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.
Herrgård
Markus J
MJ
Department of Bioengineering, University of California, San Diego, La Jolla, California 92093-0412, USA.
Swainston
Neil
N
Dobson
Paul
P
Dunn
Warwick B
WB
Arga
K Yalçin
KY
Arvas
Mikko
M
Blüthgen
Nils
N
Borger
Simon
S
Costenoble
Roeland
R
Heinemann
Matthias
M
Hucka
Michael
M
Le Novère
Nicolas
N
Li
Peter
P
Liebermeister
Wolfram
W
Mo
Monica L
ML
Oliveira
Ana Paula
AP
Petranovic
Dina
D
Pettifer
Stephen
S
Simeonidis
Evangelos
E
Smallbone
Kieran
K
Spasić
Irena
I
Weichart
Dieter
D
Brent
Roger
R
Broomhead
David S
DS
Westerhoff
Hans V
HV
Kirdar
Betül
B
Penttilä
Merja
M
Klipp
Edda
E
Palsson
Bernhard Ø
BØ
Sauer
Uwe
U
Oliver
Stephen G
SG
Mendes
Pedro
P
Nielsen
Jens
J
Kell
Douglas B
DB
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