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458The 2006 Upper Ontology Summit Joint CommuniquéApplied ontology 1 (2): 203-211. 2006.On March 14-15, 2006, at the US National Institute of Standards and Technology (NIST) in Gaithersburg, MD there took place the first Upper Ontology Summit (UOS). This was a convening of custodians of several prominent upper ontologies, key technology participants, and interested other parties, with the purpose of finding a means to relate the different ontologies to each other. The result is reflected in a joint communiqué, directed to the larger ontology community and the general public, and ex…Read more
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424Putting Biomedical Ontologies to WorkMethods of Information in Medicine 49 (2): 135-40. 2010.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 c…Read more
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981Fiat and Bona Fide Boundaries: Towards an Ontology of Spatially Extended ObjectsIn Stephen Hirtle & Andrew U. Frank (eds.), Spatial Information Theory: International Conference COSIT ‘97, Springer. 1997.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 ph…Read more
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522Creating a Controlled Vocabulary for the Ethics of Human Research: Towards a biomedical ethics ontologyJournal of Empirical Research on Human Research Ethics 4 (1): 43-58. 2009.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)…Read more
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320The New European PhilosophyIn János Kristóf Nyíri & Barry Smith (eds.), Philosophy and Political Change in Eastern Europe, Hegeler Institute. pp. 165-170. 1993.The paper seeks to indicate ways in which the crude distinction between Anglo-Saxon and Continental philosophy may have to be amended in light of recent developments in Eastern Europe. As is well known, the philosophy of science is to no small part a product of the universities of the Habsburg Empire (in Vienna, Prague, Lemberg/Lwow, etc.). Logic, too, has played a more significant role in Eastern Europe (not least in Poland) than in the philosophical cultures of Germany or France. For these and…Read more
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1032Aboutness: Towards Foundations for the Information Artifact OntologyIn Werner Ceusters & Barry Smith (eds.), Proceedings of the Sixth International Conference on Biomedical Ontology (ICBO), Ceur Vol. 1515. pp. 1-5. 2015.The Information Artifact Ontology (IAO) was created to serve as a domain‐neutral resource for the representation of types of information content entities (ICEs) such as documents, data‐bases, and digital im‐ages. We identify a series of problems with the current version of the IAO and suggest solutions designed to advance our understanding of the relations between ICEs and associated cognitive representations in the minds of human subjects. This requires embedding IAO in a larger framework of on…Read more
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26Kafka et BrentanoPhilosophiques 26 (2). 1999.Un mince fil dans la vaste littérature sur Kafka concerne la connaissance qu’avait Kafka de la philosophie, et plus précisément l’utilisation, dans les récits de Kafka, de quelques-unes des idées principales de Franz Brentano. Kafka a suivi des cours de philosophie à l’Université Charles, cours donnés par des étudiants de Brentano, Anton Marty et Christian von Ehrenfels. Il fut aussi, pendant plusieurs années, membre d’un groupe de discussion organisé par des partisans orthodoxes de la philosoph…Read more
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831What’s wrong with contemporary philosophy?Topoi 25 (1-2): 63-67. 2006.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 th…Read more
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2436On Place and Space: The Ontology of the EruvIn Christian Kanzian (ed.), Cultures: Conflict – Analysis – Dialogue, Ontos. pp. 403-416. 2007.‘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 …Read more
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659BiometaphysicsIn Robin Le Poidevin, Simons Peter, McGonigal Andrew & Ross P. Cameron (eds.), The Routledge Companion to Metaphysics, Routledge. pp. 537-544. 2009.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…Read more
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480Brentano and KafkaAxiomathes 8 (1): 83-104. 1997.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 summari…Read more
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403Textual DeferenceAmerican Philosophical Quarterly 28 (1). 1991.It is a truism that the attitude of deference to the text plays a lesser role in Anglo-Saxon philosophy than in other philosophical traditions. Works of philosophy written in English have, it is true, spawned a massive secondary literature dealing with the ideas, problems or arguments they contain. But they have almost never given rise to works of commentary in the strict sense, a genre which is however a dominant literary form not only in the Confucian, Vedantic, Islamic, Jewish and Scholastic …Read more
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336Vague Reference and Approximating JudgementsSpatial Cognition and Computation 3 (2). 2003.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 …Read more
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283We 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 o…Read more
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512We 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…Read more
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517A Theory of Granular PartitionsIn M. Duckham, M. F. Goodchild & M. F. Worboys (eds.), Foundations of Geographic Information Science, Taylor & Francis. pp. 117-151. 2003.We have a variety of different ways of dividing up, classifying, mapping, sorting and listing the objects in reality. The theory of granular partitions presented here seeks to provide a general and unified basis for understanding such phenomena in formal terms that is more realistic than existing alternatives. Our theory has two orthogonal parts: the first is a theory of classification; it provides an account of partitions as cells and subcells; the second is a theory of reference or intentional…Read more
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477Ontology and the Future of Dental Research Informatics.Journal of the American Dental Association 141 (10): 1173-75. 2010.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 way…Read more
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1105We describe a strategy for integration of data that is based on the idea of semantic enhancement. The strategy promises a number of benefits: it can be applied incrementally; it creates minimal barriers to the incorporation of new data into the semantically enhanced system; it preserves the existing data (including any existing data-semantics) in their original form (thus all provenance information is retained, and no heavy preprocessing is required); and it embraces the full spectrum of data so…Read more
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493Austrian Origins of Logical PositivismIn Barry Gower (ed.), Logical Positivism in Perspective, Croom Helm. pp. 35-68. 1988.Recent work on Austrian philosophy has revealed, hitherto, unsuspected links between Vienna circle positivism on the one hand, and the thought of Franz Brentano and his circle on the other. the paper explores these links, casting light also on the Polish analytic movement, on the development of gestalt psychology, and on the work of Schlick and Neurath.
