Health Level 7 (HL7) is an organization seeking to provide universal standards for the exchange of healthcare information. In a document entitled ‘HL7 Version 3 Standard: Data Types’, the HL7 organization advances descriptions of data types recom- mended for use as identifiers. We will argue that the descriptions supplied provide insufficient guidance as to what exactly the entities are which these data types uniquely identify. Are they real things, such as persons or pieces of equipment? Or are they representations of (...) such real things in information artifacts? We here outline the problems faced by HL7 in providing answers to such questions, problems which arise because of the lack of anything like a coherent ontology in the HL7 standard, and we make some recommendations for future improvements. (shrink)

The integration of standardized biomedical terminologies into a single, unified knowledge representation system has formed a key area of applied informatics research in recent years. The Unified Medical Language System (UMLS) is the most advanced and most prominent effort in this direction, bringing together within its Metathesaurus a large number of distinct source-terminologies. The UMLS Semantic Network, which is designed to support the integration of these source-terminologies, has proved to be a highly successful combination of formal coherence and broad scope. (...) We argue here, however, that its organization manifests certain structural problems, and we describe revisions which we believe are needed if the network is to be maximally successful in realizing its goals of supporting terminology integration. (shrink)

Ingarden distinguishes four strata making up the structure of the literary work of art: the stratum of word sounds and sound-complexes; the stratum of meaning units; the stratum of represented objectivities (characters, actions, settings, and so forth); and the stratum of schematized aspects (perspectives under which the represented objectivities are given to the reader). It is not only works of literature which manifest this four-fold structure but also certain borderline cases such as newspaper articles, scientific works, biographies, and so forth. (...) Ingarden specifies what is characteristic of a work of literature by asserting that all declarative sentences appearing in the stratum of meaning units of such work possess what he calls a quasi-judgmental character. We discuss here Ingarden’s theory of quasi-judgments and draw out its implication that all works of literature are works of fiction through and through. (shrink)

Physical reality is all the reality we have, and so physical theory in the standard sense is all the ontology we need. This, at least, was an assumption taken almost universally for granted by the advocates of exact philosophy for much of the present century. Every event, it was held, is a physical event, and all structure in reality is physical structure. The grip of this assumption has perhaps been gradually weakened in recent years as far as the sciences of (...) mind are concerned. When it comes to the sciences of external reality, however, it continues to hold sway, so that contemporary philosophers B even while devoting vast amounts of attention to the language we use in describing the world of everyday experience B still refuse to see this world as being itself a proper object of theoretical concern. Here, however, we shall argue that the usual conception of physical reality as constituting a unique bedrock of objectivity reflects a rather archaic view as to the nature of physics itself and is in fact incompatible with the development of the discipline since Newton. More specifically, we shall seek to show that the world of qualitative structures, for example of colour and sound, or the commonsense world of coloured and sounding things, can be treated scientifically (ontologically) on its own terms, and that such a treatment can help us better to understand the structures both of physical reality and of cognition. (shrink)

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. (shrink)

Basic Formal Ontology was created in 2002 as an upper-level ontology to support the creation of consistent lower-level ontologies, initially in the subdomains of biomedical research, now also in other areas, including defense and security. BFO is currently undergoing revisions in preparation for the release of BFO version 2.0. We summarize some of the proposed revisions in what follows, focusing on BFO’s treatment of material entities, and specifically of the category object.

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. (shrink)

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. (shrink)

Biomedical research is increasingly a matter of the navigation through large computerized information resources deriving from functional genomics or from the biochemistry of disease pathways. To make such navigation possible, controlled vocabularies are needed in terms of which data from different sources can be unified. One of the most influential developments in this regard is the so-called Gene Ontology, which consists of controlled vocabularies of terms used by biologists to describe cellular constituents, biological processes and molecular functions, organized into hierarchies (...) via the relation of class subsumption. Here we seek to provide a rigorous account of the logic of classification that underlies GO and similar biomedical ontologies. Drawing on Aristotle, we develop a system of axioms and definitions for the treatment of biological classes and instances. (shrink)

This is an informal presentation of the theory of niches understood as ecological contexts. The first part sets out the basic conceptual background. The second part outlines the main principles of the theory and addresses the question of how the theory can be extended to aid our thinking in relation to the special types of causal integrity that characterize niches and niched entities.

