Mimoza: web-based semantic zooming and navigation in metabolic networks

BMC Systems Biology

David J Sherman¹  Anna Zhukova¹ 

[1] Inria/Université Bordeaux/CNRS joint project-team MAGNOME, 351, cours de la Libération, Talence F-33405, France

关键词: Model generalization;    Visualization;    Metabolic modeling;   

Others  :  1159567
DOI  :  10.1186/s12918-015-0151-5

 received in 2014-08-05, accepted in 2015-02-06,  发布年份 2015

【 摘 要 】

Background

The complexity of genome-scale metabolic models makes them quite difficult for human users to read, since they contain thousands of reactions that must be included for accurate computer simulation. Interestingly, hidden similarities between groups of reactions can be discovered, and generalized to reveal higher-level patterns.

Results

The web-based navigation system Mimoza allows a human expert to explore metabolic network models in a semantically zoomable manner: The most general view represents the compartments of the model; the next view shows the generalized versions of reactions and metabolites in each compartment; and the most detailed view represents the initial network with the generalization-based layout (where similar metabolites and reactions are placed next to each other). It allows a human expert to grasp the general structure of the network and analyze it in a top-down manner

Conclusions

Mimoza can be installed standalone, or used on-line at http://mimoza.bordeaux.inria.fr/ webcite, or installed in a Galaxy server for use in workflows. Mimoza views can be embedded in web pages, or downloaded as COMBINE archives.

