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Aligning Biomedical Ontologies
Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems. Linköping University, The Institute of Technology.
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
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.

Place, publisher, year, edition, pages
Institutionen för datavetenskap , 2007. , 24 p.
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1110
Keyword [en]
ontologies, biomedical ontologies, aligning ontologies, semantic web, knowledge management
National Category
Computer Science
Identifiers
URN: urn:nbn:se:liu:diva-9487ISBN: 978-91-85831-56-2 (print)OAI: oai:DiVA.org:liu-9487DiVA: diva2:23940
Public defence
2007-09-03, Visionen, Hus B, Campus Valla, Linköpings universitet, Linköping, 13:15 (English)
Supervisors
Available from: 2007-07-03 Created: 2007-07-03 Last updated: 2017-08-15
List of papers
1. SAMBO – A System for Aligning and Merging Biomedical Ontologies
Open this publication in new window or tab >>SAMBO – A System for Aligning and Merging Biomedical Ontologies
2006 (English)In: Journal of Web Semantics, ISSN 1570-8268, E-ISSN 1873-7749, Vol. 4, no 3, 196-206 p.Article in journal (Refereed) 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.

Place, publisher, year, edition, pages
Elsevier, 2006
Keyword
Ontologies; Alignment; Merging; Biomedical informatics
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-14575 (URN)10.1016/j.websem.2006.05.003 (DOI)000247054000005 ()
Available from: 2007-07-03 Created: 2007-07-03 Last updated: 2017-12-13Bibliographically approved
2. Alignment of Biomedical Ontologies using Life Science Literature
Open this publication in new window or tab >>Alignment of Biomedical Ontologies using Life Science Literature
Show others...
2006 (English)In: Proceedings of the International Workshop on Knowledge Discovery in Life Science Literature / [ed] Eric G. Bremer, Springer Berlin/Heidelberg, 2006, 1-17 p.Chapter in book (Refereed)
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.

Place, publisher, year, edition, pages
Springer Berlin/Heidelberg, 2006
Series
Lecture Notes in Computer Science, ISSN 0302-9743 (print), 1611-3349 (online) ; 3886
National Category
Computer Science
Identifiers
urn:nbn:se:liu:diva-14035 (URN)10.1007/11683568_1 (DOI)000237198800001 ()978-3-540-32809-4 (ISBN)3-540-32809-2 (ISBN)
Available from: 2006-09-28 Created: 2006-09-28 Last updated: 2016-12-06Bibliographically approved
3. Structure-Based Filtering for Ontology Alignment
Open this publication in new window or tab >>Structure-Based Filtering for Ontology Alignment
2006 (English)In: 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, Published 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.

Place, publisher, year, edition, pages
Institute of Electrical and Electronics Engineers (IEEE), 2006
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-14577 (URN)10.1109/WETICE.2006.64 (DOI)000245542500064 ()9780769526232 (ISBN)
Conference
IEEE WETICE Workshop on Semantic Technologies in Collaborative Applications
Available from: 2007-07-03 Created: 2007-07-03 Last updated: 2016-12-06
4. A Tool for Evaluating Ontology Alignment Strategies
Open this publication in new window or tab >>A Tool for Evaluating Ontology Alignment Strategies
2007 (English)In: Journal on Data Semantics, ISSN 1861-2032, Vol. VIII, 182-202 p.Article in journal (Refereed) 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.

Place, publisher, year, edition, pages
Springer Berlin/Heidelberg, 2007
Keyword
ontologies, alignment, evaluation
National Category
Computer Science
Identifiers
urn:nbn:se:liu:diva-14578 (URN)10.1007/978-3-540-70664-9_7 (DOI)978-3-540-70663-2 (ISBN)
Available from: 2007-07-03 Created: 2007-07-03 Last updated: 2015-02-18
5. A Method for Recommending Ontology Alignment Strategies
Open this publication in new window or tab >>A Method for Recommending Ontology Alignment Strategies
2007 (English)In: Proceedings of the 6th International Semantic Web Conference and 2nd Asian Semantic Web Conference - ISWC / ASWC 07 / [ed] International Semantic Web Conference, Springer Berlin/Heidelberg, 2007, 494-507 p.Chapter in book (Refereed)
Abstract [en]

In different areas ontologies have been developed and many of these ontologies contain overlapping information. Often we would therefore want to be able to use multiple ontologies. To obtain good results, we need to find the relationships between terms in the different ontologies, i.e. we need to align them. Currently, there already exist a number of 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.

Place, publisher, year, edition, pages
Springer Berlin/Heidelberg, 2007
Series
Lecture Notes in Computer Science, ISSN 0302-9743 (print), 1611-3349 (online) ; 4825
National Category
Computer Science
Identifiers
urn:nbn:se:liu:diva-14579 (URN)10.1007/978-3-540-76298-0_36 (DOI)000251080500036 ()978-3-540-76297-3 (ISBN)
Conference
ISWC 2007
Note

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.

Available from: 2007-07-03 Created: 2007-07-03 Last updated: 2016-12-05Bibliographically approved

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