Barry Smith

Consider a game of blind chess between two chess masters that is recorded in some standard chess notation. The recording is a representation of the game. But what is the game itself? This question is, we believe, central to the entire domain of social ontology. We argue that the recorded game is a special sort of quasi-abstract pattern, something that is: (i) like abstract entities such as numbers or forms, in that it is both nonphysical and nonpsychological; but at the same time, (ii) through its association with specific players and a specific occasion, tied to time and history. We discover other abstract patterns of this sort especially in the domains of law and commerce. This essay draws on the work in social ontology, we of Hernando de Soto and of John Searle to develop an ontology of the social world based on an analysis of the peculiar interdependence between quasi-abstract patterns and their representations in documents of different sorts.

Ontologies are being ever more commonly used in biomedical informatics and we provide a survey of some of these uses, and of the relations between ontologies and other terminology resources. In order for ontologies to become truly useful, two objectives must be met. First, ways must be found for the transparent evaluation of ontologies. Second, existing ontologies need to be harmonised. We argue that one key foundation for both ontology evaluation and harmonisation is the adoption of a realist paradigm in ontology development. For science-based ontologies of the sort which concern us in the eHealth arena, it is reality that provides the common benchmark against which ontologies can be evaluated and aligned within larger frameworks. Given the current multitude of ontologies in the biomedical domain the need for harmonisation is becoming ever more urgent. We describe one example of such harmonisation within the ACGT project, which draws on ontology-based computing as a basis for sharing clinical and laboratory data on cancer research.

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.

The dominant theory of judgment in 1870 was one or other variety of combination theory: the act of judgment is an act of combining concepts or ideas in the mind of the judging subject. In the decades to follow a succession of alternative theories arose to address defects in the combination theory, starting with Bolzano’s theory of propositions in themselves, Brentano’s theory of judgment as affirmation or denial of existence, theories distinguishing judgment act from judgment content advanced by Brentano’s students Twardowski, Husserl and Meinong, and finally, Adolf Reinach’s addition of a linguistic dimension to the Brentano-Husserlian theory of judgment – an account of judgments as ways of doing things with words in what Reinach called ‘social acts’.

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.

Mereotopology faces problems when its methods are extended to deal with time and change. We offer a new solution to these problems, based on a theory of partitions of reality which allows us to simulate (and also to generalize) aspects of set theory within a mereotopological framework. This theory is extended to a theory of coarse- and fine-grained histories (or finite sequences of partitions evolving over time), drawing on machinery developed within the framework of the so-called ‘consistent histories’ interpretation of quantum mechanics.

This is the third draft of a paper that aims to clarify the apparent contradictions in the views presented in certain standards and other specifications of health informatics systems, contradictions which come to light when the latter are evaluated from the perspective of realist philosophy. One of the origins of this document was Klein’s discussion paper of 2005-07-02 entitled “Conceptology vs Reality” and the responses from Smith, as well as the several hours of discussions during the 2005 MIE meeting in Geneva.

Revised version of chapter in J. N. Mohanty and W. McKenna (eds.), Husserl’s Phenomenology: A Textbook, Lanham: University Press of America, 1989, 29–67. Logic for Husserl is a science of science, a science of what all sciences have in common in their modes of validation. Thus logic deals with universal laws relating to truth, to deduction, to verification and falsification, and with laws relating to theory as such, and to what makes for theoretical unity, both on the side of the propositions of a theory and on the side of the domain of objects to which these propositions refer. This essay presents a systematic overview of Husserl’s views on these matters as put forward in his Logical Investigations. It shows how Husserl’s theory of linguistic meanings as species of mental acts, his formal ontology of part, whole and dependence, his theory of meaning categories, and his theory of categorial intuition combine with his theory of science to form a single whole. Finally, it explores the ways in which Husserl’s ideas on these matters can be put to use in solving problems in the philosophy of language, logic and mathematics in a way which does justice to the role of mental activity in each of these domains while at the same time avoiding the pitfalls of psychologism.

We defend a view according to which Austrian economics rests on what can most properly be called an Aristotelian methodology. This implies a realist perspective, according to which the world exists independently of our thinking and reasoning activities; an essentialist perspective, according to which the world contains certain simple essences or natures which may come together in law-like ways to form more complex static and dynamic wholes, and an apriorist perspective, according to which given essences and essential structures are intelligible, in the sense that they ca be grasped non-inductively in our thinking. We show the consequences of this view for an analysis of the thinking of Mises and Hoppe, both of which – we claim – incorporate what we believe to be foreign mixtures of Kantianism in their account of the foundations of Austrian economics.

