Robert Wagner

Max Planck Institute of Molecular Plant Physiology, Potsdam, Brandenburg, Germany

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Publications (7)8.81 Total impact

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    ABSTRACT: GabiPD ("http://www.gabipd.org/":http://www.gabipd.org/) at the Max Planck Institute of Molecular Plant Physiology constitutes a repository and analysis platform of genomic, transcriptomic, proteomic, and metabolomic plant data provided by the GABI community (Riaño-Pachón et al., 2009). Beside the data, current versions of useful tools are being made accessible via GabiPD, such as MapMan (Usadel et al., 2005) and SATlotyper (Neigenfind et al., 2008). Access to GabiPD is provided via either the web interface or WebServices. In GabiPD, twenty different plant species are currently represented with the model plant A. thaliana on top followed by the crop plants S. tuberosum and H. vulgare. Innovative user interfaces allow interactive access to the different data types, e.g. (i) GreenCards to all text-based information, like sequences and comparative SNP information (e.g., Pajerowska-Mukhtar et al., 2009) (ii) YAMB to comparative genetic maps, (iii) MapManWeb to gene expression or metabolite profiling data mapped onto pathways, or (iv) 2DGelViewer to annotated 2DE gel images. All data types (e.g., clones, protein spots, gene expression data) in GabiPD are pointing to the central Gene GreenCard, where gene information is retrieved from genome annotation projects or UniGene sets (provided by NCBI). With the Gene GreenCards, we provide MapMan and Gene Ontology annotations and ortholog information (currently only between _A. thaliana_ and _O. sativa ssp. japonica_). Recently, a new graphical representation of transcripts was integrated displaying gene structure (untranslated regions, start and stop codons and exon-exon junctions). Protein domains as well as ESTs, are mapped on the transcript displays. In order to ease the transfer of knowledge from model to crop plants, we have performed similarity-based mappings between closely related species, i.e., _O. sativa ssp. japonica_ and _H. vulgare_. By the integration of complex data in a framework of existing knowledge, GabiPD provides new insights and allows for new interpretations of plant data. This work is/was supported by the BMBF (GABI grants 0312272, 0313112, 0315046). Neigenfind J et al. (2008) Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT. _BMC Genomics_ 9:356. Pajerowska-Mukhtar K et al. (2009) Single nucleotide polymorphisms in the allene oxide synthase 2 gene are associated with field resistance to late blight in populations of tetraploid potato cultivars. _Genetics_, doi:"10.1534/genetics.108.094268":http://dx.doi.org/10.1534/genetics.108.094268 Riano-Pachon DM et al. (2009) GabiPD: The GABI Primary Database - a plant integrative ‘omics’ database. _Nucleic Acids Research_ 37(Database issue):D954-9, DOI "10.1093/nar/gkn611":http://dx.doi.org/10.1093/nar/gkn611 Usadel B et al (2006) PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. _BMC Bioinformatics_ 7:535.
    Nature Precedings 05/2009;
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    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 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.
    Nucleic Acids Research 10/2008; 37(Database issue):D954-9. · 8.81 Impact Factor
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    ABSTRACT: GabiPD ("http://gabi.rzpd.de":http://gabi.rzpd.de) was established within GABI-I and further developed in GABI-II and constitutes a repository and analysis platform for a wide array of heterogeneous data arising from high throughput experiments developed by members of the GABI/WPG community. Currently, data from different fronts (genomics, transcriptomics, proteomics, metabolomics) are incorporated in GabiPD, representing 14 different biological species. Last year GabiPD moved to the Max Planck Institute of Molecular Plant Physiology. In the progressing GABI-FUTURE phase, the GabiPD team has been creating a more integrative data view, expanding the tools and information provided by our well-known GreenCards. Links to different species-specific (_Arabidopsis thaliana_ so far) GABI-resources (e.g., Aramemnon, GABI-KAT) as well as external resources (e.g., ProMEX) are being added or updated. All data types (e.g., protein spots, clones) in GabiPD are pointing to the central Gene’s GreenCard, where gene information is retrieved from genome annotation projects or large UniGene sets provided by NCBI. Moreover, the GabiPD team will perform new types of data computations, like analysis of conserved domains in protein sequences.
    Nature Precedings 08/2008;
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    ABSTRACT: The GABI Primary Database, GabiPD, was established eight years ago in the frame of the German initiative for Genome Analysis of the Plant Biological System (Genomanalyse im biologischen System Pflanze, GABI), funded by the German Federal Ministry of Education, Research and Technology (BMBF) as well as a number of private enterprise companies. The main goal of GabiPD is to collect, integrate, visualize and link primary information from GABI projects. GabiPD, in contrast to other plant databases constitutes a repository and analysis platform for a wide array of heterogeneous data arising from high-throughput experiments in several plant species. Currently, data from different 'omics' fronts are incorporated in GabiPD (i.e., genomics, transcriptomics, metabolomics, proteomics), 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 plant lines, markers). All data types are pointing to the central Gene’s GreenCard, where gene information is integrated from genome annotation projects. Within the Gene’s GreenCards links to all GabiPD data related to the corresponding genes as well as cross references to large UniGene sets from NCBI and to useful gene-based external data bases are displayed. A collection of ~400000 ESTs from different species, generated in different GABI projects, is made publicly available though GabiPD. These ESTs have been cross referenced to UniGene sets from NCBI and to sequences from different plant genome projects, in an effort to ease the transfer of functional information. The centralized Gene's GreenCard also allows visualizing ESTs aligned to annotated transcripts as well as identified protein domains and gene structure. Moreover GabiPD makes available interactive genetic maps from Solanum tuberosum (potato) and Hordeum vulgare (barley). Gene expression data in GabiPD can be visualized through MapManWeb, the web interface of MapMan. Access to the data in GabiPD is provided via either the web interface (http://www.gabipd.org) or webservices that are currently available for Arabidopsis-related information. GabiPD was accessed by more than 30000 unique visitors last year from around the world.
    Nature Precedings 01/2008;