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

View ORCID ProfileGinger Tsueng, View ORCID ProfileJulia L. Mullen, View ORCID ProfileManar Alkuzweny, View ORCID ProfileMarco Cano, View ORCID ProfileBenjamin Rush, Emily Haag, Outbreak Curators, Jason Lin, Dylan J. Welzel, View ORCID ProfileXinghua Zhou, Zhongchao Qian, Alaa Abdel Latif, Emory Hufbauer, Mark Zeller, Kristian G. Andersen, View ORCID ProfileChunlei Wu, View ORCID ProfileAndrew I. Su, Karthik Gangavarapu, View ORCID ProfileLaura D. Hughes
doi: https://doi.org/10.1101/2022.01.20.477133
Ginger Tsueng
1Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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  • For correspondence: [email protected] [email protected]
Julia L. Mullen
1Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Manar Alkuzweny
2Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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  • ORCID record for Manar Alkuzweny
Marco Cano
1Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Benjamin Rush
3Ocuvera, Lincoln, NE 68512, USA
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Emily Haag
1Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Jason Lin
1Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Dylan J. Welzel
1Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Xinghua Zhou
1Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Zhongchao Qian
1Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Alaa Abdel Latif
4Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Emory Hufbauer
4Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Mark Zeller
4Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Kristian G. Andersen
4Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
5Scripps Research Translational Institute, La Jolla, CA 92037, USA
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Chunlei Wu
1Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
5Scripps Research Translational Institute, La Jolla, CA 92037, USA
6Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
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Andrew I. Su
1Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
5Scripps Research Translational Institute, La Jolla, CA 92037, USA
6Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
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Karthik Gangavarapu
7Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
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Laura D. Hughes
1Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Abstract

To combat the ongoing COVID-19 pandemic, scientists have been conducting research at breakneck speeds, producing over 52,000 peer-reviewed articles within the first year. To address the challenge in tracking the vast amount of new research located in separate repositories, we developed outbreak.info Research Library, a standardized, searchable interface of COVID-19 and SARS-CoV-2 resources. Unifying metadata from sixteen repositories, we assembled a collection of over 350,000 publications, clinical trials, datasets, protocols, and other resources as of October 2022. We used 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 API, and R package. Finally, we discuss the challenges inherent in combining metadata from scattered and heterogeneous resources and provide recommendations to streamline this process to aid scientific research.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Manuscript revised to reflect additional resources added to research library API, updates to Methods, and Supplemental Information

  • https://github.com/outbreak-info/outbreak.info-resources

  • https://outbreak.info/resources

  • https://api.outbreak.info/try/resources

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted December 07, 2022.
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Outbreak.info Research Library: A standardized, searchable platform to discover and explore COVID-19 resources
Ginger Tsueng, Julia L. Mullen, Manar Alkuzweny, Marco Cano, Benjamin Rush, Emily Haag, Outbreak Curators, Jason Lin, Dylan J. Welzel, Xinghua Zhou, Zhongchao Qian, Alaa Abdel Latif, Emory Hufbauer, Mark Zeller, Kristian G. Andersen, Chunlei Wu, Andrew I. Su, Karthik Gangavarapu, Laura D. Hughes
bioRxiv 2022.01.20.477133; doi: https://doi.org/10.1101/2022.01.20.477133
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Outbreak.info Research Library: A standardized, searchable platform to discover and explore COVID-19 resources
Ginger Tsueng, Julia L. Mullen, Manar Alkuzweny, Marco Cano, Benjamin Rush, Emily Haag, Outbreak Curators, Jason Lin, Dylan J. Welzel, Xinghua Zhou, Zhongchao Qian, Alaa Abdel Latif, Emory Hufbauer, Mark Zeller, Kristian G. Andersen, Chunlei Wu, Andrew I. Su, Karthik Gangavarapu, Laura D. Hughes
bioRxiv 2022.01.20.477133; doi: https://doi.org/10.1101/2022.01.20.477133

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