PHA4GE overview

The Public Health Alliance for Genomic Epidemiology (PHA4GE) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatic tools and resources, and advocate for greater openness, interoperability, accessibility and reproducibility in public health microbial bioinformatics.

In the face of the current SARS-CoV-2 pandemic, PHA4GE has identified a clear and present 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 based on harmonizable, publicly available, community standards.

SARS-CoV-2 contextual data specification overview

Public health genomics contextual data includes sample metadata, lab/clinical/epidemiological data, and analysis methods information. Contextual data enables the interpretation of the sequence data, informs decision making for public health responses, and facilitates scientific understanding of infectious disease. Structured and consistent contextual data can also be more easily processed, aggregated, and reused by both humans and computers for different types of analyses. Read more!