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Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research
- Source :
- European Journal of Human Genetics, Spjuth, O, Krestyaninova, M, Hastings, J, Shen, H Y, Heikkinen, J, Waldenberger, M, Langhammer, A, Ladenvall, C, Esko, T, Persson, M Å, Heggland, J, Dietrich, J, Ose, S, Gieger, C, Ried, J S, Peters, A, Fortier, I, de Geus, E J C, Klovins, J, Zaharenko, L, Willemsen, G, Hottenga, J J, Litton, J E, Karvanen, J, Boomsma, D I, Groop, L, Rung, J, Palmgren, J, Pedersen, N L, McCarthy, M I, van Duijn, C M, Hveem, K, Metspalu, A, Ripatti, S, Prokopenko, I & Harris, J R 2016, ' Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research ', European Journal of Human Genetics, vol. 24, no. 4, pp. 521-528 . https://doi.org/10.1038/ejhg.2015.165, European Journal of Human Genetics, 24(4), 521-528. Nature Publishing Group, Eur. J. Hum. Genet. 24, 521-528 (2015), European Journal of Human Genetics; (2015)
- Publication Year :
- 2016
-
Abstract
- 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. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
- Subjects :
- 0301 basic medicine
Netherlands Twin Register (NTR)
Databases, Factual
Computer science
Information Storage and Retrieval
Sample (statistics)
Ontology (information science)
Endocrinology and Diabetes
Bioinformatics
computer.software_genre
data archives
Article
03 medical and health sciences
SDG 17 - Partnerships for the Goals
SDG 3 - Good Health and Well-being
Genetics
Use case
biomedical data
Genetics (clinical)
Biological Specimen Banks
Genetics & Heredity
0604 Genetics
Bioinformatics (Computational Biology)
ta112
ta1184
Data science
Biobank
3. Good health
cross-biotank research
030104 developmental biology
Project planning
Exchange of information
Disparate system
Privacy
Bioinformatik (beräkningsbiologi)
clinical data
computer
Data integration
Subjects
Details
- Language :
- English
- ISSN :
- 10184813 and 14765438
- Volume :
- 24
- Issue :
- 4
- Database :
- OpenAIRE
- Journal :
- European Journal of Human Genetics
- Accession number :
- edsair.doi.dedup.....b8b72203de9508f6be731677dda026a9