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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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351本体:广谱的知识集成工具In 基于基本形式化本体的本体构建, . pp. 4-8. 2020.Ontology: Tool for Broad Spectrum Knowledge Integration (Foreword to Chinese translation of Building Ontologies with Basic Formal Ontology)
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351Ontologie des Embryos: Wann beginnt menschliches LebenIn Honnefelder L. & Schmidt M. C. (eds.), Naturalismus als Paradigma - Wie weit reicht die naturwissenschaftliche Erklärung des Menschen? , 2007,, Berlin University Press. pp. 196-204. 2007.Der Abschluß der Gastrulation, der gleichzeitig auch den Anfang der Neurulation bedeutet, ist die zeitliche Grenze, die Beginn eines menschlichen Individuums markiert. Oft wird behauptet, daß jegliche natürliche Veränderung stetig ist. Wie ist es dann aber möglich, eine zeitliche Grenze auszuzeichnen, an der ein menschliches Lebewesen zu existieren beginnt? Man beachte, was geschieht, wenn wir vom Thema zeitlicher Unstetigkeit zum räumlichen übergehen. Lebewesen haben räumliche Grenzen (wie sie …Read more
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351On Creativity and the Philosophy of the Supranational StateIn Tamás Demeter (ed.), Essays on Wittgenstein and Austrian Philosophy: In Honour of J.C. Nyíri, Brill. pp. 25-39. 2004.Building on the writings of Wittgenstein on rule-following and deviance, Kristóf Nyíri advanced a theory of creativity as consisting in a fusion of conflicting rules or disciplines. Only such fusion can produce something that is both intrinsically new and yet capable of being apprehended by and passed on to a wider community. Creativity, on this view, involves not the breaking of rules, or the deliberate cultivation of deviant social habits, but rather the acceptance of enriched systems of rules…Read more
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351Ontologies for Space and Ground SystemsIn Ground System Architectures Workshop, Gsaw. pp. 1-3. 2020.We will survey a range of ontologies relevant to space and ground system domains. The ontologies form part of the Common Core Ontology ecosystem (CCO) developed under the IARPA KDD initiative. We focus specifically on the Space Domain Ontologies, a suite of ontologies to support space situational awareness, including the Spacecraft Mission Ontology, Spacecraft Ontology, Space Event Ontology and Space Object Ontology.
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350Referent Tracking for Command and Control Messaging SystemsCEUR, Volume 555. 2009.The Joint Battle Management Language (JBML) is an XML-based language designed to allow Command and Control (C2) systems to interface easily with Modeling and Simulation (M&S) systems. While some of the XML-tags defined in this language correspond to types of entities that exist in reality, others are mere syntactic artifacts used to structure the messages themselves. Because these two kinds of tags are not formally distinguishable, JBML messages in effect confuse data with what the data represen…Read more
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350On defining bruxismStudies in Health Technology and Informatics 247 551-555. 2018.In a series of recent publications, orofacial researchers have debated the question of how ‘bruxism’ should be defined for the purposes of accurate diagnosis and reliable clinical research. Following the principles of realism-based ontology, we performed an analysis of the arguments involved. This revealed that the disagreements rested primarily on inconsistent use of terms, so that issues of ontology were thus obfuscated by shortfalls in terminology. In this paper, we demonstrate how bruxism te…Read more
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350Toward 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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349Truth and the visual fieldIn Jean Petitot, Francisco J. Varela, Bernard Pachoud & Jean-Michel Roy (eds.), Naturalizing Phenomenology: Issues in Contemporary Phenomenology and Cognitive Science, Stanford University Press. pp. 317-329. 1999.The paper uses the tools of mereotopology (the theory of parts, wholes and boundaries) to work out the implications of certain analogies between the 'ecological psychology' of J. J Gibson and the phenomenology of Edmund Husserl. It presents an ontological theory of spatial boundaries and of spatially extended entities. By reference to examples from the geographical sphere it is shown that both boundaries and extended entities fall into two broad categories: those which exist independently of our…Read more
