{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,20]],"date-time":"2025-10-20T09:55:16Z","timestamp":1760954116338},"reference-count":47,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2007,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>The tools that are available to draw and to manipulate the representations of metabolism are usually restricted to metabolic pathways. This limitation becomes problematic when studying processes that span several pathways. The various attempts that have been made to draw genome-scale metabolic networks are confronted with two shortcomings: 1- they do not use contextual information which leads to dense, hard to interpret drawings, 2- they impose to fit to very constrained standards, which implies, in particular, duplicating nodes making topological analysis considerably more difficult.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We propose a method, called MetaViz, which enables to draw a genome-scale metabolic network and that also takes into account its structuration into pathways. This method consists in two steps: a clustering step which addresses the pathway overlapping problem and a drawing step which consists in drawing the clustered graph and each cluster.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>The method we propose is original and addresses new drawing issues arising from the no-duplication constraint. We do not propose a single drawing but rather several alternative ways of presenting metabolism depending on the pathway on which one wishes to focus. We believe that this provides a valuable tool to explore the pathway structure of metabolism.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1752-0509-1-29","type":"journal-article","created":{"date-parts":[[2007,7,3]],"date-time":"2007-07-03T18:13:16Z","timestamp":1183486396000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":33,"title":["Metabolic network visualization eliminating node redundance and preserving metabolic pathways"],"prefix":"10.1186","volume":"1","author":[{"given":"Romain","family":"Bourqui","sequence":"first","affiliation":[]},{"given":"Ludovic","family":"Cottret","sequence":"additional","affiliation":[]},{"given":"Vincent","family":"Lacroix","sequence":"additional","affiliation":[]},{"given":"David","family":"Auber","sequence":"additional","affiliation":[]},{"given":"Patrick","family":"Mary","sequence":"additional","affiliation":[]},{"given":"Marie-France","family":"Sagot","sequence":"additional","affiliation":[]},{"given":"Fabien","family":"Jourdan","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2007,7,3]]},"reference":[{"key":"29_CR1","volume-title":"Third International Conference on Bioinformatics and Genome Research","author":"PD Karp","year":"1994","unstructured":"Karp PD, Paley SM: Automated Drawing of Metabolic Pathways. Third International Conference on Bioinformatics and Genome Research. 1994"},{"key":"29_CR2","first-page":"392","volume":"4","author":"Salamonsen","year":"1999","unstructured":"Salamonsen , Yee , Mok , Kolatkar : BioJAKE: a tool for the creation, visualization and manipulation of metabolic pathways. Pacific Symposium on Biocomputing. 1999, 4: 392-400.","journal-title":"Pacific Symposium on Biocomputing"},{"key":"29_CR3","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780198503279.001.0001","volume-title":"Post-genome Informatics","author":"M Kanehisa","year":"2000","unstructured":"Kanehisa M: Post-genome Informatics. 2000, Oxford University Press"},{"key":"29_CR4","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1093\/bioinformatics\/17.5.461","volume":"17","author":"M Becker","year":"2001","unstructured":"Becker M, Rojas I: A Graph Layout Algorithm for Drawing Metabolic Pathways. Bioinformatics. 2001, 17: 461-467. 10.1093\/bioinformatics\/17.5.461","journal-title":"Bioinformatics"},{"issue":"7","key":"29_CR5","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1109\/MC.2002.1016905","volume":"35","author":"J Seo","year":"2002","unstructured":"Seo J, Shneiderman B: Interactively Exploring Hierarchical Clustering Results. IEEE Computer. 2002, 35 (7): 80-86.","journal-title":"IEEE Computer"},{"key":"29_CR6","first-page":"105","volume-title":"APBC 03: Proceedings of the First Asia-Pacific bioinformatics conference on Bioinformatics","author":"F Schreiber","year":"2003","unstructured":"Schreiber F: Comparison of metabolic pathways using constraint graph drawing. APBC 03: Proceedings of the First Asia-Pacific bioinformatics conference on Bioinformatics. 