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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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369Values in Contexts: An Ontological TheoryIn G. John M. Abbarno (ed.), Inherent and Instrumental Values: Excursions in Value Inquiry, University Press of America. pp. 17-29. 2014.Values exist not in isolation, but in complex wholes. Values are what they are because of the complex wholes in which they are situated. To do justice to this thesis will require a holistic ontology, a theory according to which many types of entities exist only as inseparable parts or moments of wider contexts or environments. An ontological theory of environments -- with roots in Gestalt psychology and the ecological psychology of J. J. Gibson and Roger Barker, and which is related also to the …Read more
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351A 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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328This 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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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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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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205Groups, 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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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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452Truthmaker 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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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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201A 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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233Die 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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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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1026Franz 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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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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671Towards 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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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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793Promoting 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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548Quantum 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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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
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284Anatomical 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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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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598Ten 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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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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204The 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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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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423The 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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341Vague 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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3429Applied 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
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 |