Molecular Systems Biology 6 Article number: 361 doi:10.1038/msb.2010.15
Published online: 13 April 2010
Citation: Molecular Systems Biology 6:361
Reconstruction annotation jamborees: a community approach to systems biology
Ines Thiele1,2 & Bernhard Ø Palsson3
Center for Systems Biology, University of Iceland, Reykjavik, Iceland
Faculty of Industrial Engineering, Mechanical Engineering & Computer Science, University of Iceland, Reykjavik, Iceland
Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
Published online 13 April 2010
This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits distribution and reproduction in any medium, provided the original author and source are credited. This licence does not permit commercial exploitation or the creation of derivative works without specific permission.
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?
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