메뉴 건너뛰기




Volumn 3, Issue 3, 2007, Pages 286-302

A case study of integrating protein interaction data using semantic web technology

Author keywords

Ontology map; Protein protein interactions; RDF schema; Resource description framework; Semantic data integration; Semantic web

Indexed keywords

HU PROTEIN;

EID: 34748859463     PISSN: 17445485     EISSN: 17445493     Source Type: Journal    
DOI: 10.1504/IJBRA.2007.015004     Document Type: Article
Times cited : (16)

References (33)
  • 2
    • 0035987407 scopus 로고    scopus 로고
    • The post-genomic era of interactive proteomics: Facts and perspectives
    • Auerbach, D., Thaminy, S. Auerbach, D., Thaminy, S., Hottiger, M.O. and Stagljar, I. (2002) 'The post-genomic era of interactive proteomics: facts and perspectives', Proteomics, Vol. 2, No. 6, pp.611-623.
    • (2002) Proteomics , vol.2 , Issue.6 , pp. 611-623
    • Auerbach, D.1    Thaminy, S.2    Auerbach, D.3    Thaminy, S.4    Hottiger, M.O.5    Stagljar, I.6
  • 3
    • 0036789265 scopus 로고    scopus 로고
    • Analyzing yeast protein-protein interaction data obtained from different sources
    • Bader, G.D. and Hogue, C.W. (2002) 'Analyzing yeast protein-protein interaction data obtained from different sources', Nat. Biotechnol., Vol. 20, No. 10, pp.991-997.
    • (2002) Nat. Biotechnol , vol.20 , Issue.10 , pp. 991-997
    • Bader, G.D.1    Hogue, C.W.2
  • 4
    • 0037245913 scopus 로고    scopus 로고
    • BIND: The Biomolecular interaction network database
    • Bader, G.D., Betel, D. and Hogue, C.W. (2003) 'BIND: the Biomolecular interaction network database', Nucleic Acids Res., Vol. 31, No. 1, pp.248-250.
    • (2003) Nucleic Acids Res , vol.31 , Issue.1 , pp. 248-250
    • Bader, G.D.1    Betel, D.2    Hogue, C.W.3
  • 6
    • 33644876924 scopus 로고    scopus 로고
    • Birney, E., Andrews, D., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cox, T., Cunningham, F., Curwen, V., Cutts, T., Down, T., Durbin, R., Femandez-Suarez, X.M., Flicek, P., Gräf, S., Hammond, M., Herrero, J., Howe, K., Iyer, V., Jekosch, K., Kähäri, A., Kasprzyk, A., Keefe, D., Kokocinski, F., Kulesha, E., London, D., Longden, I., Melsopp, C., Meidl, P., Overduin, B., Parker, A., Proctor, G., Prlic, A., Rae, M., Rios, D., Redmond, S., Schuster, M., Sealy, I., Searle, S., Severin, J., Slater, G., Smedley, D., Smith, J., Stabenau, A., Stalker, J., Trevanion, S., Ureta-Vidal, A., Vogel, J., White, S., Woodwark, C. and Hubbard, T.J.P. (2006) 'Ensembl', Nucleic Acids Res., 34, Database Issue, pp.D556-D561.
    • Birney, E., Andrews, D., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cox, T., Cunningham, F., Curwen, V., Cutts, T., Down, T., Durbin, R., Femandez-Suarez, X.M., Flicek, P., Gräf, S., Hammond, M., Herrero, J., Howe, K., Iyer, V., Jekosch, K., Kähäri, A., Kasprzyk, A., Keefe, D., Kokocinski, F., Kulesha, E., London, D., Longden, I., Melsopp, C., Meidl, P., Overduin, B., Parker, A., Proctor, G., Prlic, A., Rae, M., Rios, D., Redmond, S., Schuster, M., Sealy, I., Searle, S., Severin, J., Slater, G., Smedley, D., Smith, J., Stabenau, A., Stalker, J., Trevanion, S., Ureta-Vidal, A., Vogel, J., White, S., Woodwark, C. and Hubbard, T.J.P. (2006) 'Ensembl', Nucleic Acids Res., Vol. 34, Database Issue, pp.D556-D561.
  • 7
    • 35349012037 scopus 로고    scopus 로고
    • Bizer, C. Bizer, C. and Seaborne, A. (2004) 'D2RQ - treating non RDF databases as virtual RDF graphs', Poster at The 3rd International Semantic Web Conference, Hiroshima, Japan.
    • Bizer, C. Bizer, C. and Seaborne, A. (2004) 'D2RQ - treating non RDF databases as virtual RDF graphs', Poster at The 3rd International Semantic Web Conference, Hiroshima, Japan.
  • 8
    • 84866262574 scopus 로고    scopus 로고
    • Sesame: A generic architecture for storing and querying RDF and RDF schema
    • Broekstra, J., Kampman, A. and van Harmelen, F. (2002a) 'Sesame: a generic architecture for storing and querying RDF and RDF schema', The Semantic Web-ISWC, Vol. 2342, pp.54-68.
    • (2002) The Semantic Web-ISWC , vol.2342 , pp. 54-68
