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  GabiPD: the GABI primary database-a plant integrative 'omics' database

Riano-Pachon, D. M., Nagel, A., Neigenfind, J., Wagner, R., Basekow, R., Weber, E., et al. (2009). GabiPD: the GABI primary database-a plant integrative 'omics' database. Nucleic Acids Research, 37(Database issue), 954-959. doi:10.1093/Nar/Gkn611.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-24FB-C Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-F55F-0
Genre: Journal Article

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 Creators:
Riano-Pachon, D. M.1, Author              
Nagel, A.2, Author              
Neigenfind, J.2, Author              
Wagner, R.3, Author
Basekow, R.3, Author
Weber, E.3, Author
Mueller-Roeber, B.4, Author              
Diehl, S.3, Author
Kersten, B.2, Author              
Affiliations:
1BioinformaticsCRG, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753315              
2BioinformaticsCIG, Infrastructure Groups and Service Units, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753303              
3External Organizations, ou_persistent22              
4Plant Signalling, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753311              

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Free keywords: phosphorylation sites arabidopsis-thaliana information proteins families genome tool
 Abstract: 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 textbased 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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Language(s): eng - English
 Dates: 2008-09-252009
 Publication Status: Published in print
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 Identifiers: ISI: ISI:000261906200168
DOI: 10.1093/Nar/Gkn611
ISSN: 1362-4962 (Electronic)0305-1048 (Linking)
URI: ://000261906200168http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686513/pdf/gkn611.pdf?tool=pmcentrez
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Title: Nucleic Acids Research
Source Genre: Journal
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Pages: - Volume / Issue: 37 (Database issue) Sequence Number: - Start / End Page: 954 - 959 Identifier: -