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  • 1.
    Lambrix, Patrick
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Liu, Qiang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    A System for Debugging is-a Structure in Networked Taxonomies2011In: Demo proceeding of the 10th International Semantic Web Conference, 2011Conference paper (Refereed)
  • 2.
    Lambrix, Patrick
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Liu, Qiang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Debugging is-a structure in networked taxonomies,2011In: Proceedings of the Fourth International Workshop on Semantic Web Applications and Tools for Life Sciences, Association for Computing Machinery (ACM), 2011, 58-65 p.Conference paper (Refereed)
    Abstract [en]

    With the proliferation of ontologies and their use in semantically-enabled applications, the issue of finding and repairing defects in ontologies has become increasingly important. In this paper we address the problem of defects in the is-a structure of taxonomies, the currently most frequently used kind of ontologies. We deal with both missing is-a relations as well as existing wrong is-a relations. The context of our study is a taxonomy network consisting of taxonomies networked by correct mappings. We propose a semi-automatic ontology debugging approach, which supports domain experts in debugging the is-a structure in taxonomies. We develop algorithms to detect and repair wrong and missing is-a relations. Further, we discuss an implemented system, RepOSE, and an experiment on real-world ontologies.

  • 3.
    Lambrix, Patrick
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Liu, Qiang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Debugging the missing is-a structure within taxonomies networked by partial reference alignments2013In: Data & Knowledge Engineering, ISSN 0169-023X, E-ISSN 1872-6933, Vol. 86, 179-205 p.Article in journal (Refereed)
    Abstract [en]

    With the proliferation of ontologies and their use in semantically-enabled applications, the issue of finding and repairing defects in ontologies has become increasingly important. Current work mostly targets debugging semantic defects in ontologies. In our work, we focus on another kind of severe defects, modeling defects, which require domain knowledge to detect and resolve. In particular, we debug the missing structural relations (is-a hierarchy) in a fundamental kind of ontologies, i.e. taxonomies. The context of our study is an ontology network consisting of several taxonomies networked by partial reference alignments. We use the ontology network as domain knowledge to detect the missing is-a relations in these ontologies. We also propose algorithms to generate possible repairing actions, rank missing is-a relations, recommend and execute repairing actions. Further, we discuss an implemented system RepOSE and experiments on ontologies of the Ontology Alignment Evaluation Initiative and the Finnish Ontology Library Service.

  • 4.
    Lambrix, Patrick
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Liu, Qiang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Using partial reference alignments to align ontologies2009In: Proceedings of the 6th European Semantic Web Conference - ESWC09, Springer Berlin/Heidelberg, 2009, Vol. 5554 LNCS, 188-202 p.Chapter in book (Refereed)
    Abstract [en]

    In different areas ontologies have been developed and many of these ontologies contain overlapping information. Often we would therefore want to be able to use multiple ontologies. To obtain good results, we need to find the relationships between terms in the different ontologies, i.e. we need to align them. Currently, there already exist a number of ontology alignment systems. In these systems an alignment is computed from scratch. However, recently, some situations have occurred where a partial reference alignment is available, i.e. some of the correct mappings between terms are given or have been obtained. In this paper we investigate whether and how a partial reference alignment can be used in ontology alignment. We use partial reference alignments to partition ontologies, to compute similarities between terms and to filter mapping suggestions. We test the approaches on previously developed gold standards and discuss the results.

  • 5.
    Lambrix, Patrick
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Liu, Qiang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Tan, He
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    A system for repairing missing is-a structure in ontologies2009In: Semantic Web Applications and Tools for Life Sciences, 2009Conference paper (Refereed)
  • 6.
    Lambrix, Patrick
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Liu, Qiang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Tan, He
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Aligning anatomy ontologies in the Ontology Alignment Evaluation Initiative2009In: 25th Workshop of the Swedish Artificial Intelligence Society, 2009, 13-20 p.Conference paper (Refereed)
  • 7.
    Lambrix, Patrick
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Liu, Qiang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Tan, He
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Repairing the missing is-a structure of ontologies2009In: Proceedings of the 4th Asian Semantic Web Conference - ASWC09, Springer Berlin/Heidelberg, 2009, 1, 76-90 p.Chapter in book (Refereed)
    Abstract [en]

    Developing ontologies is not an easy task and often the resultingontologies are not consistent or complete. Such ontologies,although often useful, also lead to problems when used insemantically-enabled applications. Wrong conclusions may bederived or valid conclusions may be missed. To deal with thisproblem we may want to repair the ontologies. Up to date most workhas been performed on finding and repairing the semantic defectssuch as unsatisfiable concepts and inconsistent ontologies. Inthis paper we tackle the problem of repairing modeling defects andin particular, the repairing of structural relations (is-ahierarchy) in the ontologies. We study the case where missing is-arelations are given. We define the notion of a structural repairand develop algorithms to compute repairing actions that wouldallow deriving the missing is-a relations in the repairedontology. Further, we define preferences between repairs. We alsolook at how we can use external knowledge to recommend repairingactions to a domain expert. Further, we discuss an implementedprototype and its use as well as an experiment using theontologies of the Anatomy track of the Ontology AlignmentEvaluation Initiative.