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349Referent tracking for corporate memoriesIn Peter Rittgen (ed.), Handbook of Ontologies for Business Interaction, Idea Group Publishing. pp. 34-46. 2007.For corporate memory and enterprise ontology systems to be maximally useful, they must be freed from certain barriers placed around them by traditional knowledge management paradigms. This means, above all, that they must mirror more faithfully those portions of reality which are salient to the workings of the enterprise, including the changes that occur with the passage of time. The purpose of this chapter is to demonstrate how theories based on philosophical realism can contribute to this obje…Read more
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348Developing the Quantitative Histopathology Image Ontology : A case study using the hot spot detection problemJournal of Biomedical Informatics 66 129-135. 2017.Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopatholo…Read more
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346Ontology 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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346OHMI: The Ontology of Host-Microbiome InteractionsJournal of Biomedical Semantics 10 (1): 1-14. 2019.Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of H…Read more
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345An Introduction to Hard and Soft Data Fusion via Conceptual Spaces Modeling for Space Event CharacterizationIn Jeremy Chapman, David Kasmier, John L. Crassidis, James L. Llinas, Barry Smith & Alex P. Cox (eds.), National Symposium on Sensor & Data Fusion (NSSDF), Military Sensing Symposia (MSS). 2021.This paper describes an AFOSR-supported basic research program that focuses on developing a new framework for combining hard with soft data in order to improve space situational awareness. The goal is to provide, in an automatic and near real-time fashion, a ranking of possible threats to blue assets (assets trying to be protected) from red assets (assets with hostile intentions). The approach is based on Conceptual Spaces models, which combine features from traditional associative and symbolic …Read more
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345Bioportal: Ontologies and integrated data resources at the click of the mouseIn Whetzel Patricia L., Shah Nigam H., Noy Natalya F., Benjamin Dai, Michael Dorf, Nicholas Griffith, Clement Jonquet, Cherie Youn, Chris Callendar, Adrien Coulet, Smith Barry, Chute Chris & Musen Mark (eds.), Proceedings of the 2nd International Conference on Biomedical Ontology, Buffalo, NY, . 2011.BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.
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344Oncology ontology in the NCI ThesaurusArtificial Intelligence in Medicine 213-220. 2005.The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of…Read more
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343Informatics: the fuel for pharmacometric analysisAAPS Journal 9 (1). 2007.The current informal practice of pharmacometrics as a combination art and science makes it hard to appreciate the role that informatics can and should play in the future of the discipline and to comprehend the gaps that exist because of its absence. The development of pharmacometric informatics has important implications for expediting decision making and for improving the reliability of decisions made in model-based development. We argue that well-defined informatics for pharmacometrics can lea…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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340The Plant Ontology: A common reference ontology for plantsIn Walls Ramona L., Cooper Laurel D., Justin Elser, Stevenson Dennis W., Smith Barry, Chris Mungall, Gandolfo Maria A. & Pankaj Jaiswal (eds.), Proceedings of the Workshop on Bio-Ontologies, ISMB, Boston, July, 2010, . 2010.The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical stru…Read more
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339Applications of the ACGT Master Ontology on CancerIn R. Meersman & P. Herrero (eds.), Proceedings of 4th International IFIP Workshop On Semantic Web and Web Semantics (OTM 2008: Workshops), LNCS 5333, . 2008.In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the on…Read more
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338Filozofia austriacka i dziedzictwo BrentanyPrincipia 8 19-50. 1994.A study of the contrasts between Austrian and German philosophy, with special reference to the role of logic and science, of the Brentano School and the Vienna Circle, and of the different ways in which Austrian and German ways of thinking have influenced contemporary analytical and Continental philosophy.
