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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.
    Backofen, Rolf
    et al.
    Friedrich-Schiller-Universität Jena, Germany.
    Badea, Liviu
    National Institute for Research and Development in Informatics, Bucharest, Romania.
    Barahona, Pedro
    Universidade Nova de Lisboa, Portugal.
    Berndtsson, Mikael
    University of Skövde, Sweden.
    Burger, Albert
    Heriot-Watt University/MRC Human GeneticsUnit, Edinburgh, UK.
    Dawelbait, Gihan
    Technische Universität Dresden, Germany.
    Doms, Andreas
    Technische Universität Dresden, Germany.
    Fages, Francois
    INRIA Rocquencourt, Paris, France.
    Hotaran, Anca
    National Institute for Research and Development in Informatics, Bucharest, Romania.
    Jakoniené, Vaida
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems.
    Krippahl, Ludwig
    Universidade Nova de Lisboa, Portugal.
    Lambrix, Patrick
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems.
    McLeod, Kenneth
    Heriot-Watt University/MRC Human GeneticsUnit, Edinburgh, UK.
    Nutt, Werner
    Heriot-Watt University/MRC Human GeneticsUnit, Edinburgh, UK.
    Olsson, Bjorn
    University of Skövde, Sweden.
    Schroeder, Michael
    Technische Universität Dresden, Germany.
    Schroiff, Anna
    University of Skövde, Sweden.
    Royer, Luc
    Technische Universität Dresden, Germany.
    Soliman, Sylvain
    INRIA Rocquencourt, Paris, France.
    Tan, He
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems.
    Tilivea, Doina
    National Institute for Research and Development in Informatics, Bucharest, Romania.
    Will, Sebastian
    Friedrich-Schiller-Universit¨at Jena, Germany.
    Requirements and specification of bioinformatics use cases2005Report (Other academic)
  • 3.
    Backofen, Rolf
    et al.
    Friedrich-Schiller-Universität Jena, Germany.
    Badea, Mike
    Victoria University of Manchester, UK.
    Barahona, Pedro
    Universidade Nova de Lisboa, Portugal.
    Badea, Liviu
    National Institute for Research and Development in Informatics, Bucarest, Romania.
    Bry, Francois
    Ludwig-Maximilians-Universität Munchen, Germany.
    Dawelbait, Gihan
    Technical University of Dresden, Germany.
    Doms, Andreas
    Technical University of Dresden, Germany.
    Fages, Francois
    INRIA Rocquencourt, France.
    Goble, Carol
    Victoria University of Manchester, UK.
    Henschel, Andreas
    Technical University of Dresden, Germany.
    Hotaran, Anca
    National Institute for Research and Development in Informatics, Bucarest, Romania.
    Huang, Bingding
    Technical University of Dresden, Germany.
    Krippahl, Ludwig
    Universidade Nova de Lisboa, Portugal.
    Lambrix, Patrick
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems.
    Nutt, Werner
    Heriot-Watt University, Edinburgh, UK.
    Schroeder, Michael
    Technical University of Dresden, Germany.
    Soliman, Sylvain
    INRIA Rocquencourt, France.
    Will, Sebastian
    Friedrich-Schiller-Universität Jena, Germany.
    Towards a Semantic Web for Bioinformatics2004In: Bioinformatics 2004,2004, 2004, 26-26 p.Conference paper (Other academic)
  • 4.
    Backofen, Rolf
    et al.
    Friedrich-Schiller-Universität Jena, Germany.
    Badea, Mike
    Victoria University of Manchester, UK.
    Burger, Albert
    Harriot-Watt University, Edinburgh, UK.
    Fages, Francois
    INRIA Rocquencourt, France.
    Lambrix, Patrick
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems.
    Nutt, Werner
    Harriot-Watt University, Edinburgh, UK.
    Schroeder, Michael
    Technical University of Dresden, Germany.
    Soliman, Sylvain
    NRIA Rocquencourt, France.
    Will, Sebastian
    Friedrich-Schiller-Universität Jena, Germany.
    State-of-the-art in Bioinformatics2004Report (Other academic)
  • 5.
    Backofen, Rolf
    et al.
    Albert-Ludwigs-universität Freiburg, Germany.
    Burger, Albert
    Heriot-Watt university Edinburgh, UK.
    Busch, Anke
    Albert-Ludwigs-universität Freiburg, Germany.
    Dawelbait, Gihan
    TU Dresden, Germany.
    Fages, Francois
    INRIA Rocquencourt Paris, France.
    Jakoniené, Vaida
    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.
    McLeod, Kenneth
    Heriot-Watt university Edinburgh, UK.
    Soliman, Sylvain
    INRIA Rocquencourt Paris, France.
    Tan, He
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Will, Sebastian
    Albert-Ludwigs-universität Freiburg, Germany.
    Implementation of prototypes2007Report (Other academic)
  • 6.
    Backofen, Rolf
    et al.
    Friedrich-Schiller-Universität Jena, Germany.
    Mike, Badea
    Victoria University of Manchester, UK.
    Barahona, Pedro
    FCT-UNL, Lisbon.
    Burger, Albert
    Harriot-Watt University, Edinburgh, UK.
    Dawelbait, Gihan
    Technical University of Dresden, Germany.
    Doms, Andreas
    Technical University of Dresden, Germany.
    Fages, Francois
    INRIA Rocquencourt, France.
    Hotaran, Anca
    National Institute for Research and Development in Informatics, Romania.
    Jakoniené, Vaida
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems.
    Krippahl, Ludwig
    FCT-UNL, Lisbon.
    Lambrix, Patrick
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems.
    McLeod, Kenneth
    Harriot-Watt University, Edinburgh, UK.
    Möller, Steffen
    Universität Rostock, Germany.
    Nutt, Werner
    Harriot-Watt University, Edinburgh, UK.
    Olsson, Björn
    University of Skövde, Sweden.
    Schroeder, Michael
    Technical University of Dresden, Germany.
    Soliman, Sylvain
    INRIA Rocquencourt, France.
    Tan, He
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems.
    Tilivea, Doina
    National Institute for Research and Development in Informatics, Romania.
    Will, Sebastian
    Friedrich-Schiller-Universität Jena, Germany.
    Usage of bioinformatics tools and identification of information sources2005Report (Other academic)
  • 7.
    Baker, Christopher
    et al.
    University of New Brunswick, Canada.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Laurila Bergman, Jonas
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, Database and information techniques.
    Kanagasabai, Rajamaran
    ASTAR, Singapore.
    Ang, Wee Tiong
    ASTAR, Singapore.
    Slicing through the scientific literature2009In: Proceedings of the 6th International Workshop on Data Integration in the Life Sciences , Springer , 2009, 1, 127-140 p.Chapter in book (Refereed)
    Abstract [en]