【 授权许可】

   
2015 Zhukova and Sherman; licensee BioMed Central.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

【 参考文献 】

• [1]Zhukova A, Sherman DJ: Knowledge-based generalization of metabolic models. J Comput Biol 2014, 21(7):534-47. doi:10.1089/cmb.2013.0143
• [2]Bederson B, Meyer J: Implementing a zooming User Interface: experience building Pad++. Softw Prac Exp 1998, 28(10):1101-35. doi:10.1002/(SICI)1097-024X(199808)28:10<1101::AID-SPE190>3.0.CO;2-V
• [3]Nivala A-M, Brewster S, Sarjakoski TL: Usability Evaluation of Web Mapping Sites. Cartographic J 2008, 45(2):129-38. doi:10.1179/174327708X305120
• [4]Roberts JC: Exploratory visualization with multiple linked views. [http://www.sciencedirect.com/science/article/pii/B9780080445311504267] webciteIn Exploring Geovisualization Edited by Dykes J, MacEachren AM, Kraak M-J. Elsevier, Pergamon; 2005. Chap. 8. doi:10.1016/B978-008044531-1/50426-7. http://www.sciencedirect.com/science/article/pii/B9780080445311504267
• [5]Laufer L, Halacsy P, Somlai-Fischer A: Prezi meeting: Collaboration in a zoomable canvas based environment. [http://doi.acm.org/10.1145/1979742.1979673] webciteCHI ’11 Extended Abstracts on Human Factors in Computing Systems. CHI EA ’11 ACM, New York, NY, USA; 2011. doi:10.1145/1979742.1979673. http://doi.acm.org/10.1145/1979742.1979673
• [6]Pook S, Vaysseix G, Barillot E: Zomit: biological data visualization and browsing. Bioinformatics. 1998, 14(9):807-14.
• [7]Hu Z, Mellor J, Wu J, Kanehisa M, Stuart JM, DeLisi C: Towards zoomable multidimensional maps of the cell. Nat Biotechnol. 2007, 25(5):547-54. doi:10.1038/nbt1304
• [8]Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist AM, et al.: A comprehensive genome-scale reconstruction of Escherichia coli metabolism–2011. Mol Syst Biol. 2011, 7(1):535. doi:10.1038/msb.2011.65
• [9]Aung HW, Henry SA, Walker LP: Revising the Representation of Fatty Acid, Glycerolipid, and Glycerophospholipid Metabolism in the Consensus Model of Yeast Metabolism. Ind Biotechnol. 2013, 9(4):215-28. doi:10.1089/ind.2013.0013
• [10]Thiele I, Swainston N, Fleming RMT, Hoppe A, Sahoo S, Aurich MK, et al.: A community-driven global reconstruction of human metabolism. Nat Biotechnol. 2013, 31(5):419-25. doi:10.1038/nbt.2488
• [11]von Landesberger T, Kuijper A, Schreck T, Kohlhammer J, van Wijk JJ, Fekete J-D, et al.: Visual Analysis of Large Graphs: State-of-the-Art and Future Research Challenges. Comput Graph Forum. 2011, 30(6):1719-49. doi:10.1111/j.1467-8659.2011.01898.x
• [12]Herman I, Melancon G, Marshall MS: Graph visualization and navigation in information visualization: A survey. IEEE Trans Vis Comput Graph. 2000, 6(1):24-43. doi:10.1109/2945.841119
• [13]Karp PD, Paley S, Romero P: The Pathway Tools software. Bioinformatics. 2002, 18(Suppl 1):225-32. doi:10.1093/bioinformatics/18.suppl_1.S225
• [14]Agren R, Liu L, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J: The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS Comput Biol. 2013, 9(3):1002980. doi:10.1371/journal.pcbi.1002980
• [15]Wrzodek C, Büchel F, Ruff M, Dräger A, Zell A: Precise generation of systems biology models from KEGG pathways. BMC Syst Biol. 2013, 7:15. doi:10.1186/1752-0509-7-15 BioMed Central Full Text
• [16]Pitkänen E, Jouhten P, Hou J, Syed MF, Blomberg P, Kludas J, et al.: Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species. PLoS Comput Biol. 2014, 10(2):1003465. doi:10.1371/journal.pcbi.1003465
• [17]Swainston N, Smallbone K, Mendes P, Kell D, Paton N: The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks. J Integr Bioinformatics. 2011, 8(2):186. doi:10.2390/biecoll-jib-2011-186
• [18]Hamilton JJ, Reed JL: Software platforms to facilitate reconstructing genome-scale metabolic networks. Environ Microbiol. 2014, 16(1):49-59. doi:10.1111/1462-2920.12312
• [19]Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, et al.: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol. 2010, 4:92. BioMed Central Full Text
• [20]Schellenberger J, Park JO, Conrad TM, Palsson BO: BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics. 2010, 11:213. doi:10.1186/1471-2105-11-213 BioMed Central Full Text
• [21]Snoep JL, Olivier BG: JWS online cellular systems modelling and microbiology. Microbiology. 2003, 149(11):3045-7.
• [22]Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M: KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012, 40(0305-1048 (Linking):109-14.
