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

Herrgard, M J; Swainston, N; Dobson, P; Dunn, W B; Arga, K Y; Arvas, M; Bluthgen, N; Borger, S; Costenoble, R; Heinemann, M; Hucka, M; Le Novere, N; Li, P; Liebermeister, W; Mo, M L; Oliveira, A P; Petranovic, D; Pettifer, S; Simeonidis, E; Smallbone, K; Spasic, I; Weichart, D; Brent, R; Broomhead, D S; Westerhoff, H V; Kirdar, B; Penttila, M; Klipp, E; Palsson, B O; Sauer, U; Oliver, S G; Mendes, P; Nielsen, J; Kell, D B

Nature Biotechnology. 2008;26(10):1155-1160.

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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.

Bibliographic metadata

Type of resource:
Content type:
Published date:
Journal title:
ISSN:
Volume:
26
Issue:
10
Start page:
1155
End page:
1160
Total:
6
Pagination:
1155-1160
Digital Object Identifier:
10.1038/nbt1492
ISI Accession Number:
WOS:000259926000030
Related website(s):
  • Related website <Go to ISI>://WOS:000259926000030
General notes:
  • Times Cited: 91
Access state:
Active

Institutional metadata

University researcher(s):

Record metadata

Manchester eScholar ID:
uk-ac-man-scw:122122
Created by:
Dunn, Warwick
Created:
21st April, 2011, 15:30:18
Last modified by:
Dunn, Warwick
Last modified:
11th March, 2014, 21:46:06

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