TY - JOUR

T1 - Truncatulix - A data warehouse for the legume community

AU - Henckel, Kolja

AU - Runte, Kai J.

AU - Bekel, Thomas

AU - Dondrup, Michael

AU - Jakobi, Tobias

AU - Küster, Helge

AU - Goesmann, Alexander

N1 - Funding information: KH thanks the International NRW Graduate School in Bioinformatics and Genome Research for funding the project. We thank Florian Frugier (ISV, Gif-sur-Yvette) for making available data prior to publication.

PY - 2009/3/23

Y1 - 2009/3/23

N2 - 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/.

AB - 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/.

UR - http://www.scopus.com/inward/record.url?scp=62449226168&partnerID=8YFLogxK

U2 - 10.1186/1471-2229-9-19

DO - 10.1186/1471-2229-9-19

M3 - Article

C2 - 19210766

AN - SCOPUS:62449226168

VL - 9

JO - BMC plant biology

JF - BMC plant biology

SN - 1471-2229

M1 - 19

ER -