Dataset Information

Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.

ABSTRACT: The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatics tools and resources, and advocate for greater openness, interoperability, accessibility, and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a need for a fit-for-purpose, open-source SARS-CoV-2 contextual data standard. As such, we have developed a SARS-CoV-2 contextual data specification package based on harmonizable, publicly available community standards. The specification can be implemented via a collection template, as well as an array of protocols and tools to support both the harmonization and submission of sequence data and contextual information to public biorepositories. Well-structured, rich contextual data add value, promote reuse, and enable aggregation and integration of disparate datasets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19. The package is now supported by the NCBI's BioSample database.

SUBMITTER: Griffiths EJ

PROVIDER: S-EPMC8847733 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature

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Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.

Griffiths Emma J EJ Timme Ruth E RE Mendes Catarina Inês CI Page Andrew J AJ Alikhan Nabil-Fareed NF Fornika Dan D Maguire Finlay F Campos Josefina J Park Daniel D Olawoye Idowu B IB Oluniyi Paul E PE Anderson Dominique D Christoffels Alan A da Silva Anders Gonçalves AG Cameron Rhiannon R Dooley Damion D Katz Lee S LS Black Allison A Karsch-Mizrachi Ilene I Barrett Tanya T Johnston Anjanette A Connor Thomas R TR Nicholls Samuel M SM Witney Adam A AA Tyson Gregory H GH Tausch Simon H SH Raphenya Amogelang R AR Alcock Brian B Aanensen David M DM Hodcroft Emma E Hsiao William W L WWL Vasconcelos Ana Tereza R ATR MacCannell Duncan R DR

GigaScience 20220201

<h4>Background</h4>The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatics tools and resources, and advocate for greater openness, interoperability, accessibility, and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a need for a fit-for ...[more]

PMID: 35169842

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Dataset Information

Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.

Publications

Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.

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