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Nucleic Acids Research Advance Access published online on September 23, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn611
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

GabiPD: the GABI primary database—a plant integrative ‘omics’ database

Diego Mauricio Riaño-Pachón1,2, Axel Nagel1, Jost Neigenfind1, Robert Wagner1, Rico Basekow1, Elke Weber1, Bernd Mueller-Roeber2, Svenja Diehl3 and Birgit Kersten1,2,*

1GabiPD team, Bioinformatics group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 2Department of Molecular Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Haus 20, 14476 Potsdam-Golm and 3Former RZPD German Resource Center for Genome Research GmbH, Berlin, Germany

*To whom correspondence should be addressed. Tel: +49-(0)331-567-8750; Fax: +49-(0)331-567-898-750; Email: kersten{at}mpimp-golm.mpg.de

Received August 6, 2008. Accepted September 9, 2008.

The GABI Primary Database, GabiPD (http://www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyze and visualize primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. Data from different ‘omics’ fronts are incorporated (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for text-based retrieval of all data types in GabiPD (e.g. clones, genes, mutant lines). All data types point to a central Gene GreenCard, where gene information is integrated from genome projects or NCBI UniGene sets. The centralized Gene GreenCard allows visualizing ESTs aligned to annotated transcripts as well as displaying identified protein domains and gene structure. Moreover, GabiPD makes available interactive genetic maps from potato and barley, and protein 2DE gels from Arabidopsis thaliana and Brassica napus. Gene expression and metabolic-profiling data can be visualized through MapManWeb. By the integration of complex data in a framework of existing knowledge, GabiPD provides new insights and allows for new interpretations of the data.


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