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213An important part of the Unified Medical Language System (UMLS) is its Semantic Network, consisting of 134 Semantic Types connected to each other by edges formed by one or more of 54 distinct Relation Types. This Network is however for many purposes overcomplex, and various groups have thus made attempts at simplification. Here we take this work further by simplifying the relations which involve the three Semantic Types – Diagnostic Procedure, Laboratory Procedure and Therapeutic or Preventive P…Read more
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392Development of FuGO: An ontology for functional genomics investigationsOmics: A Journal of Integrative Biology 10 (2): 199-204. 2006.The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “sem…Read more
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232Dealing with elements of medical encounters: An approach based on ontological realismProceedings of the Joint International Conference on Biological Ontology and Biocreative 1747. 2016.Electronic health records (EHRs) serve as repositories of documented data collected in a health care encounter. An EHR records information about who receives, who provides the health care and about the place where the encounter happens. We also observe additional elements relating to social relations in which the healthcare consumer is involved. To provide a consensus representation of common data and to enhance interoperability between different EHR repositories we have created a solution groun…Read more
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656Adolf Reinach: An annotated bibliographyIn Kevin Mulligan (ed.), Speech Act and Sachverhalt: Reinach and the Foundations of Realist Phenomenology, M. Nijhoff. pp. 299-332. 1987.Ever since its appearance in 1913, Reinach's work on a The A Priori Foundations of the Civil Law has served as the principal representative of phenomenological, aprioristic and ontological/realist approaches to the philosophy of law. This annotated bibliography provides an overview of the reception of Reinach's thinking, which has been of influence also in the realm of speech act theory.
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414An improved ontological representation of dendritic cells as a paradigm for all cell typesBMC Bioinformatics 10 (1): 70. 2009.
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278The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and compu…Read more
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242Representing disease courses: An application of the Neurological Disease Ontology to Multiple Sclerosis TypologyIn Jensen Mark, Cox Alexander P., Diehl Alexander & Smith Barry (eds.), Proceedings of the Fourth International Conference on Biomedical Ontology (ICBO), CEUR 1060, . 2013.The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and …Read more
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287In the graphical representation of ontologies, it is customary to use graph theory as the representational background. We claim here that the standard graph-based approach has a number of limitations. We focus here on a problem in the graph-based representation of ontologies in complex domains such as biomedical, engineering and manufacturing: lack of mereotopological representation. Based on such limitation, we proposed a diagrammatic way to represent an entity’s structure and various forms of …Read more
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480Functional Anatomy: A Taxonomic ProposalActa Biotheoretica 53 (3): 153-166. 2005.It is argued that medical science requires a classificatory system that (a) puts functions in the taxonomic center and (b) does justice ontologically to the difference between the processes which are the realizations of functions and the objects which are their bearers. We propose formulae for constructing such a system and describe some of its benefits. The arguments are general enough to be of interest to all the life sciences.
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354This paper presents the Obstetric and Neonatal Ontology (OntONeo). This ontology has been created to provide a consensus representation of salient electronic health record (EHR) data and to serve interoperability of the associated data and information systems. More generally, it will serve interoperability of clinical and translational data, for example deriving from genomics disciplines and from clinical trials. Interoperability of EHR data is important to ensuring continuity of care during the…Read more
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301The ImmPort Antibody OntologyProceedings of the International Conference on Biological Ontology 1747. 2016.Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immu…Read more
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231The Ontology of DocumentsIn Mitsuhiro Okada (ed.), Proceedings of the Conference on Ontology and Analytical Metaphysics, February 24-25, 2011, Keio University Press. pp. 1-6. 2011.As is well known, speech acts such as acts of promising can have ontological consequences. For example an act of promising can give rise to a mutually correlated claim and obligation. Increasingly, speech acts in the narrow sense are being augmented by the use of documents of multiple different sorts. In this paper we analyze the results of this augmenta-tion from the ontological point of view, considering especially the domains of law and com-merce. We show how document acts are not isolated ph…Read more
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270Kognitionsforskningens topologiske grundlagSemikolon 3 (7): 91-105. 2003.The paper introduces the concepts at the heart of point-set-topology and of mereotopology (topology founded in the non-atomistic theory of parts and wholes) in an informal and intuitive fashion. It will then seek to demonstrate how mereotopological ideas can be of particular utility in cognitive science applications. The prehistory of such applications (in the work of Husserl, the Gestaltists, of Kurt Lewin and of J. J. Gibson) will be sketched, together with an indication of the field of possib…Read more
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5144OntologíaIn Hurtado G. & Nudler O. (eds.), El mobiliario del mundo. Ensayos de ontología, Universidad Autónoma De México. 2007.Presentiamo qui la traduzione di un lungo saggio sull’ontologia e i sistemi informativi. Abbiamo tradotto la parte più generale con le distinzioni base tra ontologia, metafisica e scienza. L’autore, fornendo un suo punto di vista peculiare sull’ontologia, descrive le diverse questioni e distinzioni connesse all’impresa ontologica, considerando sia il punto di vista dei filosofi che degli informatici.
