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Open Access Database

TRUNCATULIX – a data warehouse for the legume community

Kolja Henckel12345*, Kai J Runte145, Thomas Bekel145, Michael Dondrup145, Tobias Jakobi135, Helge Küster2567 and Alexander Goesmann145

Author Affiliations

1 Bioinformatics Resource Facility, Center for Biotechnology, Bielefeld University, Bielefeld, Germany

2 International Graduate School in Bioinformatics and Genome Research, Bielefeld University, Bielefeld, Germany

3 Technical Faculty, Bielefeld University, Bielefeld, Germany

4 Computational Genomics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany

5 Faculty for Biology and Genetics, Bielefeld University, Bielefeld, Germany

6 Genomics of Legume Plants, Institute for Genome Research and Systems Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany

7 Unit IV – Plant Genomics, Institute for Plant Genetics, Leibniz Universität Hannover, Germany

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BMC Plant Biology 2009, 9:19  doi:10.1186/1471-2229-9-19

Published: 11 February 2009

Abstract

Background

Databases for either sequence, annotation, or microarray experiments data are extremely beneficial to the research community, as they centrally gather information from experiments performed by different scientists. However, data from different sources develop their full capacities only when combined. The idea of a data warehouse directly adresses this problem and solves it by integrating all required data into one single database – hence there are already many data warehouses available to genetics. For the model legume Medicago truncatula, there is currently no such single data warehouse that integrates all freely available gene sequences, the corresponding gene expression data, and annotation information. Thus, we created the data warehouse TRUNCATULIX, an integrative database of Medicago truncatula sequence and expression data.

Results

The TRUNCATULIX data warehouse integrates five public databases for gene sequences, and gene annotations, as well as a database for microarray expression data covering raw data, normalized datasets, and complete expression profiling experiments. It can be accessed via an AJAX-based web interface using a standard web browser. For the first time, users can now quickly search for specific genes and gene expression data in a huge database based on high-quality annotations. The results can be exported as Excel, HTML, or as csv files for further usage.

Conclusion

The integration of sequence, annotation, and gene expression data from several Medicago truncatula databases in TRUNCATULIX provides the legume community with access to data and data mining capability not previously available. TRUNCATULIX is freely available at http://www.cebitec.uni-bielefeld.de/truncatulix/ webcite.