Abstract
BackgroundIn the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. Databases provide crucial solutions: they store, organize and allow information to be queried, they enhance the visibility of newly produced data by comparing them with previously published results, and facilitate the exploration and development of both existing hypotheses and new ideas.ResultsThe 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).ConclusionCombining 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.
Highlights
In the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern
The main design criteria included (i) using a common information system for all genomes within a unified interface, (ii) providing reliable data by combining and re-analyzing raw data derived from different sources, i.e. ridding users of format heterogeneity problems, (iii) considering data in various contexts such as chromosomal location, or gene family or orthology group membership, (iv) providing access to original data through collaboration with data producers, and (v) facilitating the formulation and testing of hypotheses based on links between gene structure and function
In order to satisfy these criteria, the choice was made to develop a data warehouse connected to original interfaces and capable of helping build hypotheses based on a number of interactive graphical displays
Summary
Through a user friendly application, FLAGdb++ offers plant biologists access to a rich array of original genomic resources. We have not described in this paper all the tools and types of display available in FLAGdb++. They are extensively documented on-line [38]. Availability and requirements The FLAGdb++ home page [38] provides both access to the installation guide and complete documentation regarding tools and data. Database architecture, integrated data and all the pipelines developed (in Perl) to fill the database are available on request for users who want to use the FLAGdb++ environment with other eukaryotic genomes. A Perl script allowing to open the FLAGdb++ application on a specific feature is available on request in order to create interactive links from other tools or databases. List of abbreviations CDS: coding sequence; GFF: gene feature format; GFT: gene family tag; GO: gene ontology; GST: gene specific tag; FST: T-DNA flanking sequence tag; MPSS: massively parallel signature sequencing; PPR: pentatricopeptide repeat; TPS: terpene synthase; TSS: transcription start site
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