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Harmonising and lin...
Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research
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- Spjuth, Ola, 1977- (author)
- Uppsala universitet,Institutionen för farmaceutisk biovetenskap,Science for Life Laboratory, SciLifeLab,Spjuth
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Krestyaninova, Maria (author)
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Hastings, Janna (author)
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Shen, Huei-Yi (author)
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Heikkinen, Jani (author)
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Waldenberger, Melanie (author)
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Langhammer, Arnulf (author)
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- Ladenvall, Claes (author)
- Lund University,Lunds universitet,Genomik, diabetes och endokrinologi,Forskargrupper vid Lunds universitet,Genomics, Diabetes and Endocrinology,Lund University Research Groups
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Esko, Tõnu (author)
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- Persson, Mats-Åke (author)
- Lund University,Lunds universitet,Genomik, diabetes och endokrinologi,Forskargrupper vid Lunds universitet,Genomics, Diabetes and Endocrinology,Lund University Research Groups
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Heggland, Jon (author)
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Dietrich, Joern (author)
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Ose, Sandra (author)
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Gieger, Christian (author)
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Ried, Janina S (author)
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Peters, Annette (author)
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Fortier, Isabel (author)
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de Geus, Eco Jc (author)
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Klovins, Janis (author)
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Zaharenko, Linda (author)
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Willemsen, Gonneke (author)
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Hottenga, Jouke-Jan (author)
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- Litton, Jan-Eric (author)
- Karolinska Institutet
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Karvanen, Juha (author)
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Boomsma, Dorret I (author)
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- Groop, Leif (author)
- Lund University,Lunds universitet,Genomik, diabetes och endokrinologi,Forskargrupper vid Lunds universitet,Genomics, Diabetes and Endocrinology,Lund University Research Groups
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- Rung, Johan (author)
- Uppsala universitet,Institutionen för immunologi, genetik och patologi
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- Palmgren, Juni (author)
- Karolinska Institutet
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- Pedersen, Nancy L (author)
- Karolinska Institutet
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McCarthy, Mark I (author)
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van Duijn, Cornelia M (author)
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Hveem, Kristian (author)
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Metspalu, Andres (author)
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Ripatti, Samuli (author)
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Prokopenko, Inga (author)
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Harris, Jennifer R (author)
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(creator_code:org_t)
- 2015-08-26
- 2016
- English.
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In: European Journal of Human Genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 24:4, s. 521-528
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Abstract
Subject headings
Close
- A wealth of biospecimen samples are stored in modern globally distributed biobanks. Biomedical researchers worldwide need to be able to combine the available resources to improve the power of large-scale studies. A prerequisite for this effort is to be able to search and access phenotypic, clinical and other information about samples that are currently stored at biobanks in an integrated manner. However, privacy issues together with heterogeneous information systems and the lack of agreed-upon vocabularies have made specimen searching across multiple biobanks extremely challenging. We describe three case studies where we have linked samples and sample descriptions in order to facilitate global searching of available samples for research. The use cases include the ENGAGE (European Network for Genetic and Genomic Epidemiology) consortium comprising at least 39 cohorts, the SUMMIT (surrogate markers for micro- and macro-vascular hard endpoints for innovative diabetes tools) consortium and a pilot for data integration between a Swedish clinical health registry and a biobank. We used the Sample avAILability (SAIL) method for data linking: first, created harmonised variables and then annotated and made searchable information on the number of specimens available in individual biobanks for various phenotypic categories. By operating on this categorised availability data we sidestep many obstacles related to privacy that arise when handling real values and show that harmonised and annotated records about data availability across disparate biomedical archives provide a key methodological advance in pre-analysis exchange of information between biobanks, that is, during the project planning phase.
Subject headings
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Endokrinologi och diabetes (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Endocrinology and Diabetes (hsv//eng)
Keyword
- Bioinformatik
- Bioinformatics
Publication and Content Type
- ref (subject category)
- art (subject category)
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To the university's database
- By the author/editor
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Spjuth, Ola, 197 ...
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Krestyaninova, M ...
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Hastings, Janna
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Shen, Huei-Yi
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Heikkinen, Jani
-
Waldenberger, Me ...
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show more...
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Langhammer, Arnu ...
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Ladenvall, Claes
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Esko, Tõnu
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Persson, Mats-Åk ...
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Heggland, Jon
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Dietrich, Joern
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Ose, Sandra
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Gieger, Christia ...
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Ried, Janina S
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Peters, Annette
-
Fortier, Isabel
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de Geus, Eco Jc
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Klovins, Janis
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Zaharenko, Linda
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Willemsen, Gonne ...
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Hottenga, Jouke- ...
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Litton, Jan-Eric
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Karvanen, Juha
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Boomsma, Dorret ...
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Groop, Leif
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Rung, Johan
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Palmgren, Juni
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Pedersen, Nancy ...
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McCarthy, Mark I
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van Duijn, Corne ...
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Hveem, Kristian
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Metspalu, Andres
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Ripatti, Samuli
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Prokopenko, Inga
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Harris, Jennifer ...
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show less...
- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Computer and Inf ...
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and Bioinformatics
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Clinical Medicin ...
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and Endocrinology an ...
- Articles in the publication
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European Journal ...
- By the university
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Uppsala University
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Lund University
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Karolinska Institutet