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  • 1.
    Achichi, Manel
    et al.
    LIRMM/University of Montpellier, France.
    Cheatham, Michelle
    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 & Univ. Grenoble Alpes, Grenoble, France.
    Faria, Daniel
    Instituto Gulbenkian de Ciencia, Lisbon, Portugal.
    Ferrara, Alfio
    Universita degli studi di Milano, Italy.
    Flouris, Giorgos
    Institute of Computer Science-FORTH, Heraklion, Greece.
    Fundulaki, Irini
    Institute of Computer Science-FORTH, Heraklion, Greece.
    Harrow, Ian
    Pistoia Alliance Inc., USA.
    Ivanova, Valentina
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Jiménez-Ruiz, Ernesto
    University of Oslo, Norway and University of Oxford, UK.
    Kuss, Elena
    University of Mannheim, Germany.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Leopold, Henrik
    Vrije Universiteit Amsterdam, The Netherlands.
    Li, Huanyu
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, Faculty of Science & Engineering.
    Meilicke, Christian
    University of Mannheim, Germany.
    Montanelli, Stefano
    Universita degli studi di Milano, Italy.
    Pesquita, Catia
    Universidade de Lisboa, Portugal.
    Saveta, Tzanina
    Institute of Computer Science-FORTH, Heraklion, Greece.
    Shvaiko, Pavel
    TasLab, Informatica Trentina, Trento, Italy.
    Splendiani, Andrea
    Novartis Institutes for Biomedical Research, Basel, Switzerland.
    Stuckenschmidt, Heiner
    University of Mannheim, Germany.
    Todorov, Konstantin
    LIRMM/University of Montpellier, France.
    Trojahn, Cassia
    IRIT & Universit ́ e Toulouse II, Toulouse, France.
    Zamazal, Ondřej
    University of Economics, Prague, Czech Republic.
    Results of the Ontology Alignment Evaluation Initiative 20162016In: Proceedings of the 11th International Workshop on Ontology Matching, Aachen, Germany: CEUR Workshop Proceedings , 2016, 73-129 p.Conference paper (Refereed)
  • 2.
    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 & Universite Toulouse II, Toulouse, France.
    Zamazal, Ondrej
    University of Economics, Prague, Czech Republic.
    Results of the Ontology Alignment Evaluation Initiative 20152015In: Ontology Matching, 2015, 60-115 p.Conference paper (Refereed)
  • 3.
    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, 21- p.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.

  • 4.
    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, 61-100 p.Conference paper (Refereed)
  • 5.
    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.

  • 6.
    Dragisic, Zlatan
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, Faculty of Science & Engineering.
    Completion of Ontologies and Ontology Networks2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The World Wide Web contains large amounts of data, and in most cases this data has no 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 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 a means for modeling a domain of interest and are used for search and integration of data.

    In recent years many ontologies have been developed. To be able to use multiple ontologies it is necessary to align them, i.e., find inter-ontology relationships. However, developing and aligning ontologies is not an easy task and it is often the case that ontologies and their alignments are incorrect and incomplete. This can be a problem for semantically-enabled applications. Incorrect and incomplete ontologies and alignments directly influence the quality of the results of such applications, as wrong results can be returned and correct results can be missed. This thesis focuses on the problem of completing ontologies and ontology networks.

    The contributions of the thesis are threefold. First, we address the issue of completing the is-a structure and alignment in ontologies and ontology networks. We have formalized the problem of completing the is-a structure in ontologies as an abductive reasoning problem and developed algorithms as well as systems for dealing with the problem. With respect to the completion of alignments, we have studied system performance in the Ontology Alignment Evaluation Initiative, a yearly evaluation campaign for ontology alignment systems. We have also addressed the scalability of ontology matching, which is one of the current challenges, by developing an approach for reducing the search space when generating the alignment.Second, high quality completion requires user involvement. As users' time and effort are a limited resource we address the issue of limiting and facilitating user interaction in the completion process. We have conducted a broad study of state-of-the-art ontology alignment systems and identified different issues related to the process. We have also conducted experiments to assess the impact of user errors in the completion process.