2003, 105-110. Australian Computer Society, Inc"},{"key":"29_CR7","first-page":"46","volume-title":"Visualization and Data Analysis, VDA","author":"F Jourdan","year":"2003","unstructured":"Jourdan F, Melan\u00e7on G: A Tool for Metabolic and Regulatory Pathways Visual Analysis. Visualization and Data Analysis, VDA. 2003, 46-55. Santa Clara Convention Center: SPIE, Http:\/\/vw.indiana.edu\/vda2003\/"},{"key":"29_CR8","first-page":"442","volume":"3383","author":"Dogrusoz","year":"2004","unstructured":"Dogrusoz , Giral , Cetintas , Civril , Demir : A Compound Graph Layout Algorithm for Biological Pathways. GD 2004. Edited by: LNCS. 2004, 3383: 442-447.","journal-title":"GD 2004"},{"key":"29_CR9","first-page":"11","volume":"2912","author":"U Brandes","year":"2004","unstructured":"Brandes U, Dwyer T, Schreiber F: Visualizing Related Metabolic Pathways in Two and Half Dimensions. LNCS. 2004, 2912: 11-122.","journal-title":"LNCS"},{"key":"29_CR10","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1186\/1471-2105-6-212","volume":"6","author":"Wegner","year":"2005","unstructured":"Wegner , Kummer : A new dynamical layout algoritmh for complex biochemical reaction networks. BMC Bioinformatics. 2005, 6: 212- 10.1186\/1471-2105-6-212","journal-title":"BMC Bioinformatics"},{"key":"29_CR11","unstructured":"Gabouje SD, Zim\u00e1nyi : A New Compound Graph Layout Algorithm for Visualizing Biochemical Networks. Poster Proceedings Volume of the 4th International Workshop on Efficient and Experimental Algorithms, WEA 05."},{"issue":"3","key":"29_CR12","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1093\/bioinformatics\/bti776","volume":"22","author":"Dogrusoz","year":"2005","unstructured":"Dogrusoz , Erson , Giral , Demir , Babur , Cetintas , Colak : PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization. Bioinformatics. 2005, 22 (3): 374-375. 10.1093\/bioinformatics\/bti776","journal-title":"Bioinformatics"},{"key":"29_CR13","doi-asserted-by":"publisher","first-page":"D428","DOI":"10.1093\/nar\/gki072","volume":"33","author":"J Tope","year":"2005","unstructured":"Tope J, Gillespie , Vastrik , DEustachio , Schmidt , de Bono , Jassal , Gopinath , Wu , Matthews , Lewis , Birney , Stein : Reactome: a knowledgebase of biological pathways. Nucleic Acids Research. 2005, 33: D428-D432. 10.1093\/nar\/gki072","journal-title":"Nucleic Acids Research"},{"issue":"13","key":"29_CR14","doi-asserted-by":"publisher","first-page":"3771","DOI":"10.1093\/nar\/gkl334","volume":"34","author":"S Paley","year":"2006","unstructured":"Paley S, Karp P: The Pathway Tools cellular overview diagram and Omics Viewer. Nucleic Acids Research. 2006, 34 (13): 3771-3778. 10.1093\/nar\/gkl334","journal-title":"Nucleic Acids Research"},{"key":"29_CR15","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1186\/1471-2105-7-109","volume":"7","author":"BH Junker","year":"2006","unstructured":"Junker BH, Klukas C, Schreiber F: VANTED: A System for Advanced Data Analysis and Visualization in the Context of Biological Networks. BMC Bioinformatics. 2006, 7: 109-EPub 10.1186\/1471-2105-7-109","journal-title":"BMC Bioinformatics"},{"key":"29_CR16","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1104\/pp.104.053793","volume":"138","author":"V Nikiforova","year":"2005","unstructured":"Nikiforova V, Kopka J, Tolstikov V, Fiehn O, Hopkins L, Hawkesford M, Hesse H, Hoefgen R: Systems Rebalancing of Metabolism in Response to Sulfur Deprivation, as Revealed by Metabolome Analysis of Arabidopsis Plants. Plant Physiology. 2005, 138: 304-318. 10.1104\/pp.104.053793","journal-title":"Plant Physiology"},{"issue":"4","key":"29_CR17","doi-asserted-by":"publisher","first-page":"360","DOI":"10.1109\/TCBB.2006.55","volume":"3","author":"V Lacroix","year":"2006","unstructured":"Lacroix V, Fernandes CG, Sagot MF: Motif search in graphs: application to metabolic networks. IEEE\/ACM Trans Comput Biol Bioinform. 2006, 3 (4): 360-368. 10.1109\/TCBB.2006.55","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"key":"29_CR18","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1057\/palgrave.ivs.9500102","volume":"4","author":"P Saraiya","year":"2005","unstructured":"Saraiya P, North C, Duca K: Visualizing biological pathways: requirements analysis, systems evaluation and research agenda. Information Visualization. 2005, 4: 1-15. 10.1057\/palgrave.ivs.9500102.","journal-title":"Information Visualization"},{"key":"29_CR19","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1038\/35036627","volume":"407","author":"H Jeong","year":"2000","unstructured":"Jeong H, Tombor B, Albert R, Oltvai Z, Barabasi A: The Large-Scale Organization of Metabolic Networks. Nature. 