Barry Smith

Ontologies describe reality in specific domains in ways that can bridge various disciplines and languages. They allow easier access and integration of information that is collected by different groups. Ontologies are currently used in the biomedical sciences, geography, and law. A Biomedical Ethics Ontology would benefit members of ethics committees who deal with protocols and consent forms spanning numerous fields of inquiry. There already exists the Ontology for Biomedical Investigations (OBI); the proposed BMEO would interoperate with OBI, creating a powerful information tool. We define a domain ontology and begin to construct a BMEO, focused on the process of evaluating human research protocols. Finally, we show how our BMEO can have practical applications for ethics committees. This paper describes ongoing research and a strategy for its broader continuation and cooperation.

This paper proposes a reformulation of the treatment of boundaries, at parts and aggregates of entities in Basic Formal Ontology. These are currently treated as mutually exclusive, which is inadequate for biological representation since some entities may simultaneously be at parts, boundaries and/or aggregates. We introduce functions which map entities to their boundaries, at parts or aggregations. We make use of time, space and spacetime projection functions which, along the way, allow us to develop a simple temporal theory

We propose a new account of vagueness and approximation in terms of the theory of granular partitions. We distinguish different kinds of crisp and non-crisp granular partitions and we describe the relations between them, concentrating especially on spatial examples. We describe the practice whereby subjects use regular grid-like reference partitions as a means for tempering the vagueness of their judgments, and we demonstrate how the theory of reference partitions can yield a natural account of this practice, which is referred to in the literature as ‘approximation’.

We describe on-going work on IAO-Intel, an information artifact ontology developed as part of a suite of ontologies designed to support the needs of the US Army intelligence community within the framework of the Distributed Common Ground System (DCGS-A). IAO-Intel provides a controlled, structured vocabulary for the consistent formulation of metadata about documents, images, emails and other carriers of information. It will provide a resource for uniform explication of the terms used in multiple existing military dictionaries, thesauri and metadata registries, thereby enhancing the degree to which the content formulated with their aid will be available to computational reasoning.

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.

Philosophy in the West divides into three parts: Analytic Philosophy (AP), Continental Philosophy (CP), and History of Philosophy (HP). But all three parts are in a bad way. AP is sceptical about the claim that philosophy can be a science, and hence is uninterested in the real world. CP is never pursued in a properly theoretical way, and its practice is tailor-made for particular political and ethical conclusions. HP is mostly developed on a regionalist basis: what is studied is determined by the nation or culture to which a philosopher belongs, rather than by the objective value of that philosopher’s work. Progress in philosophy can only be attained by avoiding these pitfalls.

When does a human being begin to exist? We argue that it is possible, through a combination of biological fact and philosophical analysis, to provide a definitive answer to this question. We lay down a set of conditions for being a human being, and we determine when, in the course of normal fetal development, these conditions are first satisfied. Issues dealt with along the way include: modes of substance-formation, twinning, the nature of the intra-uterine environment, and the nature of the relation between fetus and mother (connection, parthood, dependence).

‘Eruv’ is a Hebrew word meaning literally ‘mixture’ or ‘mingling’. An eruv is an urban region demarcated within a larger urban region by means of a boundary made up of telephone wires or similar markers. Through the creation of the eruv, the smaller region is turned symbolically (halachically = according to Jewish law) into a private domain. So long as they remain within the boundaries of the eruv, Orthodox Jews may engage in activities that would otherwise be prohibited on the Sabbath, such as pushing prams or wheelchairs, or carrying walking sticks. There are eruvim in many towns and university campuses throughout the world. There are five eruvim in Chicago, five in Brooklyn, twenty three in Queens and Long Island, and at least three in Manhattan. The US Supreme Court is (like most other major US Federal Government buildings) located within the eruv of Washington DC. In many cases, not all of those living within or near the area of an actual or proposed eruv will themselves be Orthodox Jews, and this has sometimes led to protests against eruv creation. It is such protests which triggered the writing of this essay.

The paper is an exercise in descriptive ontology, with specific applications to problems in the geographical sphere. It presents a general typology of spatial boundaries, based in particular on an opposition between bona fide or physical boundaries on the one hand, and fiat or human-demarcation-induced boundaries on the other. Cross-cutting this opposition are further oppositions in the realm of boundaries, for example between: crisp and indeterminate, complete and incomplete, enduring and transient, symmetrical and asymmetrical. The resulting typology generates a corresponding categorization of the different sorts of objects which (complete) boundaries determine or demarcate. The theory is applied first of all in the areas of geography and of administrative and property law. Indications are then given as to how the typology may be applied also in other fields where physical and fiat boundaries are at work, including the field of cognitive linguistics and the related field of the ontology of truth.

