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476The Unified Medical Language System and the Gene Ontology: Some critical reflectionsIn A. Günter, R. Kruse & B. Neumann (eds.), KI 2003: Advances in Artificial Intelligence, Springer. pp. 135-148. 2003.The Unified Medical Language System and the Gene Ontology are among the most widely used terminology resources in the biomedical domain. However, when we evaluate them in the light of simple principles for wellconstructed ontologies we find a number of characteristic inadequacies. Employing the theory of granular partitions, a new approach to the understanding of ontologies and of the relationships ontologies bear to instances in reality, we provide an application of this theory in relation to a…Read more
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191Ontologie des Mesokosmos. Soziale Objekte und UmweltenZeitschrift für Philosophische Forschung 52 (4): 521-540. 1998.The paper relates classical treatments of physics and metaphysics to contemporary work on common sense in the field of artificial intelligence (J. Hobbs, P. Hayes, et al.). It defends the universality (and truth) of certain basic principles of common-sense physics and shows why these basic principles must leave certain issues undetermined.
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511Granular Partitions and VaguenessIn Chris Welty & Barry Smith (eds.), Formal Ontology in Information Systems (FOIS), Acm Press. pp. 309-320. 2003.There are some who defend a view of vagueness according to which there are intrinsically vague objects or attributes in reality. Here, in contrast, we defend a view of vagueness as a semantic property of names and predicates. All entities are crisp, on this view, but there are, for each vague name, multiple portions of reality that are equally good candidates for being its referent, and, for each vague predicate, multiple classes of objects that are equally good candidates for being its extensio…Read more
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353A terminological and ontological analysis of the NCI thesaurusMethods of Information in Medicine 44 (4): 498-507. 2005.We performed a qualitative analysis of the Thesaurus in order to assess its conformity with principles of good practice in terminology and ontology design. We used both the on-line browsable version of the Thesaurus and its OWL-representation (version 04.08b, released on August 2, 2004), measuring each in light of the requirements put forward in relevant ISO terminology standards and in light of ontological principles advanced in the recent literature. Version 04.08b of the NCI Thesaurus suffers…Read more
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2024Building Ontologies with Basic Formal OntologyMIT Press. 2015.In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the…Read more
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330The cognitive geometry of warIn Peter Koller & Klaus Puhl (eds.), Current Issues in Political Philosophy: Justice in Society and World Order, Hölder-pichler-tempsky. pp. 394--403. 1997.When national borders in the modern sense first began to be established in early modern Europe, non-contiguous and perforated nations were a commonplace. According to the conception of the shapes of nations that is currently preferred, however, nations must conform to the topological model of circularity; their borders must guarantee contiguity and simple connectedness, and such borders must as far as possible conform to existing topographical features on the ground. The striving to conform to t…Read more
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351Annotating affective neuroscience data with the Emotion OntologyIn Janna Hastings, Werner Ceusters, Kevin Mulligan & Barry Smith (eds.), Third International Conference on Biomedical Ontology, Icbo. pp. 1-5. 2012.The Emotion Ontology is an ontology covering all aspects of emotional and affective mental functioning. It is being developed following the principles of the OBO Foundry and Ontological Realism. This means that in compiling the ontology, we emphasize the importance of the nature of the entities in reality that the ontology is describing. One of the ways in which realism-based ontologies are being successfully used within biomedical science is in the annotation of scientific research results in pu…Read more
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1179Towards an ontology of painIn Proceedings of the Conference on Ontology and Analytical Metaphysics, Keio University Press. 2011.We present an ontology of pain and of other pain-related phenomena, building on the definition of pain provided by the International Association for the Study of Pain (IASP). Our strategy is to identify an evolutionarily basic canonical pain phenomenon, involving unpleasant sensory and emotional experience based causally in localized tissue damage that is concordant with that experience. We then show how different variant cases of this canonical pain phenomenon can be distinguished, including pa…Read more
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499Mereotopology: A theory of parts and boundariesData and Knowledge Engineering 20 (3). 1996.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 ce…Read more
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453An Axiomatisation of Basic Formal Ontology with Projection FunctionsIn Kerry Taylor (ed.), Advances in Ontologies, Proceedings of the Sixth Australasian Ontology Workshop, University of Adelaide. pp. 71-80. 2010.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 de…Read more
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752Against FantologyIn Johann C. Marek & Maria E. Reicher (eds.), Experience and Analysis, Hpt&öbv. pp. 153-170. 2005.The analytical philosophy of the last hundred years has been heavily influenced by a doctrine to the effect that the key to the correct understanding of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of standard first order predicate logic. Here ‘F’ stands for what is general in reality and ‘a’ for what is individual. Hence “f(a)ntology”. Because predicate logic has exactly two syntactically different kinds of referring expressions—‘F’, ‘G’, ‘R’,…Read more
