You are here: MIMS > EPrints
MIMS EPrints

2008.89: A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

2008.89: M.J. Herrgård, N. Swainston, P. Dobson, W.B. Dunn, K.Y. Arga, M. Arvas, N. Blüthgen, S. Borger, R. Costenoble, M. Heinemann, M. Hucka, N. Le Novère, P Li, W. Liebermeister, M.L. Mo, A.P. Oliveira, D. Petranovic, S. Pettifer, E. Simeonidis, K. Smallbone, I. Spasić, D. Weichart, R. Brent, D.S. Broomhead, H.V. Westerhoff, B.I. Kırdar, M. Penttilä, E. Klipp, B.Ø. Palsson, U. Sauer, S.G. Oliver, P. Mendes, J. Nielsen and D.B. Kell (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology, 16. pp. 1155-1160. ISSN 1087-0156

Full text available as:

PDF - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader
264 Kb

DOI: 10.1038/nbt1492


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 ( 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.

Item Type:Article
Subjects:MSC 2000 > 92 Biology and other natural sciences
MIMS number:2008.89
Deposited By:Dr Kieran Smallbone
Deposited On:10 October 2008

Download Statistics: last 4 weeks
Repository Staff Only: edit this item