Barry Smith

In perceptual experience we are directed towards objects in a way which establishes a real relation between a mental act and its target. In reading works of fiction we enjoy experiences which manifest certain internal similarities to such relational acts, but which lack objects. The substitution theory of art attempts to provide a reason why we seek out such experiences and the artifacts which they generate. Briefly, we seek out works of art because we enjoy the physiology and the phenomenology of, for example, the experience of love or mountain climbing, and works of art serve as props for the promotion of substitutes for the corresponding genuine feelings. Art arose, or came to be separated out from other, related phenomena, through the discovery that the experience of substitute emotions can be pleasurable.

Tumors, abscesses, cysts, scars, fractures are familiar types of what we shall call pathological continuant entities. The instances of such types exist always in or on anatomical structures, which thereby become transformed into pathological anatomical structures of corresponding types: a fractured tibia, a blistered thumb, a carcinomatous colon. In previous work on biomedical ontologies we showed how the provision of formal definitions for relations such as is_a, part_of and transformation_of can facilitate the integration of such ontologies in ways which have the potential to support new kinds of automated reasoning. We here extend this approach to the treatment of pathologies, focusing especially on those pathological continuant entities which arise when organs become affected by carcinomas.

We have a variety of different ways of dividing up, classifying, mapping, sorting and listing the objects in reality. The theory of granular partitions presented here seeks to provide a general and unified basis for understanding such phenomena in formal terms that is more realistic than existing alternatives. Our theory has two orthogonal parts: the first is a theory of classification; it provides an account of partitions as cells and subcells; the second is a theory of reference or intentionality; it provides an account of how cells and subcells relate to objects in reality. We define a notion of well-formedness for partitions, and we give an account of what it means for a partition to project onto objects in reality. We continue by classifying partitions along three axes: (a) in terms of the degree of correspondence between partition cells and objects in reality; (b) in terms of the degree to which a partition represents the mereological structure of the domain it is projected onto; and (c) in terms of the degree of completeness with which a partition represents this domain.

We present a novel methodology for calculating the improvements obtained in successive versions of biomedical ontologies. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to those that have fostered the growth of modern evidence-based medicine. Although in this paper we focus on ontologies, the methodology can be generalized to other sorts of terminology-based artifacts, including Electronic Patient Records.

The pathbreaking scientific advances of recent years call for a new philosophical consideration of the fundamental categories of biology and its neighboring disciplines. Above all, the new information technologies used in biomedical research, and the necessity to master the continuously growing flood of data that is associated therewith, demand a profound and systematic reflection on the systematization and classification of biological data. This, however, demands robust theories of basic concepts such as kind, species, part, whole, function, process, fragment, sequence, expression, boundary, locus, environment, system, and so on. Concepts which belong to the implicit stock of knowledge of every biologist. They amount to a dimension of biological reality which remains constant in the course of biological evolution and whose theoretical treatment requires contemporary analogues of the tools developed in traditional Aristotelian metaphysics. To provide the necessary theories and definitions is a task for philosophy, which is thus called upon to play an important role as intermediary between biology and informatics.

If mind is a creature of adaptation, then our standard theories of intentionality and of mental representation are in need of considerable revision. For such theories, deriving under Cartesian inspiration from the work of Brentano, Husserl and their followers, are context-free. They conceive the subject of mental experience in isolation from any surrounding physico-biological environment. Husserl sought in his later writings to find room for the surrounding world of human practical experience, and a similar expansion of concerns can be detected also in the writings of other later phenomenologists such as Heidegger, Sartre, and Merleau-Ponty. But in none of these authors do we find sustained attempts to grapple with the intervolvements of the world of human thought, feeling and action with the environment of human behavior as this is described by physics and biology. Their work can, however, be seen in a new light when conjoined with the ideas on perception and action of J. J. Gibson and Roger Barker, both of whom (independently) conceived their work under the banner of 'ecological psychology.' It is against this background that the term 'Husserlian ecology' is to be understood in this essay.

It is a truism that the attitude of deference to the text plays a lesser role in Anglo-Saxon philosophy than in other philosophical traditions. Works of philosophy written in English have, it is true, spawned a massive secondary literature dealing with the ideas, problems or arguments they contain. But they have almost never given rise to works of commentary in the strict sense, a genre which is however a dominant literary form not only in the Confucian, Vedantic, Islamic, Jewish and Scholastic traditions of the past, but also in relation to more recent German-language philosophy (thus for example in work on Hegel, Heidegger or Wittgenstein). Moreover Anglo-Saxon philosophers have themselves embraced the commentary form when dealing with Greek or Latin philosophers outside their own tradition. The paper seeks to establish the reasons for this imbalance by examining those factors which might be conducive to the growth of a commentary literature in a given culture.

