Reconstruction annotation jamborees: a community approach to systems biology

Abstract

Mol Syst Biol. 6: 361 Genome‐scale metabolic network reconstructions represent biochemical, genetic, and genomic (BiGG) knowledge bases for a target organism (Reed et al , 2006). Thus, they correspond to two‐dimensional genome annotations: that is, they contain all nodes and links that comprise a biochemical reaction network defined by the genome (Palsson, 2004). These reconstructions allow the conversion of biological knowledge into a mathematical format and subsequent computation of physiological properties. They therefore enable the formulation of a mechanistic genotype–phenotype relationship for metabolic functions in the target organism. The metabolic network reconstruction process is now well established (Thiele and Palsson, 2010) and its workflows have recently been reviewed (Reed et al , 2006; Feist et al , 2009). The development of a consensus network reconstruction that is accepted and used by the research community necessitates a collective effort to formalize such networks that are specific to a target organism. This need has led to the concept of a 2D annotation (or a reconstruction) jamboree (Mo and Palsson, 2009), in analogy to the 1D genome annotation jamborees that lead to a community‐driven genome annotation process. You may be interested in organizing a jamboree for your favorite target organism. What do you need to do? The goal of a network reconstruction jamboree is to reconcile and refine currently available BiGG knowledge about the target organism. If available, multiple existing metabolic network reconstructions made by individual research groups provide a great starting point. A jamboree should update, re‐evaluate, refine and, later on, expand the network content. These goals are most efficiently achieved through a community approach that assembles experts from different areas. Jamborees assist in fostering collaborations as well as informing the community about the properties, content, and capabilities of the consensus reconstruction to ensure its broad use for biological, biomedical, …