CaltechAUTHORS
Published October 2008 | Version Accepted Version + Supplemental Material
Journal Article Open

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

Creators

  • 1. ROR icon University of California, San Diego
  • 2. ROR icon Synthetic Genomics (United States)
  • 3. ROR icon University of Manchester
  • 4. ROR icon Boğaziçi University
  • 5. ROR icon VTT Technical Research Centre of Finland
  • 6. ROR icon Max Planck Institute for Molecular Genetics
  • 7. ROR icon ETH Zurich
  • 8. ROR icon California Institute of Technology
  • 9. ROR icon European Bioinformatics Institute
  • 10. ROR icon Technical University of Denmark
  • 11. ROR icon Molecular Sciences Institute
  • 12. ROR icon VU Amsterdam
  • 13. ROR icon University of Cambridge
  • 14. ROR icon Virginia Tech
  • 15. ROR icon Chalmers University of Technology

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.

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.

Attached Files

Accepted Version - nihms574724.pdf

Supplemental Material - HERnbt08_supp.doc

Supplemental Material - nbt1492-S2.html

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Additional details

Identifiers

PMCID
PMC4018421
Eprint ID
14113
DOI
10.1038/nbt1492
Resolver ID
CaltechAUTHORS:20090430-074605876

Related works

Describes
10.1038/nbt1492 (DOI)

Funding

Biotechnology and Biological Sciences Research Council (BBSRC)
Engineering and Physical Sciences Research Council (EPSRC)
NIH
R01 GM071808
Yeast Systems Biology Network
LSHG-CT-2005-018942

Dates

Created
2009-08-11
Created from EPrint's datestamp field
Updated
2021-11-08
Created from EPrint's last_modified field