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

Affiliation
Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
Griffiths, Emma J.;
Affiliation
Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, United States
Timme, Ruth E.;
Affiliation
Instituto de Microbiologia, Instituto de Medicina Molecular, Universidade de Lisboa, Lisboa, Portugal
Mendes, Catarina Inês;
Affiliation
Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, United Kingdom
Page, Andrew J.;
Affiliation
Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, United Kingdom
Alikhan, Nabil-Fareed;
Affiliation
BC Centre for Disease Control Public Health Laboratory, Vancouver, Canada
Fornika, Dan;
Affiliation
Faculty of Computer Science, Dalhousie University, Halifax, Canada
Maguire, Finlay;
Affiliation
INEI-ANLIS Dr Carlos G. Malbrán, Buenos Aires, Argentina
Campos, Josefina;
Affiliation
Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, United States
Park, Daniel;
Affiliation
African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State 232103, Nigeria
Olawoye, Idowu B.;
Affiliation
African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State 232103, Nigeria
Oluniyi, Paul E.;
Affiliation
South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
Anderson, Dominique;
Affiliation
South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
Christoffels, Alan;
Affiliation
Microbiological Diagnostic Unit Public Health Laboratory, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
Da Silva, Anders Gonçalves;
Affiliation
Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
Cameron, Rhiannon;
Affiliation
Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
Dooley, Damion;
Affiliation
Center for Food Safety, University of Georgia, Atlanta, United States
Katz, Lee S.;
Affiliation
Department of Epidemiology, University of Washington, United States
Black, Allison;
Affiliation
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
Karsch-Mizrachi, Ilene;
Affiliation
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
Barrett, Tanya;
Affiliation
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
Johnston, Anjanette;
Affiliation
Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, United Kingdom
Connor, Thomas R.;
Affiliation
University of Birmingham, Birmingham, United Kingdom
Nicholls, Samuel M.;
Affiliation
Institute for Infection and Immunity, St George's, University of London, London, United Kingdom
Witney, Adam A.;
Affiliation
Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, United States
Tyson, Gregory H.;
ORCID
0000-0002-6874-233X
Affiliation
German Federal Institute for Risk Assessment (BfR), Department 4 - Biological Safety, 4 NSZ - National Study Centre for Sequencing in Risk Assessment, Berlin, Germany
Tausch, Simon H.;
Affiliation
Dept. of Biochem. and Biomed. Sci. and the Michael G. DeGroote Inst. for Infectious Disease Research, McMaster University, Hamilton, Canada
Raphenya, Amogelang R.;
Affiliation
Dept. of Biochem. and Biomed. Sci. and the Michael G. DeGroote Inst. for Infectious Disease Research, McMaster University, Hamilton, Canada
Alcock, Brian;
Affiliation
Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Cambridge, United Kingdom
Aanensen, David M.;
Affiliation
Biozentrum, University of Basel, Basel, Switzerland
Hodcroft, Emma;
Affiliation
Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
Hsiao, William W. L.;
Affiliation
Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
Vasconcelos, Ana Tereza R.;
Affiliation
Office of Advanced Molecular Detection, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, United States
MacCannell, Duncan R.; da Silva, Anders Gonçalves

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.

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Category

Published in:
GigaScience
Vol. 11, articlenr.:giac003
Volume:
11
Date Issued:
2022
Date Issued (online):
16.02.2022
DOI:
10.1093/gigascience/giac003
Other identifier (pubmed):
35169842
Scopus ID:
85124680073
Language:
English
Type of Resource:
Text
Keywords:
bioinformatics; data standards; genomics; metadata; SARS-CoV-2
DDC subject of DNB:
570 Life science
Institution:
German Federal Institute for Risk Assessment, German Federal Institute for Risk Assessment (July 2014 - 2021), Department 4 Biological Safety, National Study Centre for Sequencing in Risk Assessment 4NSZ
Physical Location:
2022004A4

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