At the University of Leipzig, microarray technology is used in various research projects for gene expression analysis. To manage the large amounts of data resulting from these experi-ments we developed a comprehensive data warehouse platform called GeWare. It supports different methods for pre-processing and analysis, e.g. to identify different expressed genes. The GeWare platform is fully operational. An extended version of the warehouse serves as the data platform for the nation-wide project “Molecular Mechanisms in Malignant Lymphoma” of Deutsche Krebshilfe. This work is performed at the Interdisciplinary Centre for Bioinformatics (IZBI) in close cooperation with the Institute for Medical Informatics, Statistics and Epidemiology at the University of Leipzig (Prof. Löffler) as well as the study partners.

The following figure shows the general architecture of GeWare.

Figure 1: Overall GeWare architecture

Currently, our work in this project focuses on flexible mechanisms for management of different kinds of annotation data, and advanced strategies for coupling analysis algorithms and tools with our data warehouse.

The current version of GeWare is available under URL: http://www.izbi.de/GEWARE

Current Project Members:

• Erhard Rahm
• Toralf Kirsten
• Jörg Lange

Previous Project Member:

• Hong-Hai Do

Master Thesis:

• Jörg Lange: Flexible Verwaltung und Spezifikation von Experimentannotationen für Genexpressionsanalysen, 2004

Further and Related Information:

• about GeWare on the IZBI homepage
• about related data integration projects at the IZBI
• Networked Computing Resources for Biomedical Research (MediGRID)

Selected Publications:

Rahm, Erhard; Kirsten, Toralf; Lange, Jörg The GeWare data warehouse platform for the analysis of molecular-biological and clinical data Journal of Integrative Bioinformatics, 4(1):47, 2007 2007-01-20

Kirsten, Toralf; Lange, Jörg; Rahm, Erhard An integrated platform for analyzing molecular-biological data within clinical studies EDBT-Workshop Information Integration in Healthcare Applications, Springer LNCS 4254, 2006 2006-03

Do, H.H.; Kirsten, T. ; Rahm, E. Comparative Evaluation of Microarray-based Gene Expression Databases Proc. 10. Fachtagung Datenbanksysteme für Business, Technologie und Web (BTW 2003), GI, Lecture Notes in Informatics (LNI), Feb. 2003 2003-02

Posters and Talks

Lange, J.; Kirsten, T.; Rahm, E.; Berger, H.; Löffler, M. An integrated platform for analyzing clinical and molecular-biological data in collaborative research projects Proc 4th Research Festival for Life Sciences, Leipzig, Dec. 2005 2005

Kirsten, T.; Do, H.H.; Rahm, E. Data Integration for Genomic Research Proc. 3rd Biotech Day, Univ. Leipzig, May 2004 2004-03

Kirsten, T.; Do, H.H.; Rahm, E. A Multidimensional Data Warehouse for Gene Expression Analysis Proc. German Conference on Bioinformatics (GCB) 2003, Munich, October 2003 2003-10

Kirsten, T.; Do, H.H.; Rahm, E. Data Integration for Analyzing Gene Expression Data Proc. 6th Meeting of Microarray Gene Expression Data Society (MGED), Aix-en-Provence (France), September 2003 2003-09

Kirsten, T.; Do, H.H.; Rahm, E. Data Integration for Analyzing Gene Expression Data Proc. 2nd Biotech Day, Univ. Leipzig, May 2003. pp. 88-89 2003-05

Rahm, E.; Do, H.H.; Kirsten, T. Data Integration for Analyzing Gene Expression Data - Selected Projects Data Integration for Analyzing Gene Expression Data. Bonn, May 2003. 2003-05

Kirsten, T.; Do, H.H.; Sosna, D.; Rahm, E.; Krohn, K.; Eszlinger, M.; Paschke, R. Gene Expression Warehousing in Leipzig Poster for the Workshop on Databases and Data Integration in Genome Research, Berlin, February 2002 2002-02

Kirsten, T.; Do, H.H.; Rahm, E.; Krohn, K. Gene Expression Warehousing in Leipzig. Poster/Abstract, Proc. Biotech Day, Univ. Leipzig, May 2002, pp. 152-153. 2002