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344This paper addresses the use of dispositions in the Infectious Disease Ontology (IDO). IDO is an ontology constructed according to the principles of the Open Biomedical Ontology (OBO) Foundry and uses the Basic Formal Ontology (BFO) as an upper ontology. After providing a brief introduction to disposition types in BFO and IDO, we discuss three general techniques for representing combinations of dispositions under the headings blocking dispositions, complementary dispositions, and collective disp…Read more
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303The 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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220Groups, sets, and wholesRivista di Estetica 43 (24): 126-127. 2003.As he recalls in his book Naive Physics, Paolo Bozzi’s experiments on naïve or phenomenological physics were partly inspired by Aristotle’s spokesman Simplicio in Galileo’s Dialogue. Aristotle’s ‘naïve’ views of physical reality reflect the ways in which we are disposed perceptually to organize the physical reality we see. In what follows I want to apply this idea to the notion of a group, a term which I shall apply as an umbrella expression embracing ordinary visible collections (of pieces of f…Read more
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295Horizontal Integration of Warfighter Intelligence Data: A Shared Semantic Resource for the Intelligence CommunityIn Barry Smith, Tatiana Malyuta, William S. Mandrick, Chia Fu, Kesny Parent & Milan Patel (eds.), Proceedings of the Conference on Semantic Technology in Intelligence, Defense and Security (STIDS), CEUR, . pp. 1-8. 2012.We describe a strategy that is being used for the horizontal integration of warfighter intelligence data within the framework of the US Army’s Distributed Common Ground System Standard Cloud (DSC) initiative. The strategy rests on the development of a set of ontologies that are being incrementally applied to bring about what we call the ‘semantic enhancement’ of data models used within each intelligence discipline. We show how the strategy can help to overcome familiar tendencies to stovepiping …Read more
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471Truthmaker realismAustralasian Journal of Philosophy 77 (3). 1999.We take as our starting point a thesis to the effect that, at least for true judgments of many varieties, there are parts of reality which make such judgments are true. We argue that two distinct components are involved in this truthmaker relation. On the one hand is the relation of necessitation, which holds between an object x and a judgment p when the existence of x entails the truth of p. On the other hand is the dual notion of projection, which holds between a judgment p and an objec…Read more
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276Biomedical informatics and granularityComparative and Functional Genomics 5 (6-7): 501-508. 2004.An explicit formal-ontological representation of entities existing at multiple levels of granularity is an urgent requirement for biomedical information processing. We discuss some fundamental principles which can form a basis for such a representation. We also comment on some of the implicit treatments of granularity in currently available ontologies and terminologies (GO, FMA, SNOMED CT).
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627An 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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1062Franz Brentano on the Ontology of MindPhilosophy and Phenomenological Research 45 (4): 627-644. 1985.This is a review article on Franz Brentano’s Descriptive Psychology published in 1982. We provide a detailed exposition of Brentano’s work on this topic, focusing on the unity of consciousness, the modes of connection and the types of part, including separable parts, distinctive parts, logical parts and what Brentano calls modificational quasi-parts. We also deal with Brentano’s account of the objects of sensation and the experience of time.
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1323Framework 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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688Towards Industrial Strength Philosophy: How Analytical Ontology Can Help Medical InformaticsInterdisciplinary Science Reviews 28 (2). 2003.Initially the problems of data integration, for example in the field of medicine, were resolved in case by case fashion. Pairs of databases were cross-calibrated by hand, rather as if one were translating from French into Hebrew. As the numbers and complexity of database systems increased, the idea arose of streamlining these efforts by constructing one single benchmark taxonomy, as it were a central switchboard, into which all of the various classification systems would need to be translated on…Read more
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607CARO: The Common Anatomy Reference OntologyIn 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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805Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI projectNature Biotechnology 26 (8): 889-896. 2008.Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental c…Read more
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555MetaphysicsIn Asbjørn Steglich-Petersen (ed.), Metaphysics: Five 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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213A Unified Framework for Biomedical Terminologies and OntologiesStudies in Health Technology and Informatics 160 1050-1054. 2010.The goal of the OBO (Open Biomedical Ontologies) Foundry initiative is to create and maintain an evolving collection of non-overlapping interoperable ontologies that will offer unambiguous representations of the types of entities in biological and biomedical reality. These ontologies are designed to serve non-redundant annotation of data and scientific text. To achieve these ends, the Foundry imposes strict requirements upon the ontologies eligible for inclusion. While these requirements are not…Read more
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365Toward an Ontological Treatment of Disease and DiagnosisIn Proceedings of the 2009 AMIA Summit on Translational Bioinformatics, 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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786Per 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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306Anatomical information scienceIn A. G. Cohn & D. M. Mark (eds.), Spatial Information Theory, Springer. pp. 149-164. 2005.The Foundational Model of Anatomy (FMA) is a map of the human body. Like maps of other sorts – including the map-like representations we find in familiar anatomical atlases – it is a representation of a certain portion of spatial reality as it exists at a certain (idealized) instant of time. But unlike other maps, the FMA comes in the form of a sophisticated ontology of its objectdomain, comprising some 1.5 million statements of anatomical relations among some 70,000 anatomical kinds. It is furt…Read more
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1687Do 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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627Ten Conditions on a Theory of Speech ActsTheoretical Linguistics 11 (3): 309-330. 1984.It is now generally recognized that figures such as Reid, Peirce, and Reinach formulated theories of speech acts avant la lettre of Austin and Searle, in Reid and Reinach’s cases under the heading ‘theory of social acts’. Here we address the question as to what conditions would have to be satisfied for such theories to count as ‘theories of speech acts’ in the now familiar sense.
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270Tracking 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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208The Formal Structure of Ecological ContextsIn Paolo Bouquet, Patrick Brezillon, Francesca Castellani & Luciano Serafini (eds.), Modeling and Using Context. Proceedings of the Second International and Interdisciplinary Conference, Springer. 1999.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.
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689Logic 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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462The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysisJournal of Biomedical Semantics 7 (53). 2016.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 collect…Read more
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361Ontology 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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3480Applied Ontology: An Introduction (edited book)ontos. 2008.Ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. This is exactly what information scientists aim for in creating structured, automated representations, called 'ontologies,' for managing information in fields such as science, government, industry, and healthcare. Currently, these systems are designed in a variety of different ways, so they cannot share data with one another. They ar…Read more
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483Bodily 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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462Towards a Reference Terminology for Ontology Research and Development in the Biomedical DomainIn Barry Smith, Waclaw Kusnierczyk, Daniel Schober & Werner Ceusters (eds.), Proceedings of KR-MED, CEUR, vol. 222, . pp. 57-65. 2006.Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have be…Read more
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391The 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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609Ontological tools for geographic representationIn Nicola Guarino (ed.), Formal Ontology in Information Systems (FOIS), Ios Press. pp. 77--85. 1998.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 p…Read more
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3216John 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
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 |