Ludger Jansen

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

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 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.

Much work in social ontology analyzes how social entities are based on collective intentionality. A neglected perspective is, however, the distinction between those social entities that are explicitly established (often called formal institutions, like marriages), those that are established but not explicitly (informal institutions, like friendships), and those that are not established at all (social macro entities, like episodes of inflation). To shed more light on this trichotomy, a collection of examples taken from the works of John Searle will be discussed, comprising money, marriages, friendship, cocktail parties, natural language, and episodes of inflation. The chapter argues that explicit establishment confers certain typical characteristics on formal institutions that informal institutions lack, thus explaining the typical differences between marriages and friendship. The focus on explicit establishment further develops Khalidi’s classification of social kinds, and it contributes to Epstein’s quest for grounds and anchors of social entities. It can thus contribute to overcoming the narrow focus on collective intentionality.

Researchers and ethicists have long been concerned about the expectations for direct medical benefit expressed by participants in early phase clinical trials. Early work on the issue considered the possibility that participants misunderstand the purpose of clinical research or that they are misinformed about the prospects for medical benefit from these trials. Recently, however, attention has turned to the possibility that research participants are simply expressing optimism or hope about their participation in these trials. The ethical significance of this therapeutic optimism remains unclear. This paper argues that there are two distinct phenomena that can be associated with the term ‘therapeutic optimism’—one is ethically benign and the other is potentially worrisome. Distinguishing these two phenomena is crucial for understanding the nature and ethical significance of therapeutic optimism. The failure to draw a distinction between these phenomena also helps to explain why different writers on the topic often speak past one another

While genomic and proteomic information describe the overall cellular machinery available to an organism, the metabolic profile of an individual at a given time provides a canvas as to the current physiological state. Concentration levels of relevant metabolites vary under different conditions, in particular, in the presence or absence of different disorders. Metabolite concentrations thus mediate an important link between chemistry and biology, contributing to a systems-wide understanding of biological processes and pathways. However, there are a number of challenges in the ontological representation of such information. Firstly, concentration information is numeric and ranges over continuous values, while ontologies consist of discrete classes. Secondly, ontologies usually model only what is certain, and their logical formalisms are adapted to reasoning from certain axioms to logical deductions, however, the link between chemicals and diseases via concentration levels, like many threshold phenomena, is both uncertain and vague. In this paper we evaluate the representation of this knowledge using a combination of concrete domains and probabilistic reasoning. We parse concentration values from HMDB and create an ontology able to distinguish normal from abnormal concentrations and able to evaluate a probabilistic risk category for the presence of an associated disorder.

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.

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.

Ontology engineering is mainly done by domain experts who are specialists in their domain but have, if at all, limited knowledge in logics, computer science, or analytic philosophy. The literature on formal ontologies and biomedical ontologies is neither suited nor intended to serve as an educational resource that would help domain experts to become good ontologists. Existing educational resources focus rather on ontology tools and languages than on good practice. The purpose of the GoodOD guideline is to pave the road for domain experts who want (or need) to become ontology engineers. It pursues the openly pragmatic approach that ontology engineers only need to know ontology theory to the extent which supports the (measurable) outcome of their work. The GoodOD Guideline builds upon given philosophical and methodological principles as well as preexisting tools and resources. In particular (pragmatic) scientific realism, first order logics and its subset OWL-DL (description logics), set theory, an upper-level ontology with high-level categories and a canonic set of relations, constraints which limit the freedom of choice when building coordinate expressions, the ontology editor Protégé 4, a complete DL reasoner, such as HermIT, ontology design patterns, and naming conventions. Given these precepts the guideline contains all the knowledge to be acquired by a user to be able to solve ontology engineering problems in a foreseeable and non-arbitrary way. The didactic concept is to convey the skills not only by theory but also by practical examples.

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.

Ontologies aim to represent what is general, by means of universal statements. In contrast, dispositional predications capture knowledge about what is likely to happen if a certain set of circumstances obtain, which is crucial in investigative research such as in drug discovery and systems biology, where entities which are constitutionally dissimilar can nevertheless have similar behavior in a biological context. While such dispositional properties are increasingly included in biomedical ontologies, the circumstances under which the dispositions are realized are seldom explicitly modeled, and doing so is problematic due to the necessary restriction to binary relations in OWL ontologies. In this paper we address this shortcoming, focusing on the bioactivity of small molecules at varying levels of concentration within a living organism as our problem domain, although our approach is generalizable to other problems. We discuss the ontological nature and representation of dispositions and their realization; consider the nature of concentrations and their representation; and finally we detail an approach to linking dispositions to the conditions for their realization which regards conditions as triggers for the process in which the disposition is realized.

Traditionally, nature has often been thought to be structured by essential forms providing the generic features of natural things and thus the foundations for scientific explanations. In contrast, human history and the social domain have been thought to be the realm of ever-changing appearances, where contingency prevails. The paper argues that the existence of essential forms is compatible with the contingent, mind-dependent and historical character of the social world, and that essential forms can also be found in the social domain. Two categories of entities are discussed that suggest themselves to be identified as social forms, namely social kinds and social identities. To this end, it is shown that standard arguments for the existence of essential forms also apply to the social domain, and objections to the existence of social forms are rebutted. Particular attention is paid to the explanatory appeal of social forms. The paper concludes by suggesting that, far from being oppressive, essential social forms are presupposed by liberating social practices.

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.

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.

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.