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BY-NC-ND 4.0 license Open Access Published by De Gruyter October 18, 2016

Using Data Warehouse Technology in Crop Plant Bioinformatics

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

Summary

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.

Published Online: 2016-10-18
Published in Print: 2007-3-1

© 2007 The Author(s). Published by Journal of Integrative Bioinformatics.

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

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