The COMPARE Data Hubs

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

doi:10.1093/database/baz136

The COMPARE Data Hubs

Clara Amid, Nima Pakseresht, Nicole Silvester, Suran Jayathilaka, Ole Lund, Lukasz D. Dynovski, Bálint Pataki, Dávid Visontai, Basil Britto Xavier, Blaise T.F. Alako, Ariane Belka, Jose L.B. Cisneros, Matthew Cotten, George B. Haringhuizen, Peter W. Harrison, Dirk Höper, Sam Holt, Camilla Hundahl, Abdulrahman Hussein, Rolf Sommer KaasXin Liu, Rasko Leinonen, Surbhi Malhotra-Kumar, David F. Nieuwenhuijse, Nadim Rahman, Carolina Dos S Ribeiro, Jeffrey Edward Skiby, Dennis Schmitz, József Stéger, János M. Szalai-Gindl, Martin Christen Frølund Thomsen, Simone M. Cacciò, István Csabai, Annelies Kroneman, Marion Koopmans, Frank Møller Aarestrup, Guy Cochrane

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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.

Original language	English
Article number	baz136
Journal	Database : the journal of biological databases and curation
Volume	2019
Pages (from-to)	1-14
ISSN	1758-0463
DOIs	https://doi.org/10.1093/database/baz136
Publication status	Published - 2019

Keywords

data hubs
data sharing platform
FAIR principles
pathogen portal
pathogen sequencing data

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Amid, C., Pakseresht, N., Silvester, N., Jayathilaka, S., Lund, O., Dynovski, L. D., Pataki, B., Visontai, D., Xavier, B. B., Alako, B. T. F., Belka, A., Cisneros, J. L. B., Cotten, M., Haringhuizen, G. B., Harrison, P. W., Höper, D., Holt, S., Hundahl, C., Hussein, A., ... Cochrane, G. (2019). The COMPARE Data Hubs. Database : the journal of biological databases and curation, 2019, 1-14. Article baz136. https://doi.org/10.1093/database/baz136

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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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author = "Clara Amid and Nima Pakseresht and Nicole Silvester and Suran Jayathilaka and Ole Lund and Dynovski, {Lukasz D.} and B{\'a}lint Pataki and D{\'a}vid Visontai and Xavier, {Basil Britto} and Alako, {Blaise T.F.} and Ariane Belka and Cisneros, {Jose L.B.} and Matthew Cotten and Haringhuizen, {George B.} and Harrison, {Peter W.} and Dirk H{\"o}per and Sam Holt and Camilla Hundahl and Abdulrahman Hussein and Kaas, {Rolf Sommer} and Xin Liu and Rasko Leinonen and Surbhi Malhotra-Kumar and Nieuwenhuijse, {David F.} and Nadim Rahman and {Dos S Ribeiro}, Carolina and Skiby, {Jeffrey Edward} and Dennis Schmitz and J{\'o}zsef St{\'e}ger and Szalai-Gindl, {J{\'a}nos M.} and Thomsen, {Martin Christen Fr{\o}lund} and Cacci{\`o}, {Simone M.} and Istv{\'a}n Csabai and Annelies Kroneman and Marion Koopmans and Aarestrup, {Frank M{\o}ller} and Guy Cochrane",

year = "2019",

doi = "10.1093/database/baz136",

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volume = "2019",

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Amid, C, Pakseresht, N, Silvester, N, Jayathilaka, S, Lund, O, Dynovski, LD, Pataki, B, 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, FM & Cochrane, G 2019, 'The COMPARE Data Hubs', Database : the journal of biological databases and curation, vol. 2019, baz136, pp. 1-14. https://doi.org/10.1093/database/baz136

TY - JOUR

T1 - The COMPARE Data Hubs

AU - Amid, Clara

AU - Pakseresht, Nima

AU - Silvester, Nicole

AU - Jayathilaka, Suran

AU - Lund, Ole

AU - Dynovski, Lukasz D.

AU - Pataki, Bálint

AU - Visontai, Dávid

AU - Xavier, Basil Britto

AU - Alako, Blaise T.F.

AU - Belka, Ariane

AU - Cisneros, Jose L.B.

AU - Cotten, Matthew

AU - Haringhuizen, George B.

AU - Harrison, Peter W.

AU - Höper, Dirk

AU - Holt, Sam

AU - Hundahl, Camilla

AU - Hussein, Abdulrahman

AU - Kaas, Rolf Sommer

AU - Liu, Xin

AU - Leinonen, Rasko

AU - Malhotra-Kumar, Surbhi

AU - Nieuwenhuijse, David F.

AU - Rahman, Nadim

AU - Dos S Ribeiro, Carolina

AU - Skiby, Jeffrey Edward

AU - Schmitz, Dennis

AU - Stéger, József

AU - Szalai-Gindl, János M.

AU - Thomsen, Martin Christen Frølund

AU - Cacciò, Simone M.

AU - Csabai, István

AU - Kroneman, Annelies

AU - Koopmans, Marion

AU - Aarestrup, Frank Møller

AU - Cochrane, Guy

PY - 2019

Y1 - 2019

N2 - 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.

AB - 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.

KW - data hubs

KW - data sharing platform

KW - FAIR principles

KW - pathogen portal

KW - pathogen sequencing data

U2 - 10.1093/database/baz136

DO - 10.1093/database/baz136

M3 - Journal article

C2 - 31868882

SN - 1758-0463

VL - 2019

SP - 1

EP - 14

JO - Database : the journal of biological databases and curation

JF - Database : the journal of biological databases and curation

M1 - baz136

ER -

The COMPARE Data Hubs

Abstract

Keywords

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