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Dragisic, Zlatan
Publications (10 of 14) Show all publications
Lambrix, P., Wei-Kleiner, F. & Dragisic, Z. (2015). Completing the is-a structure in light-weight ontologies. Journal of Biomedical Semantics, 6, Article ID 12.
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
Dragisic, Z., Lambrix, P. & Blomqvist, E. (2015). Integrating Ontology Debugging and Matching into the eXtreme Design Methodology. In: Eva Blomqvist; Pascal Hitzler; Adila Krisnadhi; Tom Narock; Monika Solanki (Ed.), Proceedings of the 6th Workshop on Ontology and Semantic Web Patterns (WOP 2015): . Paper presented at 6th Workshop on Ontology and Semantic Web Patterns (WOP 2015), Bethlehem, Pensylvania, USA, October 11, 2015. Rheinisch-Westfaelische Technische Hochschule Aachen University
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
Chiatti, A., Dragisic, Z., Cerquitelli, T. & Lambrix, P. (2015). Reducing the search space in ontology alignment using clustering techniques and topic identification. In: Proceedings of the 8th International Conference on Knowledge Capture: . Paper presented at 8th International Conference on Knowledge Capture (pp. 21). New York: ACM Digital Library
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
Cheatham, M., Dragisic, Z., Euzenat, J., Faria, D., Ferrara, A., Flouris, G., . . . Zamazal, O. (2015). Results of the Ontology Alignment Evaluation Initiative 2015. In: Ontology Matching: . Paper presented at Ontology Matching (pp. 60-115).
Open this publication in new window or tab >>Results of the Ontology Alignment Evaluation Initiative 2015
Show others...
2015 (English)In: Ontology Matching, 2015, p. 60-115Conference paper, Published paper (Refereed)
Series
CEUR Workshop Proceedings, ISSN 1613-0073 ; 1545
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-123885 (URN)
Conference
Ontology Matching
Available from: 2016-01-12 Created: 2016-01-12 Last updated: 2018-07-17
Dragisic, Z., Lambrix, P. & Wei-Kleiner, F. (2014). A System for Debugging Missing Is-a Structure in EL Ontologies. In: Proceedings of the Third International Workshop on Debugging Ontologies and Ontology Mappings - WoDOOM14: . Paper presented at Third International Workshop on Debugging Ontologies and Ontology Mappings (WoDOOM 2014), May 26, 2014, Anissaras/Hersonissou, Greece (pp. 51-58).
Open this publication in new window or tab >>A System for Debugging Missing Is-a Structure in EL Ontologies
2014 (English)In: Proceedings of the Third International Workshop on Debugging Ontologies and Ontology Mappings - WoDOOM14, 2014, p. 51-58Conference paper, Published paper (Refereed)
Series
CEUR Workshop Proceedings, ISSN 1613-0073 ; 1162
Keywords
ontologies, knowledge representation
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-107320 (URN)
Conference
Third International Workshop on Debugging Ontologies and Ontology Mappings (WoDOOM 2014), May 26, 2014, Anissaras/Hersonissou, Greece
Funder
Swedish e‐Science Research CenterSwedish Research Council, 2010-4759CUGS (National Graduate School in Computer Science)
Available from: 2014-06-10 Created: 2014-06-10 Last updated: 2018-01-11Bibliographically approved
Wei-Kleiner, F., Dragisic, Z. & Lambrix, P. (2014). Abduction Framework for Repairing Incomplete EL Ontologies:  Complexity Results and Algorithms. In: Proceedings of the 28th AAAI Conference on Artificial Intelligence: . Paper presented at 28th AAAI Conference on Artificial Intelligence (pp. 1120-1127). Palo Alto, CA, USA: AAAI Press
Open this publication in new window or tab >>Abduction Framework for Repairing Incomplete EL Ontologies:  Complexity Results and Algorithms
2014 (English)In: Proceedings of the 28th AAAI Conference on Artificial Intelligence, Palo Alto, CA, USA: AAAI Press, 2014, p. 1120-1127Conference paper, Published paper (Refereed)
Abstract [en]

In this paper we consider the problem of repairing  missing is-a relations in ontologies.We formalize the problem as a generalized TBox abduction problem (GTAP). Based on this abduction framework, we  present complexity results for the existence, relevance and necessity decision problems for the GTAP 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.

