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. 2019 Jan 1:2019:baz136.
doi: 10.1093/database/baz136.

The COMPARE Data Hubs

Clara Amid  1 , Nima Pakseresht  1 , Nicole Silvester  1 , Suran Jayathilaka  1 , Ole Lund  2 , Lukasz D Dynovski  2 , Bálint Á Pataki  3   4 , Dávid Visontai  3   4 , Basil Britto Xavier  5 , Blaise T F Alako  1 , Ariane Belka  6 , Jose L B Cisneros  2 , Matthew Cotten  7 , George B Haringhuizen  8 , Peter W Harrison  1 , Dirk Höper  6 , Sam Holt  1 , Camilla Hundahl  2 , Abdulrahman Hussein  1 , Rolf S Kaas  2 , Xin Liu  1 , Rasko Leinonen  1 , Surbhi Malhotra-Kumar  5 , David F Nieuwenhuijse  7 , Nadim Rahman  1 , Carolina Dos S Ribeiro  8 , Jeffrey E Skiby  2 , Dennis Schmitz  7   8 , József Stéger  3   4 , János M Szalai-Gindl  3   4 , Martin C F Thomsen  2 , Simone M Cacciò  9 , István Csabai  3   4 , Annelies Kroneman  8 , Marion Koopmans  7 , Frank Aarestrup  2 , Guy Cochrane  1
Affiliations

The COMPARE Data Hubs

Clara Amid et al. Database (Oxford). .

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.

Keywords: FAIR principles; data hubs; data sharing platform; pathogen portal; pathogen sequencing data.

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Figures

Figure 1
Figure 1
Example CDH user workflow.
Figure 2
Figure 2
System architecture.
Figure 3
Figure 3
PP interactive interface. 1: select a domain (e.g. read_run); 2: narrow down search (where desired) by specifying taxonomy and sample collection details (e.g. collection date and country); 3: specify (where desired) which fields should be returned in the result report (e.g. centre name, study accession, sample accession, etc); 4: result page with download options in TSV and JASON (JavaScript Object Notation).
See this image and copyright information in PMC

References

    1. Whitty C.J., Mundel T., Farrar J. et al. (2015) Providing incentives to share data early in health emergencies: the role of journal editors. Lancet, 386, 1797–1798. - PMC - PubMed
    1. Dos S., Ribeiro C., Koopmans M.P. et al. (2018) Threats to timely sharing of pathogen sequence data. Science, 362, 404–406. - PubMed
    1. Aarestrup F.M. and Koopmans M.G. (2016) Sharing data for global infectious disease surveillance and outbreak detection. Trends Microbiol., 24, 241–245. - PubMed
    1. Van Panhuis W.G., Paul P., Emerson C. et al. (2014) A systematic review of barriers to data sharing in public health. BMC Public Health, 14, 1144. - PMC - PubMed
    1. Ribeiro C.D.S., van Roode M.Y., Haringhuizen G.B. et al. (2018) How ownership rights over microorganisms affect infectious disease control and innovation: a root-cause analysis of barriers to data sharing as experienced by key stakeholders. PLoS One, 13, e0195885. - PMC - PubMed

Publication types