Ludger Jansen

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.

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

Being an "untimely review", this paper reviews Aristotle's 'Categories' as if they were published today, in the era of computerised information, where categorisation becomes more and more essential for information retrieval. I suggest a systematic ordering of Aristotle's list of categories and argue that Aristotle's discussion of ontological dependency and his focus on concrete entities are still a source of new insight and can indeed be read as a contribution to the emerging field of applied ontology and ontological engineering.

The constituents of social entities (and of social continuants in particular) determine whether or not a social thing comes to be, persists and perishes. John Searle hints at two very different accounts for the persistence of social entities, a mere past related account and an acceptance theoretic account, whereas Margaret Gilbert's account is based on deontic entities like obligations or joint commitments. I demonstrate that Gilbert's account can also accommodate Searle's examples. While oblivion, protests or violence can be historical causes of the destruction of social entities, they cannot be considered to be the ultimate causes of the perishing from Gilbert's point of view. Social entities rather perish because of the treatises or divorces that dissolve their deontic constituents.

Is a bank note identical with the piece of paper of which it consists? On the one hand, John Searle, in his reply to Barry Smith, suggests that they are “one and the same object” that is a social or non-social object only under certain descriptions. On the other hand, Lynne Rudder Baker puts forward the claim that bank note and paper are distinct entities that are bound together by the relation of material constitution. I suggest two possible analyses for Searle’s description relativity claim, the Alternative Subject Analysis and the Predicate Modification Analysis. On both accounts his identity claim gets into serious trouble. While Baker’s definition of material constitution deals well with the bank note example, it fails to account for the constitution of bearerless social entities and groups. I point out five respects in which social constitution can differ from Baker’s account of material constitution and discuss compositional, institutional and interactional constitution as additional varieties of social constitution.

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.

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.

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.

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.

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.

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.

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.