セマンティクウェブ技術のアレルギー関連知識領域への適用
我々は，XML/RDF (Resource Description Framework 技術をアレルギーに関する知識領域への適用を試みた．その領域には複雑なデータ構造と、データ要素・リソース間の意味関係が存在する．本論文の目的は次の３要素で構成される．(i)アレルギー疾患の要因に関する知識領域を最適に表現するために，概念の群およびそれら概念間の関係を記述するオントロジーを設計・開発すること；(ii)アレルギー疾患に関係する情報資源の主題索引に本オントロジーを適用すること；(iii)構築したオントロジーと索引を用いて情報資源からデータを検索することの３つである．メタデータの構造化，表現そして蓄積...
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| Published in | 情報知識学会誌 Vol. 18; no. 1; pp. 22 - 46 |
|---|---|
| Main Authors | , |
| Format | Journal Article |
| Language | Japanese |
| Published |
情報知識学会
2008
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| Subjects | |
| Online Access | Get full text |
| ISSN | 0917-1436 1881-7661 |
| DOI | 10.2964/jsik.ishi007 |
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| Abstract | 我々は，XML/RDF (Resource Description Framework 技術をアレルギーに関する知識領域への適用を試みた．その領域には複雑なデータ構造と、データ要素・リソース間の意味関係が存在する．本論文の目的は次の３要素で構成される．(i)アレルギー疾患の要因に関する知識領域を最適に表現するために，概念の群およびそれら概念間の関係を記述するオントロジーを設計・開発すること；(ii)アレルギー疾患に関係する情報資源の主題索引に本オントロジーを適用すること；(iii)構築したオントロジーと索引を用いて情報資源からデータを検索することの３つである．メタデータの構造化，表現そして蓄積はセマンティクウェブ技術であるRDF とSimple Knowledge Organisation System (SKOS)を用いて実行した．一方，Web リソース自体の構造はXML フォーマットを用いて記述した．セマンティクWeb 技術とXML によって表現された情報を検索するために，我々はWeb アプリケーションのプロトタイプを開発した．また，RDF と他のセマンティクWeb 技術がこのライフサイエンス分野に蓄積された情報の探索，ブラウジング，検索に新しい可能性を提供することも示した． |
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| AbstractList | 我々は，XML/RDF (Resource Description Framework 技術をアレルギーに関する知識領域への適用を試みた．その領域には複雑なデータ構造と、データ要素・リソース間の意味関係が存在する．本論文の目的は次の３要素で構成される．(i)アレルギー疾患の要因に関する知識領域を最適に表現するために，概念の群およびそれら概念間の関係を記述するオントロジーを設計・開発すること；(ii)アレルギー疾患に関係する情報資源の主題索引に本オントロジーを適用すること；(iii)構築したオントロジーと索引を用いて情報資源からデータを検索することの３つである．メタデータの構造化，表現そして蓄積はセマンティクウェブ技術であるRDF とSimple Knowledge Organisation System (SKOS)を用いて実行した．一方，Web リソース自体の構造はXML フォーマットを用いて記述した．セマンティクWeb 技術とXML によって表現された情報を検索するために，我々はWeb アプリケーションのプロトタイプを開発した．また，RDF と他のセマンティクWeb 技術がこのライフサイエンス分野に蓄積された情報の探索，ブラウジング，検索に新しい可能性を提供することも示した． |
| Author | 石塚, 英弘 イェレナ, ソロビヨワ |
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| References | [25] Host, A.; Halken, S.: "Can we apply clinical studies to real life? Evidence-based recommendations from studies on development of allergic diseases and allergy prevention", Allergy, Vol.57, No.5, pp.389-397, 2002. [19] Barker, R.N.; Burney, P.G.; Devereux, G.; Hardiman, M.; Holt, P.G.; O'Donnell, M.; Platts-Mills, T.A.; Seaton, A.; Strachan, D.P.; Weiss, S.T.; Woodcock, A. : "The increase in allergic disease: environment and susceptibility. Proceedings of a Symposium held at the Royal Society of Edinburgh, 4th June 2002", Clinical & Experimental Allergy, Vol.33, No.3, pp.394-406, 2003. [5] Wang, X.; Gorlitsky, R. and Almeida, J.S: "From XML to RDF: how semantic web technologies will change the design of ‘omic’ standards", Nature Biotechnology, Vol.23, No.9, pp.1099-1103, 2005. [26] Gore, C.; Custovic A.: "Can we prevent allergy?", Allergy, Vol.59, No.2, pp.151-161, 2004. [17] Golbeck, J.; Fragoso, G.; Hartel, F.W.; Hendler, J.; Oberthaler, J.; Parsia, B.: "The national cancer institute's thesaurus and Ontology", Journal of Web Semantics, Vol.1, Issue 1, pp.75-80, 2003. [37] Scalable Vector Graphics (SVG): http://www.w3.org/Graphics/SVG/ (accessed 2007.09.22). [32] Dublin Core Metadata Element Set, Ver. 1.1, http://dublincore.org/documents/2006/12/18/dces/ (accessed 2007.05.29). [4] Cheung, K.H.; Yip, K.Y.; Smith, A.; deKnikker, R.; Masiar, A. and Gerstein, M.: "YeastHub: a semantic web use case for integrating data in the life sciences domain", Bioinformatics, Vol.21, Suppl.1, pp.i85-i96, 2005. [15] National Center for Biomedical Ontology: http://www.bioontology.org/resources.html (accessed 2007.06.20). [16] Open Biomedical Ontology Syntax: http://geneontology.org/GO.format.shtml#oboflat (accessed 2007.06.20). [34] Microsoft .NET Framework http://msdn2.microsoft.com/en-us/netframework/default.aspx (accessed 2007.09.22). [6] Solovieva, E.: "Design and Development of Information System devoted to Allergic Diseases", Master's thesis, University of Library and Information Science, Tsukuba, 2004. [14] Rubin, D.L.; Lewis, S.E.; Mungall, C.J.; Misra, S.; Westerfield, M.; Ashburner, M.; Sim, I.; Chute, C.G.; Solbrig, H.; Storey, M.; Smith, B.; Day-Richter, J.; Noy, N.F.; Musen, M.A.: "National Center for Biomedical Ontology: Advancing Biomedicine through Structured Organization of Scientific Knowledge", OMICS A Journal of Integrative Biology, Vol.10, No.2, pp.185-198, 2006. [27] Anto, J.M.: "The causes of asthma: the need to look at the data with different eyes", Allergy, Vol.59, No.2, pp.121-123, 2004. [33] Patel-Schneider, P.; Hayes, P.; Horrocks, I.: "OWL Web Ontology Language Semantics and Abstract Syntax W3C Recommendation 10 February 2004", http://www.w3.org/TR/2004/REC-owl-semantics-20040210/ (accessed 2007. 05.29). [24] Miles, A.; Brickley, D.: "SKOS Core Guide W3C Working Draft 2 November 2005", http://www.w3.org/TR/2005/WD-swbp-skos-core-guide-20051102/ (accessed 2007.05.29). [30] Dublin Core Metadata Initiative (DCMI) Metadata Terms: http://dublincore.org/documents/dcmi-terms/ (accessed 2007.05.29). [23] Miles, A.; Brickley, D.: "SKOS Core Vocabulary Specification W3C Working Draft 2 November 2005", http://www.w3.org/TR/2005/ WD-swbp-skos-core-spec-20051102/ (accessed 2007.05.29). [3] Kim G.: "Metadata in Medicine", 2004, http://meld.medbiq.org/primers/metadata_in_ medicine_kim.htm (accessed 2007.05.29). [20] Baena-Cagnani, C.E.; Serra, H.; Teijeiro, A.; Croce, J.S.: "Prevention of allergy and asthma", Clinical & Experimental Allergy Reviews, Vol.3, Issue 1, pp.51-57, 2003. [12] McGuinness, D. L.; Harmelen, F. V.: "OWL Web Ontology Language Overview W3C Recommendation 10 February 2004", http://www.w3.org/TR/2004/REC-owl-features-20040210/ (accessed 2007.05.29). [9] Manola, F.; Miller, E.: "RDF Primer W3C Recommendation 10 February 2004", http://www.w3.org/TR/2004/REC-rdf-primer-20040210/ (accessed 2007.05.29). [36] Clark, J.: "XSL Transformations (XSLT) Version 1.0 W3C Recommendation 16 November 1999", http://www.w3.org/TR/1999/REC-xslt-19991116 (accessed 2007.09.22). [21] Frew, A.J: "Advances in environmental and occupational disorders", Journal of Allergy and Clinical Immunology, Vol.111, Issue 3, pp.S824-S828, 2003. [18] Kumar, A.; Smith, B.: "Oncology Ontology in the NCI Thesaurus", In Proceedings