Ludger Jansen

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.

Dieses Buch betritt Neuland. Es ist eine Einführung in das neue Gebiet der angewandten Ontologie, jenem multidisziplinären Arbeitsgebiet, in dem Philosophen gemeinsam mit Informatikern und Vertretern der jeweils thematischen Wissenschaftsbereiche, in unserem Fall mit Biologen und Medizinern, daran arbeiten, wissenschaftliches Wissen informationstechnisch zu repräsentieren. Es zeigt, wie Philosophie eine praktische Anwendung findet, die von zunehmender Wichtigkeit nicht nur in den heutigen Lebenswissenschaften ist. Und so richtet sich dieses Buch an Philosophen, aber auch an interessierte Biologen, Mediziner und Informatiker.

Es gibt Staaten und Fußballmannschaften, Fakultäten und Punkbands. Und mansollte meinen, daß diese Entitäten etwas gemeinsam haben, daß sie zu ein und derselben ontologischen Kategorie gehören. Und daß sie sich unterscheiden von Elektronen, Tischen, Grizzlybären, einem Zehn-Euro-Schein, dem neuen Präsidenten, der Amtseinführung des neuen Präsidenten und der Tatsache, daß ich einen Vortrag halte. Mein Ziel ist es, zu zeigen, daß die Kategorie, die alle Beispiele der ersten Gruppe umfaßt, aber keines der zweiten Gruppe, die Kategorie der vereinten Pluralpersonen ist. Um diese These stark zu machen, muß ich zunächst eine Reihe ontologischer Unterscheidungen diskutieren. Zunächst werde ich die Begriffe des Statusobjekts und des Pluralobjekts einführen, zwei relativ neue ontologische Kategorien. Sodann werde ich die traditionellen Kategorien der Substanz und der Person diskutieren, wobei ich mit Hilfe der zuvor eingeführten Begriffe des Statusobjekts und des Pluralobjekts verschiedene Arten von Personen unterscheiden werde. Die natürlichen Personen bilden nur eine dieser Arten, wenn auch die Art von Personen, zu der wir selber als Individuen gehören. Nach diesen Vorarbeiten stehen die Hilfsmittel bereit, die zu Beginn angeführten Beispiele zu kategorisieren.

Ontological realism is a philosophical stance that provides a definitional framework for ontologies and is referred to by various applied ontologists. From a computer science perspective, ontologies are often associated with formal languages for the representation of ontologies like the Web Ontology Language (OWL). It has, however, not been made explicit how the realist framework is related to the representation formalism. We analyse how the representational units of OWL can be used for modelling realist ontologies. While OWL is sufficiently close to the realist framework of ontologies to describe them, there are categories in OWL that are alien to realist ontologies or duplicate categories in realist ontologies. This clarification allows separating talk about ontologies in general from talk about their specific representation.

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.

Taking Thomas Aquinas's interpretation of the prologue of St John's gospel (in his Lectura super loannem Evangelium) as example, I first discuss eight differences between medieval biblical interpretation and modern exegesis, especially Aquinas's frequent use of philosophical opinions in interpreting the Bible, taken mostly from Aristotle. Second, I account for these differences by reconstructing Aquinas's hermeneutics, hinging, as is shown, upon the assumption that scripture was authored by God infallible and, therefore, only contains true statements. From this starting point Aquinas is lead to a holistic hermeneutics: The interpretation of a biblical statement can be judged on only within the context of an entire theory of God, the world, and of the interpretation of the other biblical statements. Thirdly, this view is discussed systematically and critically.

Like the doctrine of the categories in general, Aristotle’s category of the relative fulfils disparate functions: On the one hand, the category of the pros ti fulfils a dialectic or logical function that aims at the avoidance of fallacies. On the other hand, the category respects the peculiar mode of being of the relative. Taking these two different functions into consideration helps with the interpretation of Aristotle’s two definitions of the relative and his treatment of the properties of the relative in Cat. 7, with the question whether corresponding relatives are of equal priority or ontologically independent, with the genus-species problem, and with the categorical classification of potency and act.

Background Ontology Design Patterns (ODPs) are representational artifacts devised to offer solutions for recurring ontology design problems. They promise to enhance the ontology building process in terms of flexibility, re-usability and expansion, and to make the result of ontology engineering more predictable. In this paper, we analyze ODP repositories and investigate their relation with upper-level ontologies. In particular, we compare the BioTop upper ontology to the Action ODP from the NeOn an ODP repository. In view of the differences in the respective approaches, we investigate whether the Action ODP can be embedded into BioTop. We demonstrate that this requires re-interpreting the meaning of classes of the NeOn Action ODP in the light of the precepts of realist ontologies. Results As a result, the re-design required clarifying the ontological commitment of the ODP classes by assigning them to top-level categories. Thus, ambiguous definitions are avoided. Classes of real entities are clearly distinguished from classes of information artifacts. The proposed approach avoids the commitment to the existence of unclear future entities which underlies the NeOn Action ODP. Our re-design is parsimonious in the sense that existing BioTop content proved to be largely sufficient to define the different types of actions and plans. Conclusions The proposed model demonstrates that an expressive upper-level ontology provides enough resources and expressivity to represent even complex ODPs, here shown with the different flavors of Action as proposed in the NeOn ODP. The advantage of ODP inclusion into a top-level ontology is the given predetermined dependency of each class, an existing backbone structure and well-defined relations. Our comparison shows that the use of some ODPs is more likely to cause problems for ontology developers, rather than to guide them. Besides the structural properties, the explanation of classification results were particularly hard to grasp for 'self-sufficient' ODPs as compared with implemented and 'embedded' upper-level structures which, for example in the case of BioTop, offer a detailed description of classes and relations in an axiomatic network. This ensures unambiguous interpretation and provides more concise constraints to leverage on in the ontology engineering process.

This paper questions the widespread supposition that artifact kinds are kinds of artifacts. I will argue that this supposition rests on a one-sided diet of examples taken from inanimate physical things and the neglect of social and biological artifacts. I will argue that belonging to an artifact kind and being an artifact are independent Features: The first divides off artifacts from non-artifacts, the second rests on the distinction between instances of artifacts kinds and instances of natural kinds. I claim that these two distinctions are orthogonal to each other, and besides the two canonical combinations of artificial instances of artifact kinds and non-artificial instances of natural kinds there are also non-artificial instances of artifact kinds and artificial instances of natural kinds. Moreover, as some artificial living beings are self-reproducing, some instances of an artifact kind are not themselves artifacts. Hence artifact kinds are not of necessity kinds of artifacts.

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.

In order to develop the ontology of tendencies for use in the representation of medical knowledge, tendencies are compared with other kinds of entities possessing the realizable-realization structure, specifically: dispositions, propensities, abilities and virtues. The peculiarities of tendencies are discussed and a standard schema of tendency ascription is developed in order to represent the relations between the ascriptions of tendency tokens to particulars and the ascriptions of tendency types to universals. Two nonstandard cases and their epistemic variants are discussed.