This paper is concerned with certain ontological issues in the foundations of geographic representation. It sets out what these basic issues are, describes the tools needed to deal with them, and draws some implications for a general theory of spatial representation. Our approach has ramifications in the domains of mereology, topology, and the theory of location, and the question of the interaction of these three domains within a unified spatial representation theory is addressed. In the final part we also consider (...) the idea of non-standard geographies, which may be associated with geography under a classical conception in the same sense in which non-standard logics are associated with classical logic. (shrink)

We propose the beginnings of a general theory of environments, of the parts or regions of space in which organisms live and move. We draw on two sources: on the one hand on recent work on the ontology of space; and on the other hand on work by ecological scientists on concepts such as territory, habitat, and niche. An environment is in first approximation a volume of space; it is a specific habitat, location, or site that is suitable or adequate (...) for given purposes (of foraging, resting, hunting, breeding, nesting, grooming) in the life of an organism or group of organisms. This spatial notion of environment can be drawn closer to biological and ecological science by taking account of the pertinent physical attributes realized within given spatial regions. (shrink)

Where some have attempted to apply cognitive methods to the study of geography, the present paper is designed to serve as a starting point for applying methods of geographic ontology to the phenomena of cognition. Agglomerations are aggregates of entities that are dispersed through space on geographic scales. Examples include: plagues, biological species, major world religions. The paper applies standard mereotopological theories of spatial regions to agglomerations in this sense. It offers the beginnings of a general theory of the relations (...) between social, cultural, ethnic and religious agglomerations on the one hand and territorially demarcated spatial objects on the other. In this way it serves as the basis for a general ontological theory of types of human groups and also of types of conflict between these groups. At the same time it provides ontological foundations for the epidemiological study of cognitive phenomena, and especially of cognitive phenomena in the sociopolitical realm. (shrink)

We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes (occurrents) and the enduring entities (continuants) that participate therein. The theory is divided into two major categories of sub-theories: (sub-) theories of type SPAN and (sub-)theories of type SNAP. These theories represent two complementary perspectives on reality and result in distinct though compatible systems of categories. In SNAP we have enduring entities such as substances, qualities, roles, functions; in SPAN we have perduring entities such as (...) processes and their parts and aggregates. We argue that both kinds of ontological theory are required in order to give a non-reductionism account of complex domains of reality. (shrink)

Building on the writings of Wittgenstein on rule-following and deviance, Kristóf Nyíri advanced a theory of creativity as consisting in a fusion of conflicting rules or disciplines. Only such fusion can produce something that is both intrinsically new and yet capable of being apprehended by and passed on to a wider community. Creativity, on this view, involves not the breaking of rules, or the deliberate cultivation of deviant social habits, but rather the acceptance of enriched systems of rules, the adherence (...) to which presupposes simultaneous immersion in disciplines hitherto seen as being unrelated. The paper presents a demonstration of the fruitfulness of this theory by means of an account of some of the political, cultural and intellectual peculiarities of the Habsburg Monarchy. (shrink)

With the possible exception of causation, disposition concepts are as prevalent in ordinary thought as any of the nomic concepts. Progress on their nature has been hard to come by. No doubt the difficulty of saying anything illuminating and suitably general about their nature is a function of their pervasiveness.