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338On the Austrianness of Austrian economicsCritical Review: A Journal of Politics and Society 4 (1-2): 212-238. 1990.Much recent work on the intellectual background of Austrian economics reveals an unfortunate lack of awareness of the distinct nature of the Austrian contribution to philosophy, from which the Austrian economists drew many of their ideas. The present essay offers a sketch of this contribution, contrasting Austrian philosophy especially with the modes of philosophy dominant in Germany. This makes it possible to throw new light on the relations on Mises, Kant and the Vienna circle, and it allows u…Read more
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336Zur Nichtübersetzbarkeit der deutschen PhilosophieIn D. Papenfuss & O. Pöggeler (eds.), Zur philosophischen Aktualität Heideggers, vol. 3, Im Spiegel der Welt: Sprache, Übersetzung, Auseinandersetzung, Klostermann. pp. 125-147. 1992.Warum hat sich die deutsche Philosophie so sehr und so langanhaltend an Autoritäten und Texte gebunden gefühlt, fast als ob man – wie die alten Iatrophilologen – Wissen aus bloßen Worten herauspressen wollte? Warum haben sich in Deutschland so häufig philosophische Sprachstile entwickelt, die ein Hindernis fur das Verständnis der entsprechenden Texte sind?
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336La verità trionfa: Da T. G. Masaryk a Jan PatočkaDiscipline Filosofiche 2. 1991.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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334Relevance, relatedness and restricted set theoryIn Georg Schurz & Georg Jakob Wilhelm Dorn (eds.), Advances in Scientific Philosophy, Rodopi. pp. 45-56. 1991.Relevance logic has become ontologically fertile. No longer is the idea of relevance restricted in its application to purely logical relations among propositions, for as Dunn has shown in his (1987), it is possible to extend the idea in such a way that we can distinguish also between relevant and irrelevant predications, as for example between “Reagan is tall” and “Reagan is such that Socrates is wise”. Dunn shows that we can exploit certain special properties of identity within the context of s…Read more
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334The Industrial Ontologies Foundry (IOF) perspectivesProceedings: Industrial Ontology Foundry (IOF) Achieving Data Interoperability Workshop, International Conference on Interoperability for Enterprise Systems and Applications, Tarbes, France, March 17-24, 2020. 2021.In recent years there has been a number of promising technical and institutional developments regarding use of ontologies in industry. At the same time, however, most industrial ontology development work remains within the realm of academic research and is without significant uptake in commercial applications. In biomedicine, by contrast, ontologies have made significant inroads as valuable tools for achieving interoperability between data systems whose contents derive from widely heterogeneous …Read more
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332Truthmaker realism: Response to GregoryAustralasian Journal of Philosophy 80 (2): 231-234. 2002.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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331An improved ontological representation of dendritic cells as a paradigm for all cell typesBMC Bioinformatics 10 (1): 70. 2009.The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representat…Read more
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330The cognitive geometry of warIn Peter Koller & Klaus Puhl (eds.), Current Issues in Political Philosophy: Justice in Society and World Order, Hölder-pichler-tempsky. pp. 394--403. 1997.When national borders in the modern sense first began to be established in early modern Europe, non-contiguous and perforated nations were a commonplace. According to the conception of the shapes of nations that is currently preferred, however, nations must conform to the topological model of circularity; their borders must guarantee contiguity and simple connectedness, and such borders must as far as possible conform to existing topographical features on the ground. The striving to conform to t…Read more
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329Sechzehn Tage: Wann beginnt ein menschliches Leben?In Guido Imaguire & Christine Schneider (eds.), Untersuchungen zur Ontologie, Philosophia. pp. 3-40. 2006.Der Abschluß der Gastrulation, der gleichzeitig auch den Anfang der Neurulation bedeutet, ist die zeitliche Grenze, die Beginn eines menschlichen Individuums markiert. Oft wird behauptet, daß jegliche natürliche Veränderung stetig ist. Wie ist es dann aber möglich, eine zeitliche Grenze auszuzeichnen, an der ein menschliches Lebewesen zu existieren beginnt? Man beachte, was geschieht, wenn wir vom Thema zeitlicher Unstetigkeit zum räumlichen übergehen. Lebewesen haben räumliche Grenzen (wie sie …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 |