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Volumn 7, Issue , 2013, Pages

Precise generation of systems biology models from KEGG pathways

Author keywords

BioPAX; Comparison; Converter; KEGG; KGML; Modeling; Qualitative modeling; Quantitative modeling; SBML; Systems biology

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; COMPUTER LANGUAGE; COMPUTER PROGRAM; GENETIC DATABASE; GENETICS; METHODOLOGY; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

EID: 84874016103     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-7-15     Document Type: Article
Times cited : (51)

References (33)
  • 1
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto Encyclopedia of Genes and Genomes
    • 10.1093/nar/28.1.27, 102409, 10592173
    • Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 2000, 28:27-30. 10.1093/nar/28.1.27, 102409, 10592173.
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 3
    • 68749099453 scopus 로고    scopus 로고
    • Pathway databases and tools for their exploitation: benefits, current limitations and challenges
    • 2724977, 19638971
    • Bauer-Mehren A, Furlong LI, Sanz F. Pathway databases and tools for their exploitation: benefits, current limitations and challenges. Mol Syst Biol 2009, 5:290. [http://dx.doi.org/10.1038/msb.2009.47], 2724977, 19638971.
    • (2009) Mol Syst Biol , vol.5 , pp. 290
    • Bauer-Mehren, A.1    Furlong, L.I.2    Sanz, F.3
  • 4
    • 73149122136 scopus 로고    scopus 로고
    • Applications of genome-scale metabolic reconstructions
    • 2795471, 19888215
    • Oberhardt MA, Palsson B, Papin JA. Applications of genome-scale metabolic reconstructions. Mol Syst Biol 2009, 5:320. http://dx.doi.org/10.1038/msb.2009.77, 2795471, 19888215.
    • (2009) Mol Syst Biol , vol.5 , pp. 320
    • Oberhardt, M.A.1    Palsson, B.2    Papin, J.A.3
  • 5
    • 0348049802 scopus 로고    scopus 로고
    • Systems biology markup language: Level 2 and beyond
    • Finney A, Hucka M. Systems biology markup language: Level 2 and beyond. Biochem Soc Trans 2003, 31(Pt 6):1472-1473. [http://dx.doi.org/10.1042/].
    • (2003) Biochem Soc Trans , vol.31 , Issue.PART 6 , pp. 1472-1473
    • Finney, A.1    Hucka, M.2
  • 8
    • 79551587720 scopus 로고    scopus 로고
    • Cytoscape 2.8: new features for data integration and network visualization
    • 10.1093/bioinformatics/btq675, 3031041, 21149340
    • Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 2011, 27(3):431-432. [http://dx.doi.org/10.1093/bioinformatics/btq675], 10.1093/bioinformatics/btq675, 3031041, 21149340.
    • (2011) Bioinformatics , vol.27 , Issue.3 , pp. 431-432
    • Smoot, M.E.1    Ono, K.2    Ruscheinski, J.3    Wang, P.L.4    Ideker, T.5
  • 9
    • 44949099336 scopus 로고    scopus 로고
    • SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks
    • 10.1186/1752-0509-2-39, 2412839, 18447902
    • Dräger A, Hassis N, Supper J, Schröder A, Zell A. SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks. BMC Syst Biol 2008, 2:39. [http://www.biomedcentral.com/1752-0509/2/39], 10.1186/1752-0509-2-39, 2412839, 18447902.
    • (2008) BMC Syst Biol , vol.2 , pp. 39
    • Dräger, A.1    Hassis, N.2    Supper, J.3    Schröder, A.4    Zell, A.5
  • 10
    • 78651553577 scopus 로고    scopus 로고
    • FASIMU flexible software for flux-balance computation series in large metabolic networks
    • 10.1186/1471-2105-12-28, 3038154, 21255455
    • Hoppe A, Hoffmann S, Gerasch A, Gille C, Holzhütter HG. FASIMU flexible software for flux-balance computation series in large metabolic networks. BMC Bioinformatics 2011, 12:28. [http://dx.doi.org/10.1186/1471-2105-12-28], 10.1186/1471-2105-12-28, 3038154, 21255455.
