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. (shrink)

BACKGROUND -/- The importance of ontologies in the biomedical domain is generally recognized. However, their quality is often too poor for large-scale use in critical applications, at least partially due to insufficient training of ontology developers. -/- OBJECTIVE -/- To show the efficacy of guideline-based ontology development training on the performance of ontology developers. The hypothesis was that students who received training on top-level ontologies and design patterns perform better than those who only received training in the basic principles of (...) formal ontology engineering. -/- METHODS -/- A curriculum was implemented based on a guideline for ontology design. A randomized controlled trial on the efficacy of this curriculum was performed with 24 students from bioinformatics and related fields. After joint training on the fundamentals of ontology development the students were randomly allocated to two groups. During the intervention, each group received training on different topics in ontology development. In the assessment phase, all students were asked to solve modeling problems on topics taught differentially in the intervention phase. Primary outcome was the similarity of the students’ ontology artefacts compared with gold standard ontologies developed by the authors before the experiment; secondary outcome was the intra-group similarity of group members’ ontologies. -/- RESULTS -/- The experiment showed no significant effect of the guideline-based training on the performance of ontology developers (a) the ontologies developed after specific training were only slightly but not significantly closer to the gold standard ontologies than the ontologies developed without prior specific training; (b) although significant differences for certain ontologies were detected, the intra-group similarity was not consistently influenced in one direction by the differential training. -/- CONCLUSION -/- Methodologically limited, this study cannot be interpreted as a general failure of a guideline-based approach to ontology development. Further research is needed to increase insight into whether specific development guidelines and practices in ontology design are effective. (shrink)

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. (shrink)

Ontology engineering is mainly done by domain experts who are specialists in their domain but have, if at all, limited knowledge in logics, computer science, or analytic philosophy. The literature on formal ontologies and biomedical ontologies is neither suited nor intended to serve as an educational resource that would help domain experts to become good ontologists. Existing educational resources focus rather on ontology tools and languages than on good practice. The purpose of the GoodOD guideline is to pave the road (...) for domain experts who want (or need) to become ontology engineers. It pursues the openly pragmatic approach that ontology engineers only need to know ontology theory to the extent which supports the (measurable) outcome of their work. The GoodOD Guideline builds upon given philosophical and methodological principles as well as preexisting tools and resources. In particular (pragmatic) scientific realism, first order logics and its subset OWL-DL (description logics), set theory, an upper-level ontology with high-level categories and a canonic set of relations, constraints which limit the freedom of choice when building coordinate expressions, the ontology editor Protégé 4, a complete DL reasoner, such as HermIT, ontology design patterns, and naming conventions. -/- Given these precepts the guideline contains all the knowledge to be acquired by a user to be able to solve ontology engineering problems in a foreseeable and non-arbitrary way. The didactic concept is to convey the skills not only by theory but also by practical examples. (shrink)

OBJECTIVE: (a) To measure the effect of a guideline-based training on the performance of ontology developers compared with the performance after unspecific training by a competency question based evaluation; and (b) to provide empirical evidence for the applicability of competency questions in formal ontology evaluation in general. BACKGROUND: A close connection between ontology development and ontology evaluation as quality management procedure can been attained with the use of competency questions. Competency questions are often used as a semi-formal specification of requirements (...) for an ontology under development. Hence they can also be used as evaluation instruments, in order to check how far an ontology fulfills these requirements. METHODS: A randomized controlled trial was conducted with two groups of 12 students each. The intervention consisted in a differential guideline-based training on ontology development vs. unspecific training. After a group-specific training focusing on three topics per group, performance of students was assessed with 12 exercises (2 exercises per topic), in which the students had to apply their skills. Different types of competency questions were elaborated for the analysis of the students' ontologies. We used the proportion of correct answers as a measure of ontology quality. RESULTS: On single topic level, the performance of ontology developers increased after guideline-based training for two out of the six topics: it increased from a proportion of 0.46 to 0.63 for the topic Process \& Participation and from 0.44 to 0.53 for the topic Collective Material Entity. In regression analysis, a positive correlation was shown between the performance of students on untrained topics and the performance after specific guideline-based training. Moreover, in multiple regression analysis an overall effect of specific training of 0.09 was calculated (p < 0.1). CONCLUSION: The results show an effect of a specific guideline-based training on the performance of ontology developers compared to the performance after unspecific training by an increase of about 10 \% on the rate of correct competency questions. In addition, this study has shown the general applicability of competency questions in a formal ontology evaluation scenario. However, the study also shows that the training of ontology developers and their performance evaluation is a tedious task. The resulting performance of ontology developers is more dependent on the a priori individual competencies than on the specific acquired skills after training. (shrink)

The concept of a function is central both to biology and to technology. But there is an intricate debate how functions as well as related entities like dispositions and roles are to be represented in top level ontologies and how they are to be related. We review important philosophical accounts and ontological models for functions and roles and discuss three models for the relation of functions and dispositions. We conclude that mainly because of the need to account for malfunctioning, functions (...) should not be treated as a subtype of dispositions, but as their sibling category. (shrink)