Abstract
Biobanks store and manage collections of biological material (tissue, blood, cell cultures, etc.) and manage the medical and biological data associated with this material. Biobanks are invaluable resources for medical research. The diversity, heterogeneity and volatility of the domain make information systems for biobanks a challenging application domain. The European project BBMRI (Biobanking and Biomolecular Resources Research Infrastructure) has the mission to network European biobanks, to improve resources for biomedical research, an thus contribute to improve the prevention, diagnosis and treatment of diseases. We present the challenges and discuss some architectures for interconnecting European biobanks and harmonizing their data.
The work reported here was partially supported by the European Commission 7th Framework program - project BBMRI and by the Austrian Ministry of Science and Research within the program Gen-Au - project GATIB.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Biobanking and Ciomolecular Resources Research Infrastructure, http://www.bbmri.eu
Geneontology, http://www.geneontology.org
Oecd: Underpinning the future of life sciences and biotechnology (2001)
Nih guide: Informed Consent in Research Involving Human Participants (2006)
Bbmri: Construction of new Infrastructures - Preparatory Phase. In: INFRA–2007–2.2.1.16: European Bio-Banking and Biomolecular Resources (April 2007)
Uk biobank: Protocol for a large-Scale Prospective Epidemiological Resource. Protocol No: UKBB-PROT-09-06 (March 2007)
Asslaber, M., Abuja, P., Stark, K., et al.: The Genome Austria Tissue Bank (GATIB). In: Pathobiology 2007, vol. 74, pp. 251–258 (2007)
Asslaber, M., Zatloukal, K.: Biobanks: Transnational, European and Global Networks. Briefings in Functional Genomics & Proteomics 6(3), 193–201 (2007)
Chamoni, P., Stock, S.: Temporal structures in data warehousing. In: Mohania, M., Tjoa, A.M. (eds.) DaWaK 1999. LNCS, vol. 1676, pp. 353–358. Springer, Heidelberg (1999)
Eder, J., Koncilia, C.: Evolution of Dimension Data in Temporal Data Warehouses. In: Kambayashi, Y., Winiwarter, W., Arikawa, M. (eds.) DaWaK 2001. LNCS, vol. 2114, pp. 284–293. Springer, Heidelberg (2001)
Eder, J., Dabringer, C., Schicho, M., Stark, K.: Information Systems for Federated Biobanks. Transactions on Large Scale Data and Knowledge Centered Systems 1(1) (2009) (in print)
Eder, J., Koncilia, C., Morzy, T.: The COMET metamodel for temporal data warehouses. In: Pidduck, A.B., Mylopoulos, J., Woo, C.C., Ozsu, M.T. (eds.) CAiSE 2002. LNCS, vol. 2348, p. 83. Springer, Heidelberg (2002)
Goos, G., Hartmanis, J., Sripada, S., Leeuwen, J.V., Jajodia, S.: Temporal Databases: Research and Practice. Springer, New York (1998)
Litwin, W., Mark, L., Roussopoulos, N.: Interoperability of Multiple Autonomous Databases. ACM Comput. Surv. 22(3), 267–293 (1990)
Muilu, J., Peltonen, L., Litton, J.: The Federated Database - a basis for Biobank-Based Post-Genome Studies, Integrating Phenome and Genome Data from 600 000 Twin Pairs in Europe. European Journal of Human Genetics 15, 718–723 (2007)
Rebulla, P., Lecchi, L., Giovanelli, S., Butti, B., Salvaterra, E.: Biobanking in the Year 2007. Transfusion Medicine and Hemotherapy 34, 286–292 (2007)
Riegman, P., Morente, M., Betsou, F., de Blasio, P., Geary, P.: Biobanking for Better Healthcare. In: The Marble Arch International Working Group on Biobanking for Biomedical Research (2008)
Saltz, J., Oster, S., Hastings, S.: Design and Implementation of the Core Architecture of the Cancer Biomedical Informatics Grid. Bioinformatics (2006)
Schroeder, C.: Vernetzte Gewebesammlungen f. d. Forschung. Laborwelt, 5 (2007)
Schulte, J., Hampel, T., Stark, K., Eder, J., Schikuta, E.: Towards the Next Generation of Service-oriented Flexible Collaborative Systems – a basic framework applied to medical research. In: ICEIS 2008 - Proc. of the 10th Int. Conf. on Enterprise Information Systems (2008)
Sheth, A.P., Larson, J.A.: Federated Database Systems for Managing Distributed, Heterogeneous, and Autonomous Databases. ACM Comput. Surv. (1990)
Stark, K., Schulte, J., Hampel, T., Schikuta, E., Zatloukal, K., Eder, J.: GATiB-CSCW, medical research supported by a service-oriented collaborative system. In: Bellahsène, Z., Léonard, M. (eds.) CAiSE 2008. LNCS, vol. 5074, pp. 148–162. Springer, Heidelberg (2008)
Stevens, R., Zhao, J., Goble, C.: Using Provenance to Manage Knowledge of in Silico Experiments. Briefings in bioinformatics 8(3) (2007)
Yang, J.: Temporal Data Warehousing. Stanford University (2001)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Eder, J., Dabringer, C., Schicho, M., Stark, K. (2009). Data Management for Federated Biobanks. In: Bhowmick, S.S., Küng, J., Wagner, R. (eds) Database and Expert Systems Applications. DEXA 2009. Lecture Notes in Computer Science, vol 5690. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-03573-9_15
Download citation
DOI: https://doi.org/10.1007/978-3-642-03573-9_15
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-03572-2
Online ISBN: 978-3-642-03573-9
eBook Packages: Computer ScienceComputer Science (R0)