Herrgård2008_MetabolicNetwork_Yeast

  public model
Short description

This is a reconstruction of the biochemical network of the yeast Saccharomyces cerevisiae carried out at a jamboree organized in April 2007 in the Manchester Centre for Integrative Systems Biology. It is the result of a consensus merger of two previous reconstructions.

Technical notes:

  • The compartments included here have no volume defined; there are no reliable estimates available for those volumes yet.
  • There are no kinetic functions defined for the reactions because this model only represents the chemical structure of the network (stoichiometry).
  • All reactions are marked reversible because all chemical reactions are reversible.

The model is described in the article and available as supplementary material:
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.
Herrgård MJ, Swainston N et al. , Nat Biotechnol. 2008 Oct;26(10):1155-60. PMID: 18846089 , doi: 10.1038/nbt1492
Abstract:
Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same chemical entities. This makes comparisons between them difficult and underscores the desirability of a consolidated metabolic network that collects and formalizes the 'community knowledge' of yeast metabolism. We describe how we have produced a consensus metabolic network reconstruction for S. cerevisiae. In drafting it, we placed special emphasis on referencing molecules to persistent databases or using database-independent forms, such as SMILES or InChI strings, as this permits their chemical structure to be represented unambiguously and in a manner that permits automated reasoning. The reconstruction is readily available via a publicly accessible database and in the Systems Biology Markup Language (http://www.comp-sys-bio.org/yeastnet). It can be maintained as a resource that serves as a common denominator for studying the systems biology of yeast. Similar strategies should benefit communities studying genome-scale metabolic networks of other organisms.

Up to date versions can be found under http://www.comp-sys-bio.org/yeastnet/

This SBML representation of the yeast metabolic network is made available under the Creative Commons Attribution-Share Alike 3.0 Unported Licence (see www.creativecommons.org ).

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.

To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Format
SBML (L2V3)
Related Publication
  • A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.
  • Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB
  • Nature biotechnology , 10/ 2008 , Volume 26 , pages: 1155-1160
  • Department of Bioengineering, University of California, San Diego, La Jolla, California 92093-0412, USA.
  • Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same chemical entities. This makes comparisons between them difficult and underscores the desirability of a consolidated metabolic network that collects and formalizes the 'community knowledge' of yeast metabolism. We describe how we have produced a consensus metabolic network reconstruction for S. cerevisiae. In drafting it, we placed special emphasis on referencing molecules to persistent databases or using database-independent forms, such as SMILES or InChI strings, as this permits their chemical structure to be represented unambiguously and in a manner that permits automated reasoning. The reconstruction is readily available via a publicly accessible database and in the Systems Biology Markup Language (http://www.comp-sys-bio.org/yeastnet). It can be maintained as a resource that serves as a common denominator for studying the systems biology of yeast. Similar strategies should benefit communities studying genome-scale metabolic networks of other organisms.
Contributors
Lukas Endler

Metadata information

isDescribedBy
PubMed 18846089
isVersionOf
Gene Ontology regulation of growth
Curation status
Non-curated
  • Model originally submitted by : Lukas Endler
  • Submitted: 12-Aug-2009 12:19:28
  • Last Modified: 03-Feb-2012 13:12:17
Revisions
  • Version: 2 public model Download this version
    • Submitted on: 03-Feb-2012 13:12:17
    • Submitted by: Lukas Endler
    • With comment: Current version of Herrgård2008_MetabolicNetwork_Yeast
  • Version: 1 public model Download this version
    • Submitted on: 12-Aug-2009 12:19:28
    • Submitted by: Lukas Endler
    • With comment: Original import of Herrgård2008 Yeast metabolic network