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  • 1.
    Cheatham, Michelle
    et al.
    Wright State University, USA.
    Dragisic, Zlatan
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Euzenat, Jerome
    INRIA, France; Univ. Grenoble Alpes, Grenoble, France.
    Faria, Daniel
    Instituto Gulbenkian de Ciencia, Lisbon, Portugal.
    Ferrara, Alfio
    Universita degli studi di Milano, Italy.
    Flouris, Giorgios
    Institute of Computer Science-FORTH, Heraklion, Greece.
    Fundulaki, Irini
    Institute of Computer Science-FORTH, Heraklion, Greece.
    Granada, Roger
    IRIT, France; Universite Toulouse II, Toulouse, France.
    Ivanova, Valentina
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Jimenez-Ruiz, Ernesto
    University of Oxford, UK.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Montanelli, Stefano
    Universita degli studi di Milano, Italy.
    Pesquita, Catia
    LASIGE, Faculdade de Ciencias, Universidade de Lisboa, Portugal .
    Saveta, Tzanina
    Institute of Computer Science-FORTH, Heraklion, Greece.
    Shvaiko, Pavel
    TasLab, Informatica Trentina, Trento, Italy.
    Solimando, Allesandro
    INRIA-Saclay, France; Univ. Paris-Sud, Orsay, France.
    Trojahn, Cassia
    IRIT, France; Universite Toulouse II, Toulouse, France.
    Zamazal, Ondrej
    University of Economics, Prague, Czech Republic.
    Results of the Ontology Alignment Evaluation Initiative 20152015In: Ontology Matching, 2015, p. 60-115Conference paper (Refereed)
  • 2.
    Chiatti, Agnese
    et al.
    Politecnico di Torino, Italy.
    Dragisic, Zlatan
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Cerquitelli, Tania
    Politecnico di Torino, Italy.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Reducing the search space in ontology alignment using clustering techniques and topic identification2015In: Proceedings of the 8th International Conference on Knowledge Capture, New York: ACM Digital Library, 2015, p. 21-Conference paper (Refereed)
    Abstract [en]

    One of the current challenges in ontology alignment is scalability and one technique to deal with this issue is to reduce the search space for the generation of mapping suggestions. In this paper we develop a method to prune that search space by using clustering techniques and topic identification. Further, we provide experiments showing that we are able to generate partitions that allow for high quality alignments with a highly reduced effort for computation and validation of mapping suggestions for the parts of the ontologies in the partition. Other techniques will still be needed for finding mappings that are not in the partition.

  • 3.
    Cuenca Grau, Bernardo
    et al.
    University of Oxford, UK.
    Dragisic, Zlatan
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Eckert, Kai
    University of Mannheim, Germany.
    Euzenat, Jerome
    INRIA, France.
    Ferrara, Alfio
    Universita degli studi di Milano, Italy.
    Granada, Roger
    Pontifıcia Universidade Catolica do Rio Grande do Sul, Porto Alegre, Brazil.
    Ivanova, Valentina
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Jimenez-Ruiz, Ernesto
    University of Oxford, UK.
    Kempf, Oscar Alexander
    Leibniz Institute for the Social Sciences, Cologne, Germany.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Nikolov, Andriy
    Fluid operations, Walldorf, Germany.
    Paulheim, Heiko
    University of Mannheim, Germany.
    Ritze, Dominique
    University of Mannheim, Germany.
    Scharffe, Francois
    LIRMM, Montpellier, France.
    Shvaiko, Pavel
    Informatica Trentina, Trento, Italy.
    Trojahn, Cassia
    Universite Toulouse II, Toulouse, France.
    Zamazal, Ondrej
    University of Economics, Prague, Czech Republic.
    Results of the Ontology Alignment Evaluation Initiative 20132013In: International Workshop on Ontology Matching, 2013, p. 61-100Conference paper (Refereed)
  • 4.
    Dragisic, Zlatan
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Completing the Is-a Structure in Description Logics Ontologies2014Licentiate thesis, monograph (Other academic)
    Abstract [en]

    The World Wide Web contains large amounts of data and in most cases this data is without any explicit structure. The lack of structure makes it difficult for automated agents to understand and use such data. A step towards a more structured World Wide Web is the idea of the Semantic Web which aims at introducing semantics to data on the World Wide Web. One of the key technologies in this endeavour are ontologies which provide means for modeling a domain of interest.

