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Hammar, Karl
Publications (6 of 6) Show all publications
Dórea, F. C., Vial, F., Hammar, K., Lindberg, A., Lambrix, P., Blomqvist, E. & Revie, C. W. (2019). Drivers for the development of an Animal Health Surveillance Ontology (AHSO). Preventive Veterinary Medicine, 166(1), 39-48
Open this publication in new window or tab >>Drivers for the development of an Animal Health Surveillance Ontology (AHSO)
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2019 (English)In: Preventive Veterinary Medicine, ISSN 0167-5877, E-ISSN 1873-1716, Vol. 166, no 1, p. 39-48Article in journal (Refereed) Published
Abstract [en]

Comprehensive reviews of syndromic surveillance in animal health have highlighted the hindrances to integration and interoperability among systems when data emerge from different sources. Discussions with syndromic surveillance experts in the fields of animal and public health, as well as computer scientists from the field of information management, have led to the conclusion that a major component of any solution will involve the adoption of ontologies. Here we describe the advantages of such an approach, and the steps taken to set up the Animal Health Surveillance Ontological (AHSO) framework. The AHSO framework is modelled in OWL, the W3C standard Semantic Web language for representing rich and complex knowledge. We illustrate how the framework can incorporate knowledge directly from domain experts or from data-driven sources, as well as by integrating existing mature ontological components from related disciplines. The development and extent of AHSO will be community driven and the final products in the framework will be open-access.

Place, publisher, year, edition, pages
Elsevier, 2019
Keywords
syndromic surveillance classification, vocabulary, terminology, standards
National Category
Computer Sciences Veterinary Science
Identifiers
urn:nbn:se:liu:diva-155036 (URN)10.1016/j.prevetmed.2019.03.002 (DOI)000465055100006 ()30935504 (PubMedID)
Funder
Vinnova
Note

Funding agencies: Swedens innovation agency (VINNOVA)

Available from: 2019-03-09 Created: 2019-03-09 Last updated: 2019-07-26Bibliographically approved
Hammar, K. (2017). Content Ontology Design Patterns: Qualities, Methods, and Tools. (Doctoral dissertation). Linköping: Linköping University Electronic Press
Open this publication in new window or tab >>Content Ontology Design Patterns: Qualities, Methods, and Tools
2017 (English)Doctoral thesis, monograph (Other academic)
Abstract [en]

Ontologies are formal knowledge models that describe concepts and relationships and enable data integration, information search, and reasoning. Ontology Design Patterns (ODPs) are reusable solutions intended to simplify ontology development and support the use of semantic technologies by ontology engineers. ODPs document and package good modelling practices for reuse, ideally enabling inexperienced ontologists to construct high-quality ontologies. Although ODPs are already used for development, there are still remaining challenges that have not been addressed in the literature. These research gaps include a lack of knowledge about (1) which ODP features are important for ontology engineering, (2) less experienced developers' preferences and barriers for employing ODP tooling, and (3) the suitability of the eXtreme Design (XD) ODP usage methodology in non-academic contexts.

This dissertation aims to close these gaps by combining quantitative and qualitative methods, primarily based on five ontology engineering projects involving inexperienced ontologists. A series of ontology engineering workshops and surveys provided data about developer preferences regarding ODP features, ODP usage methodology, and ODP tooling needs. Other data sources are ontologies and ODPs published on the web, which have been studied in detail. To evaluate tooling improvements, experimental approaches provide data from comparison of new tools and techniques against established alternatives.

