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  • 1.
    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
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för datavetenskap, IISLAB - Laboratoriet för intelligenta informationssystem.
    Krippahl, Ludwig
    Universidade Nova de Lisboa, Portugal.
    Lambrix, Patrick
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för datavetenskap, IISLAB - Laboratoriet för intelligenta informationssystem.
    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
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för datavetenskap, IISLAB - Laboratoriet för intelligenta informationssystem.
    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 cases2005Rapport (Övrigt vetenskapligt)
  • 2.
    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
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Lambrix, Patrick
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    McLeod, Kenneth
    Heriot-Watt university Edinburgh, UK.
    Soliman, Sylvain
    INRIA Rocquencourt Paris, France.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Will, Sebastian
    Albert-Ludwigs-universität Freiburg, Germany.
    Implementation of prototypes2007Rapport (Övrigt vetenskapligt)
  • 3.
    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
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för datavetenskap, IISLAB - Laboratoriet för intelligenta informationssystem.
    Krippahl, Ludwig
    FCT-UNL, Lisbon.
    Lambrix, Patrick
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för datavetenskap, IISLAB - Laboratoriet för intelligenta informationssystem.
    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
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för datavetenskap, IISLAB - Laboratoriet för intelligenta informationssystem.
    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 sources2005Rapport (Övrigt vetenskapligt)
  • 4.
    Chen, Bi
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Lambrix, Patrick
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Structure-Based Filtering for Ontology Alignment2006Ingår i: Proceedings of the IEEE WETICE Workshop on Semantic Technologies in Collaborative Applications, Institute of Electrical and Electronics Engineers (IEEE), 2006, s. 364-369Konferensbidrag (Refereegranskat)
    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.

  • 5.
    Lambrix, Patrick
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Edberg, Anna
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Manis, Carolyn
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Merging DAML+OIL bio-ontologies2003Ingår i: International workshop on description logics, 2003Konferensbidrag (Refereegranskat)
  • 6.
    Lambrix, Patrick
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Liu, Qiang
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    A system for repairing missing is-a structure in ontologies2009Ingår i: Semantic Web Applications and Tools for Life Sciences, 2009Konferensbidrag (Refereegranskat)
  • 7.
    Lambrix, Patrick
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Liu, Qiang
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Aligning anatomy ontologies in the Ontology Alignment Evaluation Initiative2009Ingår i: 25th Workshop of the Swedish Artificial Intelligence Society, 2009, s. 13-20Konferensbidrag (Refereegranskat)
  • 8.
    Lambrix, Patrick
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Liu, Qiang
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Repairing the missing is-a structure of ontologies2009Ingår i: The Semantic Web Fourth Asian Conference, ASWC 2009, Shanghai, China, December 6-9, 2009. Proceedings / [ed] Asunción Gómez-Pérez, Yong Yu and Ying Ding, Springer Berlin/Heidelberg, 2009, 1, s. 76-90Konferensbidrag (Refereegranskat)
    Abstract [en]

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

  • 9.
    Lambrix, Patrick
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Liu, Qiang
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    RepOSE: an environment for repairing missing ontological structure2009Ingår i: The Semantic Web Fourth Asian Conference, ASWC 2009, Shanghai, China, December 6-9, 2009. Proceedings / [ed] Asunción Gómez-Pérez, Yong Yu, Ying Ding, Springer Berlin/Heidelberg, 2009, 1, s. 365-366Konferensbidrag (Refereegranskat)
    Abstract [en]

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

  • 10.
    Lambrix, Patrick
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Strömbäck, Lena
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Information integration in bioinformatics with ontologies and standards2009Ingår i: Semantic Techniques for the Web: The REWERSE perspective, Springer Berlin/Heidelberg, 2009, 1, s. 343-376Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    New experimental methods allow researchers within molecular and systems biology to rapidly generate larger and larger amounts of data. This data is often made publicly available on the Internet and although this data is extremely useful, we are not using its full capacity. One important reason is that we still lack good ways to connect or integrate information from different resources. One kind of resource is the over 1000 data sources freely available on the Web. As most data sources are developed and maintained independently, they are highly heterogeneous. Information is also updated frequently. Other kinds of resources that are not so well-known or commonly used yet are the ontologies and the standards. Ontologies aim to define a common terminology for a domain of interest. Standards provide a way to exchange data between data sources and tools, even if the internal representations of the data in the resources and tools are different. In this chapter we argue that ontological knowledge and standards should be used for integration of data. We describe properties of the different types of data sources, ontological knowledge and standards that are available on the Web and discuss how this knowledge can be used to support integrated access to multiple biological data sources. Further, we present an integration approach that combines the identified ontological knowledge and standards with traditional information integration techniques. Current integration approaches only cover parts of the suggested approach. We also discuss the components in the model on which much recent work has been done in more detail: ontology-based data source integration, ontology alignment and integration using standards. Although many of our discussions in this chapter are general we exemplify mainly using work done within the REWERSE working group on Adding Semantics to the Bioinformatics Web.