    Success in the life sciences depends on access to information in knowlegde bases and literature. Finding and extracting the relevant information depends on a user’s domain knowledge and the knowledge of the search technology. In this paper we present a system that helps users formulate queries and search the scientific literature. The system coordinates ontologies, knowledge representation, text mining and NLP techniques to generate relevant queries in response to keyword input from the user. Queries are presented in natural language, translated to formal query syntax and issued to a knowledge base of scientific literature, documents or aligned document segments. We describe the components of the system and exemplify using real-world examples.

  • 8.
    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)
  • 9.
    Chen, Bi
    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.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Structure-Based Filtering for Ontology Alignment2006In: Proceedings of the IEEE WETICE Workshop on Semantic Technologies in Collaborative Applications, Institute of Electrical and Electronics Engineers (IEEE), 2006, 364-369 p.Conference paper (Refereed)
    Abstract [en]

    Ontologies are an important technology for the Semantic Web and many ontologies have already been developed. Many ontologies also contain overlapping information and to be able to use them together effectively, we need to align them. Some of the current alignment techniques use information about the structure of the ontologies, but they have not produced good results in evaluations. We propose an approach where, in contrast to the other approaches, structural information is used as a filtering method in the alignment process. We evaluate the approach in terms of quality and performance.

  • 10.
    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.

  • 11.
    Chisalita, Ioan
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems.
    Shahmehri, Nahid
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems.
    Lambrix, Patrick
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems.
    Traffic accidents modeling and analysis using temporal reasonin2004In: ITSC 2004: 7TH INTERNATIONAL IEEE CONFERENCE ON INTELLIGENT TRANSPORTATION SYSTEMS, PROCEEDINGS, Institute of Electrical and Electronics Engineers (IEEE), 2004, 378-383 p.Conference paper (Refereed)
    Abstract [en]

    Traffic accidents account for more than half a million casualties every year. The analysis of accidents helps identifying the elements that affect traffic conditions, the relationships between them, and how they may contribute to the occurrence of dangerous situations. In this paper we present a temporal reasoning system for modeling and analyzing various types of accident scenarios. The system is based on Event Calculus and was implemented using Prolog. We exemplify the use of the system by applying it for modeling and analyzing a rear-end accident scenario.

  • 12.
    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)
  • 13.
    Dawelbait, Gihan
    et al.
    Technische Universität Dresden, Germany.
    Doms, Andreas
    Technische Universität Dresden, Germany.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Royer, Loic
    Technische Universität Dresden, Germany.
    Schroeder, Michael
    Technische Universität Dresden, Germany.
    Bioinformatics Demonstrators2006Report (Other academic)
  • 14.
    Doms, Andreas
    et al.
    Technische Universität Dresden, Germany.
    Jakoniené, Vaida
    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.
    Schroeder, Michael
    Technische Universität Dresden, Germany.
    Wächter, Thomas
    Technische Universität Dresden, Germany.
    Ontologies and Text Mining as a Basis for a Semantic Web for the Life Sciences2006In: Reasoning Web, Second International Summer School: Summer School 2006, Lisbon, Portugal, September 4-8, 2006, Tutorial Lectures / [ed] Pedro BarahonaFrançois Bry, Enrico Franconi, Nicola Henze et, Springer Berlin/Heidelberg, 2006, 164-183 p.Chapter in book (Refereed)
    Abstract [en]

    This book presents thoroughly arranged tutorial papers corresponding to lectures given by leading researchers at the Second International Summer School on Reasoning Web in Lisbon, Portugal, in September 2006. Building on the predessor school held in 2005 and published as LNCS 3564, the ten tutorial lectures presented provide competent coverage of current topics in semantic Web research and development.

  • 15.
    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.

  • 16.
    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.

  • 17.
    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.

  • 18.
    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.

  • 19.
    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)
  • 20.
    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.

  • 21.
    Duma, Claudiu
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, Database and information techniques.
    Shahmehri, Nahid
    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 flexible category-based collusion-resistant key management scheme for multicast2003In: Security and privacy in the age of uncertainty: IFIP TC11 18th International Conference on Information Security (SEC2003) May 26-28, 2003, Athens, Greece / [ed] Dimitris Gritzalis; Sabrina De Capitani di Vimercati; Pierangela Samarati; Sokratis Katsikas, Kluwer Academic Publishers, 2003, 133-144 p.Conference paper (Refereed)
    Abstract [en]

    Current key management schemes for multicast provide either no resistance to collusion or perfect resistance to collusion. However, resistance to collusion is achieved at the expense of efficiency in terms of the number of transmissions and the number of keys that are used. We argue that applications may have certain assumptions regarding the users and their access to the multicast channel that may be used to provide a broader range of choices for balancing efficiency against resistance to collusion.