    • (2011) BMC Bioinformatics , vol.12 , pp. 28
    • Hoppe, A.1    Hoffmann, S.2    Gerasch, A.3    Gille, C.4    Holzhütter, H.G.5
  • 13
    • 70449515104 scopus 로고    scopus 로고
    • KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database
    • 10.1186/1471-2105-10-324, 2764712, 19814801
    • Moutselos K, Kanaris I, Chatziioannou A, Maglogiannis I, Kolisis FN. KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database. BMC Bioinformatics 2009, 10:324. [http://dx.doi.org/10.1186/1471-2105-10-324], 10.1186/1471-2105-10-324, 2764712, 19814801.
    • (2009) BMC Bioinformatics , vol.10 , pp. 324
    • Moutselos, K.1    Kanaris, I.2    Chatziioannou, A.3    Maglogiannis, I.4    Kolisis, F.N.5
  • 14
    • 84876167761 scopus 로고    scopus 로고
    • Java DOM Parsers to Convert KGML into SBML and BioPAX Common Exchange Formats
    • 10.5808/GI.2010.8.2.094, 23569217
    • Lee KE, Jang MH, Rhie A, Thong CT, Yang S, Park HS. Java DOM Parsers to Convert KGML into SBML and BioPAX Common Exchange Formats. Genomics & Informatics 2010, 8(2):94-96. [http://ids.postech.ac.kr/~myunghaj/papers/javaDomParsers.PDF], 10.5808/GI.2010.8.2.094, 23569217.
    • (2010) Genomics & Informatics , vol.8 , Issue.2 , pp. 94-96
    • Lee, K.E.1    Jang, M.H.2    Rhie, A.3    Thong, C.T.4    Yang, S.5    Park, H.S.6
  • 15
    • 79961195281 scopus 로고    scopus 로고
    • KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats
    • 10.1093/bioinformatics/btr377, 3150042, 21700675
    • Wrzodek C, Dräger A, Zell A. KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats. Bioinformatics 2011, 27(16):2314-2315. [http://dx.doi.org/10.1093/bioinformatics/btr377], 10.1093/bioinformatics/btr377, 3150042, 21700675.
    • (2011) Bioinformatics , vol.27 , Issue.16 , pp. 2314-2315
    • Wrzodek, C.1    Dräger, A.2    Zell, A.3
  • 16
    • 84863417054 scopus 로고    scopus 로고
    • [Specification available from the KEGG homepage at, Accessed 2012, April 23], KEGG team
    • KEGG team KEGG Markup Language 2010, [http://www.genome.jp/kegg/xml/docs/]. [Specification available from the KEGG homepage at [http://www.kegg.jp/kegg/xml/docs/]. Accessed 2012, April 23], KEGG team.
    • (2010) KEGG Markup Language
  • 21
    • 84862156032 scopus 로고    scopus 로고
    • Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
    • 3245029, 22140103
    • Juty N, Le Novère N, Laibe C. Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. Nucleic Acids Res 2012, 40(Database issue):D580-D586. [http://dx.doi.org/10.1093/nar/gkr1097], 3245029, 22140103.
    • (2012) Nucleic Acids Res , vol.40 , Issue.DATABASE ISSUE
    • Juty, N.1    Le Novère, N.2    Laibe, C.3
  • 23
    • 84876186277 scopus 로고    scopus 로고
    • Groups Proposal
    • [Specification available from Accessed 2012, April 23]
    • Hucka M. Groups Proposal. 2009, [Specification available from http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/Groups_Proposal_%282009-10%29 Accessed 2012, April 23].
    • (2009)
    • Hucka, M.1
  • 24
    • 84870429670 scopus 로고    scopus 로고
    • Qualitative Models (qual)
    • [Specification available at Accessed 2012, March 22]
    • Berenguier D, Chaouiya C, Naldi A, Thieffry D, van Iersel MP. Qualitative Models (qual). 2011, [Specification available at http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/Qualitative_Models Accessed 2012, March 22].
    • (2011)
    • Berenguier, D.1    Chaouiya, C.2    Naldi, A.3    Thieffry, D.4    van Iersel, M.P.5
  • 25
    • 79960423002 scopus 로고    scopus 로고
