Truncatulix - A data warehouse for the legume community

authored by: Kolja Henckel, Kai J. Runte, Thomas Bekel, Michael Dondrup, Tobias Jakobi, Helge Küster, Alexander Goesmann
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/.
Organisation(s): Institute of Plant Genetics
External Organisation(s): Bielefeld University
Type: Article
Journal: BMC plant biology
Volume: 9
ISSN: 1471-2229
Publication date: 23.03.2009
Publication status: Published
Peer reviewed: Yes
ASJC Scopus subject areas: Plant Science
Electronic version(s): https://doi.org/10.1186/1471-2229-9-19 (Access: Open)