    We formalize the collusion requirement based upon the users' access to the multicast channel. Different user categorizations give different degrees of collusion resistance and we show that the existing work has focused on special cases of user categorizations. Further, we go on to propose and evaluate a flexible key management strategy for the general case where the accessibility relation defines the order of exclusion of the categories. The theoretical and experimental results show that our scheme has good performance regarding transmissions and keys per controller.

  • 22.
    Duma, Claudiu
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, Database and information techniques.
    Shahmehri, Nahid
    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 hybrid key tree scheme for multicast to balance security and efficiency requirement2003In: Proceedings of the Twelfth IEEE International Workshops on Enabling Technologies: Infrastructure for Collaborative Enterprises (WET ICE '03), Institute of Electrical and Electronics Engineers (IEEE), 2003, 208-213 p.Conference paper (Refereed)
    Abstract [en]

    Security and efficiency of rekeying are crucial requirements for multicast key management. However, the two requirements pull in different directions and balancing them to meet the application needs is still an open issue. In this paper we introduce a hybrid key tree scheme to balance security, namely the resistance to collusion, and the efficiency. The resistance to collusion is measured by an integer parameter. The communication and the storage requirements for the controller depend on this parameter too, and they decrease as the resistance to collusion is relaxed. We analytically evaluate the efficiency of our scheme and compare with the previous work. The results show that our scheme allows a fine-tuning of security requirements versus efficiency requirements at run-time, which is not possible with the previous key management schemes.

  • 23.
    Duma, Claudiu
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, Database and information techniques.
    Shahmehri, Nahid
    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.
    Efficient storage for category-based group key management2004In: Proceedings of the 5th Conference on Computer Science and Systems Engineering in Linköping, 2004, 139-146 p.Conference paper (Refereed)
    Abstract [en]

    In multicast group communication, efficiency- and security are competing requirements and balancing them is an acknowledged challenge. In particular, the collusion resistance has an impact on the efficiency of any scheme. In this context, the category-based group key management (category-based GKM) scheme balances the collusion resistance constraints against the communication cost and the group controller storage. However, this scheme increases the storage requirements for users. In this paper we address this problem by introducing a novel technique based on spanning hash key tree (SKT). In the worst case, using our t echnique, the storage requirement remains the same as in the original category-based GKM scheme. However, the experimentalresults show that, in general, the SKT technique greatly reduces the key storage for the users as well as for the controller.

  • 24.
    Freire, Sergio Miranda
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Sundvall, Erik
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Karlsson, Daniel
    Linköping University, Department of Biomedical Engineering, Medical Informatics. 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.
    Performance of XML Databases for Epidemiological Queries in Archetype-Based EHRs2012In: Proceedings Scandinavian Conference on Health Informatics 2012, Linköping: Linköping University Electronic Press, 2012, 51-57 p.Conference paper (Refereed)
    Abstract [en]

    There are very few published studies regarding the performance of persistence mechanisms for systems that use the openEHR multi level modelling approach. This paper addresses the performance and size of XML databases that store openEHR compliant documents. Database size and response times to epidemiological queries are described. An anonymized relational epidemiology database and associated epidemiological queries were used to generate openEHR XML documents that were stored and queried in four opensource XML databases. The XML databases were considerably slower and required much more space than the relational database. For population-wide epidemiological queries the response times scaled in order of magnitude at the same rate as the number of records (total database size) but were orders of magnitude slower than the original relational database. For individual focused clinical queries where patient ID was specified the response times were acceptable. This study suggests that the tested XML database configurations without further optimizations are not suitable as persistence mechanisms for openEHR-based systems in production if population-wide ad hoc querying is needed.

  • 25.
    Freire, Sergio Miranda
    et al.
    Linköping University, Department of Biomedical Engineering. Linköping University, Faculty of Science & Engineering. Departamento de Tecnologia da Informação e Educação em Saúde, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
    Teodoro, Douglas
    Departamento de Tecnologia da Informação e Educação em Saúde, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil .
    Wei-Kleiner, Fang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Sundvall, Erik
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Science & Engineering. Region Östergötland.
    Karlsson, Daniel
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Science & Engineering.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Comparing the Performance of NoSQL Approaches for Managing Archetype-Based Electronic Health Record Data2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 3, e0150069Article in journal (Refereed)
    Abstract [en]

    This study provides an experimental performance evaluation on population-based queries of NoSQL databases storing archetype-based Electronic Health Record (EHR) data. There are few published studies regarding the performance of persistence mechanisms for systems that use multilevel modelling approaches, especially when the focus is on population-based queries. A healthcare dataset with 4.2 million records stored in a relational database (MySQL) was used to generate XML and JSON documents based on the openEHR reference model. Six datasets with different sizes were created from these documents and imported into three single machine XML databases (BaseX, eXistdb and Berkeley DB XML) and into a distributed NoSQL database system based on the MapReduce approach, Couchbase, deployed in different cluster configurations of 1, 2, 4, 8 and 12 machines. Population-based queries were submitted to those databases and to the original relational database. Database size and query response times are presented. The XML databases were considerably slower and required much more space than Couchbase. Overall, Couchbase had better response times than MySQL, especially for larger datasets. However, Couchbase requires indexing for each differently formulated query and the indexing time increases with the size of the datasets. The performances of the clusters with 2, 4, 8 and 12 nodes were not better than the single node cluster in relation to the query response time, but the indexing time was reduced proportionally to the number of nodes. The tested XML databases had acceptable performance for openEHR-based data in some querying use cases and small datasets, but were generally much slower than Couchbase. Couchbase also outperformed the response times of the relational database, but required more disk space and had a much longer indexing time. Systems like Couchbase are thus interesting research targets for scalable storage and querying of archetype-based EHR data when population-based use cases are of interest.