    Developing and maintaining ontologies is not an easy task and it is often the case that defects are introduced into ontologies. This can be a problem for semantically-enabled applications such as ontology-based querying. Defects in ontologies directly influence the quality of the results of such applications as correct results can be missed and wrong results can be returned.

    This thesis considers one type of defects in ontologies, namely the problem of completing the is-a structure in ontologies represented in description logics. We focus on two variants of description logics, the EL family and ALC, which are often used in practice.

    The contributions of this thesis are as follows. First, we formalize the problem of completing the is-a structure as a generalized TBox abduction problem (GTAP) which is a new type of abduction problem in description logics. Next, we provide algorithms for solving GTAP in the EL family and ALC description logics. Finally, we describe two implemented systems based on the introduced algorithms. The systems were evaluated in two experiments which have shown the usefulness of our approach. For example, in one experiment using ontologies from the Ontology Alignment Evaluation Initiative 58 and 94 detected missing is-a relations were repaired by adding 54 and 101 is-a relations, respectively, introducing new knowledge to the ontologies.

  • 5.
    Dragisic, Zlatan
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Eckert, Kai
    University of Mannheim, Mannheim, Germany.
    Euzenat, Jerome
    INRIA, France; University of Grenoble-Alpes, Grenoble, France.
    Faria, Daniel
    Universidade de Lisboa, Portugal.
    Ferrara, Alfio
    Universita degli studi di Milano, Italy.
    Granada, Roger
    Pontifıcia Universidade Catolica do Rio Grande do Sul, Porto Alegre, Brazil; IRIT & Universite Toulouse II, Toulouse, France.
    Ivanova, Valentina
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Jimenez-Ruiz, Ernesto
    University of Oxford, UK.
    Kempf, Andreas
    Leibniz Institute for the Social Sciences, Cologne, Germany.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Montanelli, Stefano
    Universita degli studi di Milano, Italy.
    Paulheim, Heiko
    University of Mannheim, Mannheim, Germany.
    Ritze, Dominique
    University of Mannheim, Mannheim, Germany.
    Shvaiko, Pavel
    Informatica Trentina, Trento, Italy.
    Solimando, Alessandro
    University of Genova, Italy.
    Trojahn, Cassia
    IRIT, France; Universite Toulouse II, Toulouse, France.
    Zamazal, Ondrej
    University of Economics, Prague, Czech Republic.
    Cuenca Grau, Bernardo
    University of Oxford, UK.
    Results of the Ontology Alignment Evaluation Initiative 20142014In: International Workshop on Ontology Matching, 2014, p. 61-104Conference paper (Refereed)
    Abstract [en]

    Ontology matching consists of finding correspondences between se-mantically related entities of two ontologies. OAEI campaigns aim at comparingontology matching systems on precisely defined test cases. These test cases canuse ontologies of different nature (from simple thesauri to expressive OWL on-tologies) and use different modalities, e.g., blind evaluation, open evaluation andconsensus. OAEI 2014 offered 7 tracks with 9 test cases followed by 14 partici-pants. Since 2010, the campaign has been using a new evaluation modality which provides more automation to the evaluation. This paper is an overall presentationof the OAEI 2014 campaign.

  • 6.
    Dragisic, Zlatan
    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.
    Blomqvist, Eva
    Linköping University, Department of Computer and Information Science, Human-Centered systems. Linköping University, Faculty of Science & Engineering.
    Integrating Ontology Debugging and Matching into the eXtreme Design Methodology2015In: Proceedings of the 6th Workshop on Ontology and Semantic Web Patterns (WOP 2015) / [ed] Eva Blomqvist; Pascal Hitzler; Adila Krisnadhi; Tom Narock; Monika Solanki, Rheinisch-Westfaelische Technische Hochschule Aachen University , 2015Conference paper (Refereed)
    Abstract [en]

    Ontology design patterns (ODPs) and related ontology development methodologies were designed as ways of sharing and reusing best practices in ontology engineering. However, while the use of these reduces the number of issues in the resulting ontologies defects can still be introduced into the ontology due to improper use or misinterpretation of the patterns. Thus, the quality of the developed ontologies is still a major concern. In this paper we address this issue by describing how ontology debugging and matching can be integrated in a state-of-the-art ontology development methodology based on ontology design patterns- the eXtreme Design methodology, and show the advantages in a case study based on a real world ontology.

