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[Preprint]. 2021 Sep 17:arXiv:2109.08633v1.

An Open-Publishing Response to the COVID-19 Infodemic

Halie M Rando  1   2   3 , Simina M Boca  4 , Lucy D'Agostino McGowan  5 , Daniel S Himmelstein  3   6 , Michael P Robson  7 , Vincent Rubinetti  1   3 , Ryan Velazquez  8 ; COVID-19 Review Consortium; Casey S Greene  1   2   3   9 , Anthony Gitter  10   11
Affiliations

An Open-Publishing Response to the COVID-19 Infodemic

Halie M Rando et al. ArXiv. .

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Abstract

The COVID-19 pandemic catalyzed the rapid dissemination of papers and preprints investigating the disease and its associated virus, SARS-CoV-2. The multifaceted nature of COVID-19 demands a multidisciplinary approach, but the urgency of the crisis combined with the need for social distancing measures present unique challenges to collaborative science. We applied a massive online open publishing approach to this problem using Manubot. Through GitHub, collaborators summarized and critiqued COVID-19 literature, creating a review manuscript. Manubot automatically compiled citation information for referenced preprints, journal publications, websites, and clinical trials. Continuous integration workflows retrieved up-to-date data from online sources nightly, regenerating some of the manuscript's figures and statistics. Manubot rendered the manuscript into PDF, HTML, LaTeX, and DOCX outputs, immediately updating the version available online upon the integration of new content. Through this effort, we organized over 50 scientists from a range of backgrounds who evaluated over 1,500 sources and developed seven literature reviews. While many efforts from the computational community have focused on mining COVID-19 literature, our project illustrates the power of open publishing to organize both technical and non-technical scientists to aggregate and disseminate information in response to an evolving crisis.

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Figures

Figure 1:
Figure 1:. Growth of the CORD-19 dataset.
The number of articles has proliferated, with both traditional and preprint manuscripts in the corpus. The first release (March 16, 2020) contained 28,000 documents [3]. As of September 6, 2021, this had increased to 768,929 articles. Of these, 30,726 are preprints from arXiv, medRxiv, and bioRxiv.
Figure 2:
Figure 2:. COVID-19 review GitHub repository organization and workflows.
Manubot uses CI to combine author-contributed content with automatically updated information from outside sources. A nightly workflow updates figures and statistics derived from external resources. Authors write text and add figures to the master branch (starred) via GitHub pull requests. Manubot generates updated manuscript outputs for each new git commit, integrating the static text and figures with the dynamic statistics and figures and automatically-extracted citation information. GitHub Pages hosts the latest HTML and PDF versions of the manuscript along with permanent links to prior versions.
Figure 3:
Figure 3:. Project growth over time.
The number of authors, word count, and number of references have all grown dramatically from when the project began on March 20, 2020. As of September 10, 2021, there were 52 authors (including consortia), 1,676 references, and 138,213 words. The spike in word count during summer 2020 was caused by erroneous duplication and subsequent removal of a large appendix.
Figure 4:
Figure 4:. User contributions to the manuscript text over time.
The dot size indicates the number of words added or edited each month since March 2020. The figure does not depict other types of author contributions such as literature summaries, pull request review, visualization, or software.
See this image and copyright information in PMC

References

    1. Vlasschaert C., Topf J. M., Hiremath S., Proliferation of Papers and Preprints During the Coronavirus Disease 2019 Pandemic: Progress or Problems With Peer Review?, Advances in Chronic Kidney Disease 27 (2020) 418–426. - PMC - PubMed
    1. Zarocostas J., How to fight an infodemic, The Lancet 395 (2020) 676. - PMC - PubMed
    1. Wang L. L., Lo K., Chandrasekhar Y., Reas R., Yang J., Burdick D., Eide D., Funk K., Katsis Y., Kinney R., Li Y., Liu Z., Merrill W., Mooney P., Murdick D., Rishi D., Sheehan J., Shen Z., Stilson B., Wade A., Wang K., Wang N. X. R., Wilhelm C., Xie B., Raymond D., Weld D. S., Etzioni O., Kohlmeier S., CORD-19: The COVID-19 Open Research Dataset, arXiv (2020) 2004.10706.
    1. Lever J., Altman R. B., Analyzing the vast coronavirus literature with CoronaCentral, Proceedings of the National Academy of Sciences 118 (2021) e2100766118. - PMC - PubMed
    1. Eysenbach G., The impact of preprint servers and electronic publishing on biomedical research, Current Opinion in Immunology 12 (2000) 499–503. - PubMed

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