A meaningful life, we shall argue, is a life upon which a certain sort of valuable pattern has been imposed by the person in question - a pattern which involves in serious ways the person having an effect upon the world. Meaningfulness is thus a special kind of value which a human life can bear. Two interrelated difficulties face ths proposal. One concerns responsiblity: how are we to account for the fact that a life that satisfies the above criteria can (...) have more meaning than a life with the same positive outcomes but which lacks responsiblity on the part of the agent? The other turns on these outcomes themselves: how can the meaningfulness engendered by actions you perform now be affected by what those actions go on to produce in the future, perhaps even after your death? We provide a response to both of these difficulties. (shrink)

Imagine that your body has become attached, without your permission, to that of a sick violinist. The violinist is a human being. He will die if you detach him. Such detachment seems, nonetheless, to be morally permissible. Thomson argues that an unwantedly pregnant woman is in an analogous situation. Her argument is considered by many to have established the moral permissibility of abortion even under the assumption that the foetus is a human being. Another popular argument is that presented by (...) Singer and Unger to the effect that even those who are moderately prosperous are morally obliged to help the poor if they can do so at relatively small cost to themselves. The paper considers the question whether these two arguments can be simultaneously valid. (shrink)

This special issue of Applied Ontology is devoted to the foundation, the comparison and the application of functional theories in all areas, with particular attention to the biological and engineering domains. It includes theoretical and technical contributions related to the description, characterization, and application of functions.

The subject of this paper, Excuses, is one not to be treated, but only to be introduced, within such limits. It is, or might be, the name of a whole branch, even a ramiculated branch, of philosophy, or at least of one fashion of philosophy. I shall try, therefore, first to state what the subject is, why it is worth studying, and how it may be studied, all this at a regrettably lofty level: and then I shall illustrate, in more (...) congenial but desultory detail, some of the methods to be used, together with their limitations, and some of the unexpected results to be expected and lessons to be learned. Much, of course, of the amusement, and of the instruction, comes in drawing the coverts of the microglot, in hounding down the minutiae, and to this I can do no more here than incite you. But I owe it to the subject to say, that it has long afforded me what philosophy is so often thought, and made, barren of -- the fun of discovery, the pleasures of co-operation, and the satisfaction of reaching agreement. (shrink)

The essay constructs an ontological theory designed to capture the categories instantiated in those portions or levels of reality which are captured in our common sense conceptual scheme. It takes as its starting point an Aristotelian ontology of “substances” and “accidents”, which are treated via the instruments of mereology and topology. The theory recognizes not only individual parts of substances and accidents, including the internal and external boundaries of these, but also universal parts, such as the “humanity” which is an (...) essential part of both Tom and Dick, and also “individual relations”, such as Tom’s promise to Dick, or their current handshake. (shrink)

In a pair of very important papers, namely “Space, Time and Individuals” in the Journal of Philosophy for October 1955 and “The Indestructibility and Immutability of Substances” in Philosophical Studies for April 1956, Professor N. L. Wilson began something which badly needed beginning, namely the construction of a logically rigorous “substance-language” in which we talk about enduring and changing individuals as we do in common speech, as opposed to the “space-time” language favoured by very many mathematical logicians, perhaps most notably (...) by Quine. This enterprise of Wilson's is one with which I could hardly sympathize more heartily than I do; and one wishes for this logically rigorous “substance-language” not only when one is reading Quine but also when one is reading many other people. How fantastic it is, for instance, that Kotarbinski1 should call his metaphysics “Reism” when the very last kind of entity it has room for is things —instead of them it just has the world-lines or life-histories of things; “fourdimensional worms”, as Wilson says. Wilson, moreover, has at least one point of superiority to another rebel against space-time talk, P. F. Strawson; namely he does seriously attempt to meet formalism with formalism—to show that logical rigour is not a monopoly of the other side. At another point, however, Strawson seems to me to see further than Wilson; he is aware that substance-talk cannot be carried on without tenses, whereas Wilson tries to do without them. Wilson, in short, has indeed brought us out of Egypt; but as yet has us still wandering about the Sinai Peninsula; the Promised Land is a little further on than he has taken us. (shrink)