  • 11.
    Lambrix, Patrick
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    A Framework for Aligning Ontologies2005Ingår i: PPSWR: International Workshop on Principles and Practice of Semantic Web Reasoning Principles and Practice of Semantic Web Reasoning Third International Workshop, PPSWR 2005, Dagstuhl Castle, Germany, September 11-16, 2005 Proceedings / [ed] François Fages and Sylvain Soliman, Springer Berlin/Heidelberg, 2005, s. 17-31Konferensbidrag (Refereegranskat)
    Abstract [en]

    Ontologies are an important technology for the Semantic Web. In different areas ontologies have already been developed and many of these ontologies contain overlapping information. Often we would therefore want to be able to use multiple ontologies and thus the ontologies need to be aligned. Currently, there exist a number of systems that support users in aligning ontologies, but not many comparative evaluations have been performed. In this paper we present a general framework for aligning ontologies where different alignment strategies can be combined. Further, we exemplify the use of the framework by describing a system (SAMBO) that is developed according to this framework. Within this system we have implemented some already existing alignment algorithms as well as some new algorithms. We also show how the framework can be used to experiment with combinations of strategies. This is a first step towards defining a framework that can be used for comparative evaluations of alignment strategies. For our tests we used several well-known bio-ontologies.

  • 12.
    Lambrix, Patrick
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    A semi-automatic tool for merging bio-ontologies2004Ingår i: Fourth Swedish Bioinformatics Workshop for PhD students and PostDocs, 2004Konferensbidrag (Övrigt vetenskapligt)
  • 13.
    Lambrix, Patrick
    et al.
    Linköpings universitet, Institutionen för datavetenskap, IISLAB - Laboratoriet för intelligenta informationssystem. Linköpings universitet, Tekniska högskolan.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, IISLAB - Laboratoriet för intelligenta informationssystem. Linköpings universitet, Tekniska högskolan.
    A semi-automatic tool for merging bio-ontologies2003Ingår i: 3rd Swedish annual bioinformatics workshop for PhD students and PostDocs, 2003Konferensbidrag (Övrigt vetenskapligt)
  • 14.
    Lambrix, Patrick
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    A Semi-Automatic Tool for Merging Bio-Ontologies2004Ingår i: Bioinformatics 2004, 2004, s. 55-55Konferensbidrag (Övrigt vetenskapligt)
  • 15.
    Lambrix, Patrick
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    A Tool for Evaluating Ontology Alignment Strategies2007Ingår i: Journal on Data Semantics, ISSN 1861-2032, Vol. VIII, s. 182-202Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Ontologies are an important technology for the Semantic Web. In different areas ontologies have already been developed and many of these ontologies contain overlapping information. Often we would therefore want to be able to use multiple ontologies. To obtain good results, we need to find the relationships between terms in the different ontologies, i.e. we need to align them. Currently, there exist a number of systems that support users in aligning ontologies, but not many comparative evaluations have been performed and there exists little support to perform such evaluations. However, the study of the properties, the evaluation and comparison of the alignment strategies and their combinations, would give us valuable insight in how the strategies could be used in the best way. In this paper we propose the KitAMO framework for comparative evaluation of ontology alignment strategies and their combinations and present our current implementation. We evaluate the implementation with respect to performance. We also illustrate how the system can be used to evaluate and compare alignment strategies and their combinations in terms of performance and quality of the proposed alignments. Further, we show how the results can be analyzed to obtain deeper insights into the properties of the strategies.

  • 16.
    Lambrix, Patrick
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Aligning Biomedical Ontologies2007Ingår i: Integrative Bioinformatics Workshop,2007, 2007Konferensbidrag (Refereegranskat)
  • 17.
    Lambrix, Patrick
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Merging DAML plus OIL Ontologies2005Ingår i: Databases and Information Systems: (Selected Papers from the Sixth International Baltic Conference DB&IS'2004) / [ed] Janis Barzdins, Albertas Caplinskas, IOS Press, 2005, s. 249-258Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    Modern databases and information systems essentially differ from their predecessors. Ontology-based and knowledge-based approaches to system development, UML based IS development methodologies, XML databases and heterogeneous information models have come to the fore. All these fundamental aspects are discussed in this book. This publication contains a collection of 22 high quality papers written by 44 authors. These articles present original results in modern database technologies, database applications, data warehousing, data mining, ontologies, and modern information systems. Special emphasis is put on multimedia database systems, heterogeneous data integration methods, view optimizations, ontology engineering tools, modeling and model transformations (MDA). Theoretical aspects as well as technical development issues are considered. The intended audience for this book is researchers, advanced students and practitioners who are interested in advanced topics on databases and information systems

