Ludger Jansen

Objectives: Medical decision support and other intelligent applications in the life sciences depend on increasing amounts of digital information. Knowledge bases as well as formal ontologies are being used to organize biomedical knowledge and data. However, these two kinds of artefacts are not always clearly distinguished. Whereas the popular RDF(S) standard provides an intuitive triple-based representation, it is semantically weak. Description logics based ontology languages like OWL-DL carry a clear-cut semantics, but they are computationally expensive, and they are often misinterpreted to encode all kinds of statements, including those which are not ontological. Method: We distinguish four kinds of statements needed to comprehensively represent domain knowledge: universal statements, terminological statements, statements about particulars and contingent statements. We argue that the task of formal ontologies is solely to represent universal statements, while the non-ontological kinds of statements can nevertheless be connected with ontological representations. To illustrate these four types of representations, we use a running example from parasitology. Results: We finally formulate recommendations for semantically adequate ontologies that can efficiently be used as a stable framework for more context-dependent biomedical knowledge representation and reasoning applications like clinical decision support systems.

There are group-actions, and if actions are intentional, there should also be group-intentions. Who has got these intentions? The groups? This seems to be the natural answer. But then: Groups do not have a mind or brain of there own to form any mental attitude. Different kinds of individualistic analyses of group-intentions have been suggested in the literature. On the one hand there are suggestions to reduce group intentions to a complex of different Iattitudes. John Searle, on the other hand, suggests a special social kind of attitudes, namely we-intentions. We-intentions are being had by individual persons, though they have the form “We intend to do such-and-such”. However, because of the fallibility of Searlian we-intentions and the possibility of ignorance this concept is of no help: We-intentions are neither necessary nor sufficient for group-intentions. In this respect, Margaret Gilbert’s approach is much more successful, though it covers only a special case, namely small-scale informal groups. I suggest a generalised solution in order to cover also large-scale and formal groups.

Tun und Können erläutert und diskutiert den Gründungstext der Modalontologie: das neunte Buch der Metaphysik des Aristoteles. Aristoteles' Thesen und Argumente werden zum ersten Mal in Gänze mit formalen analytischen Mitteln rekonstruiert und auf ihre Kohärenz und Gültigkeit geprüft. Erstmals verwendet der Autor dazu eine adverbiale Analyse von Ausdrücken des Könnens und des Vermögens als Prädikatmodifikatoren. Das Buch zeigt, dass Aristoteles' Theorie der Vermögen nicht nur eine konsistente, sondern auch eine leistungsfähige Analyse von Dispositionen und Dispositionsprädikaten bietet. Die Neuausgabe wurde vollständig durchgesehen und um weiterführende Anhänge ergänzt. Der Inhalt: Können, Tun und Möglichkeit. Eine Einführung • Die kausale Dimension von Vermögen • Die ontologische Dimension von Vermögen• Eine notwendige Bedingung für Vermögen • Hindernisse und Verwirklichung • Prioritätsfragen • Aristotle’s Theory of Dispositions • Das Problem des Neuen • Planners, Deciders, Performers

It is widespread practice to define artefacts as entities that owe their existence to plan-based acts of production that aim at a certain use of the produced thing. According to this definition, artefacts are essentially intention-dependent. For this reason, artefacts are threatened by marginalisation within standard naturalised ontologies. I discuss three families of marginalisation strategies: elimination, reduction and supervenience. I argue that all of these strategies fail, as they lead to false implications, with the possible exception of four-dimensional supervenience, which might well be true, but remains completely uninformative in respect to artefacts. The crucial issue in this regard is what Peter van Inwagen calls the Duplication Principle which is undermined by thought experiments involving chance entities or duplication. Hence, materialistic ontologies are not, as Peter van Inwagen wants us to believe, a Copernican revolution in ontology; they are simply not adequate for the domain of artefacts