Place, publisher, year, edition, pages
Palo Alto, CA, USA: AAAI Press, 2014
Keywords
ontology; ontology debugging; semantic web, knowledge representation; abductive reasoning
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-109039 (URN)2-s2.0-84908159683 (Scopus ID)9781577356783 (ISBN)
Conference
28th AAAI Conference on Artificial Intelligence
Funder
Swedish e‐Science Research CenterCUGS (National Graduate School in Computer Science)
Available from: 2014-07-31 Created: 2014-07-31 Last updated: 2018-01-11
Dragisic, Z. (2014). Completing the Is-a Structure in Description Logics Ontologies. (Licentiate dissertation). Linköping: Linköping University Electronic Press
Open this publication in new window or tab >>Completing the Is-a Structure in Description Logics Ontologies
2014 (English)Licentiate thesis, monograph (Other academic)
Abstract [en]

The World Wide Web contains large amounts of data and in most cases this data is without any 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 idea of 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 means for modeling a domain of interest.

Developing and maintaining ontologies is not an easy task and it is often the case that defects are introduced into ontologies. This can be a problem for semantically-enabled applications such as ontology-based querying. Defects in ontologies directly influence the quality of the results of such applications as correct results can be missed and wrong results can be returned.

This thesis considers one type of defects in ontologies, namely the problem of completing the is-a structure in ontologies represented in description logics. We focus on two variants of description logics, the EL family and ALC, which are often used in practice.

The contributions of this thesis are as follows. First, we formalize the problem of completing the is-a structure as a generalized TBox abduction problem (GTAP) which is a new type of abduction problem in description logics. Next, we provide algorithms for solving GTAP in the EL family and ALC description logics. Finally, we describe two implemented systems based on the introduced algorithms. The systems were evaluated in two experiments which have shown the usefulness of our approach. For example, in one experiment using ontologies from the Ontology Alignment Evaluation Initiative 58 and 94 detected missing is-a relations were repaired by adding 54 and 101 is-a relations, respectively, introducing new knowledge to the ontologies.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2014. p. 88
Series
Linköping Studies in Science and Technology. Thesis, ISSN 0280-7971 ; 1683
Keywords
Knowledge representation, ontology, ontology engineering, ontology debugging, description logics
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-110935 (URN)10.3384/lic.diva-111654 (DOI)978-91-7519-201-7 (ISBN)
Presentation
2014-12-01, Alan Turing, Hus E, Campus Valla, Linköpings universitet, Linköping, 13:15 (English)
Opponent
Supervisors
Funder
Swedish e‐Science Research CenterSwedish Research Council
Available from: 2014-10-28 Created: 2014-09-30 Last updated: 2018-01-11Bibliographically approved
Dragisic, Z., Lambrix, P. & Wei-Kleiner, F. (2014). Completing the is-a structure of biomedical ontologies. In: Helena Galhardas, Erhard Rahm (Ed.), Data Integration in the Life Sciences 10th International Conference, DILS 2014, Lisbon, Portugal, July 17-18, 2014. Proceedings: . Paper presented at 10th International Conference, DILS 2014, Lisbon, Portugal, July 17-18, 2014 (pp. 66-80). Berlin: Springer Science+Business Media B.V.
Open this publication in new window or tab >>Completing the is-a structure of biomedical ontologies
2014 (English)In: Data Integration in the Life Sciences 10th International Conference, DILS 2014, Lisbon, Portugal, July 17-18, 2014. Proceedings / [ed] Helena Galhardas, Erhard Rahm, Berlin: Springer Science+Business Media B.V., 2014, p. 66-80Conference paper, Published paper (Refereed)
Abstract [en]

Ontologies in the biomedical domain are becoming a key element for data integration and search. The usefulness of the applications which use ontologies is often directly influenced by the quality of ontologies, as incorrect or incomplete ontologies might lead to wrong or incomplete results for the applications. Therefore, there is an increasing need for repairing defects in ontologies. In this paper we focus on completing ontologies. We provide an algorithm for completing the is-a structure in TeX ontologies which covers many biomedical ontologies. Further, we present an implemented system based on the algorithm as well as an evaluation using three biomedical ontologies.

