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657John Searle: Od aktów mowy do rzeczywistości społecznejRoczniki Filozoficzne 51 (1): 265-292. 2003.Polish translation of "John Searle: From Speech Acts to Social Reality", 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 te…Read more
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657Adolf Reinach: An Intellectual BiographyIn Kevin Mulligan (ed.), Speech Act and Sachverhalt: Reinach and the Foundations of Realist Phenomenology, Reidel. pp. 1-27. 1987.The essay provides an account of the development of Reinach’s philosophy of “Sachverhalte” (states of affairs) and on problems in the philosophy of law, leading up to his discovery of the theory of speech acts in 1913. Reinach’s relations to Edmund Husserl and to the Munich phenomenologists are also dealt with.
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655The National Center for Biomedical OntologyJournal of the American Medical Informatics Association 19 (2): 190-195. 2012.The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variet…Read more
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653Two 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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651Philosophical foundations of intelligence collection and analysis: a defense of ontological realismIntelligence and National Security 38. 2022.There is a common misconception across the lntelligence Community (IC) to the effect that information trapped within multiple heterogeneous data silos can be semantically integrated by the sorts of meaning-blind statistical methods employed in much of artificial intelligence (Al) and natural language processlng (NLP). This leads to the misconception that incoming data can be analysed coherently by relying exclusively on the use of statistical algorithms and thus without any shared framework for …Read more
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649Representing Mental Functioning: Ontologies for Mental Health and DiseaseIn Janna Hastings, Werner Ceusters, Mark Jensen, Kevin Mulligan & Barry Smith (eds.), Towards an Ontology of Mental Functioning (ICBO Workshop), Ceur. 2012.Mental and behavioral disorders represent a significant portion of the public health burden in all countries. The human cost of these disorders is immense, yet treatment options for sufferers are currently limited, with many patients failing to respond sufficiently to available interventions and drugs. High quality ontologies facilitate data aggregation and comparison across different disciplines, and may therefore speed up the translation of primary research into novel therapeutics. Realism-based…Read more
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648A Spatio-Temporal Ontology for Geographic Information IntegrationInternational Journal for Geographical Information Science 23 (6): 765-798. 2009.This paper presents an axiomatic formalization of a theory of top-level relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the sub-universal relation among universals and the parthood relation among individuals, as well as cross-categorial relations such as instantiation and membership. We show that an adequate understanding of the formal properties of such relations – in pa…Read more
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648Ontologies for the life sciencesIn Schulze-Kremer Steffen & Smith Barry (eds.), Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, vol. 4, Wiley. 2005.Where humans can manipulate and integrate the information they receive in subtle and ever-changing ways from context to context, computers need structured and context-free background information of a sort which ontologies can help to provide. A domain ontology captures the stable, highly general and commonly accepted core knowledge for an application domain. The domain at issue here is that of the life sciences, in particular molecular biology and bioinformatics. Contemporary life science resear…Read more
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645Naive physicsPhilosophical Psychology 7 (2). 1994.The project of a 'naive physics' has been the subject of attention in recent years above all in the artificial intelligence field, in connection with work on common-sense reasoning, perceptual representation and robotics. The idea of a theory of the common-sense world is however much older than this, having its roots not least in the work of phenomenologists and Gestalt psychologists such as K hler, Husserl, Schapp and Gibson. This paper seeks to show how contemporary naive physicists can profit…Read more
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644Definitions in ontologiesCahiers de Lexicologie 109 (2). 2016.Definitions vary according to context of use and target audience. They must be made relevant for each context to fulfill their cognitive and linguistic goals. This involves adapting their logical structure, type of content, and form to each context of use. We examine from these perspectives the case of definitions in ontologies.