There is a narrow thread in the vast literature on Kafka which pertains to Kafka’s knowledge of philosophy, and more precisely to Kafka’s use in his fictional writings of some of the main ideas of Franz Brentano. Kafka attended courses in philosophy at the Charles University given by Brentano’s students Anton Marty and Christian von Ehrenfels, and was for several years a member of a discussion-group organized by orthodox adherents of the Brentanian philosophy in Prague. The present essay summarizes what is known about Kafka’s relations to the Brentanist movement. It draws on Brentanian ideas on the evidence of inner perception, on oblique consciousness, on active introspection, on correct and incorrect judgment, and on consciousness as a species of inner tribunal, in order to throw light on central features of Kafka’s writings, including stylistic features. Special attention is directed towards Die Verwandlung and Der Prozess, and a reading of the latter is offered according to which the trial of Joseph K. occurs entirely within the mind of K. himself. The revisions in the 1997 version of the paper relate especially to the treatment of Kafka and Brentano in Arnold Heidsieck’s book The Intellectual Contexts of Kafka’s Fiction: Philosophy, Law, Religion of 1994.

If we are to develop efficient, reliable and secure means for sharing information across healthcare systems and organizations, then a careful analysis of human actions will be needed. To address this need, the HL7 organization has proposed its Reference Information Model (RIM), which is designed to provide a comprehensive representation of the entire domain of healthcare centered around the phenomenon of human action. Taking the Basic Formal Ontology as our starting point, we examine the RIM from an ontological point of view, describing how it fails to provide a representation of the healthcare domain which would enjoy the sort of clarity, coherence, rigor and completeness that is claimed on its behalf.

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.

In his The Meaning of Disgust, Colin McGinn employs elements of the phenomenological theory of disgust advanced by Aurel Kolnai in 1929. Kolnai’s treatment of what he calls “material” disgust and of its primary elicitors—putrefying organic matter, bodily wastes and secretions, sticky contaminants, vermin—anticipates more recent scientific treatments of this emotion as a mode of protective recoil. While Nina Strohminger charges McGinn with neglecting such scientific studies, we here attempt to show how Kolnai goes beyond experimental findings in his careful description of the phenomenological differences between disgust and other emotions of forceful disapproval.

How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR).

From his groundbreaking book Speech Acts to his most recent studies of consciousness, freedom and rationality John Searle has been a dominant and highly influential figure amongst contemporary philosophers. This systematic introduction to the full range of Searle's work begins with the theory of speech acts and proceeds with expositions of Searle's writings on intentionality, consciousness and perception, as well as a careful presentation of the so-called Chinese Room argument. The volume considers Searle's recent work on social ontology and his views on the nature of law and obligation. It concludes with an appraisal of Searle's spirited defence of truth and scientific method in the face of the criticisms of Derrida and other postmodernists. This is the only comprehensive introduction to Searle's work, and as such it will be of particular value to advanced undergraduates, graduates and professionals in philosophy, psychology, linguistics, cognitive and computer science and literary theory.

Analytic philosophers apply the term ‘object’ both to concreta and to abstracta of certain kinds. The theory of objects which this implies is shown to rest on a dichotomy between object-entities on the one hand and meaning-entities on the other, and it is suggested that the most adequate account of the latter is provided by Husserl’s theory of noemata. A two-story ontology of objects and meanings (concepts, classes) is defended, and Löwenheim’s work on class-representatives is cited as an indication of how the need for higher types may be obviated, even in mathematical contexts. The paper concludes with a sketch of the taxonomy of the object realm which results from the above.

It is often claimed that the beginnings of Brentano’s ontology were Aristotelian in nature; but this claim is only partially true. Certainly the young Brentano adopted many elements of Aristotle’s metaphysics, and he was deeply influenced by the Aristotelian way of doing philosophy. But he always interpreted Aristotle’s ideas in his own fashion. He accepted them selectively, and he used them in the service of ends that would not have been welcomed by Aristotle himself. The present paper is an exposition of the development of Brentano’s ontology, beginning with the Lectures on Metaphysics first delivered by Brentano in Würzburg in 1867 and concluding with his late work from 1904–1917.

We aim to provide the ontological grounds for an adequate account of persistence. We defend a perspectivalist, or moderate pluralist, position, according to which some aspects of reality can be accounted for in ontological terms only via partial and mutually complementary ontologies, each one of which captures some relevant aspect of reality. Our thesis here is that this is precisely the sort of ontological account that is needed for the understanding of persistence, specifically an account involving two independent ontologies, one for continuants, and one for occurrents.

Amongst the entities making up social reality, are there necessary relations whose necessity is not a mere reflection of the logical connections between corresponding concepts? We distinguish three main groups of answers to this question, associated with Hume and Adolf Reinach at opposite extremes, and with Searle who occupies a position somewhere in the middle. We first set forth Reinach’s views on what he calls ‘material necessities’ in the realm of social entities. We then attempt to show that Searle has not identified a sustainable position somewhere between the Humean and the Reinachian extremes. This is because Searle’s position is threatened by circularity, and to steer clear of that danger it must incorporate at least some elements of Reinach’s essentialism.