  • 26.
    Färnqvist, Tommy
    et al.
    Linköping University, Department of Computer and Information Science, Software and Systems. Linköping University, Faculty of Science & Engineering.
    Heintz, Fredrik
    Linköping University, Department of Computer and Information Science, Artificial Intelligence and Integrated Computer Systems. Linköping University, Faculty of Science & Engineering.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Mannila, Linda
    Åbo Academy, Finland.
    Wang, Chunyan
    Linköping University, Department of Computer and Information Science.
    Supporting Active Learning by Introducing an Interactive Teaching Tool in a Data Structures and Algorithms2016In: Proceedings of the 47th ACM Technical Symposium on Computer Science Education (SIGCSE 2016), ACM Publications, 2016, 663-668 p.Conference paper (Refereed)
    Abstract [en]

    Traditionally, theoretical foundations in data structures and algorithms (DSA) courses have been covered through lectures followed by tutorials, where students practise their understanding on pen-and-paper tasks. In this paper, we present findings from a pilot study on using the interactive e-book OpenDSA as the main material in a DSA course. The goal was to redesign an already existing course by building on active learning and continuous examination through the use of OpenDSA. In addition to presenting the study setting, we describe findings from four data sources: final exam, OpenDSA log data, pre and post questionnaires as well as an observation study. The results indicate that students performed better on the exam than during previous years. Students preferred OpenDSA over traditional textbooks and worked actively with the material, although a large proportion of them put off the work until the due date approaches.

  • 27.
    Färnqvist, Tommy
    et al.
    Linköping University, Department of Computer and Information Science, Software and Systems. Linköping University, Faculty of Science & Engineering.
    Heintz, Fredrik
    Linköping University, Department of Computer and Information Science, Artificial Intelligence and Integrated Computer Systems. Linköping University, Faculty of Science & Engineering.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Mannila, Linda
    Åbo Academy, Finland.
    Wang, Chunyan
    Linköping University, Department of Computer and Information Science.
    Supporting Active Learning Using an Interactive Teaching Tool in a Data Structures and Algorithms Course2015In: Proceedings of 5:e Utvecklingskonferensen för Sveriges ingenjörsutbildningar (UtvSvIng), 2015, 76-79 p.Conference paper (Other academic)
    Abstract [en]

    Traditionally, theoretical foundations in data structuresand algorithms (DSA) courses have been covered throughlectures followed by tutorials, where students practise theirunderstanding on pen-and-paper tasks. In this paper, we presentfindings from a pilot study on using the interactive e-bookOpenDSA as the main material in a DSA course. The goal was toredesign an already existing course by building on active learningand continuous examination through the use of OpenDSA. Inaddition to presenting the study setting, we describe findings fromfour data sources: final exam, OpenDSA log data, pre- and postcourse questionnaires as well as an observation study. The resultsindicate that students performed better on the exam than duringprevious years. Students preferred OpenDSA over traditionaltextbooks and worked actively with the material, although alarge proportion of them put off the work until the due dateapproaches.

  • 28.
    Ivanova, Valentina
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Bach, Benjamin
    University of Edinburgh, United Kingdom.
    Pietriga, Emmanuel
    INRIA, LRI (Univ Paris-Sud & CNRS), Universit ́ e Paris-Saclay, France.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Alignment Cubes: Interactive Visual Exploration and Evaluation of Multiple Ontology Alignments2017In: Proceedings of the ISWC 2017 Posters & Demonstrations and Industry Tracks co-located with 16th International Semantic Web Conference (ISWC 2017) / [ed] Nadeschda Nikitina, Dezhao Song, Achille Fokoue, Peter Haase, Aachen, Germany: CEUR Workshop Proceedings , 2017Conference paper (Refereed)
  • 29.
    Ivanova, Valentina
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Bach, Benjamin
    University of Edinburgh, United Kingdom.
    Pietriga, Emmanuel
    INRIA, France.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, Faculty of Science & Engineering.
    Alignment Cubes: Towards Interactive Visual Exploration and Evaluation of Multiple Ontology Alignments2017In: The Semantic Web: ISWC 2017 - 16th International Semantic Web Conference, Vienna, Austria, October 21-25, 2017, Proceedings, Part I / [ed] Claudia d'Amato, Miriam Fernandez, Valentina A. M. Tamma, Freddy Lecue, Philippe Cudre-Mauroux, Juan F. Sequeda, Christoph Lange and Jeff Heflin, Cham, Switzerland: Springer Publishing Company, 2017, 400-417 p.Chapter in book (Refereed)
    Abstract [en]

    Ontology alignment is an area of active research where many algorithms and approaches are being developed. Their performance is usually evaluated by comparing the produced alignments to a reference alignment in terms of precision, recall and F-measure. These measures, however, only provide an overall assessment of the quality of the alignments, but do not reveal differences and commonalities between alignments at a finer-grained level such as, e.g., regions or individual mappings. Furthermore, reference alignments are often unavailable, which makes the comparative exploration of alignments at different levels of granularity even more important. Making such comparisons efficient calls for a “human-in-the-loop” approach, best supported through interactive visual representations of alignments. Our approach extends a recent tool, Matrix Cubes, used for visualizing dense dynamic networks. We first identify use cases for ontology alignment evaluation that can benefit from interactive visualization, and then detail how our Alignment Cubes support interactive exploration of multiple ontology alignments. We demonstrate the usefulness of Alignment Cubes by describing visual exploration scenarios, showing how Alignment Cubes support common tasks identified in the use cases.

