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Aligning and Merging Biomedical Ontologies
Linköpings universitet, Institutionen för datavetenskap, IISLAB - Laboratoriet för intelligenta informationssystem.
2006 (English)Licentiate thesis, comprehensive summary (Other academic)
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.

Place, publisher, year, edition, pages
Linköping: Institutionen för datavetenskap , 2006. , 14 p.
Series
Linköping Studies in Science and Technology. Thesis, ISSN 0280-7971 ; 1225
Keyword [en]
Ontologies, Ontology engineering, Biomedical ontologies, Ontology alignment, Ontology merging, Information technology
National Category
Computer and Information Science
Identifiers
URN: urn:nbn:se:hj:diva-18793OAI: oai:DiVA.org:hj-18793DiVA: diva2:573274
Opponent
Supervisors
Available from: 2012-11-30 Created: 2012-06-27 Last updated: 2012-11-30Bibliographically approved
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, 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.

Keyword
Ontologies; Alignment; Merging; Biomedical informatics, TECHNOLOGY, TEKNIKVETENSKAP
National Category
Engineering and Technology
Identifiers
urn:nbn:se:hj:diva-18791 (URN)10.1016/j.websem.2006.05.003 (DOI)
Available from: 2012-07-30 Created: 2012-06-27 Last updated: 2012-11-30Bibliographically 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: Knowledge Discovery in Life Science Literature: PAKDD 2006 International Workshop, KDLL 2006, Singapore, April 9, 2006, Proceedings, 2006, 1-17 p.Conference paper, Published paper (Refereed)
Abstract [en]

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. In this paper we propose strategies for aligning ontologies based on life science literature. We propose a basic algorithm as well as extensions that take the structure of the ontologies into account. We evaluate the strategies and compare them with strategies implemented in the alignment system SAMBO. We also evaluate the combination of the proposed strategies and the SAMBO strategies.

Series
Lecture notes in computer science
Keyword
TECHNOLOGY, TEKNIKVETENSKAP
National Category
Engineering and Technology
Identifiers
urn:nbn:se:hj:diva-18792 (URN)10.1007/11683568_1 (DOI)
Conference
International Workshop on Knowledge Discovery in Life Science Literature 2006 (KDLL 2006)
Available from: 2012-07-31 Created: 2012-06-27 Last updated: 2012-11-30Bibliographically approved

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Citation style
  • apa
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Output format
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