  • 7.
    Dragisic, Zlatan
    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.
    Wei-Kleiner, Fang
    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 EL Ontologies2014In: Proceedings of the Third International Workshop on Debugging Ontologies and Ontology Mappings - WoDOOM14, 2014, p. 51-58Conference paper (Refereed)
  • 8.
    Dragisic, Zlatan
    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.
    Wei-Kleiner, Fang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Completing the is-a structure of biomedical ontologies2014In: Data Integration in the Life Sciences 10th International Conference, DILS 2014, Lisbon, Portugal, July 17-18, 2014. Proceedings / [ed] Helena Galhardas, Erhard Rahm, Berlin: Springer Science+Business Media B.V., 2014, p. 66-80Conference paper (Refereed)
    Abstract [en]

    Ontologies in the biomedical domain are becoming a key element for data integration and search. The usefulness of the applications which use ontologies is often directly influenced by the quality of ontologies, as incorrect or incomplete ontologies might lead to wrong or incomplete results for the applications. Therefore, there is an increasing need for repairing defects in ontologies. In this paper we focus on completing ontologies. We provide an algorithm for completing the is-a structure in TeX ontologies which covers many biomedical ontologies. Further, we present an implemented system based on the algorithm as well as an evaluation using three biomedical ontologies.

  • 9.
    Heintz, Fredrik
    et al.
    Linköping University, Department of Computer and Information Science, KPLAB - Knowledge Processing Lab. Linköping University, The Institute of Technology.
    Dragisic, Zlatan
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Semantic Information Integration for Stream Reasoning2012In: Proceedings of the 15th International Conference on Information Fusion (FUSION), Linköping: Linköping University Electronic Press, 2012Conference paper (Other academic)
    Abstract [en]

    The main contribution of this paper is a practicalsemantic information integration approach for stream reasoningbased on semantic matching. This is an important functionality for situation awareness applications where temporal reasoning over streams from distributed sources is needed. The integration is achieved by creating a common ontology, specifying the semantic content of streams relative to the ontology and then use semantic matching to find relevant streams. By using semantic mappings between ontologies it is also possible to do semantic matching over multiple ontologies. The complete stream reasoning approach is integrated in the Robot Operating System(ROS) and used in collaborative unmanned aircraft systems missions.

  • 10.
    Lambrix, Patrick
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Dragisic, Zlatan
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Ivanova, Valentina
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Get my pizza right: Repairing missing is-a relations in ALC ontologies2012In: Second Joint International Semantic Technology Conference, Springer Berlin/Heidelberg, 2012, p. 17-32Conference paper (Refereed)
    Abstract [en]

    With the increased use of ontologies in semantically-enabled applications, the issue of debugging defects in ontologies has become increasingly important. These defects can lead to wrong or incomplete results for the applications. Debugging consists of the phases of detection and repairing. In this paper we focus on the repairing phase of a particular kind of defects, i.e. the missing relations in the is-a hierarchy. Previous work has dealt with the case of taxonomies. In this work we extend the scope to deal with ALC ontologies that can be represented using acyclic terminologies. We present algorithms and discuss a system.

  • 11.
    Lambrix, Patrick
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Ivanova, Valentina
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Dragisic, Zlatan
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Contributions of LiU/ADIT to Debugging Ontologies and Ontology Mappings2012In: Advances in secure and networked information systems: the ADIT perspective ; Festschrift in honor of professor Nahid Shahmehri / [ed] Patrick Lambrix, Linköping: Linköping University Electronic Press, 2012, p. 109-120Chapter in book (Other academic)
    Abstract [en]

    This book contains contributions by current and former colleagues and PhD students of professor Nahid Shahmehri in celebration of her 60th birthday. Although it would be difficult to cover the full range of her academic contributions, we have at least been able to hint the importance and the breadth of her work. We have chosen the title ‘Advances in Secure and Networked Information Systems - The ADIT Perspective’ as many of the contributions of Nahid and her group have been in these areas, given a fairly broad interpretation of “networked information systems”. In this collection we have gathered both republications of past work as well as newly written articles.

