The GABI Primary Database: GABIPD - Integration of Plant 'Omics'-Data in Gene Context

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.108.094268Riano-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/gkn611Usadel B et al (2006) PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. BMC Bioinformatics 7:535.