Ludger Jansen

Background: In order to improve ontology quality, tool- and language-related tutorials are not sufficient. Care must be taken to provide optimized curricula for teaching the representational language in the context of a semantically rich upper level ontology. The constraints provided by rigid top and upper level models assure that the ontologies built are not only logically consistent but also adequately represent the domain of discourse and align to explicitly outlined ontological principles. Finally such a curriculum must take into account the pre-existing skills and knowledge of the target audience. Objective: To develop a well-structured curriculum aligned to the particular requirements of life science professionals, in order to enable them to create logically sound, domain adequate and predicable ontologies using the Web Ontology Language (OWL) in Protégè. Methods: Content selection for the curriculum was based on the literature, pre-existing tutorials, and a guideline for good ontology development (i.e ontology design enhancing domain adequacy, sustainability and interoperability) that drew on the authors previous experiences with large ontology development projects. Learning objectives were formulated according to a needs assessment of the targeted learners, who were students trained in life sciences with basic knowledge and practical skills in computer science. As instructional format we choose an approach with a high amount of practical exercises. The curriculum was first implemented with 24 Students and 7 lecturers/ tutors over 5 full days. The curriculum was evaluated by gathering the participants feedback via a questionnaire. Results: Curricular development produced 16 modules of approximately 2 hours each, which covered basic principles of Applied Ontology, description logic syntax and semantics, as well as best design practices outlined in ontology design patterns and variants of the BioTop upper ontology. An opinion survey based on questionnaires indicated that the participants took advantage from the teaching strategies applied, as they indicated good knowledge gain and acknowledged the relevance of the modules. The difficulty was rated slightly lower. Conclusion: The development of teaching material for principled ontology design and best practices is of crucial importance in order to enhance the quality of biomedical ontologies. Here, we present a curriculum for a week long workshop, leveraging on current educational principles, focusing on interactive hands-on exercises, group interactions, and problem-oriented learning. Whereas evaluation clearly showed the success of this approach, in particular regarding student’s satisfaction, the objective measurement of traceable effects on the quality of the generated ontology, although of much higher interest, has just started.

Dispositions and tendencies feature significantly in the biomedical domain and therefore in representations of knowledge of that domain. They are not only important for specific applications like an infectious disease ontology, but also as part of a general strategy for modelling knowledge about molecular interactions. But the task of representing dispositions in some formal ontological systems is fraught with several problems, which are partly due to the fact that Description Logics can only deal well with binary relations. The paper will discuss some of the results of the philosophical debate about dispositions, in order to see whether the formal relations needed to represent dispositions can be broken down to binary relations. Finally, we will discuss problems arising from the possibility of the absence of realizations, of multi-track or multi-trigger dispositions and offer suggestions on how to deal with them.

Statements about the behavior of biochemical entities (e.g., about the interaction between two proteins) abound in the literature on molecular biology and are increasingly becoming the targets of information extraction and text mining techniques. We show that an accurate analysis of the semantics of such statements reveals a number of ambiguities that have to be taken into account in the practice of biomedical ontology engineering: Such statements can not only be understood as event reporting statements, but also as ascriptions of dispositions or tendencies that may or may not refer to collectives of interacting molecules or even to collectives of interaction events.

Being an "untimely review", this paper reviews Aristotle's 'Categories' as if they were published today, in the era of computerised information, where categorisation becomes more and more essential for information retrieval. I suggest a systematic ordering of Aristotle's list of categories and argue that Aristotle's discussion of ontological dependency and his focus on concrete entities are still a source of new insight and can indeed be read as a contribution to the emerging field of applied ontology and ontological engineering.