    • Broekstra, J.1    Kampman, A.2    van Harmelen, F.3
  • 10
    • 18744376914 scopus 로고    scopus 로고
    • Online predicted human interaction database
    • Brown, K.R. and Jurisica, I. (2005) Online predicted human interaction database', Bioinformatics, Vol. 21, No. 9, pp.2076-2082.
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 2076-2082
    • Brown, K.R.1    Jurisica, I.2
  • 13
    • 33751045168 scopus 로고    scopus 로고
    • An integrated computational proteomics method to extract protein targets for fanconi anemia studies
    • Dijon, France
    • Chen, J.Y., Pinkerton, S.L., Shen, C. and Wang, M. (2006b) 'An integrated computational proteomics method to extract protein targets for fanconi anemia studies', 21st Annual ACM Symposium on Applied Computing. Dijon, France, Vol. 1, pp.173-179.
    • (2006) 21st Annual ACM Symposium on Applied Computing , vol.1 , pp. 173-179
    • Chen, J.Y.1    Pinkerton, S.L.2    Shen, C.3    Wang, M.4
  • 14
    • 39049189899 scopus 로고    scopus 로고
    • Mining alzheimer disease relevant proteins from integrated protein interactome data
    • Maui, HI
    • Chen, J.Y., Shen, C. and Sivachenko, A.Y. (2006c) 'Mining alzheimer disease relevant proteins from integrated protein interactome data', Pacific Symposium on Biocomputing, Maui, HI, Vol. 11, pp.367-378.
    • (2006) Pacific Symposium on Biocomputing , vol.11 , pp. 367-378
    • Chen, J.Y.1    Shen, C.2    Sivachenko, A.Y.3
  • 16
    • 84860531384 scopus 로고    scopus 로고
    • YeastHub: A semantic web use case for integrating data in the life sciences domain
    • Cheung, K.H., Yip, K.Y., Smith, A., deKnikker, R., Masiar, A. and Gerstein, M. (2005) 'YeastHub: a semantic web use case for integrating data in the life sciences domain', Bioinformatics, Vol. 21, No. 1, pp.i85-i96.
    • (2005) Bioinformatics , vol.21 , Issue.1
    • Cheung, K.H.1    Yip, K.Y.2    Smith, A.3    deKnikker, R.4    Masiar, A.5    Gerstein, M.6
  • 19
    • 24044466525 scopus 로고    scopus 로고
    • The DARPA agent markup language
    • Hendler, J. and McGuinness, D.L. (2000) 'The DARPA agent markup language', IEEE Intelligent Systems, Vol. 15, No. 6, pp.67-73.
    • (2000) IEEE Intelligent Systems , vol.15 , Issue.6 , pp. 67-73
    • Hendler, J.1    McGuinness, D.L.2
  • 21
    • 31144432293 scopus 로고    scopus 로고
    • Literature mining for the biologist: From information retrieval to biological discovery
    • Jensen, L.J., Saric, J. and Bork, P. (2006) 'Literature mining for the biologist: from information retrieval to biological discovery', Nat. Rev. Genet., Vol. 7, No. 2, pp.119-129.
    • (2006) Nat. Rev. Genet , vol.7 , Issue.2 , pp. 119-129
    • Jensen, L.J.1    Saric, J.2    Bork, P.3
  • 22
    • 0036500993 scopus 로고    scopus 로고
    • Systems biology: A brief overview
    • Kitano, H. (2002) 'Systems biology: a brief overview', Science, Vol. 295, No. 5560, pp.1662 1664.
    • (2002) Science , vol.295 , Issue.5560
    • Kitano, H.1
  • 23
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • Mering, C.V., Krause, R., Snel, B., Cornell, M., Oliver, S.G., Fields, S. and Bork, P. (2002) 'Comparative assessment of large-scale data sets of protein-protein interactions', Nature, Vol. 417, pp.399-403.
    • (2002) Nature , vol.417 , pp. 399-403
    • Mering, C.V.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 24
    • 0003267015 scopus 로고    scopus 로고
    • An introduction to the resource description framework
    • Miller, E. (1998) 'An introduction to the resource description framework', D-Lib Magazine, Vol. 4, No. 5, www.dlib.org/dlib/may98/ miller/05miller.html.
    • (1998) D-Lib Magazine , vol.4 , Issue.5
    • Miller, E.1
  • 25
    • 33644877439 scopus 로고    scopus 로고
