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Completion of Ontologies and Ontology Networks
Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, Faculty of Science & Engineering.
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The World Wide Web contains large amounts of data, and in most cases this data has no explicit structure. The lack of structure makes it difficult for automated agents to understand and use such data. A step towards a more structured World Wide Web is the Semantic Web, which aims at introducing semantics to data on the World Wide Web. One of the key technologies in this endeavour are ontologies, which provide a means for modeling a domain of interest and are used for search and integration of data.

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

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

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

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2017. , p. 65
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1852
Keywords [en]
knowledge representation, ontology, ontology engineering, ontology debugging, ontology completion, ontology matching, description logics
National Category
Computer Sciences
Identifiers
URN: urn:nbn:se:liu:diva-139487DOI: 10.3384/diss.diva-139487ISBN: 978-91-7685-522-5 (print)OAI: oai:DiVA.org:liu-139487DiVA, id: diva2:1134727
Public defence
2017-09-26, Ada Lovelace, Linköping University, Linköping, 13:15 (English)
Opponent
Supervisors
Funder
Swedish e‐Science Research CenterSwedish Research Council, 2010-4759CUGS (National Graduate School in Computer Science)EU, FP7, Seventh Framework Programme, FP7-IP-608142Available from: 2017-08-22 Created: 2017-08-21 Last updated: 2018-01-13Bibliographically approved
List of papers
1. Completing the is-a structure in light-weight ontologies
Open this publication in new window or tab >>Completing the is-a structure in light-weight ontologies
2015 (English)In: Journal of Biomedical Semantics, ISSN 2041-1480, E-ISSN 2041-1480, Vol. 6, article id 12Article in journal (Refereed) Published
Abstract [en]

 Background: With the increasing presence of biomedical data sources on the Internet more and more research effort is put into finding possible ways for integrating and searching such often heterogeneous sources. Ontologies are a key technology in this effort. However, developing ontologies is not an easy task and often the resulting ontologies are not complete. In addition to being problematic for the correct modelling of a domain, such incomplete ontologies, when used in semantically-enabled applications, can lead to valid conclusions being missed.

Results: We consider the problem of repairing missing is-a relations in ontologies. We formalize the problem as a generalized TBox abduction problem. Based on this abduction framework, we present complexity results for the existence, relevance and necessity decision problems for the generalized TBox abduction problem with and without some specific preference relations for ontologies that can be represented using a member of the EL family of description logics. Further, we present algorithms for finding solutions, a system as well as experiments.

Conclusions: Semantically-enabled applications need high quality ontologies and one key aspect is their completeness. We have introduced a framework and system that provides an environment for supporting domain experts to complete the is-a structure of ontologies. We have shown the usefulness of the approach in different experiments. For the two Anatomy ontologies from the Ontology Alignment Evaluation Initiative, we repaired 94 and 58 initial given missing is-a relations, respectively, and detected and repaired additionally, 47 and 10 missing is-a relations. In an experiment with BioTop without given missing is-a relations, we detected and repaired 40 new missing is-a relations.

National Category
Computer Sciences Bioinformatics (Computational Biology)
Identifiers
urn:nbn:se:liu:diva-116628 (URN)10.1186/s13326-015-0002-8 (DOI)000353197200001 ()25883780 (PubMedID)
Funder
Swedish e‐Science Research CenterCUGS (National Graduate School in Computer Science)
Available from: 2015-03-29 Created: 2015-03-29 Last updated: 2018-01-11
2. Get my pizza right: Repairing missing is-a relations in ALC ontologies
Open this publication in new window or tab >>Get my pizza right: Repairing missing is-a relations in ALC ontologies
2012 (English)In: Second Joint International Semantic Technology Conference, Springer Berlin/Heidelberg, 2012, p. 17-32Conference paper, Published paper (Refereed)
Abstract [en]

With the increased use of ontologies in semantically-enabled applications, the issue of debugging defects in ontologies has become increasingly important. These defects can lead to wrong or incomplete results for the applications. Debugging consists of the phases of detection and repairing. In this paper we focus on the repairing phase of a particular kind of defects, i.e. the missing relations in the is-a hierarchy. Previous work has dealt with the case of taxonomies. In this work we extend the scope to deal with ALC ontologies that can be represented using acyclic terminologies. We present algorithms and discuss a system.

Place, publisher, year, edition, pages
Springer Berlin/Heidelberg, 2012
Series
Lecture Notes in Computer Science, ISSN 0302-9743, E-ISSN 1611-3349 ; 7774
Keywords
ontologies, ontology engineering, ontology debugging, knowledge representation
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-91435 (URN)10.1007/978-3-642-37996-3_2 (DOI)978-3-642-37995-6 (ISBN)978-3-642-37996-3 (ISBN)
Conference
Joint International Semantic Technology Conference
Funder
Swedish e‐Science Research CenterSwedish Research Council, 2010-4759CUGS (National Graduate School in Computer Science)
Available from: 2013-04-24 Created: 2013-04-24 Last updated: 2018-07-17
3. Reducing the search space in ontology alignment using clustering techniques and topic identification
Open this publication in new window or tab >>Reducing the search space in ontology alignment using clustering techniques and topic identification
2015 (English)In: Proceedings of the 8th International Conference on Knowledge Capture, New York: ACM Digital Library, 2015, p. 21-Conference paper, Published paper (Refereed)
Abstract [en]

One of the current challenges in ontology alignment is scalability and one technique to deal with this issue is to reduce the search space for the generation of mapping suggestions. In this paper we develop a method to prune that search space by using clustering techniques and topic identification. Further, we provide experiments showing that we are able to generate partitions that allow for high quality alignments with a highly reduced effort for computation and validation of mapping suggestions for the parts of the ontologies in the partition. Other techniques will still be needed for finding mappings that are not in the partition.

