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310The Soul and Its Parts: A Study in Aristotle and BrentanoBrentano Studien 1. 1988.The piece of wax takes on the form of the seal; but this occurs in a way that is largely indifferent to the particular constitution of the seal. Similarly, Aristotle says, ‘the sense is affected by what is coloured or flavoured or sounding, but it is indifferent as to what in each case the substance is’. We show that Brentano takes this Aristotelian account of the relation between sense and its objects as the basis for his theory of mind in the Psychology from an Empirical Standpoint.
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512Framework for a protein ontologyBMC Bioinformatics 8 (Suppl 9). 2007.Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relations…Read more
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1347Framework for formal ontologyTopoi 2 (1): 73-85. 1983.The discussions which follow rest on a distinction, first expounded by Husserl, between formal logic and formal ontology. The former concerns itself with (formal) meaning-structures; the latter with formal structures amongst objects and their parts. The paper attempts to show how, when formal ontological considerations are brought into play, contemporary extensionalist theories of part and whole, and above all the mereology of Leniewski, can be generalised to embrace not only relations between c…Read more
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700The Neurath-Haller Thesis: Austria and the Rise of Scientific PhilosophyIn Keith Lehrer & Johann Christian Marek (eds.), Austrian Philosophy Past and Present: Essays in Honor of Rudolf Haller, Kluwer Academic Publishers. pp. 1-20. 1997.The term ‘Continental philosophy’ designates not philosophy on the continent of Europe as a whole, but rather a selective slice of Franco-German philosophy. Through a critical analysis of the arguments advanced by Otto Neurath, the paper addresses the issue of why Austrian philosophers in particular are not counted in the pantheon of Continental philosophers. Austrian philosophy is marked by the predominance of philosophical analysis and of the philosophy of science. The paper concludes that it …Read more
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622CARO: The Common Anatomy Reference OntologyIn Haendel Melissa, A. Neuhaus, Fabian Osumi-Sutherland, David Mabee, Paula M., Mejino Jr José L. V., Mungall Chris, J. Smith & Barry (eds.), Anatomy Ontologies for Bioinformatics: Principles and Practice, Springer. pp. 327-349. 2008.The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and…Read more
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565MetaphysicsIn Asbjørn Steglich-Petersen (ed.), Metaphysics: 5 Questions, Automatic Press. pp. 143-158. 2010.Attempts to trace a unifying thread of ontological realism extending through 1. my early writings on Frege, Brentano, Husserl, Wittgenstein, Ingarden and (with Kevin Mulligan and Peter Simons) on truthmakers; 2. work on formal theories of the common-sense world, and on mereotopology, fiat objects, geographical categories, and environments (with David Mark, Roberto Casati, Achille Varzi), to 3. current work on applied ontology in biology and medicine, and on the theory of document acts and on the…Read more
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1642The Space Object OntologyIn Alexander P. Cox, Christopher Nebelecky, Ronald Rudnicki, William Tagliaferri, John L. Crassidis & Barry Smith (eds.), 19th International Conference on Information Fusion (FUSION 2016), Ieee. 2016.Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missio…Read more
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646An Essay on Material NecessityCanadian Journal of Philosophy (sup1): 301-322. 1992.Where Humeans rule out the possibility of material or non-logical necessity, and thus of any associated knowledge a priori, the German legal philosopher Adolf Reinach defends the existence of a wide class of material necessities falling within the domain of what can be known a priori, for example in fields such as color and shape, rational psychology, law and economics. Categories such as promise or claim or obligation are, in Reinach’s view, exist as nodes in a system of necessary relations, so…Read more
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287Philosophy and Biomedical Information SystemsIn Katherine Munn & Barry Smith (eds.), Applied Ontology: An Introduction, Ontos. pp. 17-30. 2008.The pathbreaking scientific advances of recent years call for a new philosophical consideration of the fundamental categories of biology and its neighboring disciplines. Above all, the new information technologies used in biomedical research, and the necessity to master the continuously growing flood of data that is associated therewith, demand a profound and systematic reflection on the systematization and classification of biological data. This, however, demands robust theories of basic concep…Read more
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1698Do mountains exist? Towards an ontology of landformsEnvironment and Planning B (Planning and Design) 30 (3). 2003.Do mountains exist? The answer to this question is surely: yes. In fact, ‘mountain’ is the example of a kind of geographic feature or thing most commonly cited by English speakers (Mark, et al., 1999; Smith and Mark 2001), and this result may hold across many languages and cultures. But whether they are considered as individuals (tokens) or as kinds (types), mountains do not exist in quite the same unequivocal sense as do such prototypical everyday objects as chairs or people.