2000, 407: 651- 10.1038\/35036627","journal-title":"Nature"},{"key":"29_CR20","first-page":"229","volume":"6","author":"T Pfeiffer","year":"2000","unstructured":"Pfeiffer T, Dandekar T, Moldenhauer F, Schuster S: Topological analysis of metabolic networks. Application to the metabolism of Mycoplasma pneumoniae. BTK2000: Animating the Cellular Map. 2000, 6: 229-234.","journal-title":"BTK2000: Animating the Cellular Map"},{"key":"29_CR21","volume-title":"Metabolism at a Glance","author":"JG Salway","year":"2003","unstructured":"Salway JG: Metabolism at a Glance. 2003, Blackwell Science Ltd"},{"key":"29_CR22","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S0303-2647(98)00019-7","volume":"47","author":"G Michal","year":"1998","unstructured":"Michal G: On representation of metabolic pathways. BioSystems. 1998, 47: 1-7. 10.1016\/S0303-2647(98)00019-7","journal-title":"BioSystems"},{"key":"29_CR23","volume-title":"Biochemical Pathways (Poster)","author":"G Michal","year":"1993","unstructured":"Michal G: Biochemical Pathways (Poster). 1993, Boehringer Mannheim"},{"key":"29_CR24","unstructured":"BIOCARTA: Charting pathways of life. http:\/\/www.biocarta.com"},{"key":"29_CR25","first-page":"1","volume-title":"Genome Biology","author":"P Romero","year":"2004","unstructured":"Romero P, Wagg J, Green M, Kaiser D, Krummenacker M, Karp P: Computational prediction of human metabolic pathways from the complete human genome. Genome Biology. 2004, 1-17."},{"issue":"4","key":"29_CR26","first-page":"189","volume":"2","author":"H Purchase","year":"1997","unstructured":"Purchase H, Cohen RF, James M: An Experimental Study of the Basis for Graph Drawing Algorithms. ACM Journal of Experimental Algorithmics. 1997, 2 (4): 189-","journal-title":"ACM Journal of Experimental Algorithmics"},{"key":"29_CR27","volume-title":"Graph Drawing: Algorithms for the Visualization of Graphs","author":"GD Battista","year":"1999","unstructured":"Battista GD, Eades P, Tamassia R, Tollis IG: Graph Drawing: Algorithms for the Visualization of Graphs. 1999, Prentice Hall"},{"key":"29_CR28","doi-asserted-by":"publisher","DOI":"10.1007\/3-540-44969-8","volume-title":"Drawing Graphs Springer","author":"M Kaufmann","year":"2001","unstructured":"Kaufmann M, Wagner D: Drawing Graphs Springer. 2001"},{"issue":"4","key":"29_CR29","doi-asserted-by":"publisher","first-page":"876","DOI":"10.1109\/21.108304","volume":"21","author":"Sugiyama","year":"1991","unstructured":"Sugiyama , Misue : Visualisation of structural information : Automatic drawing of compound digraphs. IEEE Transactions on Systems, Man, and Cybernetics. 1991, 21 (4): 876-892. 10.1109\/21.108304.","journal-title":"IEEE Transactions on Systems, Man, and Cybernetics"},{"key":"29_CR30","volume-title":"GD'01","author":"F Brandenburg","year":"2002","unstructured":"Brandenburg F, Forster M, Pick A, Raitner M, Schreiber F: Biopath. GD'01. Edited by: Verlag S. 2002"},{"key":"29_CR31","first-page":"149","volume":"42","author":"Eades","year":"1984","unstructured":"Eades : A heuristic for graph drawing. Congressus Numerantium. 1984, 42: 149-160.","journal-title":"Congressus Numerantium"},{"key":"29_CR32","doi-asserted-by":"publisher","first-page":"388","DOI":"10.1007\/3-540-58950-3_393","volume":"894","author":"Frick","year":"1994","unstructured":"Frick , Ludwig , Mehldau : A fast adaptive layout algorithm for undirected graphs. Lecture Notes in Computer Science. 1994, 894: 388-403.","journal-title":"Lecture Notes in Computer Science"},{"key":"29_CR33","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozierand O, Baliga N, Wang J, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Research. 2003, 13: 2498-2504. 10.1101\/gr.1239303","journal-title":"Genome Research"},{"key":"29_CR34","unstructured":"SBML viewer. http:\/\/sbw.kgi.edu\/layout\/"},{"key":"29_CR35","first-page":"245","volume":"38","author":"J van Helden","year":"2002","unstructured":"van Helden J, Wernisch L, Gilbert D, Wodak S: Graph-based analysis of metabolic networks. Ernst Schering Research Foundation Workshop. 2002, 38: 245-274.","journal-title":"Ernst Schering Research Foundation Workshop"},{"key":"29_CR36","volume-title":"Computers and Intractability: A Guide to the Theory of NP-Completeness","author":"MR Garey","year":"1979","unstructured":"Garey MR, Johnson DS: Computers and Intractability: A Guide to the Theory of NP-Completeness. 