Barry Smith

This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single bearer. A definition of ‘protective resistance’ is proposed for use in the Infectious Disease Ontology (IDO) and we show how this definition can be used to characterize the antibiotic resistance in Methicillin-Resistant Staphylococcus aureus (MRSA). The ontological relations between entities in our MRSA case study are used alongside a series of logical inference rules to illustrate logical reasoning about resistance. A description logic representation of blocking dispositions is also provided. We demonstrate that our characterization of resistance is sufficiently general to cover two other cases of resistance in the infectious disease domain involving HIV and malaria.

Attempts to trace a unifying thread of ontological realism extending through 1. my early writings on Frege, Brentano, Husserl, Wittgenstein, Ingarden and (with Kevin Mulligan and Peter Simons) on truthmakers; 2. work on formal theories of the common-sense world, and on mereotopology, fiat objects, geographical categories, and environments (with David Mark, Roberto Casati, Achille Varzi), to 3. current work on applied ontology in biology and medicine, and on the theory of document acts and on the ontology of information artifacts.

We review an influential series of lectures on analytic philosophy published in 1976 by the West German philosopher Ernst Tugendhat focusing on Tugendhat's treatment of Husserl, and particularly on issues connected with the notion of dependence or Abhängigkeit central to Husserl's philosophy. These issues are of interest not only because Tugendhat's work is one of the few contributions to contemporary analytic philosophy in which they are confronted explicitly, but also because what he has to say about Husserl and dependence illustrates well both the positive and the negative thrust of his argument.

Recent work in formal philosophy has concentrated over-whelmingly on the logical problems pertaining to epistemic shortfall - which is to say on the various ways in which partial and sometimes incorrect information may be stored and processed. A directly depicting language, in contrast, would reflect a condition of epistemic perfection. It would enable us to construct representations not of our knowledge but of the structures of reality itself, in much the way that chemical diagrams allow the representation (at a certain level of abstractness) of the structures of molecules of different sorts. A diagram of such a language would be true if that which it sets out to depict exists in reality, i.e. if the structural relations between the names (and other bits and pieces in the diagram) map structural relations among the corresponding objects in the world. Otherwise it would be false. All of this should, of course, be perfectly familiar. (See, for example, Aristotle, Metaphysics, 1027 b 22, 1051 b 32ff.) The present paper seeks to go further than its predecessors, however, in offering a detailed account of the syntax of a working universal characteristic and of the ways in which it might be used.

While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the patient. We here present a view of mental disease that is based on ontological realism and which follows the principles embodied in Basic Formal Ontology and in the application of BFO in the Ontology of General Medical Science. We analyzed statements about what counts as a mental disease provided in the research agenda for the DSM-V, and in Pies' model. The results were used to assess whether the representational units of BFO and OGMS were adequate as foundations for a formal representation of the entities in reality that these statements attempt to describe. We then analyzed the representational units specific to mental disease and provided corresponding definitions. Our key contributions lie in the identification of confusions and conflations in the existing terminology of mental disease and in providing what we believe is a framework for the sort of clear and unambiguous reference to entities on the side of the patient that is needed in order to avoid these confusions in the future.

We take as our starting point a thesis to the effect that, at least for true judgments of many varieties, there are parts of reality which make such judgments are true. We argue that two distinct components are involved in this truthmaker relation. On the one hand is the relation of necessitation, which holds between an object x and a judgment p when the existence of x entails the truth of p. On the other hand is the dual notion of projection, which holds between a judgment p and an object x when the truth of p entails the existence of x. A truthmaker for a judgment p is then a necessitator for p which satisfies the further constraint that it is part of p’s projection. We offer a formal theory of the truthmaker relation thus defined, exploiting ontological tools of basic mereology and the theory of dependence. We then apply the theory to a range of problems connected with generic expressions, ellipsis, vagueness, and indexical and perceptual judgments

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.

The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries of domain ontologies in anatomy, physiology and pathology.

Affective science conducts interdisciplinary research into the emotions and other affective phenomena. Currently, such research is hampered by the lack of common definitions of te rms used to describe, categorise and report both individual emotional experiences and the results of scientific investigations of such experiences. High quality ontologies provide formal definitions for types of entities in reality and for the relationships between such entities, definitions which can be used to disambiguate and unify data across different disciplines. Heretofore, there has been little effort directed towards such formal representation for affective phenomena, in part because of widespread debates within the affective science community on matters of definition and categorization. We describe our efforts towards developing an Emotion Ontology (EMO) to serve the affective science community. We here focus on conformity to the BFO upper ontology and disambiguation of polysemous terminology.

Suppose you own a garden-variety object such as a hat or a shirt. Your property right then follows the ageold saw according to which possession is nine-tenths of the law. That is, your possession of a shirt constitutes a strong presumption in favor of your ownership of the shirt. In the case of land, however, this is not the case. Here possession is not only not a strong presumption in favor of ownership; it is not even clear what possession is. Possessing a thing like a hat or a shirt is a rather straightforward affair: the person wearing the hat or shirt possesses the shirt or the hat. But what is possession in the case of land? This essay seeks to provide an answer to this question in the form of an ontology of landed property.