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456Truthmaker ExplanationsIn Jean-Maurice Monnoyer (ed.), Metaphysics and Truthmakers, Ontos Verlag. pp. 79-98. 2007.This paper is a fresh attempt to articulate the role of a theory of truthmakers. We argue that truthmaker theory constitutes a cornerstone of good methodology in metaphysics, but that a conflation of truthmaker theory with the theory of truth has been responsible for certain excesses associated with truthmaker-based approaches in the recent literature. If truthmaker theory is not a component of a theory of truth, then truthmaker maximalism – the view that every truth has a truthmaker – loses its…Read more
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275Tracking Referents in Electronic Health RecordsStudies in Health Technology and Informatics 116. 2005.Electronic Health Records (EHRs) are organized around two kinds of statements: those reporting observations made, and those reporting acts performed. In neither case does the record involve any direct reference to what such statements are actually about. They record not: what is happening on the side of the patient, but rather: what is said about what is happening. While the need for a unique patient identifier is generally recognized, we argue that we should now move to an EHR regime in which a…Read more
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1966The Substitution Theory of ArtGrazer Philosophische Studien 25 (1): 533-557. 1985.In perceptual experience we are directed towards objects in a way which establishes a real relation between a mental act and its target. In reading works of fiction we enjoy experiences which manifest certain internal similarities to such relational acts, but which lack objects. The substitution theory of art attempts to provide a reason why we seek out such experiences and the artifacts which they generate. Briefly, we seek out works of art because we enjoy the physiology and the phenomenology …Read more
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693Logic and the SachverhaltThe Monist 72 (1): 52-69. 1989.Those who conceive logic as a science have generally favoured one of two alternative conceptions as to what the subject-matter of this science ought to be. On the one hand is the nowadays somewhat old-fashioned-seeming view of logic as the science of judgment, or of thinking or reasoning activities in general. On the other hand is the view of logic as a science of ideal meanings, 'thoughts', or 'propositions in themselves'. There is, however, a third alternative conception, which enjoyed only a …Read more
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255Individuals, Universals, Collections: On the Foundational Relations of OntologyIn Thomas Bittner, Maureen Donnelly & Barry Smith (eds.), Individuals, universals, collections: On the foundational relations of ontology, Ios Press. 2004.This paper provides an axiomatic formalization of a theory of foundational relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the is-a relation among universals and the part-of relation among individuals as well as cross-category relations such as instance-of, member-of, and partition-of. We show that an adequate understanding of the formal properties of such relations – in …Read more
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369Toward an Ontological Treatment of Disease and DiagnosisIn Richard H. Scheuermann, Werner Ceusters & Barry Smith (eds.), Toward an Ontological Treatment of Disease and Diagnosis, American Medical Informatics Association. 2009.Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological process…Read more
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792Per una storia della teoria degli atti linguisticiIn Stefano Besoli & Luca Guidetti (eds.), Il realismo fenomenologico. Sulla filosofia dei circoli di Monaco e Gottinga, Quodlibet. pp. 385-418. 2000.Provides a survey of the development of speech act theory from Aristotle through Reid and Peirce to Edmund Husserl, Anton Marty, Johannes Daubert, Adolf Reinach, and finally to Austin and Searle. A special role is played by Husserl's theory of objectifying acts (meaning, roughly, acts of naming or stating) and of the efforts by his followers to extend this theory to cover phenomena such as questioning and commanding. These efforts culminated in the work of Adolf Reinach, who developed the first …Read more
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489Bodily Systems and the Spatial-Functional Structure of the Human BodyStudies in Health and Technology Informatics 102. 2004.The human body is a system made of systems. The body is divided into bodily systems proper, such as the endocrine and circulatory systems, which are subdivided into many sub-systems at a variety of levels, whereby all systems and subsystems engage in massive causal interaction with each other and with their surrounding environments. Here we offer an explicit definition of bodily system and provide a framework for understanding their causal interactions. Medical sciences provide at best informal …Read more
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2029Basic concepts of formal ontologyIn Nicola Guarino (ed.), Formal Ontology in Information Systems, Ios Press. pp. 19-28. 1998.The term ‘formal ontology’ was first used by the philosopher Edmund Husserl in his Logical Investigations to signify the study of those formal structures and relations – above all relations of part and whole – which are exemplified in the subject-matters of the different material sciences. We follow Husserl in presenting the basic concepts of formal ontology as falling into three groups: the theory of part and whole, the theory of dependence, and the theory of boundary, continuity and contact. T…Read more
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397The Environment Ontology: Contextualising biological and biomedical entitiesJournal of Biomedical Semantics 4 (43): 1-9. 2013.As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all t…Read more
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341Some Formal Moments of TruthIn Werner Leinfellner (ed.), Language and Ontology, Hölder-pichler-tempsky / Reidel. pp. 186-90. 1982.A preliminary statement of the formal theory of the truthmaker relation advanced in the paper “Truth-makers” (Mulligan, Simons and Smith) in 1984. Correspondence theories of truth have. I give a brief account of some more or less obvious formal characteristics of this almost forgotten basic truthmaker relation. I then attempt to show how this account may be extended to provide elements of a theory of truth which is in keeping with the spirit of Wittgenstein’s Tractatus.