I wish to express, first of all, my profound gratitude to Professor J. M. Bochenski, without whose assistance the present work would have not been possible. To be concise, I would like to state that his contribution to this book may be viewed at three levels: (1) that of the general spirit, (2) that of the specific ideas, theses or approaches which are expressed in its pages, (3) that of this work qua doctoral dissertation. The general spirit which has guided (...) my research coincides with that underlying Professor :Oochenski's own works, in particular his Formale Logik (Munchen 1956). Moreover, the particular occasion which suggested my investigation was a statement included in that book according to which the literature in the field still lacked a detailed work on Frege (p. 317). I wish, likewise, to express my gratitude to other professors of the University of Fribourg for their generous help. I mention especially Professors P. Wyser, M. D. Philippe, N. Luyten, and V. Kuiper. I have also benefited from Professor E. Specker's lectures at the Eidge nossische Technische Hochschule (ZUrich) and from Professor Olof Gigon's lectures at the University of Bern. From an earlier period I wish to express my gratitude to the professors of the philosophy department of the Universidad Nacional de Buenos Aires, especially the late Professor Francisco Romero. The Swiss National Library (Bern) has greatly facilitated access to bibliographical sources, and the library of the University of Munster (Westphalien) has kindly provided microfilms of Frege's Nachlap. (shrink)

This book pursues the question of how and whether natural language allows for reference to abstract objects in a fully systematic way. By making full use of contemporary linguistic semantics, it presents a much greater range of linguistic generalizations than has previously been taken into consideration in philosophical discussions, and it argues for an ontological picture is very different from that generally taken for granted by philosophers and semanticists alike. Reference to abstract objects such as properties, numbers, propositions, and degrees (...) is considerably more marginal than generally held. (shrink)

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. (shrink)

The paper seeks to develop an account of indexical phenomena based on the highly general theory of structure and dependence set forth by Husserl in his Logical Investigations. Husserl here defends an Aristotelian theory of meaning, viewing meanings as species or universals having as their instances certain sorts of concrete meaning acts. Indexical phenomena are seen to involve the combination of such acts of meaning with acts of perception, a thesis here developed in some detail and contrasted with accounts of (...) indexicals suggested by Frege, Wittgenstein and by the later Husserl himself in his Ideas I. Implications are drawn also for our understanding of the categorial grammar sketched by Husserl in his 4th Logical Investigation, as also for our understanding of the nature of proper names and other candidate indexical expressions. (shrink)

To what in reality do the logically simple sentences with empirical content correspond? Two extreme positions can be distinguished in this regard: 'Great Fact' theories, such as are defended by Davidson; and trope-theories, which see such sentences being made the simply by those events or states to which the relevant main verbs correspond. A position midway between these two extremes is defended, one according to which sentences of the given sort are made tme by what are called 'dependence structures', or (...) in other words by certain complex concrete portions of reality between the parts of which relations of dependence are defined. Principles governing such dependence-structures are laid down, principles of an ontologically motivated sort which serve as basis for a topological semantics conceived as an altemative to standard set-theoretic approaches to semantics of the Tarskian sort. These principles are then used to resolve certain puzzles generated by the (semantically motivated) theory of events put forward by Davidson. (shrink)

As conceived by analytic philosophers ontology consists in the application of the methods of mathematical logic to the analysis of ontological discourse. As conceived by realist philosophers such as Meinong and the early Husserl, Reinach and Ingarden, it consists in the investigation of the forms of entities of various types. The suggestion is that formal methods be employed by phenomenological ontologists, and that phenomenological insights may contribute to the construction of adequate formal-ontological languages. The paper sketches an account of what (...) might be involved in this new discipline, an account which is illustrated in application to the formal-ontological problems raised by negative states of affairs. (shrink)

Increasingly, the high throughput technologies used by biomedical researchers are bringing about a situation in which large bodies of data are being described using controlled structured vocabularies—also known as ontologies—in order to support the integration and analysis of this data. Annotation of data by means of ontologies is already contributing in significant ways to the cumulation of scientific knowledge and, prospectively, to the applicability of cross-domain algorithmic reasoning in support of scientific advance. This very success, however, has led to a (...) proliferation of ontologies of varying scope and quality. We define one strategy for achieving quality assurance of ontologies—a plan of action already adopted by a large community of collaborating ontologists—which consists in subjecting ontologies to a process of peer review analogous to that which is applied to scientific journal articles. (shrink)