    • JSBML: a flexible Java library for working with SBML
    • 10.1093/bioinformatics/btr361, 3137227, 21697129
    • Dräger A, Rodriguez N, Dumousseau M, Dörr A, Wrzodek C, Le Novère N, Zell A, Hucka M. JSBML: a flexible Java library for working with SBML. Bioinformatics 2011, 27(15):2167-2168. [http://bioinformatics.oxfordjournals.org/content/27/15/2167], 10.1093/bioinformatics/btr361, 3137227, 21697129.
    • (2011) Bioinformatics , vol.27 , Issue.15 , pp. 2167-2168
    • Dräger, A.1    Rodriguez, N.2    Dumousseau, M.3    Dörr, A.4    Wrzodek, C.5    Le Novère, N.6    Zell, A.7    Hucka, M.8
  • 27
    • 79952827709 scopus 로고    scopus 로고
    • The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core
    • [Specification available from Nature Precedings, Accessed 2012, March 22]
    • Hucka M, Bergmann FT, Hoops S, Keating S, Sahle S, Schaff JC, Smith LP, Wilkinson DJ. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. 2010, [Specification available from Nature Precedings http://dx.doi.org/10.1038/npre.2010.4959.1. Accessed 2012, March 22].
    • (2010)
    • Hucka, M.1    Bergmann, F.T.2    Hoops, S.3    Keating, S.4    Sahle, S.5    Schaff, J.C.6    Smith, L.P.7    Wilkinson, D.J.8
  • 29
    • 33845387962 scopus 로고    scopus 로고
    • JSIM: Free software package for teaching phyiological modeling and research
    • Raymond GM, Butterworth E, Bassingthwaighte JB. JSIM: Free software package for teaching phyiological modeling and research. Exper Biol 2003, 280(5):p102.
    • (2003) Exper Biol , vol.280 , Issue.5
    • Raymond, G.M.1    Butterworth, E.2    Bassingthwaighte, J.B.3
  • 30
    • 40749087306 scopus 로고    scopus 로고
    • BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks
    • 10.1093/bioinformatics/btm553, 18024474
    • Zinovyev A, Viara E, Calzone L, Barillot E. BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics 2008, 24(6):876-877. [http://dx.doi.org/10.1093/bioinformatics/btm553], 10.1093/bioinformatics/btm553, 18024474.
    • (2008) Bioinformatics , vol.24 , Issue.6 , pp. 876-877
    • Zinovyev, A.1    Viara, E.2    Calzone, L.3    Barillot, E.4
  • 31
    • 54249091564 scopus 로고    scopus 로고
    • Presenting and exploring biological pathways with PathVisio
    • 10.1186/1471-2105-9-399, 2569944, 18817533
    • van Iersel MP, Kelder T, Pico AR, Hanspers K, Coort S, Conklin BR, Evelo C. Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics 2008, 9:399. [http://dx.doi.org/10.1186/1471-2105-9-399], 10.1186/1471-2105-9-399, 2569944, 18817533.
    • (2008) BMC Bioinformatics , vol.9 , pp. 399
    • van Iersel, M.P.1    Kelder, T.2    Pico, A.R.3    Hanspers, K.4    Coort, S.5    Conklin, B.R.6    Evelo, C.7
  • 32
    • 77952315185 scopus 로고    scopus 로고
    • Integration of -omics data and networks for biomedical research with VANTED
    • Klukas C, Schreiber F. Integration of -omics data and networks for biomedical research with VANTED. J Integr Bioinform 2010, 7(2):112. [http://dx.doi.org/10.2390/biecoll-jib-2010-112].
    • (2010) J Integr Bioinform , vol.7 , Issue.2 , pp. 112
    • Klukas, C.1    Schreiber, F.2
  • 33
    • 84856038703 scopus 로고    scopus 로고
    • The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks
    • Swainston N, Smallbone K, Mendes P, Kell D, Paton N. The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks. J Integr Bioinform 2011, 8(2):186. [http://dx.doi.org/10.2390/biecoll-jib-2011-186].
    • (2011) J Integr Bioinform , vol.8 , Issue.2 , pp. 186
    • Swainston, N.1    Smallbone, K.2    Mendes, P.3    Kell, D.4    Paton, N.5


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