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642The Protein Ontology: A structured representation of protein forms and complexesNucleic Acids Research 39 (1). 2011.The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate repres…Read more
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632WüsteriaStudies in Health Technology and Informatics 116 647-652. 2005.The last two decades have seen considerable efforts directed towards making Electronic Health Records interoperable through improvements in medical ontologies, terminologies and coding systems. Unfortunately, these efforts have been hampered by a number of influential ideas inherited from the work of Eugen Wüster, the father of terminology standardization and the founder of ISO TC 37. We here survey Wüster’s ideas – which see terminology work as being focused on the classification of concepts in…Read more
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631Controlled vocabularies in bioinformatics: A case study in the Gene OntologyDrug Discovery Today: Biosilico 2 (6): 246-252. 2004.The automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is …Read more
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625Basic Formal Ontology for bioinformaticsIFOMIS Reports. 2005.Two senses of ‘ontology’ can be distinguished in the current literature. First is the sense favored by information scientists, who view ontologies as software implementations designed to capture in some formal way the consensus conceptualization shared by those working on information systems or databases in a given domain. [Gruber 1993] Second is the sense favored by philosophers, who regard ontologies as theories of different types of entities (objects, processes, relations, functions) [Smith…Read more
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624Husserl, 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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620Coordinating Coronavirus Research: The COVID-19 Infectious Disease OntologyProceedings of the International Conference on Biomedical Ontologies. 2022.The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Co…Read more
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620On the Origins of Analytic Philosophy (review)Grazer Philosophische Studien 35 (1): 153-173. 1989.Analytic philosophers have until recently been reluctant to pursue historical investigations into the Central European roots of their own philosophical tradition. The most recent book by Michael Dummett, however, entitled Origins of Analytic Philosophy, shows how fruitful such investigations can be, not only as a means of coming to see familiar philosophical problems in a new light, but also as a means of clarifying what, precisely, ‘analytic philosophy’ might mean. As Dummett points out, the ne…Read more
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612Formal Ontology for Natural Language Processing and the Integration of Biomedical DatabasesInternational Journal of Medical Informatics 75 (3-4): 224-231. 2005.The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end r®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO)…Read more
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608Biomedical OntologiesIn Peter L. Elkin (ed.), Terminology, Ontology and Their Implementations: Teaching Guide and Notes, Springer. pp. 125-169. 2022.We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use of the term…Read more
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604Ontology-based knowledge representation of experiment metadata in biological data miningIn Jake Chen & Stefano Lonardi (eds.), Biological Data Mining, Chapman Hall / Taylor and Francis. pp. 529-559. 2009.According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay awar…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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597An Ontological Approach to Territorial DisputesIn Semantic Technology in Intelligence, Defense and Security (STIDS), CEUR, vol. 1304, Ceur. pp. 2-9. 2014.Disputes over territory are a major contributing factor to the disruption of international relations. We believe that a cumulative, integrated, and continuously updated resource providing information about such disputes in an easily accessible form would be of benefit to intelligence analysts, military strategists, political scientists, and also to historians and others concerned with international disputes. We propose an ontology-based strategy for creating such a resource. The resource will co…Read more
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592Aristotelianism, apriorism, essentialismIn Peter Boettke (ed.), The Elgar Companion to Austrian Economics, Edward Elgard. pp. 33-37. 1994.
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591Conceptual Spaces for Space Event Characterization via Hard and Soft Data FusionAIAA (American Institute of Aeronautics and Astronautics) Scitech 2021 Forum. 2021.The overall goal of the approach developed in this paper is to estimate the likelihood of a given kinetic kill scenario between hostile spacebased adversaries using the mathematical framework of Complex Conceptual Spaces Single Observation. Conceptual spaces are a cognitive model that provide a method for systematically and automatically mimicking human decision making. For accurate decisions to be made, the fusion of both hard and soft data into a single decision framework is required. This pre…Read more
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591In defense of extreme (fallibilistic) apriorismJournal of Libertarian Studies 12 (1). 1996.We presuppose a position of scientific realism to the effect (i) that the world exists and (ii) that through the working out of ever more sophisticated theories our scientific picture of reality will approximate ever more closely to the world as it really is. Against this background consider, now, the following question: 1. Do the empirical theories with the help of which we seek to approximate a good or true picture of reality rest on any non-empirical presuppositions? One can answer this quest…Read more
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587Ontology for the Intelligence AnalystCrossTalk 14 (Nov/Dec): 18-25. 2012.As available intelligence data and information expand in both quantity and variety, new techniques must be deployed for search and analytics. One technique involves the semantic enhancement of data through the creation of what are called ‘ontologies’ or ‘controlled vocabularies.’ When multiple different bodies of heterogeneous data are tagged by means of terms from common ontologies, then these data become linked together in ways which allow more effective retrieval and integration. We describe …Read more
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587Ontological 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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585CARO: 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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581The Neurological Disease OntologyJournal of Biomedical Semantics 4 (42): 42. 2013.We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by…Read more
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581The 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
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 |