  • 12.
    Lambrix, Patrick
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology. Swedish e-Science Research Centre, Linköping University, Sweden .
    Wei-Kleiner, Fang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Dragisic, Zlatan
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Completing the is-a structure in light-weight ontologies2015In: Journal of Biomedical Semantics, ISSN 2041-1480, E-ISSN 2041-1480, Vol. 6, article id 12Article in journal (Refereed)
    Abstract [en]

     Background: With the increasing presence of biomedical data sources on the Internet more and more research effort is put into finding possible ways for integrating and searching such often heterogeneous sources. Ontologies are a key technology in this effort. However, developing ontologies is not an easy task and often the resulting ontologies are not complete. In addition to being problematic for the correct modelling of a domain, such incomplete ontologies, when used in semantically-enabled applications, can lead to valid conclusions being missed.

    Results: We consider the problem of repairing missing is-a relations in ontologies. We formalize the problem as a generalized TBox abduction problem. Based on this abduction framework, we present complexity results for the existence, relevance and necessity decision problems for the generalized TBox abduction problem with and without some specific preference relations for ontologies that can be represented using a member of the EL family of description logics. Further, we present algorithms for finding solutions, a system as well as experiments.

    Conclusions: Semantically-enabled applications need high quality ontologies and one key aspect is their completeness. We have introduced a framework and system that provides an environment for supporting domain experts to complete the is-a structure of ontologies. We have shown the usefulness of the approach in different experiments. For the two Anatomy ontologies from the Ontology Alignment Evaluation Initiative, we repaired 94 and 58 initial given missing is-a relations, respectively, and detected and repaired additionally, 47 and 10 missing is-a relations. In an experiment with BioTop without given missing is-a relations, we detected and repaired 40 new missing is-a relations.

  • 13.
    Lambrix, Patrick
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Wei-Kleiner, Fang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Dragisic, Zlatan
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Ivanova, Valentina
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Repairing missing is-a structure in ontologies is an abductive reasoning problem2013In: Proceedings of the Second International Workshop on Debugging Ontologies and Ontology Mappings / [ed] Patrick Lambrix; Guilin Qi; Matthew Horridge; Bijan Parsia, Rheinisch-Westfaelische Technische Hochschule Aachen University , 2013, p. 33-44Conference paper (Refereed)
    Abstract [en]

    With the increased use of ontologies in semantically-enabled applications, the issue of debugging defects in ontologies has become increasingly important. These defects can lead to wrong or incomplete results for the applications. Debugging consists of the phases of detection and repairing. In this paper we focus on the repairing phase of a particular kind of defects, i.e., the missing relations in the is-a hierarchy. We show that this can be formalized as an abduction problem. Further, we define properties for the ontology, the set of is-a relations to repair and the domain expert, as well as preference criteria on solutions and discuss the influences of these properties and criteria on the existence of solutions for the abduction problem. We also discuss the consequences of our analyses of the repairing problem for the development and use of debugging systems.

  • 14.
    Wei-Kleiner, Fang
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Dragisic, Zlatan
    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.
    Abduction Framework for Repairing Incomplete EL Ontologies:  Complexity Results and Algorithms2014In: Proceedings of the 28th AAAI Conference on Artificial Intelligence, Palo Alto, CA, USA: AAAI Press, 2014, p. 1120-1127Conference paper (Refereed)
    Abstract [en]

    In this paper we consider the problem of repairing  missing is-a relations in ontologies.We formalize the problem as a generalized TBox abduction problem (GTAP). Based on this abduction framework, we  present complexity results for the existence, relevance and necessity decision problems for the GTAP with and without some specific preference relations for ontologies that can be represented using a member of the EL family of description logics. Further, we present algorithms for finding solutions, a system as well as experiments.

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