    The full text will be freely available from 2018-10-04 08:00
  • 30.
    Ivanova, Valentina
    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 aligning taxonomies and debugging taxonomies and their alignments2013In: The Semantic Web: ESWC 2013 Satellite Events, Montpellier, France, May 26-30, 2013, Revised Selected Papers / [ed] Philipp Cimiano, Miriam Fernández, Vanessa Lopez, Stefan Schlobach, Johanna Völker, Springer Berlin/Heidelberg, 2013, 152-156 p.Chapter in book (Refereed)
    Abstract [en]

    With the increased use of ontologies in semantically-enabled applications,the issues of debugging and aligning ontologies have become increasinglyimportant. The quality of the results of such applications is directly dependent onthe quality of the ontologies and mappings between the ontologies they employ. Akey step towards achieving high quality ontologies and mappings is discoveringand resolving modeling defects, e.g., wrong or missing relations and mappings.In this demonstration paper we present a system for aligning taxonomies, the mostused kind of ontologies, and debugging taxonomies and their alignments, whereontology alignment is treated as a special kind of debugging.

  • 31.
    Ivanova, Valentina
    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 Taxonomies and their Alignments2012In: Proceedings of First International Workshop on Debugging Ontologies and Ontology Mappings / [ed] Patrick Lambrix, Guilin Qi, Matthew Horridge, 2012, 37-42 p.Conference paper (Refereed)
    Abstract [en]

    Neither developing ontologies nor aligning ontologies are easy tasks, and often the resulting ontologies and alignments are not consistent or complete. Such ontologies and alignments, although often useful, also lead to problems when used in semantically-enabled applications. In this paper we briefly introduce a system that supports domain experts in detecting and repairing wrong and missing is-a relations and mappings.

  • 32.
    Ivanova, Valentina
    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 unified approach for aligning taxonomies and debugging taxonomies and their alignments2013In: The Semantic Web: Semantics and Big Data: 10th International Conference, ESWC 2013, Montpellier, France, May 26-30, 2013. Proceedings / [ed] Philipp Cimiano, Oscar Corcho, Valentina Presutti, Laura Hollink, Sebastian Rudolph, Springer Berlin/Heidelberg, 2013, 1-15 p.Chapter in book (Refereed)
    Abstract [en]

    With the increased use of ontologies in semantically-enabled applications, the issues of debugging and aligning ontologies have become increasingly important. The quality of the results of such applications is directly dependent on the quality of the ontologies and mappings between the ontologies they employ. A key step towards achieving high quality ontologies and mappings is discovering and resolving modeling defects, e.g., wrong or missing relations and mappings. In this paper we present a unified framework for aligning taxonomies, the most used kind of ontologies, and debugging taxonomies and their alignments, where ontology alignment is treated as a special kind of debugging. Our framework supports the detection and repairing of missing and wrong is-a structure in taxonomies, as well as the detection and repairing of missing (alignment) and wrong mappings between ontologies. Further, we implemented a system based on this framework and demonstrate its benefits through experiments with ontologies from the Ontology Alignment Evaluation Initiative.

  • 33.
    Ivanova, Valentina
    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.
    User Involvement for Large-Scale Ontology Alignment2014In: International Workshop on Visualizations and User Interfaces for Knowledge Engineering and Linked Data Analytics / [ed] Valentina Ivanova, Tomi Kauppinen, Steffen Lohmann, Suvodeep Mazumdar, Catia Pesquita, Kai Xu, 2014, 34-47 p.Conference paper (Refereed)
  • 34.
    Ivanova, Valentina
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Lambrix, PatrickLinköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.Lohmann, SteffenUniversity of Stuttgart, Germany.Pesquita, CatiaUniversity of Lisbon, Portugal.
    VOILA 2015 Visualizations and User Interfaces for Ontologies and Linked Data: Proceedings of the International Workshop on Visualizations and User Interfaces for Ontologies and Linked Data2015Conference proceedings (editor) (Refereed)
    Abstract [en]

    A picture is worth a thousand words, we often say, yet many areas are in demand of sophisticated visualization techniques, and the Semantic Web is not an exception. The size and complexity of ontologies and Linked Data in the Semantic Web constantly grow and the diverse backgrounds of the users and application areas multiply at the same time. Providing users with visual representations and intuitive user interfaces can significantly aid the understanding of the domains and knowledge represented by ontologies and Linked Data. There is noone size fits all solution but different use cases demand different visualization and interaction techniques. Ultimately, providing better user interfaces and visual representations will foster user engagement and likely lead to higher quality results in different applications employing ontologies and to the proliferation of Linked Data usage.

    User interfaces are essential to easily provide access to the increasing diversity of knowledge modeled in ontologies. As ontologies grow in size and complexity, the demand for comprehensive visualization and sophisticated interaction also rises. In particular, user interfaces are an integral part of ontology engineering, to help bridge the gap between domain experts and ontology engineers. Ontology visualization is not a new topic and a number of approaches have become available in recent years, with some being already well-established, particularly in the field of ontology modeling. In other areas of ontology engineering, such as ontology alignment and debugging, although several tools have recently been  developed, few provide a graphical user interface, not to mention navigational aids or comprehensive visualization techniques.

    While ontology users usually possess domain and/or knowledge representation expertise, this is not necessarily the case with potential Linked Data consumers who can come from very different backgrounds and have varying levels of expertise. Currently, the main Linked Data consumers are technology experienced users, one of the reasons being the lack of appropriate user interfaces and visualizations to support other user groups. Visual approaches are needed to assist various kinds of users, who pursue diverse goals and pose individual requirements.

