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

Publication: Research - peer-reviewJournal article – Annual report year: 2008

  • Author: Herrgard, Markus

  • Author: Swainston, Neil

    University of Manchester

  • Author: Dobson, Paul

    University of Manchester

  • Author: Dunn, Warwick B.

    University of Manchester

  • Author: Arga, K Yalçin

    Department of Chemical Engineering, Boğaziçi, Bebek 34342

  • Author: Arvas, Mikko

    VTT Biotechnology Espoo, PO Box 1500, Fin-02044

  • Author: Blüthgen, Nils

    University of Manchester

  • Author: Borger, Simon

    Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin

  • Author: Costenoble, Roeland

    Swiss Federal Institute of Technology Zurich

  • Author: Heinemann, Matthias

    Swiss Federal Institute of Technology Zurich

  • Author: Hucka, Michael

    Control and Dynamical Systems, California Institute of Technology

  • Author: Le Novère, Nicolas

    Computational Neurobiology, EMBL-EBI, Wellcome-Trust Genome Campus

  • Author: Li, Peter

    University of Manchester

  • Author: Liebermeister, Wolfram

    Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin

  • Author: Mo, Minica L.

    Department of bioengineering, Univerity of California, San Diego, 9500 Gilman Drive

  • Author: Soberano de Oliveira, Ana Paula

    Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark

  • Author: Petranovic, Dina

    Department of Systems Biology, Technical University of Denmark

  • Author: Pettifer, Stephen

    University of Manchester

  • Author: Simeonidis, Evangelos

    University of Manchester

  • Author: Smallbone, Kieran

    University of Manchester

  • Author: Spasić, Irena

    University of Manchester

  • Author: Weichart, Dieter

    University of Manchester

  • Author: Brent, Roger

    The Molecular Sciences Institute, 2168 Shattuck Avenue

  • Author: Broomhead, David S.

    University of Manchester

  • Author: Westerhoff, Hans V.

    University of Manchester

  • Author: Kirdar, Betül

    Department of Chemical Engineering, Boğaziçi, Bebek 34342

  • Author: Penttilä, Merja

    VTT Biotechnology Espoo, PO Box 1500, Fin-02044

  • Author: Klipp, Edda

    Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin

  • Author: Palsson, Bernhard Ø.

    Department of bioengineering, Univerity of California, San Diego, 9500 Gilman Drive

  • Author: Sauer, Uwe

    Swiss Federal Institute of Technology Zurich

  • Author: Oliver, Stephen G.

    University of Manchester

  • Author: Mendes, Pedro

    University of Manchester

  • Author: Nielsen, Jens

    Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, Denmark

  • Author: Kell, Douglas B.

    University of Manchester

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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.
Original languageEnglish
JournalNature Biotechnology
Publication date2008
Volume26
Issue10
Pages1155-1160
ISSN1087-0156
DOIs
StatePublished
CitationsWeb of Science® Times Cited: 222
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