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. 2024 Apr 11;7(2):ooae025.
doi: 10.1093/jamiaopen/ooae025. eCollection 2024 Jul.

The Pandemic Response Commons

Matthew Trunnell  1 , Casey Frankenberger  2 , Bala Hota  2 , Troy Hughes  3 , Plamen Martinov  1 , Urmila Ravichandran  4 , Nirav S Shah  4 , Robert L Grossman  3 ; Pandemic Response Commons Consortium
Collaborators, Affiliations

The Pandemic Response Commons

Matthew Trunnell et al. JAMIA Open. .

Abstract

Objectives: A data commons is a software platform for managing, curating, analyzing, and sharing data with a community. The Pandemic Response Commons (PRC) is a data commons designed to provide a data platform for researchers studying an epidemic or pandemic.

Methods: The PRC was developed using the open source Gen3 data platform and is based upon consortium, data, and platform agreements developed by the not-for-profit Open Commons Consortium. A formal consortium of Chicagoland area organizations was formed to develop and operate the PRC.

Results: The consortium developed a general PRC and an instance of it for the Chicagoland region called the Chicagoland COVID-19 Commons. A Gen3 data platform was set up and operated with policies, procedures, and controls for a NIST SP 800-53 revision 4 Moderate system. A consensus data model for the commons was developed, and a variety of datasets were curated, harmonized and ingested, including statistical summary data about COVID cases, patient level clinical data, and SARS-CoV-2 viral variant data.

Discussion and conclusions: Given the various legal and data agreements required to operate a data commons, a PRC is designed to be in place and operating at a low level prior to the occurrence of an epidemic, with the activities increasing as required during an epidemic. A regional instance of a PRC can also be part of a broader data ecosystem or data mesh consisting of multiple regional commons supporting pandemic response through sharing regional data.

Keywords: data commons; data sharing; data systems; pandemic; regional data commons.

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Conflict of interest statement

None declared.

Figures

Figure 1.
Figure 1.
A screenshot of the Chicagoland COVID-19 Commons.
Figure 2.
Figure 2.
A screenshot of viral variants and their geographic distribution in the Chicagoland COVID-19 Commons.
Figure 3.
Figure 3.
A screenshot of a Jupyter notebook from the Chicagoland COVID-19 Commons.
See this image and copyright information in PMC

References

    1. Grossman RL. Data lakes, clouds, and commons: a review of platforms for analyzing and sharing genomic data. Trends Genet. 2019;35(3):223-234. 10.1016/j.tig.2018.12.006 - DOI - PMC - PubMed
    1. Haendel MA, Chute CG, Bennett TD, et al.; N3C Consortium. The national COVID cohort collaborative (N3C): rationale, design, infrastructure, and deployment. J Am Med Inform Assoc. 2021;28(3):427-443. 10.1093/jamia/ocaa196 - DOI - PMC - PubMed
    1. The COVID Tracking Project. Accessed July 9, 2021. https://covidtracking.com/
    1. Centers for Disease Control and Prevention (CDC). COVID Data Tracker. 2020. Accessed July 9, 2021. https://covid.cdc.gov/covid-data-tracker
    1. Grossman RL, Dry JR, Hanlon SE, et al.BloodPAC data commons for liquid biopsy data. JCO Clin Cancer Inform. 2021;5:479-486. 10.1200/CCI.20.00179 - DOI - PMC - PubMed

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