    In the presence of a huge network of interconnected resources, one of the challenges faced by the Linked Data community is the visualization of the multidimensional datasets to provide for efficient overview, exploration and querying tasks, to mention just a few. With the focus shifting from a Web of Documents to a Web of Data, changes in the interaction paradigms are in demand as well. Novel approaches also need to take into consideration the technological challenges and opportunities given by new interaction contexts, ranging from mobile and touch interaction to visualizations on large displays, and encompassing highly responsive web applications.

    The VOILA! workshop addressed these and related issues in its call for papers and attracted 18 submissions in different paper categories. Three reviewers were assigned to each submission. Based on their reviews we selected 12 contributions for presentation at the workshop in the following categories: full research papers (5), position papers (2) and short papers (5).

    The first edition of VOILA! is co-located with the 14th International Semantic Web Conference (ISWC 2015) and will take place as a full day event on October 11, 2015 in Bethlehem, Pennsylvania, USA. It will be organized around paper presentations and discussions and will be accompanied by interactive software demonstrations, giving developers a chance to gather feedback from the community.

    We thank all authors for their submissions and all members of the VOILA! program committee for their useful reviews and comments. We are grateful to Miriam Fernandez and Krzysztof Janowicz, the ISWC workshop chairs, for their continuous support during theworkshop organization. The workshop would not be possible without all of you!

    September 2015

    Valentina Ivanova, Patrick Lambrix, Steffen Lohmann, Catia Pesquita

  • 35.
    Ivanova, Valentina
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Lambrix, PatrickLinköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.Lohmann, SteffenFraunhofer IAIS, Germany.Pesquita, CatiaUniversity of Lisbon, Portugal .
    VOILA! 2016: Proceedings of the 2nd International Workshop on Visualization and Interaction for Ontologies and Linked Data, Co-located with ISWC 2016, Kobe, Japan, October 17, 20162016Conference proceedings (editor) (Refereed)
    Abstract [en]

    A picture is worth a thousand words, we often say, yet many areas are in demand of sophisticated visualization techniques, and the Semantic Web is not an exception. The size and complexity of ontologies and Linked Data in the Semantic Web constantly grows and the diverse backgrounds of the users and application areas multiply at the same time. Providing users with visual representations and intuitive interaction techniques can significantly aid the exploration and understanding of the domains and knowledge represented by ontologies and Linked Data.

    Ontology visualization is not a new topic and a number of approaches have become available in recent years, with some being already well-established, particularly in the field of ontology modeling. In other areas of ontology engineering, such as ontology alignment and debugging, although several tools have recently been developed, few provide a graphical user interface, not to mention navigational aids or comprehensive visualization and interaction techniques.

    In the presence of a huge network of interconnected resources, one of the challenges faced by the Linked Data community is the visualization of multidimensional datasets to provide for efficient overview, exploration and querying tasks, to mention just a few. With the focus shifting from a Web of Documents to a Web of Data, changes in the interaction paradigms are in demand as well. Novel approaches also need to take into consideration the technological challenges and opportunities given by new interaction contexts, ranging from mobile, touch, and gesture interaction to visualizations on large displays, and encompassing highly responsive web applications.

    There is no one-size-fits-all solution but different use cases demand different visualization and interaction techniques. Ultimately, providing better user interfaces, visual representations and interaction techniques will foster user engagement and likely lead to higher quality results in different applications employing ontologies and proliferate the consumption of Linked Data.

    These and related issues are addressed by the VOILA! workshop series concerned with Visualization and Interaction for Ontologies and Linked Data. The second edition of VOILA! is co-located with the 15th International Semantic Web Conference (ISWC 2016) and will take place as a full day event on October 17, 2016 in Kobe, Japan. It will be organized around scientific paper presentations and discussions, and will be accompanied by interactive software demonstrations, giving developers a chance to gather feedback from the community.

    The call for papers for VOILA! 2016 attracted 22 submissions in different paper categories. Three reviewers were assigned to each submission. Based on the reviews, we selected 15 contributions for presentation at the workshop in the following categories: full papers (7), system papers (2), short papers (2), demo papers (4).

    We thank all authors for their submissions and all members of the VOILA! program committee for their useful reviews and comments. We are also grateful to Chiara Ghidini and Heiner Stuckenschmidt, the workshop chairs of ISWC 2016, for their continuous support during the workshop organization.

    October 2016

    Valentina Ivanova, Patrick Lambrix, Steffen Lohmann, Catia Pesquita

  • 36.
    Ivanova, Valentina
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Lambrix, PatrickLinköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.Lohmann, SteffenFraunhofer IAIS, Germany .Pesquita, CatiaUniversity of Lisbon, Portugal .
    VOILA! 2017: Proceedings of the Third International Workshop on Visualization and Interaction for Ontologies and Linked Data: co-located with the 16th International Semantic Web Conference, Vienna, Austria, October 22, 2017.2017Conference proceedings (editor) (Refereed)
    Abstract [en]

    A picture is worth a thousand words, we often say, yet many areas are in demand of sophisticated visualization techniques, and the Semantic Web is not an exception. The size and complexity of ontologies and Linked Data in the Semantic Web constantly grows and the diverse backgrounds of the users and application areas multiply at the same time. Providing users with visual representations and intuitive interaction techniques can significantly aid the exploration and understanding of the domains and knowledge representedby ontologies and Linked Data.

