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Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.
Griffiths, Emma J; Timme, Ruth E; Mendes, Catarina Inês; Page, Andrew J; Alikhan, Nabil-Fareed; Fornika, Dan; Maguire, Finlay; Campos, Josefina; Park, Daniel; Olawoye, Idowu B; Oluniyi, Paul E; Anderson, Dominique; Christoffels, Alan; da Silva, Anders Gonçalves; Cameron, Rhiannon; Dooley, Damion; Katz, Lee S; Black, Allison; Karsch-Mizrachi, Ilene; Barrett, Tanya; Johnston, Anjanette; Connor, Thomas R; Nicholls, Samuel M; Witney, Adam A; Tyson, Gregory H; Tausch, Simon H; Raphenya, Amogelang R; Alcock, Brian; Aanensen, David M; Hodcroft, Emma; Hsiao, William W L; Vasconcelos, Ana Tereza R; MacCannell, Duncan R.
Affiliation
  • Griffiths EJ; Faculty of Health Sciences, Simon Fraser University, Burnaby V5A 1S6, BC, Canada.
  • Timme RE; Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA.
  • Mendes CI; Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal.
  • Page AJ; Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, Norfolk NR4 7UQ, UK.
  • Alikhan NF; Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, Norfolk NR4 7UQ, UK.
  • Fornika D; BC Centre for Disease Control Public Health Laboratory, Vancouver, BC V5Z 4R4, Canada.
  • Maguire F; Faculty of Computer Science, Dalhousie University, Halifax, NS B3H 1W5, Canada.
  • Campos J; INEI-ANLIS "Dr Carlos G. Malbrán," Buenos Aires C1282AFF, Argentina.
  • Park D; Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  • Olawoye IB; African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State 232103, Nigeria.
  • Oluniyi PE; Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State 232103, Nigeria.
  • Anderson D; African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State 232103, Nigeria.
  • Christoffels A; Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State 232103, Nigeria.
  • da Silva AG; South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7530, South Africa.
  • Cameron R; South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7530, South Africa.
  • Dooley D; Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia.
  • Katz LS; Faculty of Health Sciences, Simon Fraser University, Burnaby V5A 1S6, BC, Canada.
  • Black A; Faculty of Health Sciences, Simon Fraser University, Burnaby V5A 1S6, BC, Canada.
  • Karsch-Mizrachi I; Center for Food Safety, University of Georgia, Atlanta, GA 30333, USA.
  • Barrett T; Office of Advanced Molecular Detection, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, GA 30333, USA.
  • Johnston A; Department of Epidemiology, University of Washington, WA 98109, USA.
  • Connor TR; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
  • Nicholls SM; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
  • Witney AA; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
  • Tyson GH; Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK.
  • Tausch SH; Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK.
  • Raphenya AR; University of Birmingham, Birmingham B17 2TT, UK.
  • Alcock B; Institute for Infection and Immunity, St George's, University of London, London SW17 0RE, UK.
  • Aanensen DM; Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD 20708, USA.
  • Hodcroft E; Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin 12277, Germany.
  • Hsiao WWL; Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada.
  • Vasconcelos ATR; Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada.
  • MacCannell DR; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
Gigascience ; 112022 02 16.
Article in En | MEDLINE | ID: mdl-35169842
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.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Guideline / Prognostic_studies Limits: Humans Language: En Journal: Gigascience Year: 2022 Document type: Article Affiliation country: Canada
Fulltext
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Guideline / Prognostic_studies Limits: Humans Language: En Journal: Gigascience Year: 2022 Document type: Article Affiliation country: Canada