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1 University of Groningen A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology Herrgård, Markus J.; Swainston, Neil; Dobson, Paul; Dunn, Warwick B.; Arga, K. Yalçin; Arvas, Mikko; Blüthgen, Nils; Borger, Simon; Costenoble, Roeland; Heinemann, Matthias Published in: Nature Biotechnology DOI: /nbt1492 IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2008 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Herrgård, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M.,... Kell, D. B. (2008). A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology, 26(10), DOI: /nbt1492 Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date:
2 Supplementary Figure 1. An example of some of the SBML annotations of compartments, species and reactions, using the example of the reaction catalyzed by the gene product hexokinase 2 of the HXK2 gene, as used in the reconstruction of the consensus network, illustrating its use of the Systems Biology Ontology ( and its MIRIAM-compliance. <?xml version="1.0" encoding="utf-8"?> <sbml xmlns=" level="2" version="3"> <model metaid="metaid_ymn1_0" id="ymn1_0" name="yeast metabolic network"> <notes> <body xmlns=" <p>this is a reconstruction of the biochemical network of the yeast <i>saccharomyces cerevisiae</i> carried out at a jamboree organized in April 2007 in the Manchester Centre for Integrative Systems Biology. It is the result of a consensus merger of two previous reconstructions.</p> <p>technical notes: <ul> <li>the compartments included here have no volume defined; there are no reliable estimates available for those volumes yet.</li> <li>there are no kinetic functions defined for the reactions because this model only represents the chemical structure of the network (stoichiometry).</li> <li>all reactions are marked reversible because all chemical reactions are reversible.</li> </ul> </p> <p>this SBML representation of the yeast metabolic network is made available under the Creative Commons Attribution-Share Alike 3.0 Unported Licence (see <a href=" </body> </notes> <rdf:description rdf:about="#metaid_ymn1_0"> <dc:creator rdf:parsetype="resource"> <rdf:li rdf:parsetype="resource"> <vcard:n rdf:parsetype="resource"> <vcard:family>herrgard</vcard:family> <vcard:given>markus</vcard:given> </vcard:n> <vcard: >mherrgar@ucsd.edu</vcard: > <vcard:org> <vcard:orgname>university of California, San Diego</vCard:Orgname> </vcard:org> </rdf:li> <rdf:li rdf:parsetype="resource"> <vcard:n rdf:parsetype="resource"> <vcard:family>swainston</vcard:family>
3 <vcard:given>neil</vcard:given> </vcard:n> <vcard:org> <vcard:orgname>university of Manchester</vCard:Orgname> </vcard:org> </rdf:li> </dc:creator> <dcterms:created rdf:parsetype="resource"> <dcterms:w3cdtf> t10:05:10z</dcterms:w3cdtf> </dcterms:created> <dcterms:modified rdf:parsetype="resource"> <dcterms:w3cdtf> t17:52:27z</dcterms:w3cdtf> </dcterms:modified> <rdf:li rdf:resource="urn:miriam:taxonomy:4932"/> <listofcompartments> <compartment metaid="metaid_c_1" id="c_1" name="cytoplasm" outside="c_10" sboterm="sbo: "> <rdf:description rdf:about="#metaid_c_4"> <rdf:li rdf:resource="urn:miriam:obo.go:go: "/> </compartment> </listofcompartments> </listofspecies> <species metaid="metaid_m_172" id="m_172" name="atp" compartment="c_1" sboterm="sbo: "> <in:inchi xmlns:in=" metaid="m_172_inchi"> InChI=1/C10H16N5O13P3/c ( )15(3-14-5)10-7(17)6 (16)4(26-10) (21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2, (H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1/f/h18-19,21,23H,11H2 </in:inchi>
4 <rdf:description rdf:about="#metaid_m_172"> <rdf:li rdf:resource="urn:miriam:obo.chebi:chebi:15422"/> <rdf:li rdf:resource="#m_172_inchi"/> </species> <species metaid="metaid_e_450" id="e_450" name="ycl040w" compartment="c_1" sboterm="sbo: "> <rdf:description rdf:about="#metaid_e_450"> <rdf:li rdf:resource="urn:miriam:sgd:s "/> <rdf:li rdf:resource="urn:miriam:uniprot:p17709"/> </species> </listofspecies> </listofreactions> <reaction metaid="metaid_r_1550" id="r_1550" name="hexokinase (D-glucose:ATP)" sboterm="sbo: "> <notes> <html xmlns=" <p>subsystem: Glycolysis/Gluconeogenesis</p> </html> </notes> <rdf:description rdf:about="#metaid_r_1550">
5 <rdf:li rdf:resource="urn:miriam:ec-code: "/> <bqmodel:isdescribedby> <rdf:li rdf:resource="urn:miriam:pubmed: "/> </bqmodel:isdescribedby> <listofreactants> <speciesreference species="m_172"/> <speciesreference species="m_304"/> </listofreactants> <listofproducts> <speciesreference species="m_135"/> <speciesreference species="m_292"/> <speciesreference species="m_329"/> </listofproducts> <listofmodifiers> <modifierspeciesreference species="e_450"/> </listofmodifiers> </reaction> </listofreactions> </model> </sbml>
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