Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.
Griffiths EJ., Timme RE., Mendes CI., Page AJ., Alikhan N-F., Fornika D., Maguire F., Campos J., Park D., Olawoye IB., Oluniyi PE., Anderson D., Christoffels A., da Silva AG., Cameron R., Dooley D., Katz LS., Black A., Karsch-Mizrachi I., Barrett T., Johnston A., Connor TR., Nicholls SM., Witney AA., Tyson GH., Tausch SH., Raphenya AR., Alcock B., Aanensen DM., Hodcroft E., Hsiao WWL., Vasconcelos ATR., MacCannell DR.
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.