  • 18.
    Lambrix, Patrick
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Merging DAML+OIL Ontologies2004Ingår i: International Baltic Conference on Databases and Information Systems,2004, 2004, s. 425-Konferensbidrag (Refereegranskat)
  • 19.
    Lambrix, Patrick
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Ontology alignment and merging2008Ingår i: Anatomy Ontologies for Bioinformatics: Principles and Practice / [ed] Albert Burger, Duncan Davidson, Richard Baldock, Springer Publishing Company, 2008, s. 133-150Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    In recent years many biomedical ontologies, including anatomy ontologies, have been developed. Many of these ontologies contain overlapping information and often we would want to be able to use multiple ontologies. This requires finding the relationships between terms in the different ontologies, i.e. we need to align them. Sometimes we also want to merge ontologies into a new one. In this chapter we give an overview of current ontology alignment and merging systems. We focus on systems that compute similarities between terms in the different ontologies. We present a general framework for these kind of systems and discuss the existing strategies. We also present such a system (SAMBO) and discuss its use using anatomy ontologies. Further, we take a first step in dealing with the problem of using the best alignment algorithms for the ontologies we want to align. We present and illustrate the use of a framework and a tool (KitAMO) for comparative evaluation of ontology alignment strategies and their combinations.

  • 20.
    Lambrix, Patrick
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    SAMBO – A System for Aligning and Merging Biomedical Ontologies2006Ingår i: Journal of Web Semantics, ISSN 1570-8268, E-ISSN 1873-7749, Vol. 4, nr 3, s. 196-206Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Due to the recent explosion of the amount of on-line accessible biomedical data and tools, finding and retrieving the relevant information is not an easy task. The vision of a Semantic Web for life sciences alleviates these difficulties. A key technology for the Semantic Web is ontologies. In recent years many biomedical ontologies have been developed and many of these ontologies contain overlapping information. To be able to use multiple ontologies they have to be aligned or merged. In this paper we propose a framework for aligning and merging ontologies. Further, we developed a system for aligning and merging biomedical ontologies (SAMBO) based on this framework. The framework is also a first step towards a general framework that can be used for comparative evaluations of alignment strategies and their combinations. In this paper we evaluated different strategies and their combinations in terms of quality and processing time and compared SAMBO with two other systems.

  • 21.
    Lambrix, Patrick
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Jakoniené, Vaida
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Strömbäck, Lena
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Biological Ontologies2007Ingår i: Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences / [ed] Christopher J.O. Baker and Kei-Hoi Cheung, Springer , 2007, s. 85-99Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    Biological ontologies define the basic terms and relations in biological domains and are being used among others, as community reference, as the basis for interoperability between systems, and for search, integration, and exchange of biological data. In this chapter we present examples of biological ontologies and ontology-based knowledge, show how biological ontologies are used and discuss some important issues in ontology engineering.

  • 22.
    Lambrix, Patrick
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Liu, Qiang
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    SAMBO and SAMBOdtf results for the Ontology Alignment Evaluation Initiative 20082008Ingår i: Third International Workshop on Ontology Matching, 2008, s. 190-198Konferensbidrag (Refereegranskat)
  • 23.
    Lambrix, Patrick
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Xu, Wei
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik.
    Literature-based alignment of ontologies.2008Ingår i: Third International Workshop on Ontology Matching, 2008, s. 219-223Konferensbidrag (Refereegranskat)
  • 24.
    Strömbäck, Lena
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Jakoniené, Vaida
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Lambrix, Patrick
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Representing, storing and accessing molecular interaction data: a review of models and tools2006Ingår i: Briefings in Bioinformatics, ISSN 1467-5463, E-ISSN 1477-4054, Vol. 7, nr 4, s. 331-338Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    One important aim within systems biology is to integrate disparate pieces of information, leading to discovery of higher-level knowledge about important functionality within living organisms. This makes standards for representation of data and technology for exchange and integration of data important key points for development within the area. In this article, we focus on the recent developments within the field. We compare the recent updates to the three standard representations for exchange of data SBML, PSI MI and BioPAX. In addition, we give an overview of available tools for these three standards and a discussion on how these developments support possibilities for data exchange and integration.

  • 25.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    A study on the relation between linguistics-oriented and domain-specific semantics2010Ingår i: Proceedings of the 3rd International Workshop on Semantic Web Applications and Tools for the Life Sciences, 2010Konferensbidrag (Refereegranskat)
    Abstract [en]

    In this paper we dealt with the comparison and linking between lexical resources with domain knowledge provided by ontologies. It is one of the issues for the combination of the Semantic Web Ontologies and Text Mining. We investigated the relations between the linguisticsoriented and domain-specific semantics, by associating the GO biological process concepts to the FrameNet semantic frames. The result shows the gaps between the linguistics-oriented and domain-specific semantics on the classification of events and the grouping of target words. The result provides valuable information for the improvement of domain ontologies supporting for text mining systems. And also, it will result in benefits to language understanding technology.