    While the completion of ontologies and ontology networks can be done at any point in the life-cycle of ontologies and ontology networks, some of the issues can be addressed already in the development phase. The third contribution of the thesis addresses this by introducing ontology completion and ontology alignment into an existing ontology development methodology.

    List of papers
    1. Completing the is-a structure in light-weight ontologies
    Open this publication in new window or tab >>Completing the is-a structure in light-weight ontologies
    2015 (English)In: Journal of Biomedical Semantics, ISSN 2041-1480, Vol. 6, 12Article in journal (Refereed) Published
    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.

    National Category
    Computer Science Bioinformatics (Computational Biology)
    Identifiers
    urn:nbn:se:liu:diva-116628 (URN)10.1186/s13326-015-0002-8 (DOI)000353197200001 ()25883780 (PubMedID)
    Funder
    Swedish e‐Science Research CenterCUGS (National Graduate School in Computer Science)
    Available from: 2015-03-29 Created: 2015-03-29 Last updated: 2017-08-21
    2. Get my pizza right: Repairing missing is-a relations in ALC ontologies
    Open this publication in new window or tab >>Get my pizza right: Repairing missing is-a relations in ALC ontologies
    2012 (English)In: Second Joint International Semantic Technology Conference, Springer Berlin/Heidelberg, 2012, 17-32 p.Chapter in book (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.

    Place, publisher, year, edition, pages
    Springer Berlin/Heidelberg, 2012
    Series
    Lecture Notes in Computer Science, ISSN 0302-9743 (print), 1611-3349 (online) ; 7774
    Keyword
    ontologies, ontology engineering, ontology debugging, knowledge representation
    National Category
    Computer Science
    Identifiers
    urn:nbn:se:liu:diva-91435 (URN)10.1007/978-3-642-37996-3_2 (DOI)978-3-642-37995-6 (ISBN)978-3-642-37996-3 (ISBN)
    Funder
    Swedish e‐Science Research CenterSwedish Research Council, 2010-4759CUGS (National Graduate School in Computer Science)
    Available from: 2013-04-24 Created: 2013-04-24 Last updated: 2017-08-21
    3. Reducing the search space in ontology alignment using clustering techniques and topic identification
    Open this publication in new window or tab >>Reducing the search space in ontology alignment using clustering techniques and topic identification
    2015 (English)In: Proceedings of the 8th International Conference on Knowledge Capture, New York: ACM Digital Library, 2015, 21- p.Conference paper, Published 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.

    Place, publisher, year, edition, pages
    New York: ACM Digital Library, 2015
    Keyword
    Knowledge representation, data mining, ontology alignment
    National Category
    Computer Science
    Identifiers
    urn:nbn:se:liu:diva-121838 (URN)10.1145/2815833.2816959 (DOI)978-1-4503-3849-3 (ISBN)
    Conference
    8th International Conference on Knowledge Capture
    Funder
    CUGS (National Graduate School in Computer Science)Swedish e‐Science Research CenterEU, FP7, Seventh Framework Programme, FP7-IP-608142
    Available from: 2015-10-09 Created: 2015-10-09 Last updated: 2017-08-21
    4. Experiences from the Anatomy track in the Ontology Alignment Evaluation Initiative
    Open this publication in new window or tab >>Experiences from the Anatomy track in the Ontology Alignment Evaluation Initiative
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Background: One of the longest running tracks in the Ontology Alignment Evaluation Initiative is the Anatomy track which focuses on aligning two anatomy ontologies. The Anatomy track was started in 2005. In 2005 and 2006 the task in this track was to align the Foundational Model of Anatomy and the OpenGalen Anatomy Model. Since 2007 the ontologies used in the track are the Adult Mouse Anatomy and a part of the NCI Thesaurus. Since 2015 the data in the Anatomy track is also used in the Interactive track of the Ontology Alignment Evaluation Initiative.

    Results: In this paper we focus on the Anatomy track in the years 2007-2016 and the Anatomy part of the Interactive track in 2015-2016. We describe the data set and the changes it went through during the years. Further, we give an overview of all systems that participated in the track and the techniques they have used. We discuss the performance results of the systems and summarize the general trends.