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388Rationality and Irrationality: Proceeedings of the 23rd International Wittgenstein Symposium, 13-19 August 2000, Kirchberg Am Wechsel (edited book, review)Öbv&Hpt. 2001.This volume consists of the invited papers presented at the 23rd International Wittgenstein Conference held in Kirchberg, Austria in August 2000. Among the topics treated are: truth, psychologism, science, the nature of rational discourse, practical reason, contextualism, vagueness, types of rationality, the rationality of religious belief, and Wittgenstein. Questions addressed include: Is rationality tied to special sorts of contexts? ls rationality tied to language? Is scientific rationality t…Read more
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249Bela Zalai und die Metaphysik des reinen SeinsBrentano Studien. Internationales Jahrbuch der Franz Brentano Forschung 5. 1994.Between 1910 und 1915 the Hungarian philosopher Béla Zalai (1882-1915) developed his “comparative metaphysics of systems”, which had a significant influence on both the young Georg Lukács and also on Karl Mannheim. Through an analysis of Zalai’s approach to metaphysics, we show how he served to mediate between the realist Austrian philosophy of Meinong and of the early Husserl on the one side, and the German (idealistic, Kantian) philosophy then dominant in Hungary.
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205Zalai Béla és a tiszta lét MetafizikájaMagyar Filozofiai Szemle 3. 1987.Between 1910 und 1915 the Hungarian philosopher Béla Zalai (1882-1915) developed his “comparative metaphysics of systems”, which had a significant influence on both the young Georg Lukács and also on Karl Mannheim. Through an analysis of Zalai’s approach to metaphysics, we show how he served to mediate between the realist Austrian philosophy of Meinong and of the early Husserl on the one side, and the German (idealistic, Kantian) philosophy then dominant in Hungary.
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416L'ontologia del senso communeIn Evandro Agazzi (ed.), Valore E Limiti Del Senso Comune, Milan: Francoangeli. pp. 261-284. 2004.Common sense is on the one hand a certain set of processes of natural cognition – of speaking, reasoning, seeing, and so on. On the other hand common sense is a system of beliefs (of folk physics, folk psychology and so on). Over against both of these is the world of common sense, the world of objects to which the processes of natural cognition and the corresponding belief-contents standardly relate. What are the structures of this world? How does the scientific treatment of this world relate to…Read more
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210Historicity, Value and MathematicsIn A. T. Tymieniecka (ed.), Analecta Husserliana, vol. 4, Reidel. pp. 219-239. 1975.At the beginning of the present century, a series of paradoxes were discovered within mathematics which suggested a fundamental unclarity in traditional mathematical methods. These methods rested on the assumption of a realm of mathematical idealities existing independently of our thinking activity, and in order to arrive at a firmly grounded mathematics different attempts were made to formulate a conception of mathematical objects as purely human constructions. It was, however, realised that s…Read more
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448An Essay in Formal OntologyGrazer Philosophische Studien 6 (1): 39-62. 1978.As conceived by analytic philosophers ontology consists in the application of the methods of mathematical logic to the analysis of ontological discourse. As conceived by realist philosophers such as Meinong and the early Husserl, Reinach and Ingarden, it consists in the investigation of the forms of entities of various types. The suggestion is that formal methods be employed by phenomenological ontologists, and that phenomenological insights may contribute to the construction of adequate formal-…Read more
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158On Tractarian lawIn Smith Barry (ed.), Wittgenstein, the Vienna Circle and Critical Rationalism, Vienna: Hölder-pichler-tempsky. pp. 31-35. 1979."'It is clear", wrote Wittgenstein in the Tractatus, "that ethics has nothing to do with punishment and reward in the usual sense of the terms" (6.422). But he insisted also that there must be some kind of ethical punishment and reward; "the reward", he tells us, "must be something pleasant, and the punishment something unpleasant" (ibid.). I argue that we can understand what Wittgenstein meant by "reward" and "punishment" by conceiving these notions as elements in a system of interrelated conce…Read more
