Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Apr;20(4):536-540.
doi: 10.1038/s41592-023-01770-w. Epub 2023 Feb 23.

Outbreak.info Research Library: a standardized, searchable platform to discover and explore COVID-19 resources

Ginger Tsueng  1 , Julia L Mullen  2 , Manar Alkuzweny  3   4 , Marco Cano  2 , Benjamin Rush  5 , Emily Haag  2 , Jason Lin  2 , Dylan J Welzel  2 , Xinghua Zhou  2 , Zhongchao Qian  2 , Alaa Abdel Latif  4 , Emory Hufbauer  4 , Mark Zeller  4 , Kristian G Andersen  4   6 , Chunlei Wu  2   6   7 , Andrew I Su  2   6   7 , Karthik Gangavarapu  4   8 , Laura D Hughes  9
Affiliations

Outbreak.info Research Library: a standardized, searchable platform to discover and explore COVID-19 resources

Ginger Tsueng et al. Nat Methods. 2023 Apr.

Abstract

Outbreak.info Research Library is a standardized, searchable interface of coronavirus disease 2019 (COVID-19) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) publications, clinical trials, datasets, protocols and other resources, built with a reusable framework. We developed a rigorous schema to enforce consistency across different sources and resource types and linked related resources. Researchers can quickly search the latest research across data repositories, regardless of resource type or repository location, via a search interface, public application programming interface (API) and R package.

PubMed Disclaimer

Conflict of interest statement

Competing interests

K.G.A. has received consulting fees and/or compensated expert testimony on SARS-CoV-2 and the COVID-19 pandemic. The remaining authors declare no competing interests.

Figures

Fig. 1 |
Fig. 1 |. outbreak.info centralizes and standardizes resources into a single searchable index.
a, Distribution of resources by resource type and source. ICTRP, International Clinical Trials Registry Platform; MRC GIDA, MRC Centre for Global Infectious Disease Analysis. b, Searching for ‘Delta variant’ finds heterogeneous resources.
Fig. 2 |
Fig. 2 |. Resources concerning variants within the outbreak.info Research Library.
a, Standardized searching across resource types, including Publications, Datasets, ClinicalTrials and more. b, A variant protocol discovered within the Library. c, As VOCs were designated, the proportion of research in the Library focused on variants increased. d, The increase in research on each VOC mirrored its worldwide prevalence, with research on the transmissibility, virulence and/ or immune evasion supporting their VOC designation by public health agencies, and these designations encouraging further research.
See this image and copyright information in PMC

Update of

Comment in

  • Tracking SARS-CoV-2 variants and resources.
    Oude Munnink BB, Koopmans M. Oude Munnink BB, et al. Nat Methods. 2023 Apr;20(4):489-490. doi: 10.1038/s41592-023-01833-y. Nat Methods. 2023. PMID: 36922622 No abstract available.

References

    1. Novel Coronavirus (2019-nCoV): Situation Report, 1 (WHO, 2020); https://apps.who.int/iris/handle/10665/330760
    1. Dong E.et al. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect. Dis 20, 533–534 (2020). - PMC - PubMed
    1. Kaiser J.‘Every day is a new surprise.’ Inside the effort to produce the world’s most popular coronavirus tracker. Science 10.1126/science.abc1085 (2020). - DOI
    1. Noren LE et al. Institutional Response to COVID https://docs.google.com/spreadsheets/d/1IbF_wlmldVssG5spcmNE82nR9btcbF7r... (2020).
    1. Morris A.& citizen scientists. USA COVID-19 K-12 School Closures, Quarantines, and/or Deaths https://docs.google.com/spreadsheets/d/e/2PACX-1vQSD9mm5HTXhxAiHabZA6BPU...(2020).

Publication types