| 1. |
- Dórea, Fernanda C., et al.
(författare)
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Drivers for the development of an Animal Health Surveillance Ontology (AHSO)
- 2019
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Ingår i: Preventive Veterinary Medicine. - : Elsevier. - 0167-5877 .- 1873-1716. ; 166:1, s. 39-48
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 2. |
- Lambrix, Patrick, Professor, 1965-, et al.
(författare)
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FAIR Big Data in the Materials Design Domain
- 2022
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Ingår i: Encyclopedia of Big Data Technologies. - Cham : Springer. - 9783319639628 - 9783319639628 - 9783319775241
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Bokkapitel (refereegranskat)abstract
- To speed up the progress in the field of materials design, a number of challenges related to big data need to be addressed. This entry discusses these challenges and shows the semantic technologies that alleviate the problems related to Variety, Variability, Veracity and FAIRness.
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| 3. |
- Li, Ying, et al.
(författare)
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An approach for repairing incoherent ontologies
- 2021
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Ingår i: Proceedings of the ISWC 2021 Posters, Demos and Industry Tracks: From Novel Ideas to Industrial Practice.. - Aachen, Germany : CEUR Workshop Proceedings.
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Konferensbidrag (refereegranskat)abstract
- The quality of ontologies and their alignments is crucial for developing high-quality ontology-based applications. In this paper we propose an approach for repairing incoherent ontologies and ontology networks that is based on axiom weakening and completion.
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| 4. |
- Säfvenberg, Rasmus, 1998-, et al.
(författare)
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The Importance of Special Teams in Ice Hockey
- 2023
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Ingår i: Proceedings of the Linköping Hockey Analytics Conference LINHAC 2023 Research Track. - Linköping, Sweden : Linköping University Electronic Press. ; , s. 53-65
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Konferensbidrag (refereegranskat)abstract
- This paper explores the significance of special teams, particularlypowerplay, in ice hockey. Despite the commonly held perception oftheir importance, little research has examined the impact of powerplayand penalty kill performance on overall team success. The paper usesseveral seasons of NHL data to characterize goal-scoring and manpoweropportunities, and perform analysis from several perspectives. The resultsindicate that individual even strength goals and powerplay goalshave similar value, but the larger share of even strength goals scoredover a season makes even strength play a more important contributorto team success. The paper also finds a high correlation between teamsthat perform above/below average during even strength and powerplay.This study provides valuable insights into the dynamics of ice hockeygameplay and the role of special teams in determining team success.
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| 5. |
- Jakoniené, Vaida, et al.
(författare)
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Tool for Evaluating Strategies for Grouping of Biological Data
- 2007
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Ingår i: Journal of Integrative Bioinformatics. - 1613-4516. ; 4:3
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Tidskriftsartikel (refereegranskat)abstract
- During the last decade an enormous amount of biological data has been generated and techniques and tools to analyze this data have been developed. Many of these tools use some form of grouping and are used in, for instance, data integration, data cleaning, prediction of protein functionality, and correlation of genes based on microarray data. A number of aspects influence the quality of the grouping results: the data sources, the grouping attributes and the algorithms implementing the grouping procedure. Many methods exist, but it is often not clear which methods perform best for which grouping tasks. The study of the properties, and the evaluation and the comparison of the different aspects that influence the quality of the grouping results, would give us valuable insight in how the grouping procedures could be used in the best way. It would also lead to recommendations on how to improve the current procedures and develop new procedures. To be able to perform such studies and evaluations we need environments that allow us to compare and evaluate different grouping strategies. In this paper we present a framework, KitEGA, for such an environment, and present its current prototype implementation. We illustrate its use by comparing grouping strategies for classifying proteins regarding biological function and isozymes.
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| 6. |
- Klingström, Tomas, et al.
(författare)
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Workshop on laboratory protocol standards for the molecular methods database
- 2013
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Ingår i: New Biotechnology. - : Elsevier BV. - 1871-6784 .- 1876-4347. ; 30:2, s. 109-113
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Tidskriftsartikel (refereegranskat)abstract
- Management of data to produce scientific knowledge is a key challenge for biological research in the 21st century. Emerging high-throughput technologies allow life science researchers to produce big data at speeds and in amounts that were unthinkable just a few years ago. This places high demands on all aspects of the workflow: from data capture (including the experimental constraints of the experiment), analysis and preservation, to peer-reviewed publication of results. Failure to recognise the issues at each level can lead to serious conflicts and mistakes; research may then be compromised as a result of the publication of non-coherent protocols, or the misinterpretation of published data. In this report, we present the results from a workshop that was organised to create an ontological data-modelling framework for Laboratory Protocol Standards for the Molecular Methods Database (MolMeth). The workshop provided a set of short- and long-term goals for the MolMeth database, the most important being the decision to use the established EXACT description of biomedical ontologies as a starting point.
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| 7. |
- Lambrix, Patrick, et al.
(författare)
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Completing the is-a structure in light-weight ontologies
- 2015
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Ingår i: Journal of Biomedical Semantics. - : Springer Science and Business Media LLC. - 2041-1480. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 8. |
- Lambrix, Patrick, et al.
(författare)
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Evaluation of ontology development tools for bioinformatics
- 2003
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Ingår i: Bioinformatics. - : Oxford University Press. - 1367-4803 .- 1367-4811. ; 19:12, s. 1564-1571
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Tidskriftsartikel (refereegranskat)abstract
- Ontologies are being used nowadays in many areas, including bioinformatics. To assist users in developing and maintaining ontologies a number of tools have been developed. In this paper we compare four such tools, Protégé-2000, Chimaera, DAG-Edit and OilEd. As test ontologies we have used ontologies from the Gene Ontology Consortium. No system is preferred in all situations, but each system has its own strengths and weaknesses.
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| 9. |
- Lambrix, Patrick, et al.
(författare)
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Evaluation of ontology merging tools
- 2003
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Ingår i: Pacific Symposium on Biocomputing. - : World Scientific. - 9812382178 ; , s. 589-600
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Konferensbidrag (refereegranskat)abstract
- Ontologies are being used nowadays in many areas, including bioinformatics. One of the issues in ontology research is the aligning and merging of ontologies. Tools have been developed for ontology merging, but they have not been evaluated for their use in bioinformatics. In this paper we evaluate two of the most well-known ontology merging tools with a bioinformatics perspective. As test ontologies we have used Gene Ontology and Signal-Ontology.
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| 10. |
- Lambrix, Patrick
(författare)
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Semantic Web, Ontologies and Linked Data
- 2014
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Ingår i: Comprehensive Biomedical Physics. - Amsterdam : Elsevier. - 9780444536334 ; , s. 67-76
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Bokkapitel (refereegranskat)abstract
- Researchers in various areas in the life sciences use biomedical data sources and tools for their research. However, with the explosion of the amountof available data sources and tools, researchers also face the difficulties of finding and retrieving relevant information and tools as well as integratinginformation from different sources. The vision of the Semantic Web alleviates these difficulties. In this chapter, we introduce the Semantic Web anddiscuss steps that have been taken toward this vision. We discuss ontologies as a key technology as well as the recent development of Linked Data. Further, for each of these, we list issues for future research.
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