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

@article{Herrgard08, 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.}, author = {Herrgard, Markus J. and Swainston, Neil and Dobson, Paul and Dunn, Warwick B. and Arga, K. Yalcin and Arvas, Mikko and Buthgen, Nils and Borger, Simon and Costenoble, Roeland and Heinemann, Matthias and Hucka, Michael and Le Novere, Nicolas and Li, Peter and Liebermeister, Wolfram and Mo, Monica L. and Oliveira, Ana P. and Petranovic, Dina and Pettifer, Stephen and Simeonidis, Evangelos and Smallbone, Kieran and Spasie, Irena and Weichart, Dieter and Brent, Roger and Broomhead, David S. and Westerhoff, Hans V. and Kurdar, Betul and Penttila, Merja and Klipp, Edda and Palsson, Bernhard O. and Sauer, Uwe and Oliver, Stephen G. and Mendes, Pedro and Nielsen, Jens and Kell, Douglas B.}, citeulike-article-id = {3391451}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nbt1492}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/nbt1492}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18846089}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18846089}, day = {09}, doi = {10.1038/nbt1492}, issn = {1546-1696}, journal = {Nat Biotech}, keywords = {community\_approach, mcisb, metabolism, modelling, reconstruction, sbml, semantics, systems-biology, yeast}, month = {October}, number = {10}, pages = {1155--1160}, posted-at = {2009-10-14 11:57:02}, priority = {2}, publisher = {Nature Publishing Group}, title = {A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology}, url = {http://dx.doi.org/10.1038/nbt1492}, volume = {26}, year = {2008} }

TY - JOUR ID - Herrgard08 L3 - citeulike-article-id:3391451 N2 - 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. IS - 10 JF - Nat Biotech SN - 1546-1696 EP - 1160 TI - A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology PB - Nature Publishing Group VL - 26 SP - 1155 KW - community_approach KW - mcisb KW - metabolism KW - modelling KW - reconstruction KW - sbml KW - semantics KW - systems-biology KW - yeast AU - Herrgard, Markus AU - Swainston, Neil AU - Dobson, Paul AU - Dunn, Warwick AU - Arga, Yalcin AU - Arvas, Mikko AU - Buthgen, Nils AU - Borger, Simon AU - Costenoble, Roeland AU - Heinemann, Matthias AU - Hucka, Michael AU - Le Novere, Nicolas AU - Li, Peter AU - Liebermeister, Wolfram AU - Mo, Monica AU - Oliveira, Ana AU - Petranovic, Dina AU - Pettifer, Stephen AU - Simeonidis, Evangelos AU - Smallbone, Kieran AU - Spasie, Irena AU - Weichart, Dieter AU - Brent, Roger AU - Broomhead, David AU - Westerhoff, Hans AU - Kurdar, Betul AU - Penttila, Merja AU - Klipp, Edda AU - Palsson, Bernhard AU - Sauer, Uwe AU - Oliver, Stephen AU - Mendes, Pedro AU - Nielsen, Jens AU - Kell, Douglas PY - 2008/10/09/ UR - http://dx.doi.org/10.1038/nbt1492 ER -