In what respects is Western civilization superior or inferior to its rivals? In raising this question we are addressing a particularly strong form of the problem of relativism. For in order to compare civilizations one with another we would need to be in possession of a framework based on principles of evaluation which would be acceptable, in principle, to all human beings. Morality will surely provide one axis of such a framework (and we note in passing that believers in Islam might quite reasonably claim that their fellow-believers are characteristically more moral than are many in the West). Criteria such as material wellbeing, too, will need to play a role, as also will happiness or pleasure. Even happiness (pace some proponents of the utilitarian philosophy) comes in different types, and to count in the civilization stakes the happiness involved would presumably need to be of the right kind. We propose a specification for what this ‘right kind’ of happiness might be.

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data.

The integration of information resources in the life sciences is one of the most challenging problems facing bioinformatics today. We describe how Language and Computing nv, originally a developer of ontology-based natural language understanding systems for the healthcare domain, is developing a framework for the integration of structured data with unstructured information contained in natural language texts. L&C’s LinkSuite™ combines the flexibility of a modular software architecture with an ontology based on rigorous philosophical and logical principles that is designed to comprehend the basic formal relationships that structure both reality and the ways humans perceive and communicate about reality.

Biomedical ontologies exist to serve integration of clinical and experimental data, and it is critical to their success that they be put to widespread use in the annotation of data. How, then, can ontologies achieve the sort of user-friendliness, reliability, cost-effectiveness, and breadth of coverage that is necessary to ensure extensive usage? Methods: Our focus here is on two different sets of answers to these questions that have been proposed, on the one hand in medicine, by the SNOMED CT community, and on the other hand in biology, by the OBO Foundry. We address more specifically the issue as to how adherence to certain development principles can advance the usability and effectiveness of an ontology or terminology resource, for example by allowing more accurate maintenance, more reliable application, and more efficient interoperation with other ontologies and information resources. Results: SNOMED CT and the OBO Foundry differ considerably in their general approach.Nevertheless, a general trend towards more formal rigor and cross-domain interoperability can be seen in both and we argue that this trend should be accepted by all similar initiatives in the future. Conclusions: Future efforts in ontology development have to address the need for harmonization and integration of ontologies across disciplinary borders, and for this, coherent formalization of ontologies is a prerequisite.

Human cognitive acts are directed towards objects extended in space of a wide range of different types. What follows is a new proposal for bringing order into this typological clutter. The theory of spatially extended objects should make room not only for the objects of physics but also for objects at higher levels, including the objects of geography and of related disciplines. It should leave room for different types of boundaries, including both the bona fide boundaries which we find in the physical world and the fiat (or human-demarcation-induced) boundaries with which much of geography has to deal. Two distinct axiomatic theories of boundaries are accordingly presented, and the need for both is examined in some detail. The resultant dual framework is shown to have application above all for our understanding of issues involving contact, division, and separation, issues which have posed serious difficulties for the ontological theories of boundaries that have been proposed hitherto.

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 provide a methodology for the creation of ontological partitions in biomedicine and we test the methodology via an application to the phenomenon of blood pressure. An ontology of blood pressure must do justice to the complex networks of intersecting pathways in the organism by which blood pressure is regulated. To this end it must deal not only with the anatomical structures and physiological processes involved in such regulation but also with the relations between these at different levels of granularity. For this purpose our ontology offers a variety of distinct partitions � of substances, processes and functions � and integrates these together within a single framework via transitive networks of part-whole and dependence relations among the entities in each of these categories. The paper concludes with a comparison of this methodology with the approaches of GOTM, KEGG, DIP and BIND and provides an outline of how the methodology is currently being applied in the field of biomedical database integration.

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.

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical data analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research.

