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YEASTNET: A consensus reconstruction of yeast metabolism |
Latest version: 5
Version 5 of this reconstruction was released in February 2012 and includes much improved coverage; in particular shingolipid metabolism is now included in some detail. An extensive description of version 5 is included in the following publication: Heavner BD, Smallbone K, Barker B, Mendes P, Walker LP (2012) Yeast 5 — an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. BMC Systems Biology 6:55.
Updates of the network are now hosted in SourceForge on http://yeast.sourceforge.net/ which is the primary point for accessing the SBML files. This website hosts the same data in a database that allows direct searches in the network
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. 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.
Publications
This reconstruction has been periodically reported in the peer-reviewed literature:
- 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 still access the corresponding network here).
- Dobson, Smallbone, et al. (2010) "Further
developments towards a genome-scale metabolic model of yeast" BMC Systems Biology 4:145.
- Heavner, Smallbone et al. (2012) "Yeast 5 — an expanded reconstruction of the Saccharomyces cerevisiae metabolic network." BMC Systems Biology 6:55
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).
The latest SBML files are available for download on yeast.sourceforge.net
While the SBML file is the most efficient computational resource for these data, casual users also need easy access to the network through simple queries. That is provided by a searchable database accessed directly from this website. (The database system is being updated and the most up to date version will appear soon)