    Conclusions: About 50 systems have participated in the Anatomy track. Many different techniques were used. The most popular matching techniques are string-based strategies and structure-based techniques. Many systems also use auxiliary information. The quality of the alignment has increased for the best performing systems since the beginning of the track and more and more systems check the coherence of the proposed alignment and implement a repair strategy.Further, interacting with an oracle is beneficial.

    Keyword
    ontologies, ontology matching, OAEI, anatomy
    National Category
    Computer Science
    Identifiers
    urn:nbn:se:liu:diva-139775 (URN)
    Funder
    Swedish e‐Science Research CenterCUGS (National Graduate School in Computer Science)EU, FP7, Seventh Framework Programme, FP7-IP-608142
    Available from: 2017-08-21 Created: 2017-08-21 Last updated: 2017-08-30
    5. User validation in ontology alignment
    Open this publication in new window or tab >>User validation in ontology alignment
    Show others...
    2016 (English)In: The Semantic Web - ISWC 2016: 15th International Semantic Web Conference, Kobe, Japan, October 17–21, 2016, Proceedings, Part I / [ed] Paul Groth, Elena Simperl, Alasdair Gray, Marta Sabou, Markus Krötzsch, Freddy Lecue, Fabian Flöck and Yolanda Gil, Cham, Switzerland: Springer Publishing Company, 2016, 200-217 p.Chapter in book (Refereed)
    Abstract [en]

    User validation is one of the challenges facing the ontology alignment community, as there are limits to the quality of automated alignment algorithms. In this paper we present a broad study on user validation of ontology alignments that encompasses three distinct but interrelated aspects: the profile of the user, the services of the alignment system, and its user interface. We discuss key issues pertaining to the alignment validation process under each of these aspects, and provide an overview of how current systems address them. Finally, we use experiments from the Interactive Matching track of the Ontology Alignment Evaluation Initiative (OAEI) 2015 to assess the impact of errors in alignment validation, and how systems cope with them as function of their services.

    Place, publisher, year, edition, pages
    Cham, Switzerland: Springer Publishing Company, 2016
    Series
    Lecture Notes in Computer Science, ISSN 0302-9743, E-ISSN 1611-3349 ; 9981
    Keyword
    knowledge representation, user interfaces, ontology engineering, ontology alignment
    National Category
    Computer Science
    Identifiers
    urn:nbn:se:liu:diva-131806 (URN)10.1007/978-3-319-46523-4_13 (DOI)000389086500013 ()9783319465227 (ISBN)9783319465234 (ISBN)
    Funder
    Swedish e‐Science Research CenterCUGS (National Graduate School in Computer Science)EU, FP7, Seventh Framework Programme, FP7-IP-608142
    Available from: 2016-10-07 Created: 2016-10-07 Last updated: 2017-08-25Bibliographically approved
    6. Integrating Ontology Debugging and Matching into the eXtreme Design Methodology
    Open this publication in new window or tab >>Integrating Ontology Debugging and Matching into the eXtreme Design Methodology
    2015 (English)In: 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, Published 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.

    Place, publisher, year, edition, pages
    Rheinisch-Westfaelische Technische Hochschule Aachen University, 2015
    Series
    CEUR Workshop Proceedings, ISSN 1613-0073 ; 1461
    National Category
    Media and Communication Technology
    Identifiers
    urn:nbn:se:liu:diva-121794 (URN)
    Conference
    6th Workshop on Ontology and Semantic Web Patterns (WOP 2015), Bethlehem, Pensylvania, USA, October 11, 2015
    Funder
    EU, FP7, Seventh Framework Programme, FP7-IP-608142CUGS (National Graduate School in Computer Science)Swedish e‐Science Research Center
    Available from: 2015-10-06 Created: 2015-10-06 Last updated: 2017-08-21Bibliographically approved
  • 7.
    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, 61-104 p.Conference 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.

