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

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 harmonisable, 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 harmonisation and submission of sequence data and contextual information to public biorepositories. Well-structured, rich contextual data adds value, promotes reuse, and enables aggregation and integration of disparate data sets. 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 National Center for Biotechnology (NCBI)'s BioSample database.