  • 26.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, IISLAB - Laboratoriet för intelligenta informationssystem. Linköpings universitet, Tekniska högskolan.
    Aligning and Merging Biomedical Ontologies2006Licentiatavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Due to the explosion of the amount of biomedical data, knowledge and tools that are often publicly available over the Web, a number of difficulties are experienced by biomedical researchers. For instance, it is difficult to find, retrieve and integrate information that is relevant to their research tasks. Ontologies and the vision of a Semantic Web for life sciences alleviate these difficulties. In recent years many biomedical ontologies have been developed and many of these ontologies contain overlapping information. To be able to use multiple ontologies they have to be aligned or merged. A number of systems have been developed for aligning and merging ontologies and various alignment strategies are used in these systems. However, there are no general methods to support building such tools, and there exist very few evaluations of these strategies. In this thesis we give an overview of the existing systems. We propose a general framework for aligning and merging ontologies. Most existing systems can be seen as instantiations of this framework. Further, we develop SAMBO (System for Aligning and Merging Biomedical Ontologies) according to this framework. We implement different alignment strategies and their combinations, and evaluate them in terms of quality and processing time within SAMBO. We also compare SAMBO with two other systems. The work in this thesis is a first step towards a general framework that can be used for comparative evaluations of alignment strategies and their combinations.

    Delarbeten
    1. SAMBO – A System for Aligning and Merging Biomedical Ontologies
    Öppna denna publikation i ny flik eller fönster >>SAMBO – A System for Aligning and Merging Biomedical Ontologies
    2006 (Engelska)Ingår i: Journal of Web Semantics, ISSN 1570-8268, E-ISSN 1873-7749, Vol. 4, nr 3, s. 196-206Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Due to the recent explosion of the amount of on-line accessible biomedical data and tools, finding and retrieving the relevant information is not an easy task. The vision of a Semantic Web for life sciences alleviates these difficulties. A key technology for the Semantic Web is ontologies. In recent years many biomedical ontologies have been developed and many of these ontologies contain overlapping information. To be able to use multiple ontologies they have to be aligned or merged. In this paper we propose a framework for aligning and merging ontologies. Further, we developed a system for aligning and merging biomedical ontologies (SAMBO) based on this framework. The framework is also a first step towards a general framework that can be used for comparative evaluations of alignment strategies and their combinations. In this paper we evaluated different strategies and their combinations in terms of quality and processing time and compared SAMBO with two other systems.

    Ort, förlag, år, upplaga, sidor
    Elsevier, 2006
    Nyckelord
    Ontologies; Alignment; Merging; Biomedical informatics
    Nationell ämneskategori
    Teknik och teknologier
    Identifikatorer
    urn:nbn:se:liu:diva-14575 (URN)10.1016/j.websem.2006.05.003 (DOI)000247054000005 ()
    Tillgänglig från: 2007-07-03 Skapad: 2007-07-03 Senast uppdaterad: 2017-12-13Bibliografiskt granskad
    2. Alignment of Biomedical Ontologies using Life Science Literature
    Öppna denna publikation i ny flik eller fönster >>Alignment of Biomedical Ontologies using Life Science Literature
    Visa övriga...
    2006 (Engelska)Ingår i: KDLL: International Workshop on Knowledge Discovery in Life Science LIterature Knowledge Discovery in Life Science Literature PAKDD 2006 International Workshop, KDLL 2006, Singapore, April 9, 2006. Proceedings / [ed] Eric G. Bremer, Jörg Hakenberg, Eui-Hong (Sam) Han, Daniel Berrar and Werner Dubitzky, Berlin/Heidelberg: Springer, 2006, s. 1-17Konferensbidrag, Publicerat paper (Refereegranskat)
    Abstract [en]

    This book constitutes the refereed proceedings of the International Workshop on Knowledge Discovery in Life Science Literature, KDLL 2006, held in Singapore in conjunction with the 10th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD 2006).

    The 12 revised full papers presented together with two invited talks were carefully reviewed and selected for inclusion in the book. The papers cover all topics of knowledge discovery in life science data such as text mining, identification and retrieval of documents, passage retrieval, co-reference resolution, extraction of life science entities or relationships from large collections, automated characterization of biological, biomedical and biotechnological entities and processes, extraction and characterization of more complex patterns and interaction networks, automated generation of text summaries, automated construction, expansion and curation of ontologies for different domains, and construction of controlled vocabularies.