In 1929 when Aurel Kolnai published his essay “On Disgust” in Husserl's ]ahrbuch he could truly assert that disgust was a "sorely neglected" topic. Now, however, this situation is changing as philosophers, psychologists, and historians of culture are turning their attention not only to emotions in general but more specifically to the large and disturbing set of aversive emotions, including disgust. We here provide an account of Kolnai’s contribution to the study of the phenomenon of disgust, of his general theory of emotions and of the phenomenological methodology he employed in his work.

One reason for the renewed interest in Austrian philosophy, and especially in the work of Brentano and his followers, turns on the fact that analytic philosophers have become once again interested in the traditional problems of metaphysics. It was Brentano, Husserl, and the philosophers and psychologists whom they influenced, who drew attention to the thorny problem of intentionality, the problem of giving an account of the relation between acts and objects or, more generally, between the psychological environments of cognitive subjects and the different sorts of external (physical, geographical, social) environments which they inhabit. The present essay addresses this environmental version of the problem of intentionality. It draws not only on the work of Husserl and Scheler but also on the Gestalt psychological writings of Kurt Koffka and Kurt Lewin. It considers the influential subjective idealist theory of animal environments put forward by J. von Uexküll and contrasts this with a realist theory of organism-environment interaction based on the work of the ecological psychologists J. J. Gibson and Roger Barker. This realist theory is then exploited as a basis for an ontology of social objects of a range of different sorts.

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. Finally, we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects.

The term ‘Continental philosophy’ designates not philosophy on the continent of Europe as a whole, but rather a selective slice of Franco-German philosophy. Through a critical analysis of the arguments advanced by Otto Neurath, the paper addresses the issue of why Austrian philosophers in particular are not counted in the pantheon of Continental philosophers. Austrian philosophy is marked by the predominance of philosophical analysis and of the philosophy of science. The paper concludes that it is not Austria which is the special case when seen against the background of contemporary mainstream philosophy, but rather Germany and France.

The tradition of realist phenomenology was founded in around 1902 by a group of students in Munich interested in the newly published Logical Investigations of Edmund Husserl. Initial members of the group included Johannes Daubert, Alexander Pfänder, Adolf Reinach and Max Scheler. With Reinach’s move to Göttingen the group acquired two new prominent members – Edith Stein and Roman Ingarden. The group’s method turned on Husserl’s idea that we are in possession a priori (which is to say: non-inductive) knowledge of entities (for example, colors, tones, values, shapes) of a range of different sorts. Pfänder applied this method in his descriptive psychology of willing and motivation, Reinach (anticipating the later speech act theory) to what he called ‘social acts’, Stein to the ontology of communities, and Ingarden to works of art and aesthetic phenomena. The movement latter, through Ingarden, lived on in Poland, where it influenced the young Karol Wojtyła.

Changes in an upper level ontology have obvious conse-quences for the domain ontologies that use it at lower levels. It is therefore crucial to document the changes made between successive versions of ontologies of this kind. We describe and apply a method for tracking, explaining and measuring changes between successive versions of upper level ontologies such as the Basic Formal Ontology (BFO). The proposed change-tracking method extends earlier work on Realism-Based Ontology Versioning (RBOV) and Evolutionary Terminology Auditing (ETA). We describe here the application of this evaluation method to changes between BFO 1.0, BFO 1.1, and BFO 2.0. We discuss the issues raised by this application and describe the extensions which we added to the original evaluation schema in order to account for changes in an ontology of this type. Our results show that BFO has undergone eight types of changes that can be systematically explained by the extended evaluation schema. Finally, we discuss problematic cases, possible pitfalls and certain limits of our study that we propose to address in future work.

