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Volumn 5, Issue 2, 2013, Pages 135-151

Accelerating cancer systems biology research through Semantic Web technology

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CANCER MODEL; CANCER RESEARCH; CANCER SYSTEM BIOLOGY; CLINICAL DATA REPOSITORY; COMPUTER PROGRAM; COMPUTER SYSTEM; DATA BASE; INFORMATION PROCESSING; LICENSING; NATIONAL HEALTH ORGANIZATION; SEMANTIC WEB TECHNOLOGY; WEB BROWSER;

EID: 84873853169     PISSN: 19395094     EISSN: 1939005X     Source Type: Journal    
DOI: 10.1002/wsbm.1200     Document Type: Article
Times cited : (13)

References (71)
  • 1
    • 50449088836 scopus 로고    scopus 로고
    • A wiki for the life sciences where authorship matters.
    • Hoffmann R. A wiki for the life sciences where authorship matters. Nat Genet 2008, 40:1047-1051.
    • (2008) Nat Genet , vol.40 , pp. 1047-1051
    • Hoffmann, R.1
  • 3
    • 84873879895 scopus 로고    scopus 로고
    • It's time to consider alternatives to RDBMS. Available at: (Accessed June 01, 2012).
    • James J. It's time to consider alternatives to RDBMS. Available at: http://blogs.techrepublic.com.com/programming-and-development/?p=1563. (Accessed June 01, 2012).
    • James, J.1
  • 4
    • 84873848389 scopus 로고    scopus 로고
    • Some pros & cons of relational databases. Available at: (Accessed June 01, 2012).
    • Borysowich C. Some pros & cons of relational databases. Available at: http://it.toolbox.com/blogs/ enterprise-solutions/some-pros-cons-of-relational-databases-24144. (Accessed June 01, 2012).
    • Borysowich, C.1
  • 5
    • 0030394059 scopus 로고    scopus 로고
    • A framework for the design and evaluation of reverse engineering methods for relational databases.
    • Chiang R, Barron T, Storey V. A framework for the design and evaluation of reverse engineering methods for relational databases. Data Knowl Eng 1997, 21:57-77.
    • (1997) Data Knowl Eng , vol.21 , pp. 57-77
    • Chiang, R.1    Barron, T.2    Storey, V.3
  • 7
    • 84873808561 scopus 로고    scopus 로고
    • RDF primer. Available at: (Accessed June 15, 2012).
    • Manola F, Miller E. RDF primer. Available at: http://www.w3.org/TR/2004/REC-rdf-primer-20040210/. (Accessed June 15, 2012).
    • Manola, F.1    Miller, E.2
  • 8
    • 0036490442 scopus 로고    scopus 로고
    • Smart drugs: tyrosine kinase inhibitors in cancer therapy.
    • Shawver LK, Slamon D, Ullrich A. Smart drugs: tyrosine kinase inhibitors in cancer therapy. Cancer Cell 2002, 1:117-123.
    • (2002) Cancer Cell , vol.1 , pp. 117-123
    • Shawver, L.K.1    Slamon, D.2    Ullrich, A.3
  • 9
    • 33748792021 scopus 로고    scopus 로고
    • Bio-ontologies: current trends and future directions.
    • Bodenreider O, Stevens R. Bio-ontologies: current trends and future directions. Brief Bioinform 2006, 7:256-274.
    • (2006) Brief Bioinform , vol.7 , pp. 256-274
    • Bodenreider, O.1    Stevens, R.2
  • 11
    • 84873880524 scopus 로고    scopus 로고
    • FOAF-project. Introducing FOAF. Available at: (Accessed June 01, 2012).
    • FOAF-project. Introducing FOAF. Available at: http://www.foaf-project.org/original-intro. (Accessed June 01, 2012).
  • 12
    • 84873873382 scopus 로고    scopus 로고
    • Bergen Pv. Semantic Web marvels in a relational database. Available at: (Accessed June 18, 2012).
    • Bergen Pv. Semantic Web marvels in a relational database. Available at: http://techblog.procurios.nl/k/ news/view/34300/14863/Semantic-web-marvels-in-a-relational-database-part-I-Case-Study.html. (Accessed June 18, 2012).
  • 17
    • 79959988943 scopus 로고    scopus 로고
    • BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.
    • Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res 2011, 39:W541-W545.