  • 8.
    Lambrix, Patrick
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Liu, Qiang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Tan, He
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    RepOSE: an environment for repairing missing ontological structure2009In: The Semantic Web: Fourth Asian Conference, ASWC 2009, Shanghai, China, December 6-9, 2009. Proceedings, Springer Berlin/Heidelberg, 2009, 1, 365-366 p.Chapter in book (Refereed)
    Abstract [en]

    Developing ontologies is not an easy task and often the resultingontologies are not consistent or complete. Such ontologies,although often useful, also lead to problems when used insemantically-enabled applications. Wrong conclusions may bederived or valid conclusions may be missed. To deal with thisproblem we may want to repair the ontologies. Up to date most workhas been performed on finding and repairing the semantic defectssuch as unsatisfiable concepts and inconsistent ontologies. Inthis paper we tackle the problem of repairing modeling defects andin particular, the repairing of structural relations (is-ahierarchy) in the ontologies. We study the case where missing is-arelations are given. We define the notion of a structural repairand develop algorithms to compute repairing actions that wouldallow deriving the missing is-a relations in the repairedontology. Further, we define preferences between repairs. We alsolook at how we can use external knowledge to recommend repairingactions to a domain expert. Further, we discuss an implementedprototype and its use as well as an experiment using theontologies of the Anatomy track of the Ontology AlignmentEvaluation Initiative.

  • 9.
    Lambrix, Patrick
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Tan, He
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Liu, Qiang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    SAMBO and SAMBOdtf results for the Ontology Alignment Evaluation Initiative 20082008In: Third International Workshop on Ontology Matching, 2008, 190-198 p.Conference paper (Refereed)
  • 10.
    Liu, Qiang
    Linköping University, Department of Computer and Information Science, Database and information techniques.
    Dealing with Missing Mappings and Structure in a Network of Ontologies2011Licentiate thesis, monograph (Other academic)
    Abstract [en]

    With the popularity of the World Wide Web, a large amount of data is generated and made available through the Internet everyday. To integrate and query this huge amount of heterogeneous data, the vision of Semantic Web has been recognized as a possible solution. One key technology for the Semantic Web is ontologies. Many ontologies have been developed in recent years. Meanwhile, due to the demand of applications using multiple ontologies,  mappings between entities of these ontologies are generated as well, which leads to the generation of ontology networks consisting of ontologies and mappings between these ontologies. However, neither developing ontologies nor finding mappings between ontologies is an easy task. It may happen that the ontologies are not consistent or complete, or the mappings between these ontologies are not correct or complete, or the resulting ontology network is not consistent. This may lead to problems when they are used in semantically-enabled applications.

    In this thesis, we address two issues relevant to the quality of the mappings and the structure in the ontology network. The first issue deals with the missing mappings between networked ontologies. Assuming existing mappings between ontologies are correct, we investigate whether and how to use these existing mappings, to find more mappings between ontologies. We propose and test several strategies of using the given correct mappings to align ontologies. The second issue deals with the missing structure, in particular missing is-a relations, in networked ontologies. Based on the assumption that missing is-a relations are a kind of modeling defects, we propose an ontology debugging approach to tackle this issue. We develop an algorithm for detecting missing is-a relations in ontologies, as well as algorithms which assist the user in repairing by generating and recommending possible ways of repairing and executing the repairing. Based on this approach, we develop a system and test its use and performance.

  • 11.
    Liu, Qiang
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    A system for debugging missing is-a structure in networked ontologies2010In: Proceedings of the Seventh International Conference on Data Integration in the Life Sciences / [ed] Patrick Lambrix, Graham Kemp, Springer Berlin/Heidelberg, 2010, 50-57 p.Chapter in book (Refereed)
    Abstract [en]

    Ontologies are recognized as a key technology for semantics-based integration of the many available biomedical data sources. However, developing ontologies is not an easy task and the resulting ontologies may have defects affecting the results of ontology-based data integration and retrieval. In this paper we present a system for debugging ontologies regarding an important kind of modeling defects. Our system supports a domain expert to detect and repair missing is-a structure in ontologies in a semi-automatic way. The input for our system is a set of ontologies networked by correct mappings between their terms. Our tool uses the ontologies and mappings as domain knowledge to detect missing is-a relations in these ontologies. It also assists the user in repairing the ontologies by generating and recommending possible ways of repairing and executing the chosen repairing strategy. The detection and repairing phases can be interleaved. We present our approach, an implemented system as well as an experiment with two anatomy ontologies.

  • 12.
    Liu, Qiang
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Debugging the missing is-a structure of networked ontologies2010In: The Semantic Web: Research and Applications: 7th Extended Semantic Web Conference, ESWC 2010, Heraklion, Crete, Greece, May 30 – June 3, 2010, Proceedings, Part II, Springer Berlin/Heidelberg, 2010, 478-482 p.Chapter in book (Refereed)
    Abstract [en]

    In parallel with the proliferation of ontologies and their use in semantically-enabled applications, the issue of finding and dealing with defects in ontologies has become increasingly important. Current work mostly targets detecting and repairing semantic defects in ontologies. In our work, we focus on another kind of severe defects, modeling defects, which require domain knowledge to detect and resolve. In particular, we are interested in detecting and repairing the missing structural relations (is-a hierarchy) in the ontologies. Our goal is to develop a system, which allows a domain expert to detect and repair the structure of ontologies in a semi-automatic way.

1 - 12 of 12
CiteExportLink to result list
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Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • oxford
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf