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Using Data Warehouse Technology in Crop Plant Bioinformatics

Kuenne, Christian ; Grosse, Ivo ; Matthies, Inge ; Scholz, Uwe ; Sretenovic-Rajicic, Tatjana ; Stein, Nils ; Stephanik, Andreas ; Steuernagel, Burkhard ; Weise, Stephan

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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Abstract:
Plant-specific data is managed in heterogeneous formats and is dispersed geographically. Based on this data, efficient analyses require a materialised integration, often realised with data warehouse technology today. We describe the requirements, problems and solution strategies for domain-crossing integration as the fundament for analysing plant biological data based on three current case studies. First, we introduce a system for retrieval of markers and mapping positions based on clustering of ESTs. The second case study illustrates the steps for diversity studies after genotyping a collection of about 3,000 ryegrass accessions (Lolium spp.), whereas in the third example data of approximately 250 barley cultivars (Hordeum vulgare) were used for associating haplotype- and SNP-patterns with malting parameters. For all case studies, we integrate data from different domains - sequence and marker data as well as IPK Genebank data including passport and phenotypic information. Specific problems associated with plant biological data and possible solution strategies are shown.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Kuenne, Christian ; Grosse, Ivo ; Matthies, Inge ; Scholz, Uwe ; Sretenovic-Rajicic, Tatjana ; Stein, Nils ; Stephanik, Andreas ; Steuernagel, Burkhard ; Weise, Stephan  (2007)  Using Data Warehouse Technology in Crop Plant Bioinformatics. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 4(1), 2007. Special Issue: Data Warehouse Technologies in Bioinformatics, Wittenberg, Germany, 2006

Online-Journal: http://journal.imbio.de/index.php?paper_id=88
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2008/284



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