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3265John Searle: From speech acts to social realityIn John Searle, Cambridge University Press. pp. 1-33. 2003.We provide an overview of Searle's contributions to speech act theory and the ontology of social reality, focusing on his theory of constitutive rules. In early versions of this theory, Searle proposed that all such rules have the form 'X counts as Y in context C' formula – as for example when Barack Obama (X) counts as President of the United States (Y) in the context of US political affairs. Crucially, the X and the Y terms are here identical. A problem arises for this theory for cases involvi…Read more
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385Ontological Support for Living Plan Specification, Execution and EvaluationIn Erik Thomsen, Fred Read, William Duncan, Tatiana Malyuta & Barry Smith (eds.), Semantic Technology in Intelligence, Defense and Security (STIDS), CEUR vol. 1304, . pp. 10-17. 2014.Maintaining systems of military plans is critical for military effectiveness, but is also challenging. Plans will become obsolete as the world diverges from the assumptions on which they rest. If too many ad hoc changes are made to intermeshed plans, the ensemble may no longer lead to well-synchronized and coordinated operations, resulting in the system of plans becoming itself incoherent. We describe in what follows an Adaptive Planning process that we are developing on behalf of the Air Force …Read more
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1528The evaluation of ontologies: Toward improved semantic interoperabilityIn Chris Baker & Kei H. Cheung (eds.), Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences, Springer. pp. 139-158. 2006.Recent years have seen rapid progress in the development of ontologies as semantic models intended to capture and represent aspects of the real world. There is, however, great variation in the quality of ontologies. If ontologies are to become progressively better in the future, more rigorously developed, and more appropriately compared, then a systematic discipline of ontology evaluation must be created to ensure quality of content and methodology. Systematic methods for ontology evaluation wil…Read more
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366Ontology with Human Subjects Testing: An Empirical Investigation of Geographic CategoriesAmerican Journal of Economics and Sociology 58 (2). 1998.Ontology, since Aristotle, has been conceived as a sort of highly general physics, a science of the types of entities in reality, of the objects, properties, categories and relations which make up the world. At the same time ontology has been for some two thousand years a speculative enterprise. It has rested methodologically on introspection and on the construction and analysis of elaborate world-models and of abstract formal-ontological theories. In the work of Quine and others this ontologica…Read more
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599Applying the Realism-Based Ontology-Versioning Method for Tracking Changes in the Basic Formal OntologyIn Paweł Garbacz & Oliver Kutz (eds.), Formal Ontology in Information Systems: Proceedings of the Eighth International Conference, Ios Press. pp. 227-240. 2014.Changes in an upper level ontology have obvious conse-quences for the domain ontologies that use it at lower levels. It is therefore crucial to document the changes made between successive versions of ontologies of this kind. We describe and apply a method for tracking, explaining and measuring changes between successive versions of upper level ontologies such as the Basic Formal Ontology (BFO). The proposed change-tracking method extends earlier work on Realism-Based Ontology Versioning (RBOV) …Read more
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467SNAP and SPAN: Towards dynamic spatial ontologySpatial Cognition and Computation 4 (1). 2004.We propose a modular ontology of the dynamic features of reality. This amounts, on the one hand, to a purely spatial ontology supporting snapshot views of the world at successive instants of time and, on the other hand, to a purely spatiotemporal ontology of change and process. We argue that dynamic spatial ontology must combine these two distinct types of inventory of the entities and relationships in reality, and we provide characterizations of spatiotemporal reasoning in the light of the inte…Read more
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333Endurants and Perdurants in Directly Depicting OntologiesAI Communications 13 (4). 2004.We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes and the enduring entities that participate therein. For this purpose we introduce the notion a directly depicting ontology. Directly depicting ontologies are based on relatively simple languages and fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and employ distinct though compatible systems of c…Read more
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2076On Classifying Material Entities in Basic Formal OntologyIn Barry Smith, Riichiro Mizoguchi & Sumio Nakagawa (eds.), Interdisciplinary Ontology, Vol. 3: Proceedings of the Third Interdisciplinary Ontology Meeting, Keio University Press. pp. 1-13. 2010.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
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523SachverhaltIn Historisches Wörterbuch der Philosophie, Volume 8, Basel: Schwabe. 1992.Both ‘Sachverhalt’ and ‘state of affairs’ seem to have been derived from the juridical ‘status’ in the sense of 'status rerum' meaning: state or constitution of things. ‘Status’ signifies also in an extended sense ‘the way things stand, the condition or peculiarity of a thing in regard to its circumstances, position, order’. We describe the history of usage of ‘Sachverhalt’ from these beginnings, addressing the role of Goclenius, Lotze, Stumpf, Husserl and Adolf Reinach, whose theory of the rela…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 |