The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into application domains yields a variety of improvements. L&C’s LinKBase® (...) is one of the world’s largest medical domain ontologies. Its current primary use pertains to natural language processing ap-plications, but it also supports intelligent navigation through a range of struc-tured medical and bioinformatics information resources, such as SNOMED-CT, Swiss-Prot, and the Gene Ontology (GO). In this report we discuss how and why philosophical methods improve both the internal coherence of LinKBase®, and its capacity to serve as a translation hub, improving the interoperability of the ontologies through which it navigates. (shrink)

Philosophers from Plotinus to Paul Churchland have yielded to the temptation to embrace doctrines which contradict the core beliefs of common sense. Philosophical realists have on the other hand sought to counter this temptation and to vindicate those core beliefs. The remarks which follow are to be understood as a further twist of the wheel in this never-ending battle. They pertain to the core beliefs of common sense concerning the external reality that is given in everyday experience -the beliefs of (...) folk physics, as we might call them. Just as critics of Churchland et al. have argued that the folk-psychological ontology of beliefs, desires, etc. yields the best explanation we can have of the order of cognitive phenomena conceived from the perspective of first-person experience, so we shall argue that (1) the commonsensical ontology of folk physics yields the best explanation we can have of our externally directed cognitive experience and that (2) an ontology of mesoscopic things, events and processes must play a role, in particular, in our best scientific theory of human action. (shrink)

The theory of granular partitions (TGP) is a new approach to the understanding of ontologies and other classificatory systems. The paper explores the use of this new theory in the treatment of task-based clinical guidelines as a means for better understanding the relations between different clinical tasks, both within the framework of a single guideline and between related guidelines. We used as our starting point a DAML+OIL-based ontology for the WHO guideline for hypertension management, comparing this with related guidelines and (...) attempting to show that TGP provides a flexible and highly expressive basis for the manipulation of ontologies of a sort which might be useful in providing more adequate Computer Interpretable Guideline Models (CIGMs) in the future. (shrink)

For this second edition, the editors have returned to Austin's original lecture notes, amending the printed text where it seemed necessary.

This is a welcome reprint of a book that continues to grow in importance.

Nominalizations are expressions that are particularly challenging philosophically in that they help form singular terms that seem to refer to abstract or derived objects often considered controversial. The three standard views about the semantics of nominalizations are [1] that they map mere meanings onto objects, [2] that they refer to implicit arguments, and [3] that they introduce new objects, in virtue of their compositional semantics. In the second case, nominalizations do not add anything new but pick up objects that would (...) be present anyway in the semantic structure of a corresponding sentence without a nominalization. In the first and third case, nominalizations in a sense ‘create’ new objects’, enriching the ontology on the basis of the meaning of expressions. I will argue that there is a fourth kind of nominalization which requires a quite different treatment. These are nominalizations that introduce ‘new’ objects, but only partially characterize them. Such nominalizations generally refer to events or tropes. I will explore an account according on which such nominalizations refer to truth makers. (shrink)

The paper challenges the assumption, common amongst philosophers, that the reality described in the fundamental theories of microphysics is all the reality we have. It will be argued that this assumption is in fact incompatible with the nature of such theories. It will be shown further that the macro-world of three-dimensional bodies and of such qualitative structures as colour and sound can be treated scientifically on its own terms, which is to say not only from the perspective of psychology but (...) also ontologically. A new sort of emergentist position will be defended, one which yields the basis of a method for describing the perceptually salient macroscopic world in mathematical terms. Broadly, it will be argued that the macroscopic world exists in virtue of certain specific sorts of boundary-patterns in the field of what is captured by the theories of microphysics. (shrink)