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Issue No.12 - Dec. (2012 vol.24)
pp: 2288-2300
Vincent Ranwez , Université Montpellier II, Montpellier
Sylvie Ranwez , LGI2P/EMA Research Centre, Site EERIE, Nîmes
Stefan Janaqi , LGI2P/EMA Research Centre, Site EERIE, Nîmes
ABSTRACT
Ontologies are successfully used as semantic guides when navigating through the huge and ever increasing quantity of digital documents. Nevertheless, the size of numerous domain ontologies tends to grow beyond the human capacity to grasp information. This growth is problematic for a lot of key applications that require user interactions such as document annotation or ontology modification/evolution. The problem could be partially overcome by providing users with a subontology focused on their current concepts of interest. A subontology restricted to this sole set of concepts is of limited interest since their relationships can generally not be explicit without adding some of their hyponyms and hypernyms. This paper proposes efficient algorithms to identify these additional key concepts based on the closure of two common graph operators: the least common-ancestor (lca) and greatest common descendant (gcd). The resulting method produces ontology excerpts focused on a set of concepts of interest and is fast enough to be used in interactive environments. As an example, we use the resulting program, called OntoFocus (http://www.ontotoolkit.mines-ales.fr/), to restrict, in few seconds, the large Gene Ontology (∼30,000 concepts) to a subontology focused on concepts annotating a gene related to breast cancer.
INDEX TERMS
Ontologies, Semantics, Humans, Context, Indexes, Filtering, Visualization, greatest common descendant, Subontology extraction, ontology transformation, directed acyclic graph, least common ancestor
CITATION
Vincent Ranwez, Sylvie Ranwez, Stefan Janaqi, "Subontology Extraction Using Hyponym and Hypernym Closure on is-a Directed Acyclic Graphs", IEEE Transactions on Knowledge & Data Engineering, vol.24, no. 12, pp. 2288-2300, Dec. 2012, doi:10.1109/TKDE.2011.173
REFERENCES
[1] T. Berners-Lee, J. Hendler, and O. Lassila, "The Semantic Web," Scientific Am. Magazine, vol. 5, pp. 29-37, 2001.
[2] A. Abecker and L. van Elst, "Ontologies for Knowledge Management," Handbook on Ontologies, International Handbooks on Information Systems, second ed., S. Staab and R. Studer, eds., pp. 713-734, Springer 2009.
[3] C. Wouters, T. Dillon, W. Rahayu, and E. Chang, "Large Scale Ontology Visualisation Using Ontology Extraction," Int'l J. Web and Grid Services, vol. 1, pp. 113-135, 2005.
[4] M.E. Dolan and J.A. Blake, "Using Ontology Visualization to Understand Annotations and Reason about Them," Proc. KR-MED 2006 'Biomedical Ontology in Action,' pp. 21-29, 2006.
[5] J.W. Kim, J. Conesa Caralt, and J.K. Hilliard, "Pruning Bio-Ontologies," Proc. 40th Ann. Hawaii Int'l Conf. System Sciences (HICSS '07), 2007.
[6] H.C. Chen, B. Schatz, T. Ng, J. Martinez, A. Kirchhoff, and C.T. Lin, "A Parallel Computing Approach to Creating Engineering Concept Spaces for Semantic Retrieval: The Illinois Digital Library Initiative Project," IEEE Trans. Pattern Analysis and Machine Intelligence, vol. 18, no. 8, pp. 771-782, Aug. 1996.
[7] P.C. Smits and A. Friis-Christensen, "Resource Discovery in a European Spatial Data Infrastructure," IEEE Trans. Knowledge and Data Eng., vol. 19, no. 1, pp. 85-95, Jan. 2007.
[8] R. Navigli, "Automatically Extending, Pruning and Trimming General Purpose Ontologies," Proc. IEEE Int'l Conf. Systems, Man and Cybernetics, 2002.
[9] M. Sabou, "Learning Web Service Ontologies: An Automatic Extraction Method and Its Evaluation," Ontology Learning from Text: Methods, Evaluation and Applications, Frontiers in Artificial Intelligence and Applications, P. Buitelaar, P. Cimiano, and B. Magnini, eds., vol. 123, IOS Press, 2005.