Place, publisher, year, edition, pages
Berlin: Springer Science+Business Media B.V., 2014
Series
Lecture Notes in Computer Science, ISSN 0302-9743, E-ISSN 1611-3349 ; 8574
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-108848 (URN)10.1007/978-3-319-08590-6_7 (DOI)000345519500007 ()978-3-319-08589-0 (ISBN)978-3-319-08590-6 (ISBN)
Conference
10th International Conference, DILS 2014, Lisbon, Portugal, July 17-18, 2014
Funder
Swedish e‐Science Research CenterCUGS (National Graduate School in Computer Science)
Available from: 2014-07-08 Created: 2014-07-08 Last updated: 2018-07-17Bibliographically approved
Dragisic, Z., Eckert, K., Euzenat, J., Faria, D., Ferrara, A., Granada, R., . . . Cuenca Grau, B. (2014). Results of the Ontology Alignment Evaluation Initiative 2014. In: International Workshop on Ontology Matching: . Paper presented at International Workshop on Ontology Matching (pp. 61-104).
Open this publication in new window or tab >>Results of the Ontology Alignment Evaluation Initiative 2014
Show others...
2014 (English)In: International Workshop on Ontology Matching, 2014, p. 61-104Conference paper, Published paper (Refereed)
Abstract [en]

Ontology matching consists of finding correspondences between se-mantically related entities of two ontologies. OAEI campaigns aim at comparingontology matching systems on precisely defined test cases. These test cases canuse ontologies of different nature (from simple thesauri to expressive OWL on-tologies) and use different modalities, e.g., blind evaluation, open evaluation andconsensus. OAEI 2014 offered 7 tracks with 9 test cases followed by 14 partici-pants. Since 2010, the campaign has been using a new evaluation modality which provides more automation to the evaluation. This paper is an overall presentationof the OAEI 2014 campaign.

Series
CEUR Workshop Proceedings, ISSN 1613-0073 ; 1317
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-112851 (URN)2-s2.0-84919625766 (Scopus ID)
Conference
International Workshop on Ontology Matching
Available from: 2014-12-17 Created: 2014-12-17 Last updated: 2018-01-11
Lambrix, P., Wei-Kleiner, F., Dragisic, Z. & Ivanova, V. (2013). Repairing missing is-a structure in ontologies is an abductive reasoning problem. In: Patrick Lambrix; Guilin Qi; Matthew Horridge; Bijan Parsia (Ed.), Proceedings of the Second International Workshop on Debugging Ontologies and Ontology Mappings: . Paper presented at Second International Workshop on Debugging Ontologies and Ontology Mappings (WoDOOM 2013), Montpellier, France, May 27, 2013 (pp. 33-44). Rheinisch-Westfaelische Technische Hochschule Aachen University
Open this publication in new window or tab >>Repairing missing is-a structure in ontologies is an abductive reasoning problem
2013 (English)In: Proceedings of the Second International Workshop on Debugging Ontologies and Ontology Mappings / [ed] Patrick Lambrix; Guilin Qi; Matthew Horridge; Bijan Parsia, Rheinisch-Westfaelische Technische Hochschule Aachen University , 2013, p. 33-44Conference 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. We show that this can be formalized as an abduction problem. Further, we define properties for the ontology, the set of is-a relations to repair and the domain expert, as well as preference criteria on solutions and discuss the influences of these properties and criteria on the existence of solutions for the abduction problem. We also discuss the consequences of our analyses of the repairing problem for the development and use of debugging systems.

Place, publisher, year, edition, pages
Rheinisch-Westfaelische Technische Hochschule Aachen University, 2013
Series
CEUR Workshop Proceedings, ISSN 1613-0073 ; 999
Keywords
ontology debugging, ontology engineering, knowledge representation
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-93928 (URN)
Conference
Second International Workshop on Debugging Ontologies and Ontology Mappings (WoDOOM 2013), Montpellier, France, May 27, 2013
Funder
Swedish e‐Science Research CenterSwedish Research Council, 2010-4759CUGS (National Graduate School in Computer Science)
Available from: 2013-06-12 Created: 2013-06-12 Last updated: 2018-01-11Bibliographically approved
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