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Completing the is-a structure in light-weight ontologies
Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology. Swedish e-Science Research Centre, Linköping University, Sweden . (IDA/ADIT)ORCID iD: 0000-0002-9084-0470
Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
2015 (English)In: Journal of Biomedical Semantics, ISSN 2041-1480, E-ISSN 2041-1480, Vol. 6, 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.

Place, publisher, year, edition, pages
2015. Vol. 6, 12
National Category
Computer Science Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:liu:diva-116628DOI: 10.1186/s13326-015-0002-8ISI: 000353197200001PubMedID: 25883780OAI: oai:DiVA.org:liu-116628DiVA: diva2:799065
Funder
Swedish e‐Science Research CenterCUGS (National Graduate School in Computer Science)
Available from: 2015-03-29 Created: 2015-03-29 Last updated: 2017-12-04
In thesis
1. Completion of Ontologies and Ontology Networks
Open this publication in new window or tab >>Completion of Ontologies and Ontology Networks
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. 65 p.
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1852
Keyword
knowledge representation, ontology, ontology engineering, ontology debugging, ontology completion, ontology matching, description logics
National Category
Computer Science
Identifiers
urn:nbn:se:liu:diva-139487 (URN)10.3384/diss.diva-139487 (DOI)978-91-7685-522-5 (ISBN)
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-608142
Available from: 2017-08-22 Created: 2017-08-21 Last updated: 2017-08-29Bibliographically approved

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