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259OBCS: The Ontology of Biological and Clinical StatisticsProceedings of the Fifth International Conference on Biomedical Ontology 1327 65. 2014.Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to pres…Read more
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260Investigating subsumption in DL-based terminologies: A case study in SNOMED CTIn Olivier Bodenreider, Barry Smith, Anand Kumar & Anita Burgun (eds.), Proceedings of the First International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2004), . pp. 12-20. 2004.Formalisms such as description logics (DL) are sometimes expected to help terminologies ensure compliance with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) complies with such principles. We defined seven ontological principles (for example: each class must have at least one parent, each class must differ from its parent) and examined the properties of SNOMED CT classes with respect to these principles. O…Read more
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798Finding Our Way through PhenotypesPLoS Biol 13 (1). 2015.Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systemat…Read more
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348Informatics: 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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235The emphasis on evidence based medicine (EBM) has placed increased focus on finding timely answers to clinical questions in presence of patients. Using a combination of natural language processing for the generation of clinical excerpts and information theoretic distance based clustering, we evaluated multiple approaches for the efficient presentation of context-sensitive EBM excerpts.
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3688In Defense of Truth: Skepticism, Morality, and The MatrixIn William Irwin (ed.), Philosophy and The Matrix, Open Court. pp. 16-27. 2002.The Matrix exposes us to the uncomfortable worries of philosophical skepticism in an especially compelling way. However, with a bit more reflection, we can see why we need not share the skeptic’s doubts about the existence of the world. Such doubts are appropriate only in the very special context of the philosophical seminar. When we return to normal life we see immediately that they are groundless. Furthermore, we see also the drastic mistake that Cypher commits in turning his back upon reality…Read more
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208Despite the recent advances in information and communication technology that have increased our ability to store and circulate information, the task remains of ensuring that the right sorts of information reach the right sorts of people. In what follows we defend the thesis that efforts to develop efficient means for sharing information across healthcare systems and organizations would benefit from a careful analysis of human action in healthcare organizations, and that the communication of heal…Read more
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218An 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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400Development 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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243Dealing 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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666Adolf 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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427An improved ontological representation of dendritic cells as a paradigm for all cell typesBMC Bioinformatics 10 (1): 70. 2009.
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285The 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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261Representing 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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314A diagrammatic representation for entities and mereotopological relations in ontologiesIn José M. Parente de Oliveira & Barry Smith (eds.), CEUR, vol. 1908, . 2017.In 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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486Functional 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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370This 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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314The 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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240The 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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275Kognitionsforskningens 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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5191OntologíaIn 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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393Rationality 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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254Bela 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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211Zalai 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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423L'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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225Historicity, 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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465An 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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164On 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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1598Kafka 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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193R. Schmit, Husserls Philosophie der Mathematik. Platonistische und konstruktivistische Momente in Husserls Mathematikbegriff (review)History and Philosophy of Logic 4 (2): 230. 1983.
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 |