[10] J. Seidenberg and A. Rector, "Web Ontology Segmentation: Analysis, Classification and Use," Proc. 15th Int'l Conf. World Wide Web, 2006.
[11] B.C. Grau, I. Horrocks, Y. Kazakov, and U. Sattler, "Modular Reuse of Ontologies: Theory and Practice," J. Artificial Intelligence Research, vol. 31, pp. 273-318, 2008.
[12] E. Jimenez-Ruiz, B.C. Grau, U. Sattler, T. Schneider, and R. Berlanga, "Safe and Economic Re-Use of Ontologies: A Logic-Based Methodology and Tool Support," Proc. European Semantic Web Conf. Research and Applications, vol. 5021, pp. 185-199, 2008.
[13] A. Katifori, C. Halatsis, G. Lepouras, C. Vassilakis, and E. Giannopoulou, "Ontology Visualization Methods - A Survey," ACM Computing Surveys, vol. 39, p. 10, 2007.
[14] M.E. Dolan and J.A. Blake, "Using Ontology Visualization to Coordinate Cross-Species Functional Annotation for Human Disease Genes," Proc. IEEE 19th Symp. Computer-Based Medical Systems, pp. 583-587, 2006.
[15] M. Bhatt, W. Rahayu, S.P. Soni, and C. Wouters, "OntoMove: A Knowledge Based Framework for Semantic Requirement Profiling and Resource Acquisition," Proc. 18th Australian Software Eng. Conf. (ASWEC '07), 2007.
[16] M. Bhatt, A. Flahive, C. Wouters, W. Rahayu, D. Taniar, and T. Dillon, "A Distributed Approach to Sub-Ontology Extraction," Proc. 18th Int'l Conf. Advanced Information Networking and Applications, pp. 636-641, 2004.
[17] A. Flahive, W. Rahayu, D. Taniar, B.O. Apduhan, C. Wouters, and T. Dillon, "A Service Oriented Architecture for Extracting and Extending Sub-Ontologies in the Semantic Grid," Proc. 21st Int'l Conf. Advanced Networking and Applications, pp. 831-838, 2007.
[18] S. Bauer, S. Grossmann, M. Vingron, and P.N. Robinson, "Ontologizer 2.0 - A Multifunctional Tool for GO Term Enrichment Analysis and Data Exploration," Bioinformatics, vol. 24, pp. 1650-1651, 2008.
[19] S. Grossmann, S. Bauer, P.N. Robinson, and M. Vingron, "Improved Detection of Overrepresentation of Gene-Ontology Annotations with Parentchild Analysis," Bioinformatics, vol. 23, pp. 3024-3031, 2007.
[20] V. Nebot and R. Berlanga, "Efficient Retrieval of Ontology Fragments Using an Interval Labeling Scheme," Information Sciences, vol. 179, pp. 4151-4173, 2009.
[21] C. Ben Necib and J.C. Freytag, "Ontology Based Query Processing in Database Management Systems," Proc. Sixth Int'l Conf. Ontologies, DataBases, and Applications of Semantics for Large Scale Information Systems (ODBASE '03), vol. 2888, pp. 839-857, 2003.
[22] N. Guarino, D. Oberle, and S. Staab, "What is an Ontology?," Handbook on Ontologies, International Handbooks on Information Systems, Staab, Steffen, Studer, and Rudi, eds., pp. 1-17, Heidelberg Springer, 2009.
[23] P. Ganesan, H. Garcia-Molina, and J. Widom, "Exploiting Hierarchical Domain Structure to Compute Similarity," ACM Trans. Information Systems, vol. 21, pp. 64-93, 2003.
[24] M. Baziz, M. Boughanem, G. Pasi, and H. Prade, "An Information Retrieval Driven by Ontology: From Query to Document Expansion," Proc. Eighth Int'l Conf. Recherche d'Information Assistee par Ordinateur, 2007.
[25] L. Khan, D. McLeod, and E. Hovy, "Retrieval Effectiveness of an Ontology-Based Model for Information Selection," Int'l J. Very Large Data Bases, vol. 13, pp. 71-85, 2004.