• [23]Milacic M, Haw R, Rothfels K, Wu G, Croft D, Hermjakob H, et al.: Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome. Cancers. 2012, 4(4):1180-211. doi:10.3390/cancers4041180
• [24]Croft D: Building models using Reactome pathways as templates. Methods Mol Biol. 2013, 1021:273-83. doi:10.1007/978-1-62703-450-0_14
• [25]Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, et al.: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003, 19(4):524-31.
• [26]van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, et al.: Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics (Oxford, England). 2012, 28(15):2016-21. doi:10.1093/bioinformatics/bts270
• [27]Lloyd CM, Halstead MDB, Nielsen PF: CellML: its future, present and past. Progress Biophys Mol Biol. 2004, 85(doi:10.1016/j.pbiomolbio.2004.01.004):433-50.
• [28]de Matos P, Alcántara R, Dekker A, Ennis M, Hastings J, Haug K, et al.: Chemical Entities of Biological Interest: an update. Nucleic Acids Res. 2010, 38(suppl 1):249-54. doi:10.1093/nar/gkp886
• [29]The UniProt Consortium: Activities at the Universal Protein Resource (UniProt) Nucleic Acids Res. 2014, 42(Database issue):191-8. doi:10.1093/nar/gkt1140
• [30]Thiele I, Palsson BO: A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc. 2010, 5(1):93-121. doi:10.1038/nprot.2009.203
• [31]Thiele I, Vlassis N, Fleming RMT: fastGapFill: efficient gap filling in metabolic networks. Bioinformatics. 2014, 30(17):2529-31. doi:10.1093/bioinformatics/btu321
• [32]Klamt S, Saez-Rodriguez J, Gilles ED: Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst Biol. 2007, 1:2. BioMed Central Full Text
• [33]Copeland WB, Bartley BA, Chandran D, Galdzicki M, Kim KH, Sleight SC, et al.: Computational tools for metabolic engineering. Metab Eng. 2012, 14(3):270-80.
• [34]Schulz M, Uhlendorf J, Klipp E, Liebermeister W: SBMLmerge, a system for combining biochemical network models. Genome Inform Int Conf Genome Inform. 2006, 17(1):62-71.
• [35]Krause F, Uhlendorf J, Lubitz T, Schulz M, Klipp E, Liebermeister W: Annotation and merging of SBML models with semanticSBML. Bioinformatics. 2010, 26(3):421-2. doi:10.1093/bioinformatics/btp642
• [36]Umeton R, Nicosia G, Dewey CF: OREMPdb: a semantic dictionary of computational pathway models. BMC Bioinformatics. 2012, 13 Suppl 4:6. doi:10.1186/1471-2105-13-S4-S6 BioMed Central Full Text
• [37]Coskun SA, Cicek AE, Lai N, Dash RK, Ozsoyoglu ZM, Ozsoyoglu G: An online model composition tool for system biology models. BMC Syst Biol. 2013, 7:88. doi:10.1186/1752-0509-7-88 BioMed Central Full Text
• [38]Funahashi A, Matsuoka Y, Jouraku A, Morohashi M, Kikuchi N, Kitano H: CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks. Proc IEEE. 2008, 96(8):1254-65. doi:10.1109/JPROC.2008.925458
• [39]Rohn H, Junker A, Hartmann A, Grafahrend-Belau E, Treutler H, Klapperstück M, et al.: VANTED v2: a framework for systems biology applications. BMC Syst Biol. 2012, 6(1):139. doi:10.1186/1752-0509-6-139 BioMed Central Full Text
• [40]Smoot ME, Ono K, Ruscheinski J, Wang P-L, Ideker T: Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011, 27(3):431-2. doi:10.1093/bioinformatics/btq675. http://bioinformatics.oxfordjournals.org/content/27/3/431.full.pdf+html
• [41]Fruchterman TMJ, Reingold EM: Graph drawing by force-directed placement. Softw Prac Exp. 1991, 21(11):1129-64. doi:10.1002/spe.4380211102
• [42]Tamassia R: Handbook of graph drawing and visualization (discrete mathematics and its applications). Chapman & Hall/CRC, Boca Raton; 2007.
• [43]Jensen PA, Papin JA. MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data. Bioinformatics. 2014. doi:10.1093/bioinformatics/btt758.
• [44]Barillot E, Guyon F, Cussat-Blanc C, Viara E, Vaysseix G: HuGeMap: a distributed and integrated Human Genome Map database. Nucleic Acids Res. 1998, 26(1):106-7.
• [45]Jianu R, Laidlaw DH: What Google Maps can do for biomedical data dissemination: examples and a design study. BMC Res Notes. 2013, 6(1):179. doi:10.1186/1756-0500-6-179 BioMed Central Full Text
• [46]Yates T, Okoniewski MJ, Miller CJ: X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis. Nucleic Acids Res. 2008, 36(Database issue):780-6. doi:10.1093/nar/gkm779
• [47]Arakawa K, Tamaki S, Kono N, Kido N, Ikegami K, Ogawa R, et al.: Genome Projector: zoomable genome map with multiple views. BMC Bioinformatics. 2009, 10(1):31. doi:10.1186/1471-2105-10-31 BioMed Central Full Text
• [48]Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A: ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 2003, 31(13):3784-8.