    Ort, förlag, år, upplaga, sidor
    Berlin/Heidelberg: Springer, 2006
    Serie
    Lecture Notes in Computer Science, ISSN 0302-9743, E-ISSN 1611-3349 ; 3886
    Nationell ämneskategori
    Datavetenskap (datalogi)
    Identifikatorer
    urn:nbn:se:liu:diva-14035 (URN)10.1007/11683568_1 (DOI)000237198800001 ()978-3-540-32809-4 (ISBN)3-540-32809-2 (ISBN)
    Konferens
    KDLL: International Workshop on Knowledge Discovery in Life Science LIterature Knowledge Discovery in Life Science Literature PAKDD 2006 International Workshop, KDLL 2006, Singapore, April 9, 2006
    Tillgänglig från: 2006-09-28 Skapad: 2006-09-28 Senast uppdaterad: 2018-11-27Bibliografiskt granskad
  • 27.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, IISLAB - Laboratoriet för intelligenta informationssystem. Linköpings universitet, Tekniska högskolan.
    Aligning Biomedical Ontologies2007Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    The amount of biomedical information that is disseminated over the Web increases every day. This rich resource is used to find solutions to challenges across the life sciences. The Semantic Web for life sciences shows promise for effectively and efficiently locating, integrating, querying and inferring related information that is needed in daily biomedical research. One of the key technologies in the Semantic Web is ontologies, which furnish the semantics of the Semantic Web. A large number of biomedical ontologies have been developed. Many of these ontologies contain overlapping information, but it is unlikely that eventually there will be one single set of standard ontologies to which everyone will conform. Therefore, applications often need to deal with multiple overlapping ontologies, but the heterogeneity of ontologies hampers interoperability between different ontologies. Aligning ontologies, i.e. identifying relationships between different ontologies, aims to overcome this problem. A number of ontology alignment systems have been developed. In these systems various techniques and ideas have been proposed to facilitate identification of alignments between ontologies. However, there still is a range of issues to be addressed when we have alignment problems at hand. The work in this thesis contributes to three different aspects of identification of high quality alignments: 1) Ontology alignment strategies and systems. We surveyed the existing ontology alignment systems, and proposed a general ontology alignment framework. Most existing systems can be seen as instantiations of the framework. Also, we developed a system for aligning biomedical ontologies (SAMBO) according to this framework. We implemented various alignment strategies in the system. 2) Evaluation of ontology alignment strategies. We developed and implemented the KitAMO framework for comparative evaluation of different alignment strategies, and we evaluated different alignment strategies using the implementation. 3) Recommending optimal alignment strategies for different applications. We proposed a method for making recommendations.

    Delarbeten
    1. SAMBO – A System for Aligning and Merging Biomedical Ontologies
    Öppna denna publikation i ny flik eller fönster >>SAMBO – A System for Aligning and Merging Biomedical Ontologies
    2006 (Engelska)Ingår i: Journal of Web Semantics, ISSN 1570-8268, E-ISSN 1873-7749, Vol. 4, nr 3, s. 196-206Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Due to the recent explosion of the amount of on-line accessible biomedical data and tools, finding and retrieving the relevant information is not an easy task. The vision of a Semantic Web for life sciences alleviates these difficulties. A key technology for the Semantic Web is ontologies. In recent years many biomedical ontologies have been developed and many of these ontologies contain overlapping information. To be able to use multiple ontologies they have to be aligned or merged. In this paper we propose a framework for aligning and merging ontologies. Further, we developed a system for aligning and merging biomedical ontologies (SAMBO) based on this framework. The framework is also a first step towards a general framework that can be used for comparative evaluations of alignment strategies and their combinations. In this paper we evaluated different strategies and their combinations in terms of quality and processing time and compared SAMBO with two other systems.

    Ort, förlag, år, upplaga, sidor
    Elsevier, 2006
    Nyckelord
    Ontologies; Alignment; Merging; Biomedical informatics
    Nationell ämneskategori
    Teknik och teknologier
    Identifikatorer
    urn:nbn:se:liu:diva-14575 (URN)10.1016/j.websem.2006.05.003 (DOI)000247054000005 ()
    Tillgänglig från: 2007-07-03 Skapad: 2007-07-03 Senast uppdaterad: 2017-12-13Bibliografiskt granskad
    2. Alignment of Biomedical Ontologies using Life Science Literature
    Öppna denna publikation i ny flik eller fönster >>Alignment of Biomedical Ontologies using Life Science Literature
    Visa övriga...
    2006 (Engelska)Ingår i: KDLL: International Workshop on Knowledge Discovery in Life Science LIterature Knowledge Discovery in Life Science Literature PAKDD 2006 International Workshop, KDLL 2006, Singapore, April 9, 2006. Proceedings / [ed] Eric G. Bremer, Jörg Hakenberg, Eui-Hong (Sam) Han, Daniel Berrar and Werner Dubitzky, Berlin/Heidelberg: Springer, 2006, s. 1-17Konferensbidrag, Publicerat paper (Refereegranskat)
    Abstract [en]

    This book constitutes the refereed proceedings of the International Workshop on Knowledge Discovery in Life Science Literature, KDLL 2006, held in Singapore in conjunction with the 10th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD 2006).

    The 12 revised full papers presented together with two invited talks were carefully reviewed and selected for inclusion in the book. The papers cover all topics of knowledge discovery in life science data such as text mining, identification and retrieval of documents, passage retrieval, co-reference resolution, extraction of life science entities or relationships from large collections, automated characterization of biological, biomedical and biotechnological entities and processes, extraction and characterization of more complex patterns and interaction networks, automated generation of text summaries, automated construction, expansion and curation of ontologies for different domains, and construction of controlled vocabularies.

