Data harmonization and federated analysis of population-based studies: the BioSHaRE project
Identifieur interne : 000338 ( Pmc/Checkpoint ); précédent : 000337; suivant : 000339Data harmonization and federated analysis of population-based studies: the BioSHaRE project
Auteurs : Dany Doiron [Canada] ; Paul Burton [Royaume-Uni] ; Yannick Marcon [Canada] ; Amadou Gaye [Royaume-Uni] ; Bruce H R. Wolffenbuttel [Pays-Bas] ; Markus Perola [Finlande] ; Ronald P. Stolk [Pays-Bas] ; Luisa Foco [Italie] ; Cosetta Minelli [Royaume-Uni] ; Melanie Waldenberger [Allemagne] ; Rolf Holle [Allemagne] ; Kirsti Kval Y [Norvège] ; Hans L. Hillege [Pays-Bas] ; Anne-Marie Tassé [Canada] ; Vincent Ferretti [Canada] ; Isabel Fortier [Canada]Source :
- Emerging Themes in Epidemiology [ 1742-7622 ] ; 2013.
Abstract
Individual-level data pooling of large population-based studies across research centres in international research projects faces many hurdles. The BioSHaRE (Biobank Standardisation and Harmonisation for Research Excellence in the European Union) project aims to address these issues by building a collaborative group of investigators and developing tools for data harmonization, database integration and federated data analyses.
Eight population-based studies in six European countries were recruited to participate in the BioSHaRE project. Through workshops, teleconferences and electronic communications, participating investigators identified a set of 96 variables targeted for harmonization to answer research questions of interest. Using each study’s questionnaires, standard operating procedures, and data dictionaries, harmonization potential was assessed. Whenever harmonization was deemed possible, processing algorithms were developed and implemented in an open-source software infrastructure to transform study-specific data into the target (i.e. harmonized) format. Harmonized datasets located on server in each research centres across Europe were interconnected through a federated database system to perform statistical analysis.
Retrospective harmonization led to the generation of common format variables for 73% of matches considered (96 targeted variables across 8 studies). Authenticated investigators can now perform complex statistical analyses of harmonized datasets stored on distributed servers without actually sharing individual-level data using the DataSHIELD method.
New Internet-based networking technologies and database management systems are providing the means to support collaborative, multi-center research in an efficient and secure manner. The results from this pilot project show that, given a strong collaborative relationship between participating studies, it is possible to seamlessly co-analyse internationally harmonized research databases while allowing each study to retain full control over individual-level data. We encourage additional collaborative research networks in epidemiology, public health, and the social sciences to make use of the open source tools presented herein.
Url:
DOI: 10.1186/1742-7622-10-12
PubMed: 24257327
PubMed Central: 4175511
Affiliations:
- Allemagne, Canada, Finlande, Italie, Norvège, Pays-Bas, Royaume-Uni
- Angleterre, Grand Londres, Groningue (province), Québec, Trøndelag, Uusimaa
- Groningue, Helsinki, Londres, Montréal, Trondheim
- Université d'Helsinki, Université de Groningue
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<author><name sortKey="Hillege, Hans L" sort="Hillege, Hans L" uniqKey="Hillege H" first="Hans L" last="Hillege">Hans L. Hillege</name>
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<author><name sortKey="Tasse, Anne Marie" sort="Tasse, Anne Marie" uniqKey="Tasse A" first="Anne-Marie" last="Tassé">Anne-Marie Tassé</name>
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<author><name sortKey="Fortier, Isabel" sort="Fortier, Isabel" uniqKey="Fortier I" first="Isabel" last="Fortier">Isabel Fortier</name>
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<country xml:lang="fr">Canada</country>
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<series><title level="j">Emerging Themes in Epidemiology</title>
<idno type="eISSN">1742-7622</idno>
<imprint><date when="2013">2013</date>
</imprint>
</series>
</biblStruct>
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<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><sec><title>Abstracts</title>
<sec><title>Background</title>
<p>Individual-level data pooling of large population-based studies across research centres in international research projects faces many hurdles. The BioSHaRE (Biobank Standardisation and Harmonisation for Research Excellence in the European Union) project aims to address these issues by building a collaborative group of investigators and developing tools for data harmonization, database integration and federated data analyses.</p>
