Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package
Emma Griffiths, Ruth Timme, Catarina Inês Mendes, Andrew J. Page, Nabil-Fareed Alikhan, Daniel Fornika, Finlay Maguire, Josefina Campos, Daniel J. Park, Idowu B. Olawoye, Paul E. Oluniyi, Dominique Anderson, Alan Christoffels, Anders Gonçalves da Silva, Rhiannon Cameron, Damion Dooley, Lee S. Katz, Allison Black, Ilene Karsch‐Mizrachi, Tanya Barrett, Anjanette Johnston, Thomas R. Connor, Samuel M. Nicholls, Adam A. Witney, Gregory H. Tyson, Simon H. Tausch, Amogelang R. Raphenya, Brian Alcock, David M. Aanensen, Emma B. Hodcroft, William Hsiao, Ana Tereza Ribeiro de Vasconcelos, Duncan MacCannell
Abstract
BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.