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

Emma J. Griffiths; Ruth E. Timme; Catarina Inês Mendes; Andrew J. Page; Nabil Fareed Alikhan; Dan Fornika; Finlay Maguire; Josefina Campos; Daniel Park; Idowu B. Olawoye; Paul E. Oluniyi; Dominique Anderson; Alan Christoffels; Anders Gonçalves Da Silva; Rhiannon Cameron; Damion Dooley; Lee S. Katz; Allison Black; Ilene Karsch-Mizrachi; Tanya Barrett; Anjanette Johnston; Thomas R. Connor; Samuel M. Nicholls; Adam A. Witney; Gregory H. Tyson; Simon H. Tausch; Amogelang R. Raphenya; Brian Alcock; David M. Aanensen; Emma Hodcroft; William W.L. Hsiao; Ana Tereza R. Vasconcelos; Duncan R. MacCannell

doi:10.1093/gigascience/giac003

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

Emma J. Griffiths, Ruth E. Timme, Catarina Inês Mendes, Andrew J. Page, Nabil Fareed Alikhan, Dan Fornika, Finlay Maguire, Josefina Campos, Daniel Park, Idowu B. Olawoye, Paul E. Oluniyi, Dominique Anderson, Alan Christoffels, Anders Gonçalves Da Silva, Rhiannon Cameron, Damion Dooley, Lee S. Katz, Allison Black, Ilene Karsch-Mizrachi, Tanya BarrettAnjanette Johnston, Thomas R. Connor, Samuel M. Nicholls, Adam A. Witney, Gregory H. Tyson, Simon H. Tausch, Amogelang R. Raphenya, Brian Alcock, David M. Aanensen, Emma Hodcroft, William W.L. Hsiao, Ana Tereza R. Vasconcelos, Duncan R. MacCannell

Medicine

Research output: Contribution to journal › Article › peer-review

26 Citations (Scopus)

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.

Original language	English
Article number	giac003
Journal	GigaScience
Volume	11
DOIs	https://doi.org/10.1093/gigascience/giac003
Publication status	Published - 2022

Bibliographical note

Publisher Copyright:
© 2022 The Author(s) 2022. Published by Oxford University Press GigaScience.

ASJC Scopus Subject Areas

Health Informatics
Computer Science Applications

PubMed: MeSH publication types

Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1093/gigascience/giac003

Cite this

Griffiths, E. J., Timme, R. E., Mendes, C. I., Page, A. J., Alikhan, N. F., Fornika, D., Maguire, F., Campos, J., Park, D., Olawoye, I. B., Oluniyi, P. E., Anderson, D., Christoffels, A., Da Silva, A. G., Cameron, R., Dooley, D., Katz, L. S., Black, A., Karsch-Mizrachi, I., ... MacCannell, D. R. (2022). Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package. GigaScience, 11, Article giac003. https://doi.org/10.1093/gigascience/giac003

Griffiths, EJ, Timme, RE, Mendes, CI, Page, AJ, Alikhan, NF, 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 2022, 'Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package', GigaScience, vol. 11, giac003. https://doi.org/10.1093/gigascience/giac003

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

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.",

author = "Griffiths, {Emma J.} and Timme, {Ruth E.} and Mendes, {Catarina In{\^e}s} and Page, {Andrew J.} and Alikhan, {Nabil Fareed} and Dan Fornika and Finlay Maguire and Josefina Campos and Daniel Park and Olawoye, {Idowu B.} and Oluniyi, {Paul E.} and Dominique Anderson and Alan Christoffels and {Da Silva}, {Anders Gon{\c c}alves} and Rhiannon Cameron and Damion Dooley and Katz, {Lee S.} and Allison Black and Ilene Karsch-Mizrachi and Tanya Barrett and Anjanette Johnston and Connor, {Thomas R.} and Nicholls, {Samuel M.} and Witney, {Adam A.} and Tyson, {Gregory H.} and Tausch, {Simon H.} and Raphenya, {Amogelang R.} and Brian Alcock and Aanensen, {David M.} and Emma Hodcroft and Hsiao, {William W.L.} and Vasconcelos, {Ana Tereza R.} and MacCannell, {Duncan R.}",

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year = "2022",

doi = "10.1093/gigascience/giac003",

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T1 - Future-proofing and maximizing the utility of metadata

T2 - The PHA4GE SARS-CoV-2 contextual data specification package

AU - Griffiths, Emma J.

AU - Timme, Ruth E.

AU - Mendes, Catarina Inês

AU - Page, Andrew J.

AU - Alikhan, Nabil Fareed

AU - Fornika, Dan

AU - Maguire, Finlay

AU - Campos, Josefina

AU - Park, Daniel

AU - Olawoye, Idowu B.

AU - Oluniyi, Paul E.

AU - Anderson, Dominique

AU - Christoffels, Alan

AU - Da Silva, Anders Gonçalves

AU - Cameron, Rhiannon

AU - Dooley, Damion

AU - Katz, Lee S.

AU - Black, Allison

AU - Karsch-Mizrachi, Ilene

AU - Barrett, Tanya

AU - Johnston, Anjanette

AU - Connor, Thomas R.

AU - Nicholls, Samuel M.

AU - Witney, Adam A.

AU - Tyson, Gregory H.

AU - Tausch, Simon H.

AU - Raphenya, Amogelang R.

AU - Alcock, Brian

AU - Aanensen, David M.

AU - Hodcroft, Emma

AU - Hsiao, William W.L.

AU - Vasconcelos, Ana Tereza R.

AU - MacCannell, Duncan R.

PY - 2022

Y1 - 2022

N2 - 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.

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

Abstract

Bibliographical note

ASJC Scopus Subject Areas

PubMed: MeSH publication types

UN SDGs

Access to Document

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