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186AgglomerationsIn C. Freksa & David M. Mark (eds.), Spatial Information Theory. Cognitive and Computational Foundations of Geographic Information Science, Springer. pp. 267-282. 1999.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 …Read more
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704Fiat objectsTopoi 20 (2): 131-148. 2001.Human cognitive acts are directed towards entities of a wide range of different types. What follows is a new proposal for bringing order into this typological clutter. A categorial scheme for the objects of human cognition should be (1) critical and realistic. Cognitive subjects are liable to error, even to systematic error of the sort that is manifested by believers in the Pantheon of Olympian gods. Thus not all putative object-directed acts should be recognized as having objects of their own. …Read more
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857Sixteen daysJournal of Medicine and Philosophy 28 (1). 2003.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 rel…Read more
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957The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic AnalysesPlant and Cell Physiology 54 (2). 2013.The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabi…Read more
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503On drawing lines on a mapIn Frank A. U., Kuhn W. & Mark D. M. (eds.), Spatial Information Theory: Proceedings of COSIT '95, Springer. pp. 475-484. 1995.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 trans…Read more
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232L’ontologie de la realité socialeIn P. Livet & R. Ogien (eds.), L’Enquête ontologique, du mode de l'existence des objets sociaux, Editions Ehess. pp. 185--208. 2000.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 banks computers, however, the formula fails, because these are cases of what he calls ‘free-st…Read more
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59Wittgenstein and the Background of Austrian PhilosophyIn Elisabeth Leinfellner (ed.), Wittgenstein and his impact on contemporary thought: proceedings of the Second International Wittgenstein Symposium, 29th August to 4th September 1977, Kirchberg/Wechsel (Austria) ; editors, Elisabeth Leinfellner... [et al.], D. Reidel Pub. Co.. pp. 31-35. 1978.Surveys the evidence for an influence of Austrian philosophers – specifically Brentano, Meinong, Husserl, Twardowski and Mach – on the early Wittgenstein. Such influence might either have been direct, for instance through Wittgenstein’s reading of Mach, or indirect, through the mediation of Russell and Moore. The paper concludes by addressing the possible influence of Stumpf and Reinach on Wittgenstein’s technical usage of the term ‘Sachverhalt’ in the Tractatus.
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654Two Idealisms: Lask and HusserlKant Studien 84 (4): 448-466. 1993.Neo-Kantianism is common conceived as a philosophy ‘from above’, excelling in speculative constructions – as opposed to the attitude of patient description which is exemplified by the phenomenological turn ‘to the things themselves’. When we study the work of Emil Lask in its relation to that of Husserl and the phenomenologists, however, and when we examine the influences moving in both directions, then we discover that this idea of a radical opposition is misconceived. Lask himself was influenc…Read more
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550Quantum mereotopologyAnnals of Mathematics and Artificial Intelligence 36 (1): 153-175. 2002.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 hist…Read more
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496Traditional vs. Analytic Philosophy (review)Grazer Philosophische Studien 21 (1): 193-202. 1984.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 sa…Read more
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234Die Struktur der Common-Sense WeltLogos. Anales Del Seminario de Metafísica [Universidad Complutense de Madrid, España] 1 422-449. 1994.Die zeitgenössischen Philosophen haben zwar der Sprache, die wir verwenden, um die Welt der alltäglichen Erfahrung zu beschreiben oder um uns in dieser Welt zurechtzufinden, große Aufmerksamkeit geschenkt, sie haben sich jedoch – von einigen Ausnahmen abgesehen – geweigert, diese Welt selbst als passendes Objekt theoretischer Betrachtungen anzusehen. Im folgenden werde ich versuchen zu zeigen, wie es möglich ist, die Common-Sense-Welt als ontologisch eigenständiges Untersuchungsobjekt zu v…Read more
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32John Searle (edited book)Cambridge University Press. 2003.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 consid…Read more
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27Kafka 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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2039The Relevance of Philosophical Ontology to Information and Computer ScienceIn Ruth Hagenbruger & Uwe V. Riss (eds.), Philosophy, computing and information science, Pickering & Chattoo. pp. 75-83. 2014.The discipline of ontology has enjoyed a checkered history since 1606, with a significant expansion in recent years. We focus here on those developments in the recent history of philosophy which are most relevant to the understanding of the increased acceptance of ontology, and especially of realist ontology, as a valuable method also outside the discipline of philosophy.
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462The 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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431Putting 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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779Dispositions and Processes in the Emotion OntologyIn Proceedings of the 2nd International Conference on Biomedical Ontology, Ceur Workshop Proceedings. pp. 71-78. 2011.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 disamb…Read more
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529Creating 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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1035Aboutness: 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
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 |