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GabiPD


NAR Molecular Biology Database Collection entry number 672
Riaño-Pachón, D.M.1,2, Nagel, A.1, Neigenfind, J.1, Wagner, R.1, Basekow, R.1, Weber, E.1, Mueller-Roeber, B.2, Diehl, S.3, and Kersten, B.1,2
1GabiPD Team, Bioinformatics Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
2Department of Molecular Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Haus 20, 14476 Potsdam-Golm, Germany.
3Former RZPD German Resource Center for Genome Research, Berlin, Germany.

Database Description

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 centralised Gene GreenCard allows the visualization of ESTs aligned to annotated transcripts as well as the display of identified protein domains and gene structure. Moreover GabiPD makes available interactive genetic maps from potato and barley, and 2DE-gels from Arabidopsis thaliana and Brassica napus. Gene expression and metabolic profiling data can be visualized through MapManWeb. Furthermore, the newest version of the MapMan desktop [1,2] and the SATlotyper tool [3] are made available for download. Through the integration of complex data in a framework of existing knowledge, GabiPD provides new insights and allows for new interpretations of the data.

Acknowledgements

GabiPD is supported by the German Ministry for Education and Research (BMBF) [GABI I: 0312272, GABI II: 0313112 and GABI-FUTURE: 0315046], the former German Resource Center for Genome Research (RZPD) GmbH and the Max Planck Society.

References

1. Thimm, O., Bläsing, O., Gibon, Y., Nagel, A., Meyer, S., Krüger, P., Selbig, J., Müller, L.A., Rhee, S.Y., and Stitt, M. (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 37: 914-939.
2. Usadel, B., Nagel, A., Thimm, O., Redestig, H., Bläsing, O.E., Palacios-Rojas, N., Selbig, J., Hannemann, J., Piques, M.C., Steinhauser, D., Scheible, W.R., Gibon, Y., Morcuende, R., Weicht, D., Meyer, S., and Stitt, M. (2005) Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses. Plant Physiol. 138: 1195-1204.
3. Neigenfind, J., Gyetvai, G., Basekow, R., Diehl, S., Achenbach, U., Gebhardt, C., Selbig, J., and Kersten, B. (2008) Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT. BMC Genomics 9: 356.

Category: Plant databases

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