    • Mishra, G.R., Suresh, M., Kumaran, K., Kannabiran, N., Suresh, S., Bala, P., Shivakumar, K., Anuradha, N., Reddy, R., Raghavan, T.M., Menon, S., Hanumanthu, G., Gupta, M., Upendran, S., Gupta, S., Mahesh, M., Jacob, B., Mathew, P., Chatterjee, P., Arun, K.S., Sharma, S., Chandrika, K.N., Deshpande, N., Palvankar, K., Raghavnath, R., Krishnakanth, R., Karathia, H., Rekha, B., Nayak R., Vishnupriya, G., Kumar, H.G., Nagini, M., Kumar, G.S., Jose, R., Deepthi, P., Mohan, S.S., Gandhi, T.K., Harsha, H.C., Deshpande, K.S., Sarker, M., Prasad T.S. and Pandey, A. (2006) 'Human protein reference database-2006 update', Nucleic Acids Res., 34, Database Issue, pp.D411-D414.
    • Mishra, G.R., Suresh, M., Kumaran, K., Kannabiran, N., Suresh, S., Bala, P., Shivakumar, K., Anuradha, N., Reddy, R., Raghavan, T.M., Menon, S., Hanumanthu, G., Gupta, M., Upendran, S., Gupta, S., Mahesh, M., Jacob, B., Mathew, P., Chatterjee, P., Arun, K.S., Sharma, S., Chandrika, K.N., Deshpande, N., Palvankar, K., Raghavnath, R., Krishnakanth, R., Karathia, H., Rekha, B., Nayak R., Vishnupriya, G., Kumar, H.G., Nagini, M., Kumar, G.S., Jose, R., Deepthi, P., Mohan, S.S., Gandhi, T.K., Harsha, H.C., Deshpande, K.S., Sarker, M., Prasad T.S. and Pandey, A. (2006) 'Human protein reference database-2006 update', Nucleic Acids Res., Vol. 34, Database Issue, pp.D411-D414.
  • 27
    • 0036083294 scopus 로고    scopus 로고
    • Extraction of knowledge on protein-protein interaction by association rule discovery
    • Oyama, T., Kitano, K., Satou, K. and Ito, T. (2002) 'Extraction of knowledge on protein-protein interaction by association rule discovery', Bioinformatics, Vol. 18, No. 5, pp.705-714.
    • (2002) Bioinformatics , vol.18 , Issue.5 , pp. 705-714
    • Oyama, T.1    Kitano, K.2    Satou, K.3    Ito, T.4
  • 28
    • 0347511691 scopus 로고    scopus 로고
    • Next generation simulation tools: The systems biology workbench and BioSPICE integration
    • Sauro, H.M., Hucka, M., Finney, A., Wellock, C., Bolouri, H., Doyle, J. and Kitano, H. (2003) 'Next generation simulation tools: the systems biology workbench and BioSPICE integration', Omics, Vol. 7, No. 4, pp.355-72.
    • (2003) Omics , vol.7 , Issue.4 , pp. 355-372
    • Sauro, H.M.1    Hucka, M.2    Finney, A.3    Wellock, C.4    Bolouri, H.5    Doyle, J.6    Kitano, H.7
  • 29
    • 33646761733 scopus 로고    scopus 로고
    • Protein knowledge base: Making of protein ontology
    • American Society for Biochemistry and Molecular Biology, Beijing, China
    • Sidhu, A.S., Dillon, T.S. and Chang, E. (2004) 'Protein knowledge base: making of protein ontology', HUPO 3rd Annual World Congress, American Society for Biochemistry and Molecular Biology, Beijing, China, Vol. 3, p.S262.
    • (2004) HUPO 3rd Annual World Congress , vol.3
    • Sidhu, A.S.1    Dillon, T.S.2    Chang, E.3
  • 30
    • 1642457154 scopus 로고    scopus 로고
    • RDF-based architecture for semantic integration of heterogeneous information sources
    • Rio de Janeiro, Brazil, pp
    • Vdovjak, R. and Houben, G.J. (2001) 'RDF-based architecture for semantic integration of heterogeneous information sources', Workshop on Information Integration on the Web, Rio de Janeiro, Brazil, pp.51-57, http://citeseer.ist.psu.edu/vdovjak01rdf.html.
    • (2001) Workshop on Information Integration on the Web , pp. 51-57
    • Vdovjak, R.1    Houben, G.J.2
  • 31
    • 13444249988 scopus 로고    scopus 로고
    • von Mering, C., Jensen, L.J., Snel, B., Hooper, S.D., Krupp, M., Foglierini, M., Jouffre, N., Huynen, M.A. and Bork, P. (2005) 'STRING: known and predicted protein-protein associations, integrated and transferred across organisms', Nucleic Acids Res., 33, Database Issue, pp.D433-D437.
    • von Mering, C., Jensen, L.J., Snel, B., Hooper, S.D., Krupp, M., Foglierini, M., Jouffre, N., Huynen, M.A. and Bork, P. (2005) 'STRING: known and predicted protein-protein associations, integrated and transferred across organisms', Nucleic Acids Res., Vol. 33, Database Issue, pp.D433-D437.
  • 32
    • 0037580112 scopus 로고    scopus 로고
    • Technologies for integrating biological data
    • Wong, L. (2002) 'Technologies for integrating biological data', Brief Bioinform., Vol. 3, No. 4, pp.389-404.
    • (2002) Brief Bioinform , vol.3 , Issue.4 , pp. 389-404
    • Wong, L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.