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

Markus J Herrgård ; Neil Swainston ; Paul Dobson ; Warwick B Dunn ; K Yalçin Arga ; Mikko Arvas ; Nils Blüthgen ; Simon Borger ; Roeland Coestenoble ; Matthias Heinemann ; Michael Hucka ; Nicolas Le Novère ; Peter Li ; Wolfram Liebermeister ; Monica L Mo ; Ana Paula Oliveira ; Dina Petranovic (Institutionen för kemi- och bioteknik, Systembiologi) ; Stephen Pettifer ; Evangelos Simeonidis ; Kieran Smallbone ; Irena Spasić ; Dieter Weichart ; Roger Brent ; David S Broomhead ; Hans W Westerhoff ; Betül Kırdar ; Merja Penttilä ; Edda Klipp ; Bernhard Ø Palsson ; Uwe Sauer ; Stephen G Oliver ; Pedro Mendes ; Jens B. Nielsen (Institutionen för kemi- och bioteknik, Systembiologi) ; Douglas B Kell
Nature Biotechnology Vol. 26 (2008), 10, p. 1155-1160.
[Artikel, refereegranskad vetenskaplig]

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 make 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 InChl 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.

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Denna post skapades 2009-04-06. Senast ändrad 2014-10-27.
CPL Pubid: 92245


Institutioner (Chalmers)

Institutionen för kemi- och bioteknik, Systembiologi (2008-2014)


Cell- och molekylärbiologi
Industriell bioteknik

Chalmers infrastruktur