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Amid C, Pakseresht N, Silvester N, Jayathilaka S, Lund O, Dynovski LD, Pataki BÁ, Visontai D, Xavier BB, Alako BTF, Belka A, Cisneros JLB, Cotten M, Haringhuizen GB, Harrison PW, Höper D, Holt S, Hundahl C, Hussein A, Kaas RS, Liu X, Leinonen R, Malhotra-Kumar S, Nieuwenhuijse DF, Rahman N, dos S Ribeiro C, Skiby JE, Schmitz D, Stéger J, Szalai-Gindl JM, Thomsen MCF, Cacciò SM, Csabai I, Kroneman A, Koopmans M, Aarestrup F, Cochrane G. The COMPARE Data Hubs. Database (Oxford) 2019; 2019:baz136. [PMID: 31868882 PMCID: PMC6927095 DOI: 10.1093/database/baz136] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 11/12/2022]
Abstract
Data sharing enables research communities to exchange findings and build upon the knowledge that arises from their discoveries. Areas of public and animal health as well as food safety would benefit from rapid data sharing when it comes to emergencies. However, ethical, regulatory and institutional challenges, as well as lack of suitable platforms which provide an infrastructure for data sharing in structured formats, often lead to data not being shared or at most shared in form of supplementary materials in journal publications. Here, we describe an informatics platform that includes workflows for structured data storage, managing and pre-publication sharing of pathogen sequencing data and its analysis interpretations with relevant stakeholders.
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Affiliation(s)
- Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nima Pakseresht
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nicole Silvester
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Suran Jayathilaka
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ole Lund
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Lukasz D Dynovski
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Bálint Á Pataki
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest 1117, Hungary
- Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest 1121, Hungary
| | - Dávid Visontai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest 1117, Hungary
- Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest 1121, Hungary
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk 2610, Belgium
| | - Blaise T F Alako
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ariane Belka
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald 17493, Germany
| | - Jose L B Cisneros
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Matthew Cotten
- Department of Viroscience, Erasmus Medical Center, Rotterdam 3015, Netherlands
| | - George B Haringhuizen
- National Institute for Public Health and the Environment (RIVM), Bilthoven 3720, The Netherlands
| | - Peter W Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald 17493, Germany
| | - Sam Holt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Camilla Hundahl
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Abdulrahman Hussein
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rolf S Kaas
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Xin Liu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk 2610, Belgium
| | | | - Nadim Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carolina dos S Ribeiro
- National Institute for Public Health and the Environment (RIVM), Bilthoven 3720, The Netherlands
| | - Jeffrey E Skiby
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Dennis Schmitz
- Department of Viroscience, Erasmus Medical Center, Rotterdam 3015, Netherlands
- National Institute for Public Health and the Environment (RIVM), Bilthoven 3720, The Netherlands
| | - József Stéger
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest 1117, Hungary
- Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest 1121, Hungary
| | - János M Szalai-Gindl
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest 1117, Hungary
- Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest 1121, Hungary
| | - Martin C F Thomsen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Simone M Cacciò
- European Union Reference Laboratory for Parasites, Istituto Superiore di Sanità (ISS), Rome 00161, Italy
| | - István Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest 1117, Hungary
- Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest 1121, Hungary
| | - Annelies Kroneman
- National Institute for Public Health and the Environment (RIVM), Bilthoven 3720, The Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam 3015, Netherlands
| | - Frank Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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