The analysis of the gathered data resulted in a set of measurable quality indicators that cover aspects of ODP documentation, formal representation or axiomatisation, and usage by ontologists. These indicators highlight quality trade-offs: for instance, between ODP Learnability and Reusability, or between Functional Suitability and Performance Efficiency. Furthermore, the results demonstrate a need for ODP tools that support three novel property specialisation strategies, and highlight the preference of inexperienced developers for template-based ODP instantiation---neither of which are supported in prior tooling. The studies also resulted in improvements to ODP search engines based on ODP-specific attributes. Finally, the analysis shows that XD should include guidance for the developer roles and responsibilities in ontology engineering projects, suggestions on how to reuse existing ontology resources, and approaches for adapting XD to project-specific contexts.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2017. p. 238
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1879
Keywords
Ontology, Ontology Design Pattern, Quality Model, eXtreme Design, XDP, WebProtégé
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-139584 (URN)10.3384/diss.diva-139584 (DOI)9789176854549 (ISBN)
Public defence
2017-09-29, Ada Lovelace, Hus B, Campus Valla, Linköping, 13:15 (English)
Opponent
Supervisors
Available from: 2017-09-06 Created: 2017-08-15 Last updated: 2019-10-11Bibliographically approved
Hammar, K. (2017). Content Ontology Design Patterns: Qualities, Methods, and Tools - Supplementary Materials. Linköping: Linköping University Electronic Press
Open this publication in new window or tab >>Content Ontology Design Patterns: Qualities, Methods, and Tools - Supplementary Materials
2017 (English)Data set, Primary data
Abstract [en]

Data and code supporting Karl Hammar's 2017 PhD dissertation.

Place, publisher, year
Linköping: Linköping University Electronic Press, 2017
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-138724 (URN)
Available from: 2017-06-21 Created: 2017-06-21 Last updated: 2019-10-11Bibliographically approved
Hammar, K. (2014). Ontology Design Pattern Property Specialisation Strategies. In: KNOWLEDGE ENGINEERING AND KNOWLEDGE MANAGEMENT, EKAW 2014: . Paper presented at 19th International Conference on Knowledge Engineering and Knowledge Management (EKAW) (pp. 165-180). SPRINGER-VERLAG BERLIN, 8876
Open this publication in new window or tab >>Ontology Design Pattern Property Specialisation Strategies
2014 (English)In: KNOWLEDGE ENGINEERING AND KNOWLEDGE MANAGEMENT, EKAW 2014, SPRINGER-VERLAG BERLIN , 2014, Vol. 8876, p. 165-180Conference paper, Published paper (Refereed)
Abstract [en]

Ontology Design Patterns (ODPs) show potential in enabling simpler, faster, and more correct Ontology Engineering by laymen and experts. For ODP adoption to take off, improved tool support for ODP use in Ontology Engineering is required. This paper studies and evaluates the effects of strategies for object property specialisation in ODPs, and suggests tool improvements based on those strategies. Results indicate the existence of three previously unstudied strategies for ODP specialisation, the uses of which affect reasoning performance and integration complexity of resulting ontologies.

Place, publisher, year, edition, pages
SPRINGER-VERLAG BERLIN, 2014
Series
Lecture Notes in Artificial Intelligence, ISSN 0302-9743 ; 8876
National Category
Computer and Information Sciences
Identifiers
urn:nbn:se:liu:diva-119282 (URN)10.1007/978-3-319-13704-9_13 (DOI)000354879800013 ()978-3-319-13704-9 (ISBN)978-3-319-13703-2 (ISBN)
Conference
19th International Conference on Knowledge Engineering and Knowledge Management (EKAW)
Available from: 2015-06-12 Created: 2015-06-12 Last updated: 2018-01-11
Hammar, K. (2013). Towards an Ontology Design Pattern Quality Model. (Licentiate dissertation). Linköping: Linköping University Electronic Press
Open this publication in new window or tab >>Towards an Ontology Design Pattern Quality Model
2013 (English)Licentiate thesis, monograph (Other academic)
Abstract [en]

The use of semantic technologies and Semantic Web ontologies in particular have enabled many recent developments in information integration, search engines, and reasoning over formalised knowledge. Ontology Design Patterns have been proposed to be useful in simplifying the development of Semantic Web ontologies by codifying and reusing modelling best practices.