1979, New York, NY, USA: W. H. Freeman & Co"},{"key":"29_CR37","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1093\/comjnl\/10.1.85","volume":"10","author":"Welsh","year":"1967","unstructured":"Welsh , Powell : An upper Bound to the chromatic number of a graph and its application to timetabling problems. The Computer journal. 1967, 10: 85-86. 10.1093\/comjnl\/10.1.85.","journal-title":"The Computer journal"},{"key":"29_CR38","doi-asserted-by":"crossref","unstructured":"Auber D: Graph Drawing Software. Springer-Verlag 2003 chap. Tulip- A Huge Graph Visualization Framework","DOI":"10.1007\/978-3-642-18638-7_5"},{"key":"29_CR39","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1007\/3-540-37623-2_13","volume-title":"Graph Drawing '98 (Proc.)","author":"C Gutwenger","year":"1998","unstructured":"Gutwenger C, Mutzel P: Planar Polyline Drawings with Good Angular Resolution. Graph Drawing '98 (Proc.). 1998, 1547: 167-182. Springer-Verlag, Lecture Notes in Computer Science"},{"key":"29_CR40","first-page":"727","volume-title":"Proceeding on the 10th conf. on Comb., Graph Theory, and Comp","author":"P Lui","year":"1977","unstructured":"Lui P, Geldmacher R: On the deletion of nonplanar edges of a graph. Proceeding on the 10th conf. on Comb., Graph Theory, and Comp. 1977, 727-738."},{"key":"29_CR41","doi-asserted-by":"publisher","first-page":"1","DOI":"10.7155\/jgaa.00032","volume":"5","author":"A Liebers","year":"2001","unstructured":"Liebers A: Planarizing Graphs \u2013 A Survey and Annotated Bibliography. Journal of Graph Algorithms and Applications. 2001, 5: 1-74.","journal-title":"Journal of Graph Algorithms and Applications"},{"key":"29_CR42","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1093\/nar\/28.1.56","volume":"28","author":"P Karp","year":"2000","unstructured":"Karp P, Riley M, Saier M, Paulsen I: The EcoCyc and MetaCyc databases. Nucleic Acids Research. 2000, 28: 56-59. 10.1093\/nar\/28.1.56","journal-title":"Nucleic Acids Research"},{"issue":"Suppl 1","key":"29_CR43","doi-asserted-by":"publisher","first-page":"S225","DOI":"10.1093\/bioinformatics\/18.suppl_1.S225","volume":"18","author":"PD Karp","year":"2002","unstructured":"Karp PD, Paley S, Romero P: The Pathway Tools software. Bioinformatics. 2002, 18 (Suppl 1): S225-32.","journal-title":"Bioinformatics"},{"issue":"16","key":"29_CR44","doi-asserted-by":"publisher","first-page":"3454","DOI":"10.1093\/bioinformatics\/bti546","volume":"21","author":"M Krummenacker","year":"2005","unstructured":"Krummenacker M, Paley S, Mueller L, Yan T, Karp PD: Querying and computing with BioCyc databases. Bioinformatics. 2005, 21 (16): 3454-3455. 10.1093\/bioinformatics\/bti546","journal-title":"Bioinformatics"},{"issue":"2","key":"29_CR45","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1007\/s002850200143","volume":"45","author":"S Schuster","year":"2002","unstructured":"Schuster S, Hilgetag C, Woods JH, Fell DA: Reaction routes in biochemical reaction systems: algebraic properties, validated calculation procedure and example from nucleotide metabolism. J Math Biol. 2002, 45 (2): 153-181. 10.1007\/s002850200143","journal-title":"J Math Biol"},{"issue":"3","key":"29_CR46","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1006\/jtbi.2000.1073","volume":"203","author":"CH Schilling","year":"2000","unstructured":"Schilling CH, Letscher D, Palsson BO: Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J Theor Biol. 2000, 203 (3): 229-248. 10.1006\/jtbi.2000.1073","journal-title":"J Theor Biol"},{"key":"29_CR47","first-page":"1472","volume-title":"Biochem Soc Trans","author":"AHM Finney","year":"2003","unstructured":"Finney AHM: Systems biology markup language: Level 2 and beyond. Biochem Soc Trans. 2003, 1472-3."}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-1-29.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,15]],"date-time":"2024-02-15T18:23:25Z","timestamp":1708021405000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-1-29"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,7,3]]},"references-count":47,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2007,12]]}},"alternative-id":["29"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-1-29","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,7,3]]},"assertion":[{"value":"17 January 2007","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 July 2007","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 July 2007","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"29"}}