It is only by fixing on agreed meanings of terms in biomedical terminologies that we will be in a position to achieve that accumulation and integration of knowledge that is indispensable to progress at the frontiers of biomedicine. Standardly, the goal of fixing meanings is seen as being realized through the alignment of terms on what are called ‘concepts’. Part I addresses three versions of the concept-based approach – by Cimino, by Wüster, and by Campbell and associates – and surveys some of the problems to which they give rise, all of which have to do with a failure to anchor the terms in terminologies to corresponding referents in reality. Part II outlines a new, realist solution to this anchorage problem, which sees terminology construction as being motivated by the goal of alignment not on concepts but on the universals (kinds, types) in reality and thereby also on the corresponding instances (individuals, tokens). We outline the realist approach, and show how on its basis we can provide a benchmark of correctness for terminologies which will at the same time allow a new type of integration of terminologies and electronic health records. We conclude by outlining ways in which the framework thus defined might be exploited for purposes of diagnostic decision-support.

Given the assertion of a relation between two types, like: “Epidermis has part some Keratinocyte”, we define silent change as any kind of change of the instance-relata of the relation in question that does not change the truth-value of the respective type-level assertion. Such assertions are notoriously difficult to model in OWL 2. To address this problem, we distinguish different modes of type-level relatedness giving rise to this problem and describe a conservative extension to the BFO top-level ontology that allows expressing these modes.

The paper investigates the role played by ethical deliberation and ethical judgment in Wittgenstein's early thought in the light of twentieth?century German legal philosophy. In particular the theories of the phenomenologists Adolf Reinach, Wilhelm Schapp, and Gerhart Husserl are singled out, as resting on ontologies which are structurally similar to that of the Tractatus: in each case it is actual and possible Sachverhalte which constitute the prime ontological category. The study of the relationship between the states of affairs depicted, e.g., in the sentences of a legal trial and prior fact?complexes to which these may correspond suggests one possible connecting link between the logical and ontological sections of the Tractatus and the ethical reflections appearing at the end. It is argued that the latter can best be understood in terms of the idea of a ?last judgment? (with its associated ethical rewards and punishments) which would relate to the world as a whole as a penal trial relates to individual complexes of facts.

Values exist not in isolation, but in complex wholes. Values are what they are because of the complex wholes in which they are situated. To do justice to this thesis will require a holistic ontology, a theory according to which many types of entities exist only as inseparable parts or moments of wider contexts or environments. An ontological theory of environments -- with roots in Gestalt psychology and the ecological psychology of J. J. Gibson and Roger Barker, and which is related also to the theory of motivation sketched by Edmund Husserl as part of his theory of the lifeworld or Lebenswelt -- will help us to understand the ontology of values. It will help us to understand what values are. It will not, however, tell us what is good or bad. From facts of ontology, no value propositions follow.

We propose a typology of representational artifacts for health care and life sciences domains and associate this typology with different kinds of formal ontology and logic, drawing conclusions as to the strengths and limitations for ontology in a description logics framework. The four types of domain representation we consider are: (i) lexico-semantic representation, (ii) representation of types of entities, (iii) representations of background knowledge, and (iv) representation of individuals. We advocate a clear distinction of the four kinds of representation in order to provide a more rational basis for using ontologies and related artifacts to advance integration of data and enhance interoperability of associated reasoning systems. We highlight the fact that only a minor portion of scientifically relevant facts in a domain such as biomedicine can be adequately represented by formal ontologies as long as the latter are conceived as representations of entity types. In particular, the attempt to encode default or probabilistic knowledge using ontologies so conceived is prone to produce unintended, erroneous models.

Die bahnbrechenden wissenschaftlichen Ergebnisse der letzten Jahre erzwingen eine neue philosophische Auseinandersetzung mit den Grundkategorien der Biologie und der benachbarten Disziplinen. Insbesondere die Anwendung neuer informationstechnischer Mittel in der biomedizinischen Forschung und die damit verbundene, kontinuierlich zunehmende Datenflut sowie die Notwendigkeit, ihrer Herr zu werden, erfordern ein konsequentes Nachdenken darüber, wie biologische Daten systematisiert und klassifiziert werden können. Dafür wiederum bedarf es robuster Theorien von Grundbegriffen wie Art, Spezies, Teil, Ganzes, Funktion, Prozess, Fragment, Sequenz, Expression, Grenze, Locus, Umwelt, System usw. Solche Begriffe gehören zum impliziten Wissen jedes Biologen. Sie spiegeln einerseits eine Dimension der biologischen Wirklichkeit wider, die auch vor dem Hintergrund der biologischen Evolution unverändert bleibt. Andererseits verlangt deren theoretische Behandlung nach zeitgemäßen Analoga der in der traditionellen aristotelischen Metaphysik entwickelten Methoden. Zugleich können so die explizit formulierten Theorien und Definitionen bereitgestellt werden, die für computergestützte Informationssysteme unabdingbar sind. Das Entwickeln derartiger Theorien und Definitionen ist eine Aufgabe der Philosophie, die in diesem Sinne herausgefordert ist, zwischen Biologie und Informatik zu vermitteln.

