Barry Smith

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

The essay surveys recent developments in ontology and defends a strategy for improvement of ontologies based on ontological realism. As a thought experiment, we consider central theses of Aristotelian metaphysics, and show how they fall short of what we believe to be the requirements of ontology today. Above all, Aristotle provides us with no strategy for the reconciliation of common-sense realism and scientific realism where these diverge. We focus specifically on shortfalls in Aristotle’s treatment of individual accidents, especially in regard to the category of place. We then show how Aristotle’s metaphysics needs to be supplemented by a theory of holes, of fiat boundaries, of granularity, and of vagueness.

French translation of "Truth-Makers" (1984). A realist theory of truth for a class of sentence holds that there are entities in virtue of which these sentences are true or false. We call such entities ‘truthmakers’ and contend that those for a wide range of sentences about the real world are moments (dependent particulars). Since moments are unfamiliar we provide a definition and a brief philosophical history, anchoring them in our ontology by showing that they are objects of perception. The core of our theory is the account of truthmaking for atomic sentences, in which we expose a pervasive ‘dogma of logical form’, which says that atomic sentences cannot have more than one truthmaker. The authors uphold the mutual independence of logical and ontological complexity. The theory is compared with that of Wittgenstein’s Tractatus, and the authors outline formal principles of truthmaking taking account of both kinds of complexity and suggesting how to overcome Wittgenstein’s problem of negation.

We propose a modular ontology of the dynamic features of reality. This amounts, on the one hand, to a purely spatial ontology supporting snapshot views of the world at successive instants of time and, on the other hand, to a purely spatiotemporal ontology of change and process. We argue that dynamic spatial ontology must combine these two distinct types of inventory of the entities and relationships in reality, and we provide characterizations of spatiotemporal reasoning in the light of the interconnections between them.

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.

A collection of material on Husserl's Logical Investigations, and specifically on Husserl's formal theory of parts, wholes and dependence and its influence in ontology, logic and psychology. Includes translations of classic works by Adolf Reinach and Eugenie Ginsberg, as well as original contributions by Wolfgang Künne, Kevin Mulligan, Gilbert Null, Barry Smith, Peter M. Simons, Roger A. Simons and Dallas Willard. Documents work on Husserl's ontology arising out of early meetings of the Seminar for Austro-German Philosophy.

We describe an ontology of philosophy that is designed to aid navigation through philosophical literature, including literature in the form of encyclopedia articles and textbooks and in both printed and digital forms. The ontology is designed also to serve integration and structuring of data pertaining to the philosophical literature, and in the long term also to support reasoning about the provenance and contents of such literature, by providing a representation of the philosophical domain that is oriented around what philosophical literature is about

The paper is a contribution to formal ontology. It seeks to use topological means in order to derive ontological laws pertaining to the boundaries and interiors of wholes, to relations of contact and connectedness, to the concepts of surface, point, neighbourhood, and so on. The basis of the theory is mereology, the formal theory of part and whole, a theory which is shown to have a number of advantages, for ontological purposes, over standard treatments of topology in set-theoretic terms. One central goal of the paper is to provide a rigorous formulation of Brentano's thesis to the effect that a boundary can exist as a matter of necessity only as part of a whole of higher dimension which it is the boundary of. It concludes with a brief survey of current applications of mereotopology in areas such as natural-language analysis, geographic information systems, machine vision, naive physics, and database and knowledge engineering.

If Mont Blanc is a vague object, then its vagueness will depend on the context in which reference is made. In a geological context the mountain might include only rock, perhaps together with a certain amount of air in the crevices and tunnels which have been formed beneath its surface. In a context of soil chemistry we might include also a surrounding thin layer of organic matter. In a skiing context we might include some snow. This essay sketches in informal terms the theory of granular partitions, which is designed to do justice to this context-dependence of vagueness by means of what might be described as a contextualized supervaluationism. Granularity and vagueness, it is argued, are two sides of a single coin: what is vague at one level of granularity may appear crisp at another. The resultant theory can be shown to resolve certain problems in our description of perceptual content, for example when John says that he sees the wall, but that he does not see the molecules by which the wall is constituted.