This thesis investigates the quality of Ontology Design Patterns. The main contribution of the thesis is a theoretically grounded and partially empirically evaluated quality model for such patterns including a set of quality characteristics, indicators, measurement methods and recommendations. The quality model is based on established theory on information system quality, conceptual model quality, and ontology evaluation. It has been tested in a case study setting and in two experiments.

The main findings of this thesis are that the quality of Ontology Design Patterns can be identified, formalised and measured, and furthermore, that these qualities interact in such a way that ontology engineers using patterns need to make tradeoffs regarding which qualities they wish to prioritise. The developed model may aid them in making these choices.

This work has been supported by Jönköing University.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2013. p. 159
Series
Linköping Studies in Science and Technology. Thesis, ISSN 0280-7971 ; 1606
Keywords
Ontology, OWL, Ontology Design Pattern, Semantic Web, Quality Model
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-93370 (URN)LiU–Tek–Lic–2013:40 (Local ID)978-91-7519-570-4 (ISBN)LiU–Tek–Lic–2013:40 (Archive number)LiU–Tek–Lic–2013:40 (OAI)
Presentation
2013-09-17, E1405, hus E, Tekniska Högskolan i Jönköping, Gjuterigatan 5, Jönköping, 10:30 (English)
Opponent
Supervisors
Available from: 2013-08-27 Created: 2013-05-31 Last updated: 2019-12-08Bibliographically approved
Gunnarsson, C., Jerevall, P.-L., Hammar, K., Olsson, B., Nordenskjöld, B., Jansson, A. & Stål, O. (2008). Amplification of HSD17B1 has prognostic significance in postmenopausal breast cancer. Breast Cancer Research and Treatment, 108(1), 35-41
Open this publication in new window or tab >>Amplification of HSD17B1 has prognostic significance in postmenopausal breast cancer
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2008 (English)In: Breast Cancer Research and Treatment, ISSN 0167-6806, E-ISSN 1573-7217, Vol. 108, no 1, p. 35-41Article in journal (Refereed) Published
Abstract [en]

In situ synthesis of estrogens is believed to be of great importance for the progression of breast cancer. In postmenopausal women most estrogens are synthesized in peripheral hormone-target tissues from circulating precursor steroids, by the enzymes involved in formation of active estrogens. One of the enzymes involved in this process is 17β-hydroxysteroid dehydrogenase (17β-HSD) type 1. This enzyme catalyzes the interconversion of estrone (E1) to the biologically more potent estradiol (E2). The gene coding for 17β-HSD type 1 (HSD17B1) is located at 17q12-21. The aim of this study was to investigate altered gene copy number of HSD17B1 in breast cancer. We used real-time PCR and examined 387 postmenopausal breast tumors for amplification of HSD17B1, and if an increased mRNA level of this enzyme is associated with amplification of the gene. We also investigated whether amplification of HSD17B1 has a prognostic value. There was a significant correlation between gene copy number of HSD17B1 and mRNA expression level (P = 0.00002). ER-positive patients with amplification of HSD17B1 showed lower breast cancer survival than patients without amplification (P = 0.025). Among ER-negative patients there was no significant correlation between increased gene copy number of HSD17B1 and prognosis. Furthermore, we found that amplification of the gene had prognostic significance in multivariate analysis adjusting for other clinicopathological variables. © 2007 Springer Science+Business Media, LLC.

Keywords
Breast Neoplasms/*genetics/mortality Disease-Free Survival Estradiol Dehydrogenases/*genetics Female *Gene Amplification Humans Kaplan-Meiers Estimate Middle Aged Postmenopause Prognosis RNA, Messenger/analysis Receptors, Estrogen/metabolism Reverse Trans
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:liu:diva-43344 (URN)10.1007/s10549-007-9579-7 (DOI)73588 (Local ID)73588 (Archive number)73588 (OAI)
Available from: 2009-10-10 Created: 2009-10-10 Last updated: 2017-12-13Bibliographically approved
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