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

lenov's picture
TitleA consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.
Publication TypeJournal Article
Year of Publication2008
AuthorsHerrgård, MJ, Swainston, N, Dobson, P, Dunn, WB, Arga, YK, 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
JournalNat Biotechnol
Volume26
Issue10
Pagination1155-60
Date Published2008 Oct
ISSN1546-1696
KeywordsComputer Simulation, Databases, Protein, Information Storage and Retrieval, Models, Biological, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Signal Transduction, Systems Biology, Systems Integration
Abstract

<p>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.</p>

DOI10.1038/nbt1492
Alternate JournalNat. Biotechnol.
PubMed ID18846089
PubMed Central IDPMC4018421
Grant ListBB/C008219/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
BB/E006248/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
BB/E016065/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
BB/F010516/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
R01 GM071808 / GM / NIGMS NIH HHS / United States
R01 GM071808 / GM / NIGMS NIH HHS / United States
R01 GM097479 / GM / NIGMS NIH HHS / United States
/ / Biotechnology and Biological Sciences Research Council / United Kingdom