The paradigm of referent tracking is based on a realist presupposition which rejects so-called negative entities (congenital absent nipple, and the like) as spurious. How, then, can a referent tracking-based Electronic Health Record deal with what are standardly called ‘negative findings’? To answer this question we carried out an analysis of some 748 sentences drawn from patient charts and containing some form of negation. Our analysis shows that to deal with these sentences we need to introduce a new ontological relationship between a particular and a universal, which holds when no instance of the universal has a specific qualified ontological relation with the particular. This relation is found to be able to accommodate nearly all occurrences of negative findings in the examined sample, in ways which involve no reference to negative entities.

The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities that is designed to serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems. We diagnose certain characteristic errors in the treatment of these relations and show how these errors can be avoided through adoption of the formalism we describe. We then illustrate how a consistently applied formal treatment of taxonomy and partonomy can support the alignment of ontologies.

Those who conceive logic as a science have generally favoured one of two alternative conceptions as to what the subject-matter of this science ought to be. On the one hand is the nowadays somewhat old-fashioned-seeming view of logic as the science of judgment, or of thinking or reasoning activities in general. On the other hand is the view of logic as a science of ideal meanings, 'thoughts', or 'propositions in themselves'. There is, however, a third alternative conception, which enjoyed only a brief flowering in the years leading up to the first World War, but whose lingering presence can be detected in the background of more recent ontologising trends in logic, as for example in the 'situation semantics' of Barwise and Perry. This third conception sees logic as a science of special objects called 'Sachverhalte' or 'states of affairs'. A view of this sort is present in simplified form in the works of Meinong, but it received its definitive formulation in the writings of Adolf Reinach, a student of Husserl who is otherwise noteworthy for having anticipated, in a monograph of 1913, large chunks of what later became known as the theory of speech acts.(1).

The pivotal role of the relation part-of in the description of living organisms is widely acknowledged. Organisms are open systems, which means that in contradistinction to mechanical artifacts they are characterized by a continuous flow and exchange of matter. A closer analysis of the spatial relations in biological organisms reveals that the decision as to whether a given particular is part-of a second particular or whether it is only contained-in the second particular is often controversial. We here propose a rule-based approach which allows us to decide on the basis of well-defined criteria which of the two relations holds between two anatomical objects, given that one spatially includes the other. We discuss the advantages and limitations of this approach, using concrete examples from human anatomy.

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.

Current approaches to formal representation in biomedicine are characterized by their focus on either the static or the dynamic aspects of biological reality. We here outline a theory that combines both perspectives and at the same time tackles the by no means trivial issue of their coherent integration. Our position is that a good ontology must be capable of accounting for reality both synchronically (as it exists at a time) and diachronically (as it unfolds through time), but that these are two quite different tasks, whose simultaneous realization is by no means trivial. The paper is structured as follows. We begin by laying out the methodological and philosophical background of our approach. We then summarize the structure and elements of the Basic Formal Ontology on which it rests, in particular the SNAP ontology of objects and the SPAN ontology of processes. Finally, we apply the general framework to the specific domain of biomedicine.

Common sense is on the one hand a certain set of processes of natural cognition - of speaking, reasoning, seeing, and so on. On the other hand common sense is a system of beliefs (of folk physics, folk psychology and so on). Over against both of these is the world of common sense, the world of objects to which the processes of natural cognition and the corresponding belief-contents standardly relate. What are the structures of this world? How does the scientific treatment of this world relate to traditional and contemporary metaphysics and formal ontology? Can we embrace a thesis of common-sense realism to the effect that the world of common sense exists uniquely? Or must we adopt instead a position of cultural relativism which would assign distinct worlds of common sense to each group and epoch? The present paper draws on recent work in computer science (especially in the fields of naive and qualitative physics), in perceptual and developmental psychology, and in cognitive anthropology, in order to consider in a new light these and related questions and to draw conclusions for the methodology and philosophical foundations of the cognitive sciences.

