AgBase: a tool for systems biology in agricultural species.

Abstract

Abstract Genome sequences are available for several agriculturally important species (both eukaryotic and prokaryotic) and genome sequences and '-omics' technologies show promise for translating genomics data into increased production efficiency, sustainable agriculture and advances for the bio-economy. However, predictive and preventative systems modelling depends on biological information and not just genomics data. Systems biology approaches allow the integration of various '-omics' data to produce valuable models to understand complex biological systems. The two approaches for doing systems biology are bottom-up modelling and top-down modelling. We focus on top-down systems biology, which entails four fundamental and overlapping steps: the enumeration of the system's parts, elucidation of interactions between these parts, modelling regulation of these interaction networks and generating predictive and dynamic models. Systems biology in agriculturally important species is truly possible only when all the elements required for systems biology become available for these species. The AgBase databases provide critical components for systems biology modelling in agriculture as they provide experimentally based structural annotation of genomic sequences and highly curated functional annotations of gene products using Gene Ontology (GO). The GO underpins network analysis and can also be used to model physiological function in biological systems. Like the '-omics' data being modelled, agricultural databases (and agricultural researchers) need to be better integrated to support the multidisciplinary research required for systems biology.