    • (2011) Nucleic Acids Res , vol.39
    • Whetzel, P.L.1    Noy, N.F.2    Shah, N.H.3    Alexander, P.R.4    Nyulas, C.5    Tudorache, T.6    Musen, M.A.7
  • 18
    • 34547886125 scopus 로고    scopus 로고
    • BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations.
    • Kerhornou A, Guigo R. BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations. Bioinformatics 2007, 23:1831-1833.
    • (2007) Bioinformatics , vol.23 , pp. 1831-1833
    • Kerhornou, A.1    Guigo, R.2
  • 19
    • 84873826540 scopus 로고    scopus 로고
    • The CardioVascular research grid. Available at: (Accessed October 05, 2012).
    • The CardioVascular research grid. Available at: http://cvrgrid.org/. (Accessed October 05, 2012).
  • 20
    • 44649168910 scopus 로고    scopus 로고
    • RDFScape: Semantic Web meets systems biology.
    • Splendiani A. RDFScape: Semantic Web meets systems biology. BMC Bioinformatics 2008, 9(suppl 4):s6.
    • (2008) BMC Bioinformatics , vol.9 , Issue.SUPPL 4
    • Splendiani, A.1
  • 21
    • 36448963071 scopus 로고    scopus 로고
    • A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data.
    • Post LJ, Roos M, Marshall MS, van Driel R, Breit TM. A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data. Bioinformatics 2007, 23:3080-3087.
    • (2007) Bioinformatics , vol.23 , pp. 3080-3087
    • Post, L.J.1    Roos, M.2    Marshall, M.S.3    van Driel, R.4    Breit, T.M.5
  • 25
    • 74049122828 scopus 로고    scopus 로고
    • Cancer systems biology: a network modeling perspective.
    • Kreeger PK, Lauffenburger DA. Cancer systems biology: a network modeling perspective. Carcinogenesis 2010, 31:2-8.
    • (2010) Carcinogenesis , vol.31 , pp. 2-8
    • Kreeger, P.K.1    Lauffenburger, D.A.2
  • 27
    • 33845410054 scopus 로고    scopus 로고
    • Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments.
    • van Riel NA. Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments. Brief Bioinform 2006, 7: 364-374.
    • (2006) Brief Bioinform , vol.7 , pp. 364-374
    • van Riel, N.A.1
  • 30
    • 61349156235 scopus 로고    scopus 로고
    • Computational modeling of brain tumors: discrete, continuum or hybrid?
    • Wang Z, Deisboeck TS. Computational modeling of brain tumors: discrete, continuum or hybrid? Scientific Model Simul 2008, 15:381-393.
    • (2008) Scientific Model Simul , vol.15 , pp. 381-393
    • Wang, Z.1    Deisboeck, T.S.2
  • 32
    • 37549013776 scopus 로고    scopus 로고
    • A microenvironmental model of carcinogenesis.
    • Gatenby RA, Gillies RJ. A microenvironmental model of carcinogenesis. Nat Rev Cancer 2008, 8:56-61.
    • (2008) Nat Rev Cancer , vol.8 , pp. 56-61
    • Gatenby, R.A.1    Gillies, R.J.2
  • 33
    • 68149138796 scopus 로고    scopus 로고
    • Biophysical models of tumour growth.
    • Tracqui P. Biophysical models of tumour growth. Rep Prog Phys 2009, 72:056701.
    • (2009) Rep Prog Phys , vol.72 , pp. 056701
    • Tracqui, P.1
  • 35
    • 68749099453 scopus 로고    scopus 로고
    • Pathway databases and tools for their exploitation: benefits, current limitations and challenges.
    • 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.
    • (2009) Mol Syst Biol , vol.5 , pp. 290
    • Bauer-Mehren, A.1    Furlong, L.I.2    Sanz, F.3
  • 37
    • 33847626655 scopus 로고    scopus 로고
    • Multiscale modeling in biology - new insights into cancer illustrate how mathematical tools are enhancing the understanding of life from the smallest scale to the grandest.
    • Schnell S, Grima R, Maini PK. Multiscale modeling in biology - new insights into cancer illustrate how mathematical tools are enhancing the understanding of life from the smallest scale to the grandest. Am Sci 2007, 95:134-142.
