A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.
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.
Department of Bioengineering, University of California, San Diego, La Jolla, California 92093-0412, USA.
Markus J
MJ
Herrgård
Neil
N
Swainston
Paul
P
Dobson
Warwick B
WB
Dunn
K Yalçin
KY
Arga
Mikko
M
Arvas
Nils
N
Blüthgen
Simon
S
Borger
Roeland
R
Costenoble
Matthias
M
Heinemann
Michael
M
Hucka
Nicolas
N
Le Novère
Peter
P
Li
Wolfram
W
Liebermeister
Monica L
ML
Mo
Ana Paula
AP
Oliveira
Dina
D
Petranovic
Stephen
S
Pettifer
Evangelos
E
Simeonidis
Kieran
K
Smallbone
Irena
I
Spasić
Dieter
D
Weichart
Roger
R
Brent
David S
DS
Broomhead
Hans V
HV
Westerhoff
Betül
B
Kirdar
Merja
M
Penttilä
Edda
E
Klipp
Bernhard Ø
BØ
Palsson
Uwe
U
Sauer
Stephen G
SG
Oliver
Pedro
P
Mendes
Jens
J
Nielsen
Douglas B
DB
Kell
D003198:Computer Simulation; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods; D008954:Models, Biological; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D049490:Systems Biology / Q000379:methods*; D018511:Systems Integration
D029701:Saccharomyces cerevisiae Proteins