Ludger Jansen

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.

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.

After a short sketch of Lowe's account of his four basic categories, I discuss his theory of formal ontological relations and how Lowe wants to account for dispositional predications. I argue that on the ontic level Lowe is a pan-categoricalist, while he is a language dualist and an exemplification dualist with regard to the dispositional/categorical distinction. I argue that Lowe does not present an adequate account of disposition. From an Aristotelian point of view, Lowe conflates dispositional predication with 'hôs epi to poly' statements about what is normally or mostly the case.

Starting from the early treatise "On Being and Essence", I review issues concerning substances composed of matter and form: their hylomorphic composition, individuation, essence as part and as whole, and the analogy between genus/difference and matter/form. Then I discuss substances separated from matter, which may range from human souls and angels (or intelligences) to God. I then turn to Aquinas's later 'Summa Theologica', where he argues that in the end God cannot possibly belong to the category of substance and discuss possible reasons for Aquinas conflicting accounts on this question.

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

After a short sketch of Lowe’s account of his four basic categories, I discuss his theory of formal ontological relations and how Lowe wants to account for dispositional predications. I argue that on the ontic level Lowe is a pan-categoricalist, while he is a language dualist and an exemplification dualist with regard to the dispositional/categorical distinction. I argue that Lowe does not present an adequate account of disposition. From an Aristotelian point of view, Lowe conflates dispositional predication with hôs epi to poly statements about what is normally or mostly the case

Wether the chicken or the egg came first, is not only a mind-boggling but a substantial question. Its answer depends on the biological background theory one assumes. I review recent work on the topic (by Teichmann, Sorensen, Waller and Raatzsch) and resolve some of the disputes between these authors by borrowing from Aristotle the distinction between chicken-producing eggs. I then introduce the concept of a quasi-species to make explicit the vagueness involved in species-terms and prove 13 different priority-claims within a Darwinian framework.

Statements about the behavior of biological 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 is necessary to take into account in the practice of biomedical ontology engineering. Several concurring formalizations are proposed. Emphasis is laid on the discussion of biological dispositions.

This chapter summarizes Aristotle's teaching about human nature. It reviews passages about human beings from his treatises on logic, psychology, ethics, politics, and biology, and discusses his famous characterizations of man as a rational and political animal (zoon logon echon; zoon politikon). It is argued that while Aristotle insists on the distinctive methods and varying reliability of different disciplines, his teachings about human nature can integrate into a unified picture. The notorious disputes among his interpreters about his stand on the immortality of the soul (or of one of its parts, the 'nous poietikos'), however, find their roots in the fact that Aristotle is vague and tentative in these more speculative bits of his anthropological thoughts.

In 'Metaphysics IX.6' (1048b 18-35) Aristotle presents a test to distinguish between "kinesis" and "energeia," based on relations between the perfective and the imperfective aspect of the verb. This passage has been interpreted as drawing a linguistic distinction between classes of verbs (e.g., stative verbs) by means of a linguistic criterion (Ackrill, Graham). But such an interpretation is in conflict with the text. Aristotle's test must, therefore, be understood as a metaphysical criterion between items in the world (rather than lingual items) by means of a metaphysical criterion, exploiting properties of these items. These items are events, and 'Metaphysics IX.6' exhibits Aristotle's awareness to certain topics discussed in modern event ontology.

It has long been a standard practice for the natural sciences to classify things. Thus, it is no wonder that, for two and a half millennia, philosophers have been reflecting on classifications, from Plato and Aristotle to contemporary philosophy of science. Some of the results of these reflections will be presented in this chapter. I will start by discussing a parody of a classification, namely: the purportedly ancient Chinese classification of animals described by Jorge Luis Borges. I will show that many of the mistakes that account for the comic features of this parody appear in real-life scientific databases as well. As examples of the latter, I will discuss the terminology database of the National Cancer Institute (NCI) of the United States, the NCI Thesaurus.

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 non-standard cases and their epistemic variants are discussed.

Zuweilen werden der Geschichtsschreibung der Wissenschaftscharakter und historischen Aussagen die Wahrheitsfähigkeit abgesprochen. Ich werde erstens zeigen, dass Aussagen über Vergangenes nicht nur wahrheitsfähig sind, sondern dass einige Aussagen über Vergangenes tatsächlich wahr sind. Zweitens argumentiere ich dafür, dass weder die Gebundenheit an Quellen und die Möglichkeit des Irrtums, noch die Zeit- und Standortgebundenheit historischer Aussagen und eine eventuelle Werthaltigkeit historischer Urteile eine zwingende Gefahr für den Wissenschaftscharakter der Geschichtsschreibung sind. Sie stellen aber besondere Ansprüche an die wissenschaftlichen Tugenden, die ein guter Historiker besitzen muss. Drittens zeige ich, dass die Suche nach historischer Wahrheit nicht nur möglich, sondern für ein funktionierendes gesellschaftliches Zusammenleben auch von größter Bedeutung ist