    • (2007) Am Sci , vol.95 , pp. 134-142
    • Schnell, S.1    Grima, R.2    Maini, P.K.3
  • 38
    • 69849103228 scopus 로고    scopus 로고
    • Cross-scale, cross-pathway evaluation using an agent-based non-small cell lung cancer model.
    • Wang Z, Birch CM, Sagotsky J, Deisboeck TS. Cross-scale, cross-pathway evaluation using an agent-based non-small cell lung cancer model. Bioinformatics 2009, 25:2389-2396.
    • (2009) Bioinformatics , vol.25 , pp. 2389-2396
    • Wang, Z.1    Birch, C.M.2    Sagotsky, J.3    Deisboeck, T.S.4
  • 39
    • 77958151212 scopus 로고    scopus 로고
    • Tumour-stromal interactions in acid-mediated invasion: a mathematical model.
    • Martin NK, Gaffney EA, Gatenby RA, Maini PK. Tumour-stromal interactions in acid-mediated invasion: a mathematical model. J Theor Biol 2010, 267:461-470.
    • (2010) J Theor Biol , vol.267 , pp. 461-470
    • Martin, N.K.1    Gaffney, E.A.2    Gatenby, R.A.3    Maini, P.K.4
  • 40
    • 35748935235 scopus 로고    scopus 로고
    • Proteins, drug targets and the mechanisms they control: the simple truth about complex networks.
    • Araujo RP, Liotta LA, Petricoin EF. Proteins, drug targets and the mechanisms they control: the simple truth about complex networks. Nat Rev Drug Discov 2007, 6:871-880.
    • (2007) Nat Rev Drug Discov , vol.6 , pp. 871-880
    • Araujo, R.P.1    Liotta, L.A.2    Petricoin, E.F.3
  • 41
    • 24744472075 scopus 로고    scopus 로고
    • A validated mathematical model of cell-mediated immune response to tumor growth.
    • de Pillis LG, Radunskaya AE, Wiseman CL. A validated mathematical model of cell-mediated immune response to tumor growth. Cancer Res 2005, 65:7950-7958.
    • (2005) Cancer Res , vol.65 , pp. 7950-7958
    • de Pillis, L.G.1    Radunskaya, A.E.2    Wiseman, C.L.3
  • 42
    • 84856082746 scopus 로고    scopus 로고
    • Computational modeling of pancreatic cancer reveals kinetics of metastasis suggesting optimum treatment strategies.
    • Haeno H, Gonen M, Davis MB, Herman JM, Iacobuzio-Donahue CA, Michor F. Computational modeling of pancreatic cancer reveals kinetics of metastasis suggesting optimum treatment strategies. Cell 2012, 148:362-375.
    • (2012) Cell , vol.148 , pp. 362-375
    • Haeno, H.1    Gonen, M.2    Davis, M.B.3    Herman, J.M.4    Iacobuzio-Donahue, C.A.5    Michor, F.6
  • 43
    • 84859349606 scopus 로고    scopus 로고
    • Exploiting evolution to treat drug resistance: combination therapy and the double bind.
    • Basanta D, Gatenby RA, Anderson AR. Exploiting evolution to treat drug resistance: combination therapy and the double bind. Mol Pharm 2012, 9:914-921.
    • (2012) Mol Pharm , vol.9 , pp. 914-921
    • Basanta, D.1    Gatenby, R.A.2    Anderson, A.R.3
  • 45
    • 79951795485 scopus 로고    scopus 로고
    • Discovering Molecular Targets in Cancer with Multiscale Modeling.
    • Wang Z, Bordas V, Deisboeck TS. Discovering Molecular Targets in Cancer with Multiscale Modeling. Drug Dev Res 2011, 72:45-52.
    • (2011) Drug Dev Res , vol.72 , pp. 45-52
    • Wang, Z.1    Bordas, V.2    Deisboeck, T.S.3
  • 46
    • 84863229594 scopus 로고    scopus 로고
    • Identifying therapeutic targets in a combined EGFR-TGFbetaR signalling cascade using a multiscale agent-based cancer model.
    • Wang Z, Bordas V, Sagotsky J, Deisboeck TS. Identifying therapeutic targets in a combined EGFR-TGFbetaR signalling cascade using a multiscale agent-based cancer model. Math Med Biol 2012, 29: 95-108.