Medical terminology collects and organizes the many different kinds of terms employed in the biomedical domain both by practitioners and also in the course of biomedical research. In addition to serving as labels for biomedical classes, these names reflect the organizational principles of biomedical vocabularies and ontologies. Some names represent invariant features (classes, universals) of biomedical reality (i.e., they are a matter for ontology). Other names, however, convey also how this reality is perceived, measured, and understood by health professionals (i.e., they belong to the domain of epistemology). We analyze terms from several biomedical vocabularies in order to throw light on the interactions between ontological and epistemological components of these terminologies. We identify four cases: 1) terms containing classification criteria, 2) terms reflecting detectability, modality, uncertainty, and vagueness, 3) terms created in order to obtain a complete partition of a given domain, and 4) terms reflecting mere fiat boundaries. We show that epistemology-loaded terms are pervasive in biomedical vocabularies, that the “classes” they name often do not comply with sound classification principles, and that they are therefore likely to cause problems in the evolution and alignment of terminologies and associated ontologies.

The thesis that an analysis of property rights is essential to an adequate analysis of the state is a mainstay of political philosophy. The contours of the type of government a society has are shaped by the system regulating the property rights prevailing in that society. Views of this sort are widespread. They range from Locke to Nozick and encompass pretty much everything else in between. Defenders of this sort of view accord to property rights supreme importance. A state that does not sufficiently respect property rights is likely to be a totalitarian state, and will also be likely to fail to respect rights of other sorts.

: For Meinong, familiarly, fictional entities are not created, but rather merely discovered (or picked out) from the inexhaustible realm of Aussersein (beyond being and non-being). The phenomenologist Roman Ingarden, in contrast, offers in his Literary Work of Art of 1931 a constructive ontology of fiction, which views fictional objects as entities which are created by the acts of an author (as laws, for example, are created by acts of parliament). We outline the logic of fiction which is implied by Ingarden’s approach, showing how it distinguishes the properties possessed by fictional objects (for instance of having been created by such and such an author in such and such a work) from characteristics (for instance of smoking a pipe, of living in Baker Street) which are merely associated with such objects.

One of the tasks of ontology in information science is to support the classification of entities according to their kinds and qualities. We hold that to realize this task as far as entities such as material objects are concerned we need to distinguish four kinds of entities: substance particulars, quality particulars, substance universals, and quality universals. These form, so to speak, an ontological square. We present a formal theory of classification based on this idea, including both a semantics for the theory and a provably sound axiomatization.

In their paper “Sixteen Days” Barry Smith and Berit Brogaard try to answer the question: when does a human being begin to exist? In this paper we will address some methodological issues connected with this exercise in ontology. We shall begin by sketching the argument of “Sixteen Days”. We shall then attempt to characterize what is special about the ontological realism of “Sixteen Days” as contrasted to the linguistic constructivism which represents the more dominant current in contemporary analytic philosophy. This will allow us to infer guidelines for assessing the quality of ontological theories of various types. We shall argue that ontological parsimony, groundedness, faithfulness to ordinary language, consistency with science, coherence, and fruitfulness are at least part of the adequacy criteria for such theories. These criteria will then be applied to the theory presented in “Sixteen Days”, and they will lead us to some revisions of this theory as well as to some reflections on its ethical implications.

While Darwin is commonly supposed to have demonstrated the inapplicability of the Aristotelian ontology of species to biological science, recent developments, especially in the wake of the Human Genome Project, have given rise to a new golden age of classification in which ontological ideas -- as for example in the Gene Ontology, the Cell Ontology, the Protein Ontology, and so forth -- are once again playing an important role. In regard to species, on the other hand, matters are more complex. We provide a brief overview of recent proposals concerning the ontology of species, dealing with species as sets, classes and as collections, the views of Ernst Meyr, and mereological views.