Using Data Warehouse Technology in Crop Plant Bioinformatics
Full article [PDF] (1,52 MB)
doi:10.2390/biecoll-jib-2007-88
November 16, 2006
February 21, 2008
Christian Kuenne, Ivo Grosse, Inge Matthies, Uwe Scholz, Tatjana Sretenovic-Rajicic, Nils Stein, Andreas Stephanik, Burkhard Steuernagel and Stephan Weise
Correspondence should be addressed to:
Stephan Weise
Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, D-06466 Gatersleben
ed.nebelsretag-kpi@nullesiew
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.