• [49]Kuperstein I, Cohen DP, Pook S, Viara E, Calzone L, Barillot E, et al.: NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. BMC Syst Biol. 2013, 7(1):100. doi:10.1186/1752-0509-7-100 BioMed Central Full Text
• [50]Latendresse M, Karp PD: Web-based metabolic network visualization with a zooming user interface. BMC Bioinformatics. 2011, 12(1):176. BioMed Central Full Text
• [51]Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, et al.: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2012, 40(Database issue):742-53. doi:10.1093/nar/gkr1014
• [52]Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, et al.: A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol. 2008, 26(10):1155-60. doi:10.1038/nbt1492
• [53]Metzler DE, Metzler CM: Biochemistry: The Chemical Reactions of Living Cells, 2nd Edition, 2nd edn. Biochemistry: The Chemical Reactions of Living Cells, vol. v. 1. Academic Press, San Diego; 2001.
• [54]Zhukova A, Sherman DJ. Knowledge-based metabolic model generalization library web page. http://metamogen.gforge.inria.fr.
• [55]Hucka M, Hoops S, Keating SM, Le Novère N, Sahle S, Wilkinson DJ. Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions. 2008. doi:10.1038/npre.2008.2715.1.
• [56]Hucka M. SBML Level 3 Groups Proposal. 2012. http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/Groups_Proposal_Updated_\%282012-06\%29.
• [57]Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, et al.: Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst Biol. 2013, 7(1):116. doi:10.1186/1752-0509-7-116 BioMed Central Full Text
• [58]Diestel R. Graph Theory: Springer Graduate Text GTM 173: Reinhard Diestel; 2012, p. 451. http://identifiers.org/isbn/978-3-642-14278-9.
• [59]Auber D: Tulip – A Huge Graph Visualization Framework. [http://dx.doi.org/10.1007/978-3-642-18638-7_5] webciteIn Graph Drawing Software. Mathematics and Visualization Edited by Jünger M, Mutzel P, Farin G, Hege H-C, Hoffman D, Johnson CR, Polthier K, Rumpf M. Springer, Berlin Heidelberg; 2004. http://dx.doi.org/10.1007/978-3-642-18638-7_5
• [60]Bornstein BJ, Keating SM, Jouraku A, Hucka M: LibSBML: an API library for SBML. Bioinformatics. 2008, 24(6):880-1.
• [61]Unwin A, Theus M, Hofmann H: Graphics of large datasets: visualizing a million. Springer, New York; 2006.
• [62]Gabow HN: Path-based depth-first search for strong and biconnected components. Inf Process Lett. 2000, 74(3-4):107-14. doi:10.1016/S0020-0190(00)00051-X
• [63]Hachul S, Jünger M. Large-graph layout with the fast multipole multilevel method. Technical report, Universität zu Köln, Institut für Informatik, Köln. 2005. http://e-archive.informatik.uni-koeln.de/509/.
• [64]Sugiyama K, Tagawa S, Toda M: Methods for Visual Understanding of Hierarchical System Structures. IEEE Trans Syst Man Cybernet. 1981, 11(2):109-25. doi:10.1109/TSMC.1981.4308636
• [65]Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al.: Gene Ontology: tool for the unification of biology. Nat Genet. 2000, 25(1):25-9. doi:10.1038/75556
• [66]Gauges R, Rost U, Sahle S, Wengler K, Bergmann FT. SBML Level 3 Layout Package Version 1 Release 1. 2013. http://identifiers.org/combine.specifications/sbml.level-3.version-1.layout.version-1.release-1 Accessed 23/10/14.
• [67]Agafonkin V. Leaflet - a JavaScript library for mobile-friendly maps. http://leafletjs.com/.
• [68]Butler H, Daly M, Doyle A, Gillies S, Schaub T, Schmidt C. GeoJSON Specification. http://geojson.org/geojson-spec.html.
• [69]Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, et al.: The Systems Biology Graphical Notation. Nat Biotechnol. 2009, 27(8):735-41. doi:10.1038/nbt.1558
• [70]NCBI. NCBI Gene. http://www.ncbi.nlm.nih.gov/gene.
• [71]Zhukova A, Sherman DJ. Mimoza web page. http://mimoza.bordeaux.inria.fr.
• [72]Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M, et al. One file to share them all: Using the COMBINE Archive and the OMEX format to share all information about a modeling project. 2014. 1407.4992.
• [73]Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, et al.: Galaxy: a web-based genome analysis tool for experimentalists. Current Protoc Mol Biol. 2010, 19:19-10121. doi:10.1002/0471142727.mb1910s89
• [74]Böhringer K-F, Paulisch FN. Using constraints to achieve stability in automatic graph layout algorithms. In: Proceedings of the chi — conference on human factors in computing systems. ACM: 1990. p. 43–51. http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.35.7000.