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2039Building 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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373Ontological 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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646Husserl, Language and the Ontology of the ActIn Dino Buzzetti & M. Ferriani (eds.), Speculative Grammar, Universal Grammar, and Philosophical Analysis of Language, John Benjamins. pp. 205-227. 1987.The ontology of language is concerned with the relations between uses of language, both overt and covert, and other entities, whether in the world or in the mind of the thinking subject. We attempt a first survey of the sorts of relations which might come into question for such an ontology, including: relations between referring uses of expressions and their objects, relations between the use of a (true) sentence and that in the world which makes it true, relations between mental acts on the one…Read more
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1249When the U.S. conducts warfare, elements of a force are drawn from different services and work together as a single team to accomplish an assigned mission. To achieve such unified action, it is necessary that the doctrines governing the actions of members of specific services be both consistent with and subservient to joint Doctrine. Because warfighting today increasingly involves not only live forces but also automated systems, unified action requires that information technology that is used in…Read more
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961Features, Objects, and other Things: Ontological Distinctions in the Geographic DomainIn Daniel R. Montello (ed.), Spatial Information Theory: Foundations of Geographic Information Science, Springer. pp. 489-502. 2001.Two hundred and sixty-three subjects each gave examples for one of five geographic categories: geographic features, geographic objects, geographic concepts, something geographic, and something that could be portrayed on a map. The frequencies of various responses were significantly different, indicating that the basic ontological terms feature, object, etc., are not interchangeable but carry different meanings when combined with adjectives indicating geographic or mappable. For all of the test p…Read more
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525Mereotopology: 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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456SNAP 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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773Against 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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2055On Classifying Material Entities in Basic Formal OntologyIn Interdisciplinary Ontology: Proceedings of the Third Interdisciplinary Ontology Meeting, Keio University Press. pp. 1-13. 2012.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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193Von T. G. Masaryk bis Jan Patočka: Eine philosophische SkizzeIn J. Zumr & T. Binder (eds.), T. G. Masaryk und die Brentano-Schule, Czech Academy of Sciences. pp. 94-110. 1993.Thomas Garrigue Masaryk, later founder and President of the Republic of Czechoslovakia, studied philosophy in the University of Vienna from 1872 to 1876, where he came under the powerful influence of Franz Brentano. We survey the role of Brentano’s philosophy, and especially of his ethics, in Masaryk’s life and work.
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719Fiat 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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360Annotating 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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242L’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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687Two 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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1Interdisciplinary Ontology, Vol. 3: Proceedings of the Third Interdisciplinary Ontology Meeting (edited book)Keio University Press. 2010.
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579Quantum 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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408The Role of Foundational Relations in the Alignment of Biomedical OntologiesIn M. Fieschi, E. Coiera & Y.-C. J. Li (eds.), Medinfo, Ios Press. pp. 444-448. 2004.The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities that is designed to serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems. We diagnose certain characte…Read more
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241Die 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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969The 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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41Austrian Economics (Routledge Revivals): Historical and Philosophical Background (edited book)Croom Helm / Routledge. 1986.First published in 1986 and reprinted in 2010 in the Routledge Revivals series, this book presents the first detailed confrontation between the Austrian school of economics and Austrian philosophy, especially the philosophy of the Brentano school. It contains a study of the roots of Austrian economics in the liberal political theory of the nineteenth-century Hapsburg empire, and a study of the relations between the general theory of value underlying Austrian economics and the new economic approa…Read more
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473The 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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437Putting 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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608The metaphysics of real estateTopoi 20 (2): 161-172. 2001.The thesis that an analysis of property rights is essential to an adequate analysis of the state is a mainstay of political philosophy. The contours of the type of government a society has are shaped by the system regulating the property rights prevailing in that society. Views of this sort are widespread. They range from Locke to Nozick and encompass pretty much everything else in between. Defenders of this sort of view accord to property rights supreme importance. A state that does not suffici…Read more
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534Creating 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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877Ontologies as Integrative Tools for Plant ScienceAmerican Journal of Botany 99 (8). 2012.Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and rela…Read more
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1070Aboutness: 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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312LinkSuite™: Software Tools for Formally Robust Ontology-Based Data and Information IntegrationIn Werner Ceusters, Barry Smith & James Matthew Fielding (eds.), Proceedings of DILS 2004 (Data Integration in the Life Sciences), (Lecture Notes in Bioinformatics, 2994), Springer. pp. 1-16. 2004.The integration of information resources in the life sciences is one of the most challenging problems facing bioinformatics today. We describe how Language and Computing nv, originally a developer of ontology-based natural language understanding systems for the healthcare domain, is developing a framework for the integration of structured data with unstructured information contained in natural language texts. L&C’s LinkSuite™ combines the flexibility of a modular software architecture with an on…Read more
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29Kafka 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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860What’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
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 |