Two hundred and sixty-three subjects each gave examples for one of five geographic categories: geographic features, geographic objects, geographic concepts, something geographic, and something that could be portrayed on a map. The frequencies of various responses were significantly different, indicating that the basic ontological terms feature, object, etc., are not interchangeable but carry different meanings when combined with adjectives indicating geographic or mappable. For all of the test phrases involving geographic, responses were predominantly natural features such as mountain, river, lake, ocean, hill. Artificial geographic features such as town and city were listed hardly at all for geographic categories, an outcome that contrasts sharply with the disciplinary self-understanding of academic geography. However, geographic artifacts and fiat objects, such as roads, cities, boundaries, countries, and states, were frequently listed by the subjects responding to the phrase something that could be portrayed on a map. In this paper, we present the results of these experiments in visual form, and provide interpretations and implications for further research.

There are two important ways in which, when dealing with documents, we go beyond the boundaries of linear text. First, by incorporating diagrams into documents, and second, by creating complexes of intermeshed documents which may be extended in space and evolve and grow through time. The thesis of this paper is that such aggregations of documents are today indispensable to practically all complex human achievements from law and finance to orchestral performance and organized warfare. Documents provide for what we can think of as a division of intellectual, instructional, and deontic labour, allowing plans, orders, and obligations to be enmeshed together in a way that often involves the use of diagrammatic elements, as for example in a musical score.

Ontologies are today being applied in almost every field to support the alignment and retrieval of data of distributed provenance. Here we focus on new ontological work on dance and on related cultural phenomena belonging to what UNESCO calls the “intangible heritage.” Currently data and information about dance, including video data, are stored in an uncontrolled variety of ad hoc ways. This serves not only to prevent retrieval, comparison and analysis of the data, but may also impinge on our ability to preserve the data that already exists. Here we explore recent technological developments that are designed to counteract such problems by allowing information to be retrieved across disciplinary, cultural, linguistic and technological boundaries. Software applications such as the ones envisaged here will enable speedier recovery of data and facilitate its analysis in ways that will assist both archiving of and research on dance.

Kotarbiński is one of the leading figures in the Lvov-Warsaw school of Polish philosophy. We summarize the development of Kotarbiński’s thought from his early nominalism and ‘pansomatistic reism’ to the later doctrine of ‘temporal phases’. We show that the surface clarity and simplicity of Kotarbiński’s writings mask a number of profound philosophical difficulties, connected above all with the problem of giving an adequate account of the truth of contingent (tensed) predications. The paper will examine in particular the attempts to resolve these difficulties on the part of Leśniewski. It will continue with an account of the relations of Kotarbińskian reism to the ontology of things or entia realia defended by the later Brentano. Kotarbiński’s identification of Brentano as a precursor of reism is, it will be suggested, at least questionable, and the paper will conclude with a more careful attempt to situate the Brentanian and Kotarbińskian ontologies within the spectrum of competing ontological views.

First published in 1986 and reprinted in 2010 in the Routledge Revivals series, this book presents the first detailed confrontation between the Austrian school of economics and Austrian philosophy, especially the philosophy of the Brentano school. It contains a study of the roots of Austrian economics in the liberal political theory of the nineteenth-century Hapsburg empire, and a study of the relations between the general theory of value underlying Austrian economics and the new economic approach to human behaviour propounded by Gary Becker and others in Chicago. In addition, it considers the connections between Austrian methodology and contemporary debates in the philosophy of the social sciences.

Medical science conceives the human body as a system comprised of many subsystems at a variety of levels. At the highest level are bodily systems proper, such as the endocrine system, which are central to our understanding of human anatomy, and play a key role in diagnosis and in dynamic modeling as well as in medical pedagogy and computer visualization. But there is no explicit definition of what a bodily system is; such informality is acceptable in documentation created for human beings, but falls short of what is needed for computer representations. Our analysis is intended as a first step towards filling this gap.