    Ort, förlag, år, upplaga, sidor
    Berlin/Heidelberg: Springer, 2006
    Serie
    Lecture Notes in Computer Science, ISSN 0302-9743, E-ISSN 1611-3349 ; 3886
    Nationell ämneskategori
    Datavetenskap (datalogi)
    Identifikatorer
    urn:nbn:se:liu:diva-14035 (URN)10.1007/11683568_1 (DOI)000237198800001 ()978-3-540-32809-4 (ISBN)3-540-32809-2 (ISBN)
    Konferens
    KDLL: International Workshop on Knowledge Discovery in Life Science LIterature Knowledge Discovery in Life Science Literature PAKDD 2006 International Workshop, KDLL 2006, Singapore, April 9, 2006
    Tillgänglig från: 2006-09-28 Skapad: 2006-09-28 Senast uppdaterad: 2018-11-27Bibliografiskt granskad
    3. Structure-Based Filtering for Ontology Alignment
    Öppna denna publikation i ny flik eller fönster >>Structure-Based Filtering for Ontology Alignment
    2006 (Engelska)Ingår i: Proceedings of the IEEE WETICE Workshop on Semantic Technologies in Collaborative Applications, Institute of Electrical and Electronics Engineers (IEEE), 2006, s. 364-369Konferensbidrag, Publicerat paper (Refereegranskat)
    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.

    Ort, förlag, år, upplaga, sidor
    Institute of Electrical and Electronics Engineers (IEEE), 2006
    Nationell ämneskategori
    Teknik och teknologier
    Identifikatorer
    urn:nbn:se:liu:diva-14577 (URN)10.1109/WETICE.2006.64 (DOI)000245542500064 ()9780769526232 (ISBN)
    Konferens
    IEEE WETICE Workshop on Semantic Technologies in Collaborative Applications
    Tillgänglig från: 2007-07-03 Skapad: 2007-07-03 Senast uppdaterad: 2016-12-06
    4. A Tool for Evaluating Ontology Alignment Strategies
    Öppna denna publikation i ny flik eller fönster >>A Tool for Evaluating Ontology Alignment Strategies
    2007 (Engelska)Ingår i: Journal on Data Semantics, ISSN 1861-2032, Vol. VIII, s. 182-202Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Ontologies are an important technology for the Semantic Web. In different areas ontologies have already been developed and many of these ontologies contain overlapping information. Often we would therefore want to be able to use multiple ontologies. To obtain good results, we need to find the relationships between terms in the different ontologies, i.e. we need to align them. Currently, there exist a number of systems that support users in aligning ontologies, but not many comparative evaluations have been performed and there exists little support to perform such evaluations. However, the study of the properties, the evaluation and comparison of the alignment strategies and their combinations, would give us valuable insight in how the strategies could be used in the best way. In this paper we propose the KitAMO framework for comparative evaluation of ontology alignment strategies and their combinations and present our current implementation. We evaluate the implementation with respect to performance. We also illustrate how the system can be used to evaluate and compare alignment strategies and their combinations in terms of performance and quality of the proposed alignments. Further, we show how the results can be analyzed to obtain deeper insights into the properties of the strategies.

    Ort, förlag, år, upplaga, sidor
    Springer Berlin/Heidelberg, 2007
    Nyckelord
    ontologies, alignment, evaluation
    Nationell ämneskategori
    Datavetenskap (datalogi)
    Identifikatorer
    urn:nbn:se:liu:diva-14578 (URN)10.1007/978-3-540-70664-9_7 (DOI)978-3-540-70663-2 (ISBN)
    Tillgänglig från: 2007-07-03 Skapad: 2007-07-03 Senast uppdaterad: 2018-01-13
    5. A Method for Recommending Ontology Alignment Strategies
    Öppna denna publikation i ny flik eller fönster >>A Method for Recommending Ontology Alignment Strategies
    2007 (Engelska)Ingår i: ISWC: International Semantic Web Conference ASWC: Asian Semantic Web Conference The Semantic Web 6th International Semantic Web Conference, 2nd Asian Semantic Web Conference, ISWC 2007 + ASWC 2007, Busan, Korea, November 11-15, 2007. Proceedings / [ed] Karl Aberer, Key-Sun Choi, Natasha Noy, Dean Allemang, Kyung-Il Lee, Lyndon Nixon, Jennifer Golbeck, Peter Mika, Diana Maynard, Riichiro Mizoguchi, Guus Schreiber, Philippe Cudré-Mauroux, Springer Berlin/Heidelberg, 2007, s. 494-507Konferensbidrag, Publicerat paper (Refereegranskat)
    Abstract [en]

    In different areas ontologies have been developed and many of these ontologies contain overlapping information. Often we would therefore want to be able to use multiple ontologies. To obtain good results, we need to find the relationships between terms in the different ontologies, i.e. we need to align them. Currently, there already exist a number of different alignment strategies. However, it is usually difficult for a user that needs to align two ontologies to decide which of the different available strategies are the most suitable. In this paper we propose a method that provides recommendations on alignment strategies for a given alignment problem. The method is based on the evaluation of the different available alignment strategies on several small selected pieces from the ontologies, and uses the evaluation results to provide recommendations. In the paper we give the basic steps of the method, and then illustrate and discuss the method in the setting of an alignment problem with two well-known biomedical ontologies. We also experiment with different implementations of the steps in the method.

