PMID- 18846089
OWN - NLM
STAT- MEDLINE
DA  - 20081010
DCOM- 20081229
IS  - 1546-1696 (Electronic)
IS  - 1087-0156 (Linking)
VI  - 26
IP  - 10
DP  - 2008 Oct
TI  - A consensus yeast metabolic network reconstruction obtained from a community
      approach to systems biology.
PG  - 1155-60
LID - 10.1038/nbt1492 [doi]
AB  - 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.
FAU - Herrgard, Markus J
AU  - Herrgard MJ
AD  - Department of Bioengineering, University of California, San Diego, La Jolla,
California 92093-0412, USA.
FAU - Swainston, Neil
AU  - Swainston N
FAU - Dobson, Paul
AU  - Dobson P
FAU - Dunn, Warwick B
AU  - Dunn WB
FAU - Arga, K Yalcin
AU  - Arga KY
FAU - Arvas, Mikko
AU  - Arvas M
FAU - Bluthgen, Nils
AU  - Bluthgen N
FAU - Borger, Simon
AU  - Borger S
FAU - Costenoble, Roeland
AU  - Costenoble R
FAU - Heinemann, Matthias
AU  - Heinemann M
FAU - Hucka, Michael
AU  - Hucka M
FAU - Le Novere, Nicolas
AU  - Le Novere N
FAU - Li, Peter
AU  - Li P
FAU - Liebermeister, Wolfram
AU  - Liebermeister W
FAU - Mo, Monica L
AU  - Mo ML
FAU - Oliveira, Ana Paula
AU  - Oliveira AP
FAU - Petranovic, Dina
AU  - Petranovic D
FAU - Pettifer, Stephen
AU  - Pettifer S
FAU - Simeonidis, Evangelos
AU  - Simeonidis E
FAU - Smallbone, Kieran
AU  - Smallbone K
FAU - Spasic, Irena
AU  - Spasic I
FAU - Weichart, Dieter
AU  - Weichart D
FAU - Brent, Roger
AU  - Brent R
FAU - Broomhead, David S
AU  - Broomhead DS
FAU - Westerhoff, Hans V
AU  - Westerhoff HV
FAU - Kirdar, Betul
AU  - Kirdar B
FAU - Penttila, Merja
AU  - Penttila M
FAU - Klipp, Edda
AU  - Klipp E
FAU - Palsson, Bernhard O
AU  - Palsson BO
FAU - Sauer, Uwe
AU  - Sauer U
FAU - Oliver, Stephen G
AU  - Oliver SG
FAU - Mendes, Pedro
AU  - Mendes P
FAU - Nielsen, Jens
AU  - Nielsen J
FAU - Kell, Douglas B
AU  - Kell DB
LA  - eng
GR  - R01 GM071808/GM/NIGMS NIH HHS/United States
GR  - Biotechnology and Biological Sciences Research Council/United Kingdom
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Nat Biotechnol
JT  - Nature biotechnology
JID - 9604648
RN  - 0 (Saccharomyces cerevisiae Proteins)
SB  - IM
MH  - Computer Simulation
MH  - *Databases, Protein
MH  - Information Storage and Retrieval/methods
MH  - *Models, Biological
MH  - Saccharomyces cerevisiae/*metabolism
MH  - Saccharomyces cerevisiae Proteins/*metabolism
MH  - Signal Transduction/*physiology
MH  - Systems Biology/*methods
MH  - Systems Integration
EDAT- 2008/10/11 09:00
MHDA- 2008/12/30 09:00
CRDT- 2008/10/11 09:00
AID - nbt1492 [pii]
AID - 10.1038/nbt1492 [doi]
PST - ppublish
SO  - Nat Biotechnol. 2008 Oct;26(10):1155-60. doi: 10.1038/nbt1492.