An Application of the Semantic Web Technologies in the Knowledge Domain related to the Allergy
The authors tried to apply XML/RDF (Resource Description Framework) technologies to the knowledge domain related to the allergy which includes complicated data structures and semantic relationships among data elements and resources. The purpose of this work is threefold: (i) The design and the devel...
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| Published in | Joho Chishiki Gakkaishi Vol. 18; no. 1; pp. 22 - 46 |
|---|---|
| Main Authors | , |
| Format | Journal Article |
| Language | English Japanese |
| Published |
Japan Society of Information and Knowledge
19.02.2008
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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 | The authors tried to apply XML/RDF (Resource Description Framework) technologies to the knowledge domain related to the allergy which includes complicated data structures and semantic relationships among data elements and resources. The purpose of this work is threefold: (i) The design and the development of the ontology representing a set of the concepts and the relationships between these concepts for the knowledge domain devoted to the factors of allergic diseases; (ii) The application of this ontology for subject-indexing of resources related to the allergic diseases; (iii) The use of the created ontology and the indexing for retrieving the data from the resources. The structurization, representation and storage of metadata have been performed by using the Semantic Web technologies such as RDF and the Simple Knowledge Organisation System (SKOS). On the other hand, the structure of the web resources themselves is described by using the XML format. In order to retrieve the information, represented by the Semantic Web technologies and XML, we developed a prototype web application. We further demonstrate that RDF and other Semantic Web technologies provide new possibilities for searching, browsing and retrieving the information accumulated in the life sciences. |
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| AbstractList | The authors tried to apply XML/RDF (Resource Description Framework) technologies to the knowledge domain related to the allergy which includes complicated data structures and semantic relationships among data elements and resources. The purpose of this work is threefold: (i) The design and the development of the ontology representing a set of the concepts and the relationships between these concepts for the knowledge domain devoted to the factors of allergic diseases; (ii) The application of this ontology for subject-indexing of resources related to the allergic diseases; (iii) The use of the created ontology and the indexing for retrieving the data from the resources. The structurization, representation and storage of metadata have been performed by using the Semantic Web technologies such as RDF and the Simple Knowledge Organisation System (SKOS). On the other hand, the structure of the web resources themselves is described by using the XML format. In order to retrieve the information, represented by the Semantic Web technologies and XML, we developed a prototype web application. We further demonstrate that RDF and other Semantic Web technologies provide new possibilities for searching, browsing and retrieving the information accumulated in the life sciences. |
| Author | ISHIZUKA, Hidehiro SOLOVIEVA, Elena |
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| Cites_doi | 10.1111/j.1398-9995.2003.00480.x 10.1007/11527770_30 10.1089/omi.2006.10.185 10.1034/j.1398-9995.2002.00154.x 10.1067/mai.2003.151 10.1016/j.websem.2003.07.007 10.1093/bioinformatics/bti1026 10.1046/j.1365-2222.2003.01621.x 10.1046/j.1472-9725.2003.00052.x 10.1093/bioinformatics/btg015 10.1046/j.1398-9995.2003.00358.x 10.2964/jsik.16.1_52 |
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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). 22 23 24 25 26 27 28 29 30 31 10 32 11 33 12 34 13 35 14 36 15 16 17 18 19 1 2 3 4 5 6 7 8 9 20 21 |
| 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). – ident: 26 doi: 10.1111/j.1398-9995.2003.00480.x – ident: 17 doi: 10.1007/11527770_30 – ident: 12 – ident: 13 doi: 10.1089/omi.2006.10.185 – ident: 35 – ident: 33 – ident: 10 – ident: 14 – ident: 31 – ident: 24 doi: 10.1034/j.1398-9995.2002.00154.x – ident: 28 – ident: 20 doi: 10.1067/mai.2003.151 – ident: 16 doi: 10.1016/j.websem.2003.07.007 – ident: 4 doi: 10.1093/bioinformatics/bti1026 – ident: 9 – ident: 7 – ident: 22 – ident: 3 – ident: 5 – ident: 18 doi: 10.1046/j.1365-2222.2003.01621.x – ident: 19 doi: 10.1046/j.1472-9725.2003.00052.x – ident: 36 – ident: 11 – ident: 34 – ident: 15 – ident: 32 – ident: 29 – ident: 30 – ident: 1 doi: 10.1093/bioinformatics/btg015 – ident: 25 doi: 10.1046/j.1398-9995.2003.00358.x – ident: 6 – ident: 8 – ident: 21 – ident: 27 – ident: 2 doi: 10.2964/jsik.16.1_52 – ident: 23 |
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