</sec>
<sec><title>Methods</title>
<p>Eight population-based studies in six European countries were recruited to participate in the BioSHaRE project. Through workshops, teleconferences and electronic communications, participating investigators identified a set of 96 variables targeted for harmonization to answer research questions of interest. Using each study’s questionnaires, standard operating procedures, and data dictionaries, harmonization potential was assessed. Whenever harmonization was deemed possible, processing algorithms were developed and implemented in an open-source software infrastructure to transform study-specific data into the target (i.e. harmonized) format. Harmonized datasets located on server in each research centres across Europe were interconnected through a federated database system to perform statistical analysis.</p>
</sec>
<sec><title>Results</title>
<p>Retrospective harmonization led to the generation of common format variables for 73% of matches considered (96 targeted variables across 8 studies). Authenticated investigators can now perform complex statistical analyses of harmonized datasets stored on distributed servers without actually sharing individual-level data using the DataSHIELD method.</p>
</sec>
<sec><title>Conclusion</title>
<p>New Internet-based networking technologies and database management systems are providing the means to support collaborative, multi-center research in an efficient and secure manner. The results from this pilot project show that, given a strong collaborative relationship between participating studies, it is possible to seamlessly co-analyse internationally harmonized research databases while allowing each study to retain full control over individual-level data. We encourage additional collaborative research networks in epidemiology, public health, and the social sciences to make use of the open source tools presented herein.</p>
</sec>
</sec>
</div>
</front>
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<pmc article-type="research-article" xml:lang="en"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Emerg Themes Epidemiol</journal-id>
<journal-id journal-id-type="iso-abbrev">Emerg Themes Epidemiol</journal-id>
<journal-title-group><journal-title>Emerging Themes in Epidemiology</journal-title>
</journal-title-group>
<issn pub-type="epub">1742-7622</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">24257327</article-id>
<article-id pub-id-type="pmc">4175511</article-id>
<article-id pub-id-type="publisher-id">1742-7622-10-12</article-id>
<article-id pub-id-type="doi">10.1186/1742-7622-10-12</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Analytic Perspective</subject>
</subj-group>
</article-categories>
<title-group><article-title>Data harmonization and federated analysis of population-based studies: the BioSHaRE project</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" corresp="yes" id="A1"><name><surname>Doiron</surname>
<given-names>Dany</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>ddoiron@maelstrom-research.org</email>
</contrib>
<contrib contrib-type="author" id="A2"><name><surname>Burton</surname>
<given-names>Paul</given-names>
</name>
<xref ref-type="aff" rid="I4">4</xref>
<email>pb51@leicester.ac.uk</email>
</contrib>
<contrib contrib-type="author" id="A3"><name><surname>Marcon</surname>
<given-names>Yannick</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>yannick.marcon@obiba.org</email>
</contrib>
<contrib contrib-type="author" id="A4"><name><surname>Gaye</surname>
<given-names>Amadou</given-names>
</name>
<xref ref-type="aff" rid="I4">4</xref>
<email>ag239@le.ac.uk</email>
</contrib>
<contrib contrib-type="author" id="A5"><name><surname>Wolffenbuttel</surname>
<given-names>Bruce H R</given-names>
</name>
<xref ref-type="aff" rid="I5">5</xref>
<email>bwo@umcg.nl</email>
</contrib>
<contrib contrib-type="author" id="A6"><name><surname>Perola</surname>
<given-names>Markus</given-names>
</name>
<xref ref-type="aff" rid="I6">6</xref>
<xref ref-type="aff" rid="I7">7</xref>
<email>markus.perola@thl.fi</email>
</contrib>
<contrib contrib-type="author" id="A7"><name><surname>Stolk</surname>
<given-names>Ronald P</given-names>
</name>
<xref ref-type="aff" rid="I8">8</xref>
<email>r.p.stolk@umcg.nl</email>
</contrib>
<contrib contrib-type="author" id="A8"><name><surname>Foco</surname>
<given-names>Luisa</given-names>
</name>
<xref ref-type="aff" rid="I9">9</xref>
<email>luisa.foco@eurac.edu</email>
</contrib>
<contrib contrib-type="author" id="A9"><name><surname>Minelli</surname>
<given-names>Cosetta</given-names>
</name>
<xref ref-type="aff" rid="I13">13</xref>
<email>cosetta.minelli@eurac.edu</email>
</contrib>
<contrib contrib-type="author" id="A10"><name><surname>Waldenberger</surname>
