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.

BackgroundThe concept of function is central to both biology and technology, but neither in philosophy nor in formal ontology is there a generally accepted theory of functions. In particular, there is no consensus how to include functions into a top-level ontology or whether to include them at all.MethodsWe first review current conceptions of functions in philosophy and formal ontology and evaluate them against a set of criteria. These evaluation criteria are derived from a synopsis of theoretical and practical requirements that have been suggested for formal accounts of functions. In a second step, we elucidate in particular the relation between functions and dispositions.ResultsWe argue that functions should not be taken as a subtype of dispositions. The strongest reason for this is that any view that identifies functions with certain dispositions cannot account for malfunctioning, which is having a function but lacking the matching disposition. As a result, we suggest a cross-classification of realizables with dispositions supervening on the physical structure of their bearer, whereas both functions and roles also have some external grounding. While bearers can survive the gain, loss and change of roles, functions are rigid properties that are essentially connected to their particular bearers. Therefore, Function should not be regarded as a subtype of Disposition; rather, the classes of functions and dispositions are disjoint siblings of Realizable.

The concept of a mechanism has become a standard proposal for explanations in biology. It has been claimed that mechanistic explanations are appropriate for systems biology, because they occupy a middle ground between strict reductionism and holism. Because of their importance in the field a formal ontological description of mechanisms is desirable. The standard philosophical accounts of mechanisms are often ambiguous and lack the clarity that can be provided by a formal-ontological framework. The goal of this paper is to clarify some of these ambiguities and suggest such a framework for mechanisms. Taking some hints from an "ontology of devices" I suggest as a general approach for this task the introduction of functional kinds and functional parts by which the particular relations between a mechanism and its components can be captured.

BackgroundThe 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.ObjectiveTo 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.MethodsA 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.ResultsThe 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.ConclusionMethodologically 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.

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