    Ort, förlag, år, upplaga, sidor
    Springer Berlin/Heidelberg, 2007
    Serie
    Lecture Notes in Computer Science, ISSN 0302-9743, E-ISSN 1611-3349 ; 4825
    Nationell ämneskategori
    Datavetenskap (datalogi)
    Identifikatorer
    urn:nbn:se:liu:diva-14579 (URN)10.1007/978-3-540-76298-0_36 (DOI)000251080500036 ()978-3-540-76297-3 (ISBN)
    Konferens
    The Semantic Web 6th International Semantic Web Conference, 2nd Asian Semantic Web Conference, ISWC 2007 + ASWC 2007, Busan, Korea, November 11-15, 2007
    Anmärkning

    The book is based on the proceedings presented at the 6th International Semantic Web Conference, 2nd Asian Semantic Web Conference, Busan, Korea, November 11-15, 2007.

    Tillgänglig från: 2007-07-03 Skapad: 2007-07-03 Senast uppdaterad: 2018-11-27Bibliografiskt granskad
  • 28.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Knowledge-based Gene Symbol Disambiguation2008Ingår i: Second International Workshop on Data and Text Mining in Bioinformatics,2008, New York: ACM , 2008, s. 73-76Konferensbidrag (Refereegranskat)
    Abstract [en]

    Since there is no standard naming convention for genes and gene products, gene symbol disambiguation (GSD) has become a big challenge when mining biomedical literature. Several GSD methods have been proposed based on Medline references to genes. However, nowadays gene databases, e.g. Entrez Gene, provide plenty of information about genes, and many biomedical ontologies, e.g. UMLS Metathesaurus and Semantic Network, have been developed. These knowledge sources could be used for disambiguation, in this paper we propose a method which relies on information about gene candidates from gene databases, contexts of gene symbols and biomedical ontologies. We implement our method, and evaluate the performance of the implementation using BioCreAtIvE II data sets.

  • 29.
    Tan, He
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Jakoniené, Vaida
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Lambrix, Patrick
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Åberg, Johan
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Shahmehri, Nahid
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Alignment of Biomedical Ontologies using Life Science Literature2006Ingår i: KDLL: International Workshop on Knowledge Discovery in Life Science LIterature Knowledge Discovery in Life Science Literature PAKDD 2006 International Workshop, KDLL 2006, Singapore, April 9, 2006. Proceedings / [ed] Eric G. Bremer, Jörg Hakenberg, Eui-Hong (Sam) Han, Daniel Berrar and Werner Dubitzky, Berlin/Heidelberg: Springer, 2006, s. 1-17Konferensbidrag (Refereegranskat)
    Abstract [en]

    This book constitutes the refereed proceedings of the International Workshop on Knowledge Discovery in Life Science Literature, KDLL 2006, held in Singapore in conjunction with the 10th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD 2006).

    The 12 revised full papers presented together with two invited talks were carefully reviewed and selected for inclusion in the book. The papers cover all topics of knowledge discovery in life science data such as text mining, identification and retrieval of documents, passage retrieval, co-reference resolution, extraction of life science entities or relationships from large collections, automated characterization of biological, biomedical and biotechnological entities and processes, extraction and characterization of more complex patterns and interaction networks, automated generation of text summaries, automated construction, expansion and curation of ontologies for different domains, and construction of controlled vocabularies.

  • 30.
    Tan, He
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Kaliyaperumal, Rajaram
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Benis, Nirupama
    Linköpings universitet, Institutionen för medicinsk teknik. Linköpings universitet, Tekniska högskolan.
    Building frame-based corpus on the basis of ontological domain knowledge2011Ingår i: Proceedings of the Workshop on BioNLP, Association for Computational Linguistics, 2011, s. 74-82Konferensbidrag (Refereegranskat)
    Abstract [en]

    Semantic Role Labeling (SRL) plays a key role in many NLP applications. The development of SRL systems for the biomedical domain is frustrated by the lack of large domain-specific corpora that are labeled with semantic roles. Corpus development has been very expensive and time-consuming. In this paper we propose a method for building frame-based corpus on the basis of domain knowledge provided by ontologies. We believe that ontologies, as a structured and semantic representation of domain knowledge, can instruct and ease the tasks in building the corpora. In the paper we present a corpus built by using the method. We compared it to BioFrameNet, and examined the gaps between the semantic classification of the target words in the domain-specific corpus and in FrameNet and Prop-Bank/VerbNet.

  • 31.
    Tan, He
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Kaliyaperumal, Rajaram
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Benis, Nirupama
    Linköpings universitet, Institutionen för medicinsk teknik. Linköpings universitet, Tekniska högskolan.
    Ontology-driven Construction of Corpus with Frame Semantics Annotations2011Ingår i: poster at The Fourth International Symposium on Languages in Biology and Medicine, 2011Konferensbidrag (Refereegranskat)
  • 32.
    Tan, He
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Kaliyaperumal, Rajaram
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Benis, Nirupama
    Linköpings universitet, Institutionen för medicinsk teknik. Linköpings universitet, Tekniska högskolan.
    Ontology-Driven Construction of Domain Corpus with Frame Semantics Annotations2012Ingår i: Computational linguistics and intelligent text processing, Springer Berlin/Heidelberg, 2012, s. 54-65Konferensbidrag (Refereegranskat)
    Abstract [en]