[26] Y. Tao, E.A. Mendonca, and Y.A. Lussier, "A Tool for Abstracting Relevant Classes of Concepts: The Common Ancestry Summarizer," Proc. 11th World Congress on Medical Informatics (Medinfo '04), vol. 107, pp. 449-453, 2004.
[27] Z. Liu and Y. Chen, "Identifying Meaningful Return Information for XML Keyword Search," Proc. ACM SIGMOD Int'l Conf. Management of Data, 2007.
[28] Y. Xu and Y. Papakonstantinou, "Efficient Keyword Search for Smallest LCAs in XML Databases," Proc. ACM SIGMOD Int'l Conf. Management of Data, 2005.
[29] J.A. Bondy and U.S.R. Murty, Graph Theory with Appplications. Am. Elsevier Co., 1976.
[30] M.A. Bender, G. Pemmasani, S. Skiena, and P. Sumazin, "Finding Least Common Ancestors in Directed Acyclic Graphs," Proc. 12th Ann. ACM-SIAM Symp. Discrete Algorithms, pp. 845-854, 2001.
[31] R. Yuster, "All-Pairs Disjoint Paths from a Common Ancestor in O (n(omega)) Time," Theoretical Computer Science, vol. 396, pp. 145-150, 2008.
[32] D. Harel and R.E. Tarjan, "Fast Algorithms for Finding Nearest Common Ancestors," SIAM J. Computing, vol. 13, pp. 338-355, 1984.
[33] B. Schieber and U. Vishkin, "On Finding Lowest Common Ancestors - Simplification and Parallelization," SIAM J. Computing, vol. 17, pp. 1253-1262, 1988.
[34] A. Czumaj, M. Kowaluk, and A. Lingas, "Faster Algorithms for Finding Lowest Common Ancestors in Directed Acyclic Graphs," Theory of Computer Science, vol. 380, pp. 37-46, 2007.
[35] S. Eckhardt, A.M. Mühling, and J. Nowak, "Fast Lowest Common Ancestor Computations in Dags," Proc. 15th Ann. European Conf. Algorithms, 2007.
[36] H. Thomas Cormen, E. Charles Leiserson, and L. Ronald Rivest, "Graph Algorithms," Introduction to Algorithms, sixth ed., The MIT Press, 1992.
[37] A.D. Maedche, Ontology Learning for the Semantic Web, vol. 16. Kluwer Academic, 2002.
[38] J. Lindberg, E. af Klint, A.I. Catrina, P. Nilsson, L. Klareskog, A.K. Ulfgren, and J. Lundeberg, "Effect of Infliximab on mRNA Expression Profiles in Synovial Tissue of Rheumatoid Arthritis Patients," Arthritis Research Therapy, vol. 8, p. R179, 2006.
[39] A. Alexa, J. Rahnenfuhrer, and T. Lengauer, "Improved Scoring of Functional Groups from Gene Expression Data by Decorrelating GO Graph Structure," Bioinformatics, vol. 22, pp. 1600-1607, 2006.
[40] A. del Pozo, F. Pazos, and A. Valencia, "Defining Functional Distances over Gene Ontology," BMC Bioinformatics, vol. 9, article 50, 2008.
[41] K.P. O'Brien, I. Westerlund, and E.L. Sonnhammer, "OrthoDisease: A Database of Human Disease Orthologs," Human Mutation, vol. 24, pp. 112-119, 2004.
[42] W.N. Lee, N. Shah, K. Sundlass, and M. Musen, "Comparison of Ontology-Based Semantic-Similarity Measures," Proc. AMIA Ann. Symp., pp. 384-388, 2008.
[43] S. Ranwez, V. Ranwez, J. Villerd, and M. Crampes, "Ontological Distance Measures for Information Visualisation on Conceptual Maps," Proc. On the Move to Meaningful Internet Systems Workshops (OTM '06), vol. 4278, pp. 1050-1061, 2006.
[44] M.-F. Sy, S. Ranwez, J. Montmain, A. Regnault, M. Crampes, and V. Ranwez, "User Centered and Ontology Based Information Retrieval System for Life Sciences," BMC Bioinformatics, vol. 13 (Suppl1), article S4, 2012.
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