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1564Kafka and Brentano: A Study in Descriptive PsychologyIn Structure and Gestalt: Philosophy and Literature in Austria-Hungary and Her Successor States, John Benjamins. pp. 113-144. 1981.There is a narrow thread in the vast literature on Kafka which pertains to Kafka’s knowledge of philosophy, and more precisely to Kafka’s use in his fictional writings of some of the main ideas of Franz Brentano. Kafka attended courses in philosophy at the Charles University given by Brentano’s students Anton Marty and Christian von Ehrenfels, and was for several years a member of a discussion-group organized by orthodox adherents of the Brentanian philosophy in Prague. The present essay summari…Read more
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187R. Schmit, Husserls Philosophie der Mathematik. Platonistische und konstruktivistische Momente in Husserls Mathematikbegriff (review)History and Philosophy of Logic 4 (2): 230. 1983.
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510Acta cum fundamentis in reDialectica 38 (2‐3): 157-178. 1984.It will be the thesis of this paper that there are among our mental acts some which fall into the category of real material relations. That is: some acts are necessarily such as to involve a plurality of objects as their relata or fundamenta. Suppose Bruno walks into his study and sees a cat. To describe the seeing, here, as a relation, is to affirm that it serves somehow to tie Bruno to the cat. Bruno's act of seeing, unlike his feeling depressed, his putative thinking-about-Santa-Claus or his …Read more
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251Phänomenologie und angelsächsische PhilosophiePhilosophischer Literaturanzeiger 37 387-405. 1984.Review article on recent publications in phenomenology
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23E. Husserl, Studien zur Arithmetik und Geometrie. Texte aus dem Nachlass (review)History and Philosophy of Logic 6 (2): 223-249. 1985.
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357Wittgenstein und das ethische GesetzIn Dieter Birnbacher & Armin Burkhardt (eds.), Sprachspiel und Methode: zum Stand der Wittgenstein-Diskussion, Walter De Gruyter. pp. 191-211. 1985.Der vorliegende Aufsatz stellt den Versuch dar, die normative Seite von Wittgensteins Frühwerk herauszuarbeiten und dabei an seinem Ansatz insofern Kritik zu üben, als gezeigt wird, wie sehr dessen Implikationen mit unseren üblichen ethischen Vorstellungen in Konflikt stehen. Die Arbeit hat aber auch einen etwas wohlwollenderen Aspekt: Sie versucht zu zeigen, wie Wittgensteins scheinbar widersinnige Ansichten so formuliert werden können, daß sie zumindest begreifbar erscheinen. Zu diesem Zweck b…Read more
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283A theory of AustriaIn Nyiri J. N. (ed.), From Bolzano to Wittgenstein: The Tradition of Austrian Philosophy, Hölder-pichler-tempsky. pp. 11-30. 1986.The present essay seeks, by way of the Austrian example, to make a contribution to what might be called the philosophy of the supranational state. More specifically, we shall attempt to use certain ideas on the philosophy of Gestalten as a basis for understanding some aspects of that political and cultural phenomenon which was variously called the Austrian Empire, the Habsburg Empire, the Danube Monarchy or Kakanien.
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275Edmund Husserl, Logische Untersuchungen, II. Band, 1. und 2 (review)Grazer Philosophische Studien 27 (1): 199-207. 1986.
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512A Husserlian Theory of IndexicalityGrazer Philosophische Studien 28 (1): 133-163. 1986.The paper seeks to develop an account of indexical phenomena based on the highly general theory of structure and dependence set forth by Husserl in his Logical Investigations. Husserl here defends an Aristotelian theory of meaning, viewing meanings as species or universals having as their instances certain sorts of concrete meaning acts. Indexical phenomena are seen to involve the combination of such acts of meaning with acts of perception, a thesis here developed in some detail and contrasted w…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 |