<given-names>Melanie</given-names>
</name>
<xref ref-type="aff" rid="I10">10</xref>
<email>waldenberger@helmholtz-muenchen.de</email>
</contrib>
<contrib contrib-type="author" id="A11"><name><surname>Holle</surname>
<given-names>Rolf</given-names>
</name>
<xref ref-type="aff" rid="I10">10</xref>
<email>holle@helmholtz-muenchen.de</email>
</contrib>
<contrib contrib-type="author" id="A12"><name><surname>Kvaløy</surname>
<given-names>Kirsti</given-names>
</name>
<xref ref-type="aff" rid="I11">11</xref>
<email>kirsti.kvaloy@ntnu.no</email>
</contrib>
<contrib contrib-type="author" id="A13"><name><surname>Hillege</surname>
<given-names>Hans L</given-names>
</name>
<xref ref-type="aff" rid="I12">12</xref>
<email>h.hillege@umcg.nl</email>
</contrib>
<contrib contrib-type="author" id="A14"><name><surname>Tassé</surname>
<given-names>Anne-Marie</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>anne-marie.tasse@mcgill.ca</email>
</contrib>
<contrib contrib-type="author" equal-contrib="yes" id="A15"><name><surname>Ferretti</surname>
<given-names>Vincent</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
<email>vincent.ferretti@oicr.on.ca</email>
</contrib>
<contrib contrib-type="author" equal-contrib="yes" id="A16"><name><surname>Fortier</surname>
<given-names>Isabel</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>isabel.fortier@mail.mcgill.ca</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Research Institute of the McGill University Health Centre, 2155 Guy, office 458, Montreal, Quebec H3H 2R9, Canada</aff>
<aff id="I2"><label>2</label>
Public Population Project in Genomics and Society, Montreal, Canada</aff>
<aff id="I3"><label>3</label>
Ontario Institute for Cancer Research, MaRS Centre, Toronto, Canada</aff>
<aff id="I4"><label>4</label>
D2K Research Group, School of Social and Community Medicine, University of Bristol, Bristol, UK</aff>
<aff id="I5"><label>5</label>
Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands</aff>
<aff id="I6"><label>6</label>
Department of Chronic Disease Prevention, Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland</aff>
<aff id="I7"><label>7</label>
Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland</aff>
<aff id="I8"><label>8</label>
Department of Epidemiology, University Medical Center Groningen, Groningen, The Netherlands</aff>
<aff id="I9"><label>9</label>
European Academy of Bolzano/Bozen (EURAC), Center for Biomedicine, Bolzano, Italy</aff>
<aff id="I10"><label>10</label>
Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany</aff>
<aff id="I11"><label>11</label>
Department of Public Health and General Practice, HUNT Research Center, Norwegian University of Science and Technology, Trondheim, Norway</aff>
<aff id="I12"><label>12</label>
Department of Cardiology and Epidemiology, University Medical Centre Groningen, Groningen, The Netherlands</aff>
<aff id="I13"><label>13</label>
Respiratory Epidemiology, Occupational Medicine and Public Health, National Heart and Lung Institute, Imperial College, London, UK</aff>
<pub-date pub-type="collection"><year>2013</year>
</pub-date>
<pub-date pub-type="epub"><day>21</day>
<month>11</month>
<year>2013</year>
</pub-date>
<volume>10</volume>
<fpage>12</fpage>
<lpage>12</lpage>
<history><date date-type="received"><day>3</day>
<month>7</month>
<year>2013</year>
</date>
<date date-type="accepted"><day>11</day>
<month>11</month>
<year>2013</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2013 Doiron et al.; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2013</copyright-year>
<copyright-holder>Doiron et al.; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an open access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<self-uri xlink:href="http://www.ete-online.com/content/10/1/12"></self-uri>
<abstract><sec><title>Abstracts</title>
<sec><title>Background</title>
<p>Individual-level data pooling of large population-based studies across research centres in international research projects faces many hurdles. The BioSHaRE (Biobank Standardisation and Harmonisation for Research Excellence in the European Union) project aims to address these issues by building a collaborative group of investigators and developing tools for data harmonization, database integration and federated data analyses.</p>
</sec>
<sec><title>Methods</title>
<p>Eight population-based studies in six European countries were recruited to participate in the BioSHaRE project. Through workshops, teleconferences and electronic communications, participating investigators identified a set of 96 variables targeted for harmonization to answer research questions of interest. Using each study’s questionnaires, standard operating procedures, and data dictionaries, harmonization potential was assessed. Whenever harmonization was deemed possible, processing algorithms were developed and implemented in an open-source software infrastructure to transform study-specific data into the target (i.e. harmonized) format. Harmonized datasets located on server in each research centres across Europe were interconnected through a federated database system to perform statistical analysis.</p>