of the Artificial Intelligence in Medicine Europe conference AIME 2005, pp.213-220, 2005. [7] Summary Report: W3C Workshop on Semantic Web for Life sciences on October 27-28 2004, http://www.w3.org/2004/10/swls-workshop-report.html (accessed 2007.05.29). [13] Miles, A.: "SKOS: Requirements for Standardization", Proceedings of the 2006 international conference on Dublin Core and Metadata Applications, pp.55-64, 2006. [29] Miles, A.; Matthews, B.; Wilson, M.D.; Brickley, D.: "SKOS Core: Simple Knowledge Organisation for the Web", International Conference on Dublin Core and Metadata Applications (DC-2005), Sep 2005, available: http://epubs.cclrc.ac.uk/work-details?w=33977 (accessed 2007.05.29). [35] Visual C#: http://msdn2.microsoft.com/en-us/vcsharp/default.aspx (accessed 2007.09.22). [10] Beckett, D.: "RDF/XML Syntax Specification (Revised) W3C Recommendation 10 February 2004", http://www.w3.org/TR/2004/REC-rdf-syntax-grammar-20040210/ (accessed 2007.06.18). [11] Brickley, D.; Guha, R.V.: "RDF Vocabulary Description Language 1.0: RDF Schema W3C Recommendation 10 February 2004", http://www.w3.org/TR/2004/REC-rdf-schema-20040210/ (accessed 2007.05.29). [2] Yamakawa, T. and Yamazaki, Y.: "The Application of XML Technology in Genetic Resource Database", Journal of Japan Society of Information and Knowledge, Vol.16, No.1, pp.52-59, 2006. [31] Brickley, D.; Miller, L.: "FOAF Vocabulary Specification 0.9": http://xmlns.com/foaf/spec/20070524.html (accessed 2007.05.29). [1] Hucka, M.; Finney, A.; Sauro, H.M.; Bolouri, H.; Doyle, J.C.; Kitano, H.; Arkin, A.P.; Bornstein, B.J.; Bray, D.; Cornish-Bowden, A. et al.: "The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models", Bioinformatics, Vol.19, No.4, pp.524-531, 2003. [28] Miles, A.; Matthews, B.; Beckett, D.; Brickley, D.; Wilson, M.; Rogers, N.: "SKOS: A language to describe simple knowledge structures for the web", XTech 2005, available:http://epubs.cclrc.ac.uk/ work-details?w=33893 (accessed 2007.05.29). [8] Baker, C.J.O.; Cheung, K.-H (Eds.): "Semantic Web: Revolutionizing Knowledge Discovery in Life Sciences", Springer, 450p., 2006. [22] National Library of Medicine, Unified Medical Language System, About the UMLS Resources, http://www.nlm.nih.gov/research/umls/ (accessed 2007.05.29). |
| References_xml | – reference: [4] Cheung, K.H.; Yip, K.Y.; Smith, A.; deKnikker, R.; Masiar, A. and Gerstein, M.: "YeastHub: a semantic web use case for integrating data in the life sciences domain", Bioinformatics, Vol.21, Suppl.1, pp.i85-i96, 2005. – reference: [5] Wang, X.; Gorlitsky, R. and Almeida, J.S: "From XML to RDF: how semantic web technologies will change the design of ‘omic’ standards", Nature Biotechnology, Vol.23, No.9, pp.1099-1103, 2005. – reference: [15] National Center for Biomedical Ontology: http://www.bioontology.org/resources.html (accessed 2007.06.20). – reference: [30] Dublin Core Metadata Initiative (DCMI) Metadata Terms: http://dublincore.org/documents/dcmi-terms/ (accessed 2007.05.29). – reference: [9] Manola, F.; Miller, E.: "RDF Primer W3C Recommendation 10 February 2004", http://www.w3.org/TR/2004/REC-rdf-primer-20040210/ (accessed 2007.05.29). – reference: [31] Brickley, D.; Miller, L.: "FOAF Vocabulary Specification 0.9": http://xmlns.com/foaf/spec/20070524.html (accessed 2007.05.29). – reference: [11] Brickley, D.; Guha, R.V.: "RDF Vocabulary Description Language 1.0: RDF Schema W3C Recommendation 10 February 2004", http://www.w3.org/TR/2004/REC-rdf-schema-20040210/ (accessed 2007.05.29). – reference: [29] Miles, A.; Matthews, B.; Wilson, M.D.; Brickley, D.: "SKOS Core: Simple Knowledge Organisation for the Web", International Conference on Dublin Core and Metadata Applications (DC-2005), Sep 2005, available: http://epubs.cclrc.ac.uk/work-details?w=33977 (accessed 2007.05.29). – reference: [3] Kim G.: "Metadata in Medicine", 2004, http://meld.medbiq.org/primers/metadata_in_ medicine_kim.htm (accessed 2007.05.29). – reference: [18] Kumar, A.; Smith, B.: "Oncology Ontology in the NCI Thesaurus", In Proceedings of the Artificial Intelligence in Medicine Europe conference AIME 2005, pp.213-220, 2005. – reference: [16] Open Biomedical Ontology Syntax: http://geneontology.org/GO.format.shtml#oboflat (accessed 2007.06.20). – reference: [34] Microsoft .NET Framework http://msdn2.microsoft.com/en-us/netframework/default.aspx (accessed 2007.09.22). – reference: [13] Miles, A.: "SKOS: Requirements for Standardization", Proceedings of the 2006 international conference on Dublin Core and Metadata Applications, pp.55-64, 2006. – reference: [28] Miles, A.; Matthews, B.; Beckett, D.; Brickley, D.; Wilson, M.; Rogers, N.: "SKOS: A language to describe simple knowledge structures for the web", XTech 2005, available:http://epubs.cclrc.ac.uk/ work-details?w=33893 (accessed 2007.05.29). – reference: [19] Barker, R.N.; Burney, P.G.; Devereux, G.; Hardiman, M.; Holt, P.G.; O'Donnell, M.; Platts-Mills, T.A.; Seaton, A.; Strachan, D.P.; Weiss, S.T.; Woodcock, A. : "The increase in allergic disease: environment and susceptibility. Proceedings of a Symposium held at the Royal Society of Edinburgh, 4th June 2002", Clinical & Experimental Allergy, Vol.33, No.3, pp.394-406, 2003. – reference: [20] Baena-Cagnani, C.E.; Serra, H.; Teijeiro, A.; Croce, J.S.: "Prevention of allergy and asthma", Clinical & Experimental Allergy Reviews, Vol.3, Issue 1, pp.51-57, 2003. – reference: [17] Golbeck, J.; Fragoso, G.; Hartel, F.W.; Hendler, J.; Oberthaler, J.; Parsia, B.: "The national cancer institute's thesaurus and Ontology", Journal of Web Semantics, Vol.1, Issue 1, pp.75-80, 2003. – reference: [36] Clark, J.: "XSL Transformations (XSLT) Version 1.0 W3C Recommendation 16 November 1999", http://www.w3.org/TR/1999/REC-xslt-19991116 (accessed 2007.09.22). – reference: [7] Summary Report: W3C Workshop on Semantic Web for Life sciences on October 27-28 2004, http://www.w3.org/2004/10/swls-workshop-report.html (accessed 2007.05.29). – reference: [14] Rubin, D.L.; Lewis, S.E.; Mungall, C.J.; Misra, S.; Westerfield, M.; Ashburner, M.; Sim, I.; Chute, C.G.; Solbrig, H.; Storey, M.; Smith, B.; Day-Richter, J.; Noy, N.F.; Musen, M.A.: "National Center for Biomedical Ontology: Advancing Biomedicine through Structured Organization of Scientific Knowledge", OMICS A Journal of Integrative