    Ontology visualization is not a new topic and a number of approaches have become available in recent years, with some being already well-established, particularly in the field of ontology modeling. In other areas of ontology engineering, such as ontology alignment and debugging, although several tools have recently been developed, few provide a graphical user interface, not to mention navigational aids or comprehensive visualization and interaction techniques.

    In the presence of a huge network of interconnected resources, one of the challenges facedby the Linked Data community is the visualization of multidimensional datasets to provide for efficient overview, exploration and querying tasks, to mention just a few. With the focus shifting from a Web of Documents to a Web of Data, changes in the interaction paradigms are in demand as well. Novel approaches also need to take into consideration the technological challenges and opportunities given by new interaction contexts, ranging from mobile, touch, and gesture interaction to visualizations on large displays, and encompassing highly responsive web applications.

    There is no one-size-fits-all solution but different use cases demand different visualizationand interaction techniques. Ultimately, providing better user interfaces, visual representations and interaction techniques will foster user engagement and likely lead to higher quality results in different applications employing ontologies and proliferate the consumption of Linked Data.

    These and related issues are addressed by the VOILA! workshop series concerned with Vi-sualization and Interaction for Ontologies and Linked Data. The third edition of VOILA! is co-located with the 16th International Semantic Web Conference (ISWC 2017) and will take place as a full day event on October 22, 2017 in Vienna, Austria. It will be organized around scientific paper presentations and discussions, and will be accompanied by interactive software demonstrations, giving developers a chance to gather feedback from the community.

    The call for papers for VOILA! 2017 attracted 20 submissions in different paper categories. At least three reviewers were assigned to each submission. Based on the reviews, we selected 13 contributions for presentation at the workshop in the following categories: full papers (10), position papers (2) and experience papers (1).

    We thank all authors for their submissions and all members of the VOILA! program committee for their useful reviews and comments. We are also grateful to Aidan Hogan and Valentina Presutti, the workshop chairs of ISWC 2017, for their continuous support during the workshop organization.

    September 2017

    Valentina Ivanova, Patrick Lambrix, Steffen Lohmann, Catia Pesquita

  • 37.
    Ivanova, Valentina
    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.
    Åberg, Johan
    Linköping University, Department of Computer and Information Science, Human-Centered systems. Linköping University, Faculty of Science & Engineering.
    Requirements for and Evaluation of User Support for Large-Scale Ontology Alignment2015In: The Semantic Web. Latest Advances and New Domains: 12th European Semantic Web Conference, ESWC 2015, Portoroz, Slovenia, May 31 -- June 4, 2015. Proceedings, Springer Science+Business Media B.V., 2015, 3-20 p.Chapter in book (Refereed)
    Abstract [en]

    Currently one of the challenges for the ontology alignment community is the user involvement in the alignment process. At the same time, the focus of the community has shifted towards large-scale matching which introduces an additional dimension to this issue. This paper aims to provide a set of requirements that foster the user involvement for large-scale ontology alignment tasks.Further, we present and discuss the results of a literature study for 7 ontology alignments systems as well as a heuristic evaluation and an observational user study for 3 ontology alignment systems to reveal the coverage of the requirements in the systems and the support for the requirements in the user interfaces.

  • 38.
    Ivanova, Valentina
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Laurila Bergman, Jonas
    Division of Information Technology, National Food Agency, Uppsala, Sweden.
    Hammerling, Ulf
    Department of Risk Benefit Assessment, National Food Agency, Uppsala, Sweden.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Debugging Taxonomies and their Alignments: the ToxOntology - MeSH Use Case2012In: Proceedings of the First International Workshop on Debugging Ontologies and Ontology Mappings / [ed] Patrick Lambrix, Guilin Qi, Matthew Horridge, Linköping University Electronic Press, 2012, 25-36 p.Conference paper (Refereed)
    Abstract [en]

    As part of an initiative to facilitate adequate identification and display of substance-associated health effects a toxicological ontology - ToxOntology - was created. Further, an alignent with MeSH was accomplished to obtain an indirect index to the scientific literature.

    To arrive at satisfactory results in the semantically-enabled applications, high-quality ontologies and alignments are both necessary. A key step towards high quality in this area is debugging the ontologies and their alignments. In this paper we present an experience report on the debugging of ToxOntology and MeSH as well as an alignment.

  • 39.
    Jakoniene, Vaida
    et al.
    Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems. Linköping University, The Institute of Technology.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems. Linköping University, The Institute of Technology.
    Monitoring performance and access to biological databases2002In: 3rd swedish annual workshop in bioinformatics for PhD students and Postdocs, 2002Conference paper (Other academic)
  • 40.
    Jakoniené, Vaida
    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 tool for evaluating strategies for grouping of biological data2006In: Seventh Swedish Bioinformatics Workshop for PhD students and PostDocs,2006, 2006, 23-24 p.Conference paper (Other academic)
  • 41.
    Jakoniené, Vaida
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems.
    Lambrix, Patrick
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems.
    Implementation of a System for Integrated Access to Biological Data Sources2004In: Bioinformatics 2004,2004, 2004, 44-44 p.Conference paper (Other academic)
  • 42.
    Jakoniené, Vaida
    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.
    Information integration systems for biological data source requirements and opportunities2006Report (Other (popular science, discussion, etc.))
  • 43.
    Jakoniené, Vaida
    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.
    Ontology-based integration for bioinformatics2005In: Proceedings of the VLDB Workshop on Ontologies-bases techniques for DataBases and Information Systems - ODBIS, 2005, 55-58 p.Conference paper (Refereed)
    Abstract [en]

    Information integration systems support researchers in bioinformatics to retrieve data from multiple biological data sources. In this paper we argue that the current approaches should be enhanced by ontological knowledge. We identify the dierent types of ontological knowledge that are available on the Web and propose an approach to use this knowledge to support integrated access to multiple biological data sources. We also show that current ontology-based integration approaches only cover parts of our approach.

