This is a portal to the consensus yeast metabolic network as reconstructed from the genome sequence and literature. It is a highly annotated metabolic map that is periodically updated by a team of collaborators from various research groups.
We started on the shoulders of a number of reconstructions of the metabolic network of yeast based on genomic and literature data that were published separately (iMM904 and iLL672). However, due to the different approaches utilized in them, those earlier reconstructions had a significant number of differences. In addition they suffered from the use of non-standard names and overall they were not annotated with methods that are machine-readable. A community effort in 2007, led by the Manchester Centre for Integrative Systems Biology and the YSBN resulted in a consensus network representation of yeast metabolism, reconciling the earlier results. This first version of this reconstruction was published in Herrgård, Swainston et al. (2008) "A consensus yeast metabolic reconstruction obtained from a community approach to systems biology" Nature Biotechnol 26:1155-1160.
That effort is now ongoing under the leadership of the MCISB and with collaboration with colleagues under the UNICELLSYS FP7 and BioPreDyn projects. Version 4 was published in Dobson, Smallbone et al. (2010) "Further developments towards a genome-scale metabolic model of yeast" BMC Syst Biol 4145. The most recent version, Yeast 5, was released in September 2011.
The network reconstruction is primarily assembled and provided as an SBML file enriched with MIRIAM-compliant annotations (which are embedded in the SBML through RDF). All small and macro- molecules are referenced to an authoritative database such as Uniprot or ChEBI. All molecules and reactions are also annotated with appropriate publications that contain supporting evidence. Thus this network is entirely traceable and is presented in a computational framework. SBML is a format that is understood by a large number of software applications (see sbml.org).
See also ecoli.sf.net.