Place, publisher, year, edition, pages
New York: ACM Digital Library, 2015
Keywords
Knowledge representation, data mining, ontology alignment
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-121838 (URN)10.1145/2815833.2816959 (DOI)978-1-4503-3849-3 (ISBN)
Conference
8th International Conference on Knowledge Capture
Funder
CUGS (National Graduate School in Computer Science)Swedish e‐Science Research CenterEU, FP7, Seventh Framework Programme, FP7-IP-608142
Available from: 2015-10-09 Created: 2015-10-09 Last updated: 2018-01-11
4. Experiences from the Anatomy track in the Ontology Alignment Evaluation Initiative
Open this publication in new window or tab >>Experiences from the Anatomy track in the Ontology Alignment Evaluation Initiative
2017 (English)In: Journal of Biomedical Semantics, ISSN 2041-1480, E-ISSN 2041-1480, Vol. 8, article id 56Article, review/survey (Refereed) Published
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.

Place, publisher, year, edition, pages
BioMed Central, 2017
Keywords
ontologies, ontology matching, OAEI, anatomy
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-139775 (URN)10.1186/s13326-017-0166-5 (DOI)000416915300001 ()29202830 (PubMedID)
Funder
Swedish e‐Science Research CenterCUGS (National Graduate School in Computer Science)EU, FP7, Seventh Framework Programme, FP7-IP-608142
Note

Funding agencies: Swedish e-Science Research Centre (SeRC); Swedish national graduate school in computer science (CUGS); EU project VALCRI [FP7-IP-608142]

Available from: 2017-08-21 Created: 2017-08-21 Last updated: 2018-01-13
5. User validation in ontology alignment
Open this publication in new window or tab >>User validation in ontology alignment
Show others...
2016 (English)In: The Semantic Web - ISWC 2016: 15th International Semantic Web Conference, Kobe, Japan, October 17–21, 2016, Proceedings, Part I / [ed] Paul Groth, Elena Simperl, Alasdair Gray, Marta Sabou, Markus Krötzsch, Freddy Lecue, Fabian Flöck and Yolanda Gil, Cham, Switzerland: Springer Publishing Company, 2016, p. 200-217Conference paper, Published paper (Refereed)
Abstract [en]

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

Place, publisher, year, edition, pages
Cham, Switzerland: Springer Publishing Company, 2016
Series
Lecture Notes in Computer Science, ISSN 0302-9743, E-ISSN 1611-3349 ; 9981
Keywords
knowledge representation, user interfaces, ontology engineering, ontology alignment
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-131806 (URN)10.1007/978-3-319-46523-4_13 (DOI)000389086500013 ()9783319465227 (ISBN)9783319465234 (ISBN)
Conference
International Semantic Web Conference
Funder
Swedish e‐Science Research CenterCUGS (National Graduate School in Computer Science)EU, FP7, Seventh Framework Programme, FP7-IP-608142
Available from: 2016-10-07 Created: 2016-10-07 Last updated: 2018-07-17Bibliographically approved
6. Integrating Ontology Debugging and Matching into the eXtreme Design Methodology
Open this publication in new window or tab >>Integrating Ontology Debugging and Matching into the eXtreme Design Methodology
2015 (English)In: Proceedings of the 6th Workshop on Ontology and Semantic Web Patterns (WOP 2015) / [ed] Eva Blomqvist; Pascal Hitzler; Adila Krisnadhi; Tom Narock; Monika Solanki, Rheinisch-Westfaelische Technische Hochschule Aachen University , 2015Conference paper, Published paper (Refereed)
Abstract [en]

Ontology design patterns (ODPs) and related ontology development methodologies were designed as ways of sharing and reusing best practices in ontology engineering. However, while the use of these reduces the number of issues in the resulting ontologies defects can still be introduced into the ontology due to improper use or misinterpretation of the patterns. Thus, the quality of the developed ontologies is still a major concern. In this paper we address this issue by describing how ontology debugging and matching can be integrated in a state-of-the-art ontology development methodology based on ontology design patterns- the eXtreme Design methodology, and show the advantages in a case study based on a real world ontology.

Place, publisher, year, edition, pages
Rheinisch-Westfaelische Technische Hochschule Aachen University, 2015
Series
CEUR Workshop Proceedings, ISSN 1613-0073 ; 1461
National Category
Media and Communication Technology
Identifiers
urn:nbn:se:liu:diva-121794 (URN)
Conference
6th Workshop on Ontology and Semantic Web Patterns (WOP 2015), Bethlehem, Pensylvania, USA, October 11, 2015
Funder
EU, FP7, Seventh Framework Programme, FP7-IP-608142CUGS (National Graduate School in Computer Science)Swedish e‐Science Research Center
Available from: 2015-10-06 Created: 2015-10-06 Last updated: 2018-01-11Bibliographically approved

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