Ludger Jansen

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

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.

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.

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.

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.

Aristoteles unterscheidet zwischen zwei Arten, das Wort „dynaton" zu gebrauchen. Die erste dieser beiden Verwendungsweisen dient zur Zuschreibung von Vermögen (dynaton kata dynamin), die zweite entspricht unserer Verwendung des logisch-alethischen Modaloperators „Es ist möglich, dass" (dynaton ou kata dynamin). Ich argumentiere dafür, dass wichtige Unterschiede zwischen Vermögensprädikationen und Modalaussagen bestehen. Ich nenne mehrere Gründe dafür, dass Vermögensprädikationen keine Modalaussagen sind, zeige aber auch, dass Vermögensprädikationen zwei modale Elemente haben: Sie implizieren erstens nichttriviale Modalaussagen, weil es keine Vermögen für Unmögliches gibt. Und sie implizieren zweitens nichttriviale Aussagen über kontrafaktische Situationen, weil sie Aussagen über kausale Rollen sind.

BACKGROUND The need for detailed description and modeling of cells drives the continuous generation of large and diverse datasets. Unfortunately, there exists no systematic and comprehensive way to organize these datasets and their information. CELDA (Cell: Expression, Localization, Development, Anatomy) is a novel ontology for the association of primary experimental data and derived knowledge to various types of cells of organisms. RESULTS CELDA is a structure that can help to categorize cell types based on species, anatomical localization, subcellular structures, developmental stages and origin. It targets cells in vitro as well as in vivo. Instead of developing a novel ontology from scratch, we carefully designed CELDA in such a way that existing ontologies were integrated as much as possible, and only minimal extensions were performed to cover those classes and areas not present in any existing model. Currently, ten existing ontologies and models are linked to CELDA through the top-level ontology BioTop. Together with 15.439 newly created classes, CELDA contains more than 196.000 classes and 233.670 relationship axioms. CELDA is primarily used as a representational framework for modeling, analyzing and comparing cells within and across species in CellFinder, a web based data repository on cells (http://cellfinder.org). CONCLUSIONS CELDA can semantically link diverse types of information about cell types. It has been integrated within the research platform CellFinder, where it exemplarily relates cell types from liver and kidney during development on the one hand and anatomical locations in humans on the other, integrating information on all spatial and temporal stages. CELDA is available from the CellFinder website: http://cellfinder.org/about/ontology.

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.

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.

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.

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