</sec>
<sec><title>Results</title>
<p>Retrospective harmonization led to the generation of common format variables for 73% of matches considered (96 targeted variables across 8 studies). Authenticated investigators can now perform complex statistical analyses of harmonized datasets stored on distributed servers without actually sharing individual-level data using the DataSHIELD method.</p>
</sec>
<sec><title>Conclusion</title>
<p>New Internet-based networking technologies and database management systems are providing the means to support collaborative, multi-center research in an efficient and secure manner. The results from this pilot project show that, given a strong collaborative relationship between participating studies, it is possible to seamlessly co-analyse internationally harmonized research databases while allowing each study to retain full control over individual-level data. We encourage additional collaborative research networks in epidemiology, public health, and the social sciences to make use of the open source tools presented herein.</p>
</sec>
</sec>
</abstract>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Allemagne</li>
<li>Canada</li>
<li>Finlande</li>
<li>Italie</li>
<li>Norvège</li>
<li>Pays-Bas</li>
<li>Royaume-Uni</li>
</country>
<region><li>Angleterre</li>
<li>Grand Londres</li>
<li>Groningue (province)</li>
<li>Québec</li>
<li>Trøndelag</li>
<li>Uusimaa</li>
</region>
<settlement><li>Groningue</li>
<li>Helsinki</li>
<li>Londres</li>
<li>Montréal</li>
<li>Trondheim</li>
</settlement>
<orgName><li>Université d'Helsinki</li>
<li>Université de Groningue</li>
</orgName>
</list>
<tree><country name="Canada"><noRegion><name sortKey="Doiron, Dany" sort="Doiron, Dany" uniqKey="Doiron D" first="Dany" last="Doiron">Dany Doiron</name>
</noRegion>
<name sortKey="Doiron, Dany" sort="Doiron, Dany" uniqKey="Doiron D" first="Dany" last="Doiron">Dany Doiron</name>
<name sortKey="Ferretti, Vincent" sort="Ferretti, Vincent" uniqKey="Ferretti V" first="Vincent" last="Ferretti">Vincent Ferretti</name>
<name sortKey="Fortier, Isabel" sort="Fortier, Isabel" uniqKey="Fortier I" first="Isabel" last="Fortier">Isabel Fortier</name>
<name sortKey="Marcon, Yannick" sort="Marcon, Yannick" uniqKey="Marcon Y" first="Yannick" last="Marcon">Yannick Marcon</name>
<name sortKey="Tasse, Anne Marie" sort="Tasse, Anne Marie" uniqKey="Tasse A" first="Anne-Marie" last="Tassé">Anne-Marie Tassé</name>
</country>
<country name="Royaume-Uni"><noRegion><name sortKey="Burton, Paul" sort="Burton, Paul" uniqKey="Burton P" first="Paul" last="Burton">Paul Burton</name>
</noRegion>
<name sortKey="Gaye, Amadou" sort="Gaye, Amadou" uniqKey="Gaye A" first="Amadou" last="Gaye">Amadou Gaye</name>
<name sortKey="Minelli, Cosetta" sort="Minelli, Cosetta" uniqKey="Minelli C" first="Cosetta" last="Minelli">Cosetta Minelli</name>
</country>
<country name="Pays-Bas"><region name="Groningue (province)"><name sortKey="Wolffenbuttel, Bruce H R" sort="Wolffenbuttel, Bruce H R" uniqKey="Wolffenbuttel B" first="Bruce H R" last="Wolffenbuttel">Bruce H R. Wolffenbuttel</name>
</region>
<name sortKey="Hillege, Hans L" sort="Hillege, Hans L" uniqKey="Hillege H" first="Hans L" last="Hillege">Hans L. Hillege</name>
<name sortKey="Stolk, Ronald P" sort="Stolk, Ronald P" uniqKey="Stolk R" first="Ronald P" last="Stolk">Ronald P. Stolk</name>
</country>
<country name="Finlande"><noRegion><name sortKey="Perola, Markus" sort="Perola, Markus" uniqKey="Perola M" first="Markus" last="Perola">Markus Perola</name>
</noRegion>
<name sortKey="Perola, Markus" sort="Perola, Markus" uniqKey="Perola M" first="Markus" last="Perola">Markus Perola</name>
</country>
<country name="Italie"><noRegion><name sortKey="Foco, Luisa" sort="Foco, Luisa" uniqKey="Foco L" first="Luisa" last="Foco">Luisa Foco</name>
</noRegion>
</country>
<country name="Allemagne"><noRegion><name sortKey="Waldenberger, Melanie" sort="Waldenberger, Melanie" uniqKey="Waldenberger M" first="Melanie" last="Waldenberger">Melanie Waldenberger</name>
</noRegion>
<name sortKey="Holle, Rolf" sort="Holle, Rolf" uniqKey="Holle R" first="Rolf" last="Holle">Rolf Holle</name>
</country>
<country name="Norvège"><region name="Trøndelag"><name sortKey="Kval Y, Kirsti" sort="Kval Y, Kirsti" uniqKey="Kval Y K" first="Kirsti" last="Kval Y">Kirsti Kval Y</name>
</region>
</country>
</tree>
</affiliations>
</record>
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