    Semantic Role Labeling plays a key role in many text mining applications. The development of SRL systems for the biomedical domain is frustrated by the lack of large domain specific corpora that are labeled with semantic roles. In this paper we proposed a method for building corpus that are labeled with semantic roles for the domain of biomedicine. The method is based on the theory of frame semantics, and uses domain knowledge provided by ontologies. By using the method, we have built a corpus for transport events strictly following the domain knowledge provided by GO biological process ontology. We compared one of our frames to a BioFrameNet frame. We also examined the gaps between the semantic classification of the target words in this domain-specific corpus and in FrameNet and PropBank/VerbNet data. The successful corpus construction demonstrates that ontologies, as a formal representation of domain knowledge, can instruct us and ease all the tasks in building this kind of corpus. Furthermore, ontological domain knowledge leads to well-defined semantics exposed on the corpus, which will be very valuable in text mining applications.

  • 33.
    Tan, He
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Lambrix, Patrick
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    A Method for Recommending Ontology Alignment Strategies2007Ingår i: ISWC: International Semantic Web Conference ASWC: Asian Semantic Web Conference The Semantic Web 6th International Semantic Web Conference, 2nd Asian Semantic Web Conference, ISWC 2007 + ASWC 2007, Busan, Korea, November 11-15, 2007. Proceedings / [ed] Karl Aberer, Key-Sun Choi, Natasha Noy, Dean Allemang, Kyung-Il Lee, Lyndon Nixon, Jennifer Golbeck, Peter Mika, Diana Maynard, Riichiro Mizoguchi, Guus Schreiber, Philippe Cudré-Mauroux, Springer Berlin/Heidelberg, 2007, s. 494-507Konferensbidrag (Refereegranskat)
    Abstract [en]

    In different areas ontologies have been developed and many of these ontologies contain overlapping information. Often we would therefore want to be able to use multiple ontologies. To obtain good results, we need to find the relationships between terms in the different ontologies, i.e. we need to align them. Currently, there already exist a number of different alignment strategies. However, it is usually difficult for a user that needs to align two ontologies to decide which of the different available strategies are the most suitable. In this paper we propose a method that provides recommendations on alignment strategies for a given alignment problem. The method is based on the evaluation of the different available alignment strategies on several small selected pieces from the ontologies, and uses the evaluation results to provide recommendations. In the paper we give the basic steps of the method, and then illustrate and discuss the method in the setting of an alignment problem with two well-known biomedical ontologies. We also experiment with different implementations of the steps in the method.

  • 34.
    Tan, He
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Lambrix, Patrick
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Aligning and merging biomedical ontologies2006Ingår i: Seventh Swedish Bioinformatics Workshop for PhD students and PostDocs,2006, 2006, s. 18-18Konferensbidrag (Övrigt vetenskapligt)
  • 35.
    Tan, He
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Lambrix, Patrick
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    SAMBO results for the Ontology Alignment Evaluation Initiative 20072007Ingår i: International Workshop on Ontology Matching,2007, CEURWS , 2007, s. 236-Konferensbidrag (Refereegranskat)
    Abstract [en]

    This article describes a system for ontology alignment, SAMBO, and presents its results for the benchmark and anatomy tasks in the 2007 Ontology Alignment Evaluation Initiative. For the benchmark task we have used a strategy based on string matching as well as the use of a thesaurus, and obtained good results in many cases. For the anatomy task we have used a combination of string matching and the use of domain knowledge. This combination performed well in former evaluations using other anatomy ontologies.

  • 36.
    Tan, He
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Lambrix, Patrick
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Selecting an ontology for biomedical text mining2009Ingår i: 17th Conference on Intelligent Systems for Molecular Biology, 2009Konferensbidrag (Refereegranskat)
  • 37.
    Tan, He
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Lambrix, Patrick
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Selecting an ontology for biomedical text mining2009Ingår i: Workshop on BioNLP, 2009, s. 55-62Konferensbidrag (Refereegranskat)
  • 38.
    Wächter, Thomas
    et al.
    Biotechnologisches Zentrum, TU Dresden, Germany.
    Tan, He
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Wobst, André
    Biotechnologisches Zentrum, TU Dresden, Germany.
    Lambrix, Patrick
    Linköpings universitet, Institutionen för datavetenskap, Databas och informationsteknik. Linköpings universitet, Tekniska högskolan.
    Schroeder, Michael
    Biotechnologisches Zentrum, TU Dresden, Germany.
    A Corpus-driven Approach for Design, Evolution and Alignment of Ontologies2006Ingår i: Winter Simulation Conference,2006, 2006, s. 1595-Konferensbidrag (Refereegranskat)
    Abstract [en]

    Bio-ontologies are hierarchical vocabularies, which are used to annotate other data sources such as sequence and structure databases. With the wide use of ontologies their integration, design, and evolution becomes an important problem. We show how textmining on relevant text corpora can be used to identify matching ontology terms of two separate ontologies and to propose new ontology terms for a given term. We evaluate these approaches on the GeneOntology.

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