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374The Benefits of Realism: A Realist Logic with ApplicationsIn Katherine Munn & Barry Smith (eds.), Applied Ontology: An Introduction, Ontos. pp. 109-124. 2008.We propose a formalization of a realist ontology using first order logic with identity and allowing quantification over terms representing both individuals and universals. In addition to identity, the ontology includes also relational predicates such as subtype, instantiation, parthood, location, and inherence. Inspired in part by Davidson’s treatment of events, the ontology includes also various relations linking events to their participants and to the times at which they occur.
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187Referent tracking for treatment optimisation in schizophrenic patientsJournal of Web Semantics 4 (3): 229-236. 2006.The IPAP Schizophrenia Algorithm was originally designed in the form of a flow chart to help physicians optimise the treatment of schizophrenic patients. We examined the current version from the perspective of recent work on terminologies and ontologies thereby drawing on the resources of Basic Formal Ontology, and this with the objective to make the algorithm appropriate for Semantic Web applications. We found that Basic Formal Ontology is a rich enough theory to represent all the entities invo…Read more
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207If 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 fro…Read more
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369Adapting Clinical Ontologies in Real-World EnvironmentsJournal of Universal Computer Science 14 (22): 3767-3780. 2008.The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. T…Read more
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190Comment: Kolnai’s DisgustEmotion Review 6 (3): 219-220. 2014.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 sh…Read more
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512Laws of Essence or Constitutive Rules? Reinach vs. Searle on the Ontology of Social EntitiesIn Francesca De Vecchi (ed.), Eidetica del Diritto e Ontologia Sociale. Il Realismo di Adolf Reinach, Mimesis. pp. 83-108. 2012.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 tha…Read more
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579Ontology and Geographic KindsIn T. Poiker & N. Chrisman (eds.), Proceedings of the 8th International Symposium on Spatial Data Handling, International Geographic Union. pp. 308-320. 1998.Cognitive categories in the geographic realm appear to manifest certain special features as contrasted with categories for objects at surveyable scales. We have argued that these features reflect specific ontological characteristics of geographic objects. This paper presents hypotheses as to the nature of the features mentioned, reviews previous empirical work on geographic categories, and presents the results of pilot experiments that used English-speaking subjects to test our hypotheses. Our e…Read more
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1171Austrian and Hungarian Philosophy: On the Logic of Wittgenstein and PaulerIn Anne Reboul (ed.), Mind, Meaning and Metaphysics. Philosophical Papers Dedicated to Kevin Mulligan, Springer. pp. 387-486. 2014.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…Read more
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174Signs and MeaningsIn Peer Bundgaard & Frederik Stjernfelt (eds.), Signs and Meanings: Five Questions, Automatic Press. pp. 199--206. 2009.A background piece on the role of ontology in technology research, focusing especially on the use-mention confusion.
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18Review of Ernest Davis: Representations of Commonsense Knowledge (review)Minds and Machines 4 (2): 245-249. 1994.Review of a compendium of alternative formal representations of common-sense knowledge. The book is centered largely on formal representations drawn from first-order logic, and thus lies in the tradition of Kenneth Forbus, Patrick Hayes and Jerry Hobbs.
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507Normalizing medical ontologies using Basic Formal OntologyIn K. Versorgung & V. Forschung (eds.), Ubiquitäre Information (Proceedings of GMDS 2004), Videel Ohg. pp. 199-201. 2004.Description Logics are nowadays widely accepted as formalisms which provide reasoning facilities which allow us to discover inconsistencies in ontologies in an automatic fashion. Where ontologies are developed in modular fashion, they allow changes in one module to propogated through the system of ontologies automatically in a way which helps to maintain consistency and stability. For this feature to be utilized effectively, however, requires that domain ontologies be represented in a normalized…Read more
Barry Smith
University at Buffalo
National Center for Ontological Research
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University at BuffaloDepartment of Philosophy
Biomedical Informatics
Neurology
Computer Science and EngineeringDistinguished Professor, Julian Park Chair -
National Center for Ontological ResearchAdministrator
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APA Eastern Division
Buffalo, New York, United States of America
Areas of Specialization
Metaphysics |
Ontology |
Philosophy of Artificial Intelligence |
Philosophy of Biology |