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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.

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Change history

  • 07 May 2012

    In the HTML version of this article initially published, Nils Blüthgen’s name was spelled as Büthgen. The error has been corrected in the HTML version of the article.

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Acknowledgements

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 information

Author notes

    • Markus J Herrgård
    •  & Dina Petranovic

    Present addresses: Synthetic Genomics, Inc., 11149 N. Torrey Pines Rd., La Jolla, California 92037, USA (M.J.H.) and Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden (D.P.).

    • Markus J Herrgård
    •  & Neil Swainston

    These authors contributed equally to this work.

Affiliations

  1. Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, USA.

    • Markus J Herrgård
    • , Monica L Mo
    •  & Bernhard Ø Palsson
  2. School of Computer Science, The University of Manchester, Oxford Rd., Manchester M13 9PL, UK.

    • Neil Swainston
    • , Peter Li
    • , Stephen Pettifer
    • , Irena Spasié
    •  & Pedro Mendes
  3. The Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess St., Manchester M1 7DN, UK.

    • Neil Swainston
    • , Paul Dobson
    • , Warwick B Dunn
    • , Nils Blüthgen
    • , Peter Li
    • , Stephen Pettifer
    • , Evangelos Simeonidis
    • , Kieran Smallbone
    • , Irena Spasié
    • , Dieter Weichart
    • , David S Broomhead
    • , Hans V Westerhoff
    • , Stephen G Oliver
    • , Pedro Mendes
    •  & Douglas B Kell
  4. School of Chemistry, The University of Manchester, Manchester M13 9PL, UK.

    • Paul Dobson
    • , Warwick B Dunn
    • , Dieter Weichart
    •  & Douglas B Kell
  5. Department of Chemical Engineering, Boğaziçi University, Bebek 34342, Istanbul, Turkey.

    • K Yalçin Arga
    •  & Betül Kürdar
  6. VTT Biotechnology Espoo, PO Box 1500, FIN-02044, Finland.

    • Mikko Arvas
    •  & Merja Penttilä
  7. School of Chemical Engineering and Analytical Science, The University of Manchester, UK.

    • Nils Blüthgen
    • , Evangelos Simeonidis
    •  & Hans V Westerhoff
  8. Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, Germany.

    • Simon Borger
    • , Wolfram Liebermeister
    •  & Edda Klipp
  9. Institut für Molekulare Systembiologie, ETH Zurich Wolfgang-Pauli-Str. 16, 8093 Zürich, Switzerland.

    • Roeland Costenoble
    • , Matthias Heinemann
    •  & Uwe Sauer
  10. Control and Dynamical Systems, California Institute of Technology, Pasadena, California 91125, USA.

    • Michael Hucka
  11. Computational Neurobiology, EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

    • Nicolas Le Novère
  12. Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, Building 223, DK-2800 Kgs. Lyngby, Denmark.

    • Ana Paula Oliveira
    • , Dina Petranovic
    •  & Jens Nielsen
  13. School of Mathematics, The University of Manchester, Manchester M13 9PL, UK.

    • Kieran Smallbone
    •  & David S Broomhead
  14. The Molecular Sciences Institute, 2168 Shattuck Avenue, Berkeley, California 94704, USA.

    • Roger Brent
  15. Department of Molecular Cell Physiology, Vrije Universiteit, de Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.

    • Hans V Westerhoff
  16. Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK.

    • Stephen G Oliver
  17. Virginia Bioinformatics Institute, Virginia Tech, Washington St. 0477, Blacksburg, Virginia 24061, USA.

    • Pedro Mendes
  18. Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.

    • Jens Nielsen

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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.

Corresponding author

Correspondence to Douglas B Kell.

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DOI

https://doi.org/10.1038/nbt1492

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