     

  • 44.
    Jakoniené, Vaida
    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.
    Tool for Evaluating Strategies for Grouping of Biological Data2007In: Journal of Integrative Bioinformatics, ISSN 1613-4516, Vol. 4, no 3Article in journal (Refereed)
    Abstract [en]

    During the last decade an enormous amount of biological data has been generated and techniques and tools to analyze this data have been developed. Many of these tools use some form of grouping and are used in, for instance, data integration, data cleaning, prediction of protein functionality, and correlation of genes based on microarray data. A number of aspects influence the quality of the grouping results: the data sources, the grouping attributes and the algorithms implementing the grouping procedure. Many methods exist, but it is often not clear which methods perform best for which grouping tasks. The study of the properties, and the evaluation and the comparison of the different aspects that influence the quality of the grouping results, would give us valuable insight in how the grouping procedures could be used in the best way. It would also lead to recommendations on how to improve the current procedures and develop new procedures. To be able to perform such studies and evaluations we need environments that allow us to compare and evaluate different grouping strategies. In this paper we present a framework, KitEGA, for such an environment, and present its current prototype implementation. We illustrate its use by comparing grouping strategies for classifying proteins regarding biological function and isozymes.

  • 45.
    Jakoniené, Vaida
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Rundqvist, David
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, Database and information techniques.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    A Method for Similarity-Based Grouping of Biological Data2006In: Data Integration in the Life Sciences: Third International Workshop, DILS 2006, Hinxton, UK, July 20-22, 2006. Proceedings / [ed] Ulf Leser, Felix Naumann, Barbara Eckman, Springer Berlin/Heidelberg, 2006, 136-151 p.Chapter in book (Refereed)
    Abstract [en]

    Similarity-based grouping of data entries in one or more data sources is a task underlying many different data management tasks, such as, structuring search results, removal of redundancy in databases and data integration. Similarity-based grouping of data entries is not a trivial task in the context of life science data sources as the stored data is complex, highly correlated and represented at different levels of granularity. The contribution of this paper is two-fold. 1) We propose a method for similarity-based grouping and 2) we show results from test cases. As the main steps the method contains specification of grouping rules, pairwise grouping between entries, actual grouping of similar entries, and evaluation and analysis of the results. Often, different strategies can be used in the different steps. The method enables exploration of the influence of the choices and supports evaluation of the results with respect to given classifications. The grouping method is illustrated by test cases based on different strategies and classifications. The results show the complexity of the similarity-based grouping tasks and give deeper insights in the selected grouping tasks, the analyzed data source, and the influence of different strategies on the results.

  • 46.
    Janowicz, Krzysztof
    et al.
    University of California, USA.
    Schlobach, StefanVrije Universiteit Amsterdam, The Netherlands.Lambrix, PatrickLinköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.Hyvönen, EeroAalto University, Finland.
    Knowledge Engineering and Knowledge Management: 19th International Conference, EKAW 2014, Linköping, Sweden, November 24-28, 2014, Proceedings2014Conference proceedings (editor) (Refereed)
  • 47.
    Klingström, Tomas
    et al.
    Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Soldatova, Larissa
    Aberystwyth University, UK.
    Stevens, Robert
    Universtity of Manchester, UK.
    Roos, T. Erik
    University of Groningen, The Netherlands.
    Swertz, Morris A.
    University of Groningen, The Netherlands.
    Müller, Kristian M.
    University of Potsdam, Germany.
    Kalas, Matus
    University of Bergen, Norway.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Taussig, Michael J.
    Babraham Bioscience Technologies, Cambridge, UK.
    Litton, Jan-Eric
    Karolinska Institutet, Stockholm, Sweden.
    Landegren, Ulf
    Uppsala University, Sweden.
    Bongcam-Rudloff, Erik
    Swedish University of Agricultural Sciences and Uppsala University, Sweden.
    Workshop on laboratory protocol standards for the molecular methods database2013In: New Biotechnology, ISSN 1871-6784, Vol. 30, no 2, 109-113 p.Article in journal (Refereed)
    Abstract [en]

    Management of data to produce scientific knowledge is a key challenge for biological research in the 21st century. Emerging high-throughput technologies allow life science researchers to produce big data at speeds and in amounts that were unthinkable just a few years ago. This places high demands on all aspects of the workflow: from data capture (including the experimental constraints of the experiment), analysis and preservation, to peer-reviewed publication of results. Failure to recognise the issues at each level can lead to serious conflicts and mistakes; research may then be compromised as a result of the publication of non-coherent protocols, or the misinterpretation of published data. In this report, we present the results from a workshop that was organised to create an ontological data-modelling framework for Laboratory Protocol Standards for the Molecular Methods Database (MolMeth). The workshop provided a set of short- and long-term goals for the MolMeth database, the most important being the decision to use the established EXACT description of biomedical ontologies as a starting point.

  • 48.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    A framework for session-based ontology alignment2011In: Proceedings of the 6th International Workshop on Ontology Matching, CEUR Workshop Proceedings , 2011, 238-239 p.Conference paper (Refereed)
    Abstract [en]

    [No abstract available]

  • 49.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Advances in Secure and Networked Information Systems – The ADIT Perspective: Festschrift in honor of professor NAHID SHAHMEHRI2012Collection (editor) (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.

     

  • 50.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Extending Standard Description Logics1994In: Proceedings of the International Workshop on Description Logics, 1994, 42-44 p.Conference paper (Refereed)
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