There is a basic distinction, in the realm of spatial boundaries, between bona fide boundaries on the one hand, and fiat boundaries on the other. The former are just the physical boundaries of old. The latter are exemplified especially by boundaries induced through human demarcation, for example in the geographic domain. The classical problems connected with the notions of adjacency, contact, separation and division can be resolved in an intuitive way by recognizing this two-sorted ontology of boundaries. Bona fide boundaries yield a notion of contact that is effectively modeled by classical topology; the analogue of contact involving fiat boundaries calls, however, for a different account, based on the intuition that fiat boundaries do not support the open/closed distinction on which classical topology is based. In the presence of this two-sorted ontology it then transpires that mereotopology—topology erected on a mereological basis—is more than a trivial formal variant of classical point-set topology.

As Kevin Mulligan, more than anyone else, has demonstrated, there is a distinction within the philosophy of the German-speaking world between two principal currents: of idealism / transcendentalism, characteristic of Northern Germany; and of realism / objectivism, characteristic of Austria and the South. We explore some of the implications of this distinction with reference to the influence of Austrian (and German) philosophy on philosophical developments in Hungary, focusing on the work of Ákos von Pauler, and especially on Pauler’s reading of Wittgenstein’s Tractatus.

The concept of niche (setting, context, habitat, environment) has been little studied by ontologists, in spite of its wide application in a variety of disciplines from evolutionary biology to economics. What follows is a first formal theory of this concept, a theory of the relations between objects and their niches. The theory builds upon existing work on mereology, topology, and the theory of spatial location as tools of formal ontology. It will be illustrated above all by means of simple biological examples, but the concept of niche should be understood as being, like concepts such as part, boundary, and location, a structural concept that is applicable in principle to a wide range of different domains

This paper presents an axiomatic formalization of a theory of top-level relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the sub-universal relation among universals and the parthood relation among individuals, as well as cross-categorial relations such as instantiation and membership. We show that an adequate understanding of the formal properties of such relations – in particular their behavior with respect to time – is critical for geographic information processing. The axiomatic theory is developed using Isabelle, a computational system for implementing logical formalisms. All proofs are computer verified and the computational representation of the theory is available online.

The goal of referent tracking is to create an ever-growing pool of data relating to the entities existing in concrete spatiotemporal reality. In the context of Electronic Healthcare Records (EHRs) the relevant concrete entities are not only particular patients but also their parts, diseases, therapies, lesions, and so forth, insofar as these are salient to diagnosis and treatment. Within a referent tracking system, all such entities are referred to directly and explicitly, something which cannot be achieved when familiar concept-based systems are used in what is called “clinical coding”. In this paper we describe the components of a referent tracking system in an informal way and we outline the procedures that would have to be followed by healthcare personnel in using such a system. We argue that the referent tracking paradigm can be introduced with only minor – though nevertheless ontologically important – technical changes to existing EHR infrastructures, but that it will require a radically different mindset on the part of those involved in clinical coding and terminology development from that which has prevailed hitherto.

Vor dem Hintergrund einer von Durkheim ausgehenden Selbstmordarten-Typologie wird das Phänomen von terroristischen Selbstmordattentaten untersucht: Diese scheinen ein spezifisch nicht-westliches Phänomen zu sein. Der deutliche Unterschied zwischen der Strategie westlicher Terrorgruppen und solchen Terrorgruppen, die Selbstmordattentate ausüben, geht auf ein besonderes Merkmal der Geschichte und der Eigenart des Westens zurück; und dies wiederum ist tief im Mittelalter verwurzelt. Against the background of a taxonomy of types of suicide advanced by Durkheim we propose an analysis of the phenomenon of terrorist suicide attacks. We argue that suicide of this sort is a specifically non-Western phenomenon. The significant difference between the strategy of Western terrorist groups and those terrorist groups engaged in suicide attacks is rooted in a peculiar feature of the history and character of the West extending back to the Middle Ages.

Some would conceive philosophy as being divided into Analytic and Continental. This, as John Searle points out, is rather like conceiving America as being divided into Business and Kansas. Searle’s wise saying has not, as yet, received the theoretical attention it deserves. In both cases we have a certain domain, which is conceived as being divided into two parts, one defined in spatial terms, the other defined in terms of objects, practices or features widely spread through some spatial area. We present a draft theory of such divides, and of the agglomerations (populations, movements, systems of beliefs) which are the vehicles for their division. It offers a general, ontological theory of Us and Them, of Analytics and Continentals, of the Hegemonic Colonizing Self and the Indigenous Colonized Other. Presented at a conference on Bridging the Analytic-Continental Divide, Tel Aviv University, January 17-20, 1999.