Due to importance of data FAIRness (Findable, Accessible, Interoperable, Reusable), ontologies as a means to make data FAIR have attracted more and more attention in different communities and are being used in semantically-enabled applications. However, to obtain good results while using ontologies in these applications, high quality ontologies are needed of which completeness is one of the important aspects. An ontology lacking information can lead to missing results. In this paper we present a tool, Phrase2Onto, that supports users in extending ontologies to make the ontologies more complete. It is particularly suited for ontology extension using a phrase-based topic model approach, but the tool can support any extension approach where a user needs to make decisions regarding the appropriateness of using phrases to define new concepts. We describe the functionality of the tool and a user study using Pizza Ontology. The user study showed a good usability of the system and high task completion. Further, we report on a real application where we extend the Materials Design Ontology.

Traditionally, theoretical foundations in data structures and algorithms (DSA) courses have been covered through lectures followed by tutorials, where students practise their understanding on pen-and-paper tasks. In this paper, we present findings from a pilot study on using the interactive e-book OpenDSA as the main material in a DSA course. The goal was to redesign an already existing course by building on active learning and continuous examination through the use of OpenDSA. In addition to presenting the study setting, we describe findings from four data sources: final exam, OpenDSA log data, pre and post questionnaires as well as an observation study. The results indicate that students performed better on the exam than during previous years. Students preferred OpenDSA over traditional textbooks and worked actively with the material, although a large proportion of them put off the work until the due date approaches.

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.

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.

One important aim within systems biology is to integrate disparate pieces of information, leading to discovery of higher-level knowledge about important functionality within living organisms. This makes standards for representation of data and technology for exchange and integration of data important key points for development within the area. In this article, we focus on the recent developments within the field. We compare the recent updates to the three standard representations for exchange of data SBML, PSI MI and BioPAX. In addition, we give an overview of available tools for these three standards and a discussion on how these developments support possibilities for data exchange and integration.

MOTIVATION: Analysis and simulation of pathway data is of high importance in bioinformatics. Standards for representation of information about pathways are necessary for integration and analysis of data from various sources. Recently, a number of representation formats for pathway data, SBML, PSI MI and BioPAX, have been proposed. RESULTS: In this paper we compare these formats and evaluate them with respect to their underlying models, information content and possibilities for easy creation of tools. The evaluation shows that the main structure of the formats is similar. However, SBML is tuned towards simulation models of molecular pathways while PSI MI is more suitable for representing details about particular interactions and experiments. BioPAX is the most general and expressive of the formats. These differences are apparent in allowed information and the structure for representation of interactions. We discuss the impact of these differences both with respect to information content in existing databases and computational properties for import and analysis of data.

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.

The Information Technology curriculum at Linköping University has as goal to form engineers with an integrated view of engineering. The teaching philosophy in this curriculum is Problem-Based Learning. The education in each term is organised in a number of themes where topics from different disciplines are integrated. We describe a particular term in the Information Technology curriculum as an example of the approach and the integration of computer science teaching with the teaching of other disciplines. An important advantage of the approach is that the students discover interactions between different disciplines and view the different topics as naturally connected. Also, the students seem to have a better understanding of the topics and are better motivated. Further, they obtain improved communication and co-operation skills. Another advantage is that the approach is appreciated by our female students, which has led to a higher percentage of female students in this curriculum compared to our other computer science curricula.