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

Herrgård, Markus J. and Swainston, Neil and Dobson, Paul and Dunn, Warwick B. and Arga, K. Yalçin and Arvas, Mikko and Büthgen, Nils and Borger, Simon and Costenoble, Roeland and Heinemann, Matthias and Hucka, Michael and Le Novère, Nicolas and Li, Peter and Liebermeister, Wolfram and Mo, Monica L. and Oliveira, Ana Paula and Petranovic, Dina and Pettifer, Stephen and Simeonidis, Evangelos and Smallbone, Kieran and Spasié, Irena and Weichart, Dieter and Brent, Roger and Broomhead, David S. and Westerhoff, Hans V. and Kürdar, Betül and Penttilä, Merja and Klipp, Edda and Palsson, Bernhard Ø. and Sauer, Uwe and Oliver, Stephen G. and Mendes, Pedro and Nielsen, Jens and Kell, Douglas B. (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology, 26 (10). pp. 1155-1160. ISSN 1087-0156. PMCID PMC4018421. http://resolver.caltech.edu/CaltechAUTHORS:20090430-074605876

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1038/nbt1492DOIArticle
http://www.nature.com/nbt/journal/v26/n10/abs/nbt1492.htmlPublisherArticle
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4018421/PubMed CentralArticle
ORCID:
AuthorORCID
Hucka, Michael0000-0001-9105-5960
Additional Information:© 2009 Nature Publishing Group. Published online 9 October 2008. The Manchester groups thank the UK Biotechnology and Biological Sciences Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC) for financial support including for the Manchester Centre for Integrative Systems Biology (http://www.mcisb.org/). The UCSD participants thank the National Institutes of Health for financial support (NIH R01 GM071808). We thank Diane Kelly, Sarah Keating and Norman Paton for many useful discussions. The Jamboree was held under the auspices and with the sponsorship of the Yeast Systems Biology Network (EC Contract: LSHG-CT-2005-018942). Author Contributions: All authors conceived the idea of the consensus reconstruction, the majority were present during the jamboree itself and all contributed to the writing of, and approved, the manuscript.
Funders:
Funding AgencyGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)UNSPECIFIED
Engineering and Physical Sciences Research Council (EPSRC)UNSPECIFIED
NIHR01 GM071808
Yeast Systems Biology NetworkLSHG-CT-2005-018942
PubMed Central ID:PMC4018421
Record Number:CaltechAUTHORS:20090430-074605876
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20090430-074605876
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:14113
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:11 Aug 2009 16:42
Last Modified:25 Jul 2017 16:49

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