    • (2012) Math Med Biol , vol.29 , pp. 95-108
    • Wang, Z.1    Bordas, V.2    Sagotsky, J.3    Deisboeck, T.S.4
  • 49
    • 45849117153 scopus 로고    scopus 로고
    • Advancing cancer systems biology: introducing the Center for the Development of a Virtual Tumor, CViT.
    • Deisboeck TS, Zhang L, Martin S. Advancing cancer systems biology: introducing the Center for the Development of a Virtual Tumor, CViT. Cancer Inform 2007, 5:1-8.
    • (2007) Cancer Inform , vol.5 , pp. 1-8
    • Deisboeck, T.S.1    Zhang, L.2    Martin, S.3
  • 50
    • 84873847934 scopus 로고    scopus 로고
    • DCMI. Metadata basics. Available at: (Accessed July 01, 2012).
    • DCMI. Metadata basics. Available at: http://dublincore.org/metadata-basics/. (Accessed July 01, 2012).
  • 51
    • 84873822445 scopus 로고    scopus 로고
    • NCI Thesaurus Available at: (Accessed July 01, 2012).
    • NCI Thesaurus Available at: http://ncit.nci.nih.gov/ncitbrowser/. (Accessed July 01, 2012).
  • 52
    • 84873845501 scopus 로고    scopus 로고
    • Getting Started with OpenAnzo. Available at: (Accessed July 01, 2012).
    • DuCharme R, Getting Started with OpenAnzo. Available at: http://www.snee.com/bobdc.blog/2009/03/getting-started-with-open-anzo.html. (Accessed July 01, 2012).
    • DuCharme, R.1
  • 53
    • 84873810070 scopus 로고    scopus 로고
    • SPARQL query language for RDF. Available at: (Accessed July 01, 2012).
    • Prud'hommeaux E, Seaborne A. SPARQL query language for RDF. Available at: http://www.w3.org/TR/rdf-sparql-query/. (Accessed July 01, 2012).
    • Prud'hommeaux, E.1    Seaborne, A.2
  • 54
    • 84873880356 scopus 로고    scopus 로고
    • CViT. CViT license. Available at: (Accessed June 15, 2012).
    • CViT. CViT license. Available at: https://www.cvit.org/license.pdf. (Accessed June 15, 2012).
  • 55
    • 40149101292 scopus 로고    scopus 로고
    • Simulating non-small cell lung cancer with a multiscale agent-based model.
    • Wang Z, Zhang L, Sagotsky J, Deisboeck TS. Simulating non-small cell lung cancer with a multiscale agent-based model. Theor Biol Med Model 2007, 4:50.
    • (2007) Theor Biol Med Model , vol.4 , pp. 50
    • Wang, Z.1    Zhang, L.2    Sagotsky, J.3    Deisboeck, T.S.4
  • 59
    • 84878112178 scopus 로고    scopus 로고
    • Semantic Web meets Integrative Biology: a survey.
    • Chen H, Yu T, Chen JY. Semantic Web meets Integrative Biology: a survey. Brief Bioinform 2012.
    • (2012) Brief Bioinform
    • Chen, H.1    Yu, T.2    Chen, J.Y.3
  • 64
    • 77953888300 scopus 로고    scopus 로고
    • BioModels.net Web Services, a free and integrated toolkit for computational modelling software.
    • Li C, Courtot M, Le Novere N, Laibe C. BioModels.net Web Services, a free and integrated toolkit for computational modelling software. Brief Bioinform 11:270-277.
    • Brief Bioinform , vol.11 , pp. 270-277
    • Li, C.1    Courtot, M.2    Le Novere, N.3    Laibe, C.4
  • 69
    • 77957143904 scopus 로고    scopus 로고
    • Professional networks in the life sciences: linking the linked.
    • Deisboeck TS, Sagotsky J. Professional networks in the life sciences: linking the linked. Cancer Inform 9:189-195.
    • Cancer Inform , vol.9 , pp. 189-195
    • Deisboeck, T.S.1    Sagotsky, J.2
  • 71
    • 84873824180 scopus 로고    scopus 로고
    • TUMOR: Transatlantic Tumour Model Repositories. Available at: (Accessed July 12, 2012).
    • TUMOR: Transatlantic Tumour Model Repositories. Available at: http://tumor-project.eu/. (Accessed July 12, 2012).


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.