  • 8.
    Dragisic, Zlatan
    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.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Faria, Daniel
    Gulbenkian Science Institute, Oeiras, Portugal.
    Jimenez-Ruiz, Ernesto
    University of Oxford, Oxford, UK.
    Pesquita, Catia
    LaSIGE, Faculdade de Ciencias, Universidade de Lisboa, Lisboa, Portugal.
    User validation in ontology alignment2016In: The Semantic Web - ISWC 2016: 15th International Semantic Web Conference, Kobe, Japan, October 17–21, 2016, Proceedings, Part I / [ed] Paul Groth, Elena Simperl, Alasdair Gray, Marta Sabou, Markus Krötzsch, Freddy Lecue, Fabian Flöck and Yolanda Gil, Cham, Switzerland: Springer Publishing Company, 2016, 200-217 p.Chapter in book (Refereed)
    Abstract [en]

    User validation is one of the challenges facing the ontology alignment community, as there are limits to the quality of automated alignment algorithms. In this paper we present a broad study on user validation of ontology alignments that encompasses three distinct but interrelated aspects: the profile of the user, the services of the alignment system, and its user interface. We discuss key issues pertaining to the alignment validation process under each of these aspects, and provide an overview of how current systems address them. Finally, we use experiments from the Interactive Matching track of the Ontology Alignment Evaluation Initiative (OAEI) 2015 to assess the impact of errors in alignment validation, and how systems cope with them as function of their services.

  • 9.
    Dragisic, Zlatan
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, Faculty of Science & Engineering.
    Ivanova, Valentina
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, Faculty of Science & Engineering.
    Li, Huanyu
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, Faculty of Science & Engineering.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, Faculty of Science & Engineering.
    Experiences from the Anatomy track in the Ontology Alignment Evaluation InitiativeManuscript (preprint) (Other academic)
    Abstract [en]

    Background: One of the longest running tracks in the Ontology Alignment Evaluation Initiative is the Anatomy track which focuses on aligning two anatomy ontologies. The Anatomy track was started in 2005. In 2005 and 2006 the task in this track was to align the Foundational Model of Anatomy and the OpenGalen Anatomy Model. Since 2007 the ontologies used in the track are the Adult Mouse Anatomy and a part of the NCI Thesaurus. Since 2015 the data in the Anatomy track is also used in the Interactive track of the Ontology Alignment Evaluation Initiative.

    Results: In this paper we focus on the Anatomy track in the years 2007-2016 and the Anatomy part of the Interactive track in 2015-2016. We describe the data set and the changes it went through during the years. Further, we give an overview of all systems that participated in the track and the techniques they have used. We discuss the performance results of the systems and summarize the general trends.

    Conclusions: About 50 systems have participated in the Anatomy track. Many different techniques were used. The most popular matching techniques are string-based strategies and structure-based techniques. Many systems also use auxiliary information. The quality of the alignment has increased for the best performing systems since the beginning of the track and more and more systems check the coherence of the proposed alignment and implement a repair strategy.Further, interacting with an oracle is beneficial.

  • 10.
    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.

  • 11.
    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, 51-58 p.Conference paper (Refereed)
  • 12.
    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, Berlin: Springer Science+Business Media B.V., 2014, 66-80 p.Chapter in book (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.

  • 13.
    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.

  • 14.
    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, 17-32 p.Chapter in book (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.

  • 15.
    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.
    Anslow, Craig
    Middlesex University, London, UK.
    Visualization for Ontology Evolution2016In: VOILA 2016 Visualization and Interaction for Ontologies and Linked Data: Proceedings of the 2nd  International Workshop on Visualization and Interaction for Ontologies and Linked Data / [ed] Valentina Ivanova; Patrick Lambrix; Steffen Lohmann; Catia Pesquita, Rheinisch-Westfaelische Technische Hochschule Aachen University , 2016, 54-67 p.Conference paper (Refereed)
    Abstract [en]

    One of the challenges for the ontology engineering community is theuser involvement in the engineering process. Ontologies are not static entities andthere is a demand for tools to support the user during the ontology evolution pro-cess. This paper aims to provide a set of functionality requirements for ontologyevolution systems, with a particular focus on the visualization of the ontologies,their versions and information needed for ontology evolution tasks. Further, wereview the current state of the art in ontology evolution systems with respect tothe requirements and the visualization. We also view ontologies as software anddiscuss approaches from the software visualization area that could be used forontology evolution visualization.

  • 16.
    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, 109-120 p.Chapter 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.

  • 17.
    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, Vol. 6, 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.

  • 18.
    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, 33-44 p.Conference 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.

  • 19.
    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, 1120-1127 p.Conference 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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