The author attempts to show how mereology, taken together with certain topological notions, can yield the foundations for future investigations in formal ontology. He also attempts to show how the mereological framework allows for the direct and natural formulation of a series of theses - for example pertaining to the concept of a boundary - which can be only indirectly formulated (if at all) in set-theoretic terms. The far-reaching ain of the present framework is to serve as a basis for a formal ontology of the common-sense world. The author is interested in producing formally precise theories of structures of certain sorts in such a way that it is the structures themselves that intrest him and not formal machinery that has been set up to describe them. Hence the axioms are chosen primarily for the sake of the light they throw on the intended subject-matters (and not for their logical independence). The world itself - or its picture given in ordinary experience - is the only model the paper concentrates upon. Thus for example the presented system allows to prove that every boundary is the boundary of something, and that in particular no point exists in isolation from a large extended whole that is its boundary

The shape of the Earth's surface, its topography, is a fundamental dimension of the environment, shaping or mediating many other environmental flows or functions. But there is a major divergence in the way that topography is conceptualized in different domains. Topographic cartographers, information scientists, geomorphologists and environmental modelers typically conceptualize topographic variability as a continuous field of elevations or as some discrete approximation to such a field. Pilots, explorers, anthropologists, ecologists, hikers, and archeologists, on the other hand, typically conceptualize this same variability in terms of hills and valleys, mountains and plains, barrows and trenches, that is, as (special sorts of) objects, with locations, shapes, and often names of their own. In this chapter, we sketch an approach to bridging this fundamental gap in geographic information infrastructure.

Part 1 of this exchange consists in a critique by Smith of Searle’s The Construction of Social Reality focusing on Searle’s use of the formula ‘X counts as Y in context C’. Smith argues that this formula works well for social objects such as dollar bills and presidents where the corresponding X terms (pieces of paper, human beings) are easy to identify. In cases such as debts and prices and money in a bank's computers, however, the formula fails, because these are cases of what he calls ‘free-standing Y terms’, since there is here no X which can count as the corresponding Y. In his response in Part 2, Searle argues that Smith’s critique rests on three misunderstandings: 1. in wrongly presupposing that Searle is trying to analyze the nature of what he calls “social objects”, rather than of social facts; 2. in thinking that the counts as formula is intended as a definition, rather than as a mere mnemonic; and 3. in neglecting the naturalism of Searle’s account.

The ontology of language is concerned with the relations between uses of language, both overt and covert, and other entities, whether in the world or in the mind of the thinking subject. We attempt a first survey of the sorts of relations which might come into question for such an ontology, including: relations between referring uses of expressions and their objects, relations between the use of a (true) sentence and that in the world which makes it true, relations between mental acts on the one hand and underlying mental states (attitudes, beliefs), on the other, relations between my acts and states, associated uses of language and overt actions on my part and on the part of those other subjects with whom I communicate.

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.

Why have Polish philosophers fared so badly as concerns their admission into the pantheon of Continental Philosophers? Why, for example, should Heidegger and Derrida be included in this pantheon, but not Ingarden or Tarski? Why, to put the question from another side, should there be so close an association in Poland between philosophy and logic, and between philosophy and science? We distinguish a series of answers to this question, which are dealt with under the following headings: (a) the role of socialism; (b) the disciplinary association between philosophy and mathematics; (c) the influence of Austrian philosophy in general and of Brentanian philosophy in particular; (d) the serendipitous role of Twardowski; (e) the role of Catholicism. The conclusion of the paper is that there is no such thing as 'Polish philosophy' because philosophy in Poland is philosophy per se; it is part and parcel of the mainstream of world philosophy simply because, in contrast to French or German philosophy, it meets international standards of training, rigour, professionalism and specialization.

What follows is a contribution to the theory of space and of spatial objects. It takes as its starting point the philosophical subfield of ontology, which can be defined as the science of what is: of the various types and categories of objects and relations in all realms of being. More specifically, it begins with ideas set forth by Aristotle in his Categories and Metaphysics, two works which constitute the first great contributions to ontological science. Because Aristotle’s ontological ideas were developed prior to the scientific discoveries of the modern era, he approached the objects and relations of everyday reality with the same ontological seriousness with which scientists today approach the objects of physics. We shall seek to show that what Aristotle has to say about these commonsensical objects and relations can, when translated into more formal terms, be of use also to contemporary ontologists. More precisely, we shall argue that his ideas can contribute to the development of a rigorous theory of those social and institutional components of everyday reality – the settings of human behavior – which are the subject of this volume. When modern-day philosophers turn their attentions to ontology they begin not with Aristotle but rather, in almost every case, with a set-theoretic ontology of the sort which is employed in standard model-theoretic semantics. Set-theoretic ontology sees the world in atomistic terms: it postulates a lowest level of atoms or urelements, from out of which successively higher levels of set-theoretic objects are then constructed. The approach to ontology to be defended here, in contrast, starts not with atoms but with the mesoscopic objects by which we are surrounded in our normal day-to-day..