Biology, Vol.10, No.2, pp.185-198, 2006. – reference: [27] Anto, J.M.: "The causes of asthma: the need to look at the data with different eyes", Allergy, Vol.59, No.2, pp.121-123, 2004. – reference: [1] Hucka, M.; Finney, A.; Sauro, H.M.; Bolouri, H.; Doyle, J.C.; Kitano, H.; Arkin, A.P.; Bornstein, B.J.; Bray, D.; Cornish-Bowden, A. et al.: "The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models", Bioinformatics, Vol.19, No.4, pp.524-531, 2003. – reference: [10] Beckett, D.: "RDF/XML Syntax Specification (Revised) W3C Recommendation 10 February 2004", http://www.w3.org/TR/2004/REC-rdf-syntax-grammar-20040210/ (accessed 2007.06.18). – reference: [8] Baker, C.J.O.; Cheung, K.-H (Eds.): "Semantic Web: Revolutionizing Knowledge Discovery in Life Sciences", Springer, 450p., 2006. – reference: [12] McGuinness, D. L.; Harmelen, F. V.: "OWL Web Ontology Language Overview W3C Recommendation 10 February 2004", http://www.w3.org/TR/2004/REC-owl-features-20040210/ (accessed 2007.05.29). – reference: [23] Miles, A.; Brickley, D.: "SKOS Core Vocabulary Specification W3C Working Draft 2 November 2005", http://www.w3.org/TR/2005/ WD-swbp-skos-core-spec-20051102/ (accessed 2007.05.29). – reference: [35] Visual C#: http://msdn2.microsoft.com/en-us/vcsharp/default.aspx (accessed 2007.09.22). – reference: [2] Yamakawa, T. and Yamazaki, Y.: "The Application of XML Technology in Genetic Resource Database", Journal of Japan Society of Information and Knowledge, Vol.16, No.1, pp.52-59, 2006. – reference: [24] Miles, A.; Brickley, D.: "SKOS Core Guide W3C Working Draft 2 November 2005", http://www.w3.org/TR/2005/WD-swbp-skos-core-guide-20051102/ (accessed 2007.05.29). – reference: [6] Solovieva, E.: "Design and Development of Information System devoted to Allergic Diseases", Master's thesis, University of Library and Information Science, Tsukuba, 2004. – reference: [25] Host, A.; Halken, S.: "Can we apply clinical studies to real life? Evidence-based recommendations from studies on development of allergic diseases and allergy prevention", Allergy, Vol.57, No.5, pp.389-397, 2002. – reference: [26] Gore, C.; Custovic A.: "Can we prevent allergy?", Allergy, Vol.59, No.2, pp.151-161, 2004. – reference: [21] Frew, A.J: "Advances in environmental and occupational disorders", Journal of Allergy and Clinical Immunology, Vol.111, Issue 3, pp.S824-S828, 2003. – reference: [32] Dublin Core Metadata Element Set, Ver. 1.1, http://dublincore.org/documents/2006/12/18/dces/ (accessed 2007.05.29). – reference: [37] Scalable Vector Graphics (SVG): http://www.w3.org/Graphics/SVG/ (accessed 2007.09.22). – reference: [33] Patel-Schneider, P.; Hayes, P.; Horrocks, I.: "OWL Web Ontology Language Semantics and Abstract Syntax W3C Recommendation 10 February 2004", http://www.w3.org/TR/2004/REC-owl-semantics-20040210/ (accessed 2007. 05.29). – reference: [22] National Library of Medicine, Unified Medical Language System, About the UMLS Resources, http://www.nlm.nih.gov/research/umls/ (accessed 2007.05.29). |
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| ispartofPNX | 情報知識学会誌, 2008/02/19, Vol.18(1), pp.22-46 |
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