Exploration of plant genomes in the FLAGdb++ environment

The FLAGdb++ information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches. Available through a JAVA application, original interfaces and tools assist the functional study of plant genes by considering them in their specific context: chromosome, gene family, orthology group, co-expression cluster and functional network. FLAGdb++ is mainly dedicated to the exploration of large gene groups in order to decipher functional connections, to highlight shared or specific structural or functional features, and to facilitate translational tasks between plant species (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera).Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb++ presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge. First launched in 2002, a 15th version of FLAGdb++ is now available and comprises four model plant genomes and over eight million genomic features.Holistic approaches require the organization of data and metadata in order to allow the hypothesis-driven querying of heterogeneous objects. In many systems biology considerations, data management and integrative approaches are identified as key to the thorough exploitation of omics data and their translation into knowledge [1]. Many biologists that would like to take advantage of the rapid increase in the number and size of sequenced genomes do not have the skills required to derive function from sequence or vice versa. They encounter a major problem, i.e. connecting heterogeneous pieces of information quickly and accurately in the absence of a methodological approach to organizing them efficiently. Indeed, huge quantities of data are stored and managed by different