GabiPD: The GABI Primary Database - a plant integrative ‘omics’ database

Abstract

AbstractThe 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, analyse and visualise 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 visualising 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 2DE-gels from Arabidopsis thaliana and Brassica napus. Gene expression and metabolic profiling data can be visualised 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.