Was ist der Mensch? Das ist eine der "großen" philosophischen Fragen, und immer wieder werden bei der Beantwortung dieser Frage antike Denker zitiert. Das vorliegende Buch ist die erste Gesamtdarstellung des anthropologischen Denkens in der Antike. In fünfzehn Beiträgen behandelt der Band alle wichtigen antiken Philosophen und Philosophenschulen, von den Vorsokratikern bis zu Augustinus. Bewusst schaut der Band dabei über die Grenzen dessen hinaus, was wir heute "Philosophie" nennen, und wendet sich auch Denkern aus den Gebieten der antiken Literatur, Theologie und Medizin zu. Der Band richtet sich an Philosophen und Altphilologen ebenso wie Historiker und Theologen. Die Beiträge eignen sich auch als Einführung in die jeweiligen Autoren und Schulen für Studierende und interessierte Leser aus anderen Disziplinen. Speziell für diesen Leserkreis liefern die Beiträge Hinweise für die weitere Lektüre. (publisher) Mit Beiträgen von Ursula Bittrich, Yves Bossart, Jan N. Bremmer, Thomas Buchheim, Christoph Horn, Ludger Jansen, Christoph Jedan, Geurt Henk van Kooten, Zbigniew Nerczuk, Matthias Perkams, Joachim Söder, Niko Strobach, Hartmut Westermann und Jula Wildberger

The construction of complex ontologies can be facilitated by adapting existing vocabularies. There is little clarity and in fact little consensus as to what modifications of vocabularies are necessary in order to re-engineer them into ontologies. In this paper we present a method that provides clear steps to follow when re-engineering a thesaurus. The method makes use of top-level ontologies and was derived from the structural differences between thesauri and ontologies as well as from best practices in modeling, some of which have been advocated in the biomedical domain. We illustrate each step of our method with examples from a re-engineering case study about agricultural fertilizers based on the AGROVOC thesaurus. Our method makes clear that re-engineering thesauri requires far more than just a syntactic conversion into a formal language or other easily automatable steps. The method can not only be used for re-engineering thesauri, but does also summarize steps for building ontologies in general, and can hence be adapted for the re-engineering of other types of vocabularies or terminologies.

BACKGROUND Understanding, modelling and influencing the transition between different states of cells, be it reprogramming of somatic cells to pluripotency or trans-differentiation between cells, is a hot topic in current biomedical and cell-biological research. Nevertheless, the large body of published knowledge in this area is underused, as most results are only represented in natural language, impeding their finding, comparison, aggregation, and usage. Scientific understanding of the complex molecular mechanisms underlying cell transitions could be improved by making essential pieces of knowledge available in a formal (and thus computable) manner. RESULTS We describe the outline of two ontologies for cell phenotypes and for cellular mechanisms which together enable the representation of data curated from the literature or obtained by bioinformatics analyses and thus for building a knowledge base on mechanisms involved in cellular reprogramming. In particular, we discuss how comprehensive ontologies of cell phenotypes and of changes in mechanisms can be designed using the entity-quality (EQ) model. CONCLUSIONS We show that the principles for building cellular ontologies published in this work allow deeper insights into the relations between the continuants (cell phenotypes) and the occurrents (cell mechanism changes) involved in cellular reprogramming, although implementation remains for future work. Further, our design principles lead to ontologies that allow the meaningful application of similarity searches in the spaces of cell phenotypes and of mechanisms, and, especially, of changes of mechanisms during cellular transitions.

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.

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.

BACKGROUND In biomedical ontologies, mereological relations have always been subject to special interest due to their high relevance in structural descriptions of anatomical entities, cells, and biomolecules. This paper investigates two important subrelations of has_proper_part, viz. the relation has_grain, which relates a collective entity to its multiply occurring uniform parts (e.g., water molecules in a portion of water), and the relation has_component, which relates a compound to its constituents (e.g., molecules to the atoms they consist of). METHOD We distinguish between four kinds of complex entities and characterize them in first order logic. We then discuss whether similar characterizations could be given in description logics, and finally apply the results to mixtures. RESULTS At first sight, collectives and compounds seem to be disjoint categories. Their disjointness, however, relies on agreement about what are uniform entities, and thus on the granularity of description. For instance, the distinction between isomeric subtypes of a molecule can be important in one use case but might be neglected in another one. We demonstrate that, as implemented in the BioTop domain upper level ontology, equivalence or subsumption between different descriptions of same or similar entities cannot be achieved. Using OWL-DL, we propose a new design pattern that avoids primitive subrelations at the expense of more complex descriptions and thus supports the needed inferences.