary.com]
Figure 4
Figure 4
Example entry form for COVID‐19 patient information given in the Implementation Guide
Figure 5
Figure 5
SNOMED CT COVID‐19 symptoms value set shown in the Shrimp browser [Colour figure can be viewed at wileyonlinelibrary.com]
See this image and copyright information in PMC

References

    1. Banu, S., Jolly, B., Mukherjee, P., Singh, P., Khan, S., Zaveri, L., & Sowpati, D. T. (2020). A distinct phylogenetic cluster of Indian SARS‐CoV‐2 isolates. Open Forum Infectious Diseases, 7(11), 10.1093/ofid/ofaa434 - DOI - PMC - PubMed
    1. Bauer, D. C., Tay, A. P., Wilson, L. O. W., Reti, D., Hosking, C., McAuley, A. J., Vasan, S. S. (2020). Supporting pandemic response using genomics and bioinformatics: a case study on the emergent SARS‐CoV‐2 outbreak. Transboundary and Emerging Diseases, 67(4), 1453–1462. 10.1111/tbed.13588. - DOI - PMC - PubMed
    1. Chu, H., Chan, J.‐F.‐W., Yuen, T.‐T.‐T., Shuai, H., Yuan, S., Wang, Y., & Yuen, K.‐Y. (2020). Comparative tropism, replication kinetics, and cell damage profiling of SARS‐CoV‐2 and SARS‐CoV with implications for clinical manifestations, transmissibility, and laboratory studies of COVID‐19: An observational study. The Lancet Microbe, 1(1), E14–E23. 10.1016/S2666-5247(20)30004-5 - DOI - PMC - PubMed
    1. Dyer, C. (2020). Covid‐19: Rules on sharing confidential patient information are relaxed in England. BMJ (Clinical Research Ed.), 369, m1378. 10.1136/bmj.m1378 - DOI - PubMed
    1. Elbe, S., & Buckland‐Merrett, G. (2017). Data, disease and diplomacy: GISAID’s innovative contribution to global health. Global Challenges, 1(1), 33–46. 10.1002/gch2.1018 - DOI - PMC - PubMed