|
|
YEASTNET: A consensus reconstruction of yeast metabolism |
Latest version: Yeast consensus reconstructions are now made available at yeast.sf.net, this page is left here only for historical purposes
Version 2
Version 2 of this reconstruction was released in June 2009, and incorporates 989 new reactions, 899 new species types (of which 26 are new distinct metabolites) and 1 new compartment (lipid particle). Part of the new data originated from the iIN800 (Nookaew et al.) reconstruction that includes lipid metabolism; in addition the team managed to find literature evidence for a large number of transporters that were originally identified by computational hypothesis. This resulted in a total of 2576 reactions and 2491 chemical species.
As usual, the entire network is supplied in a single SBML file and is also available as a searchable database.
About this resource
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. The 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 (you can access that network here). A second version has now been released and is awaiting publication. We plan on continuing to update this resource towards a complete metabolic network of yeast. All versions will remain accessible for historical purposes, however it is highly recommended that you always use the latest one since that is the most up to date.
This effort 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. That effort is now ongoing under the leadership of the MCISB and with collaboration with colleagues under the UNICELLSYS FP7 project.
Availability
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 (e.g. Uniprot, ChEBI, etc.). 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).
This reconstruction is provided in the following formats:
- an SBML file containing the reaction network and annotations, located to specific sub-cellular compartments
- an SBML file containing the reaction network and annotations without subcellular compartmentation (all reactions happening in a single compartment).