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

  • 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 availabThe 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.show moreshow less

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Metadaten
Author:Diego Mauricio Riano-Pachon, Axel Nagel, Jost Neigenfind, Robert Wagner, Rico Basekow, Elke Weber, Bernd Müller-Röber, Svenja Diehl, Birgit Kersten
URN:urn:nbn:de:kobv:517-opus-45075
Series (Serial Number):Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe (paper 137)
Document Type:Postprint
Language:English
Date of Publication (online):2010/07/19
Year of Completion:2009
Publishing Institution:Universität Potsdam
Release Date:2010/07/19
Tag:Arabidopsis thaliana; Families; Information; Phosphorylation sites; Proteins
Source:Nucleic acids research 37 (2009), Database issue, S. D954 - D959, DOI: 10.1093/nar/gkn611
Organizational units:Mathematisch-Naturwissenschaftliche Fakultät / Institut für Biochemie und Biologie
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Licence (German):License LogoCreative Commons - Namensnennung, Nicht kommerziell, Weitergabe zu gleichen Bedingungen 2.0 Deutschland
Notes extern:
The article was originally published by Oxford University Press:
Nucleic Acids Research. - 37 (2009), Database issue, S. D954-D959
ISSN 0305-1048
DOI 10.1093/nar/gkn611