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212An ontology for carcinoma classification for clinical bioinformaticsStudies in Health Technology and Informatics 116 (1): 635-640. 2005.There are a number of existing classifications and staging schemes for carcinomas, one of the most frequently used being the TNM classification. Such classifications represent classes of entities which exist at various anatomical levels of granularity. We argue that in order to apply such representations to the Electronic Health Records one needs sound ontologies which take into consideration the diversity of the domains which are involved in clinical bioinformatics. Here we outline a formal the…Read more
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212The 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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211A general framework for implementation of clinical guidelines by healthcare organizationsIn Pisanelli D. M. (ed.), Ontologies in Medicine: Proceedings of the Workshop on Medical Ontologies (Rome October 2003), Ios Press. pp. 95-107. 2003.The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also …Read more
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211Social ObjectsPhilosophiques 26 (2): 315-347. 1999.One reason for the renewed interest in Austrian philosophy, and especially in the work of Brentano and his followers, turns on the fact that analytic philosophers have become once again interested in the traditional problems of metaphysics. It was Brentano, Husserl, and the philosophers and psychologists whom they influenced, who drew attention to the thorny problem of intentionality, the problem of giving an account of the relation between acts and objects or, more generally, between the psycho…Read more
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210Les objets sociauxPhilosophiques 26 (2): 315-347. 1999.One reason for the renewed interest in Austrian philosophy, and especially in the work of Brentano and his followers, turns on the fact that analytic philosophers have become once again interested in the traditional problems of metaphysics. It was Brentano, Husserl, and the philosophers and psychologists whom they influenced, who drew attention to the thorny problem of intentionality, the problem of giving an account of the relation between acts and objects or, more generally, between the psycho…Read more
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209Where there’s no will, there’s no wayUkcolumn. 2023.An interview by Alex Thomson of UKColumn on Landgrebe and Smith's book: Why Machines Will Never Rule the World. The subtitle of the book is Artificial Intelligence Without Fear, and the interview begins with the question of the supposedly imminent takeover of one profession or the other by artificial intelligence. Is there truly reason to be afraid that you will lose your job? The interview itself is titled 'Where this is no will there is no way', drawing on one thesis of the book to the effect …Read more
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209How to Distinguish Parthood from Location in BioontologiesIn Proceedings of the AMIA Symposium, American Medical Informatics Association. pp. 669-673. 2005.The pivotal role of the relation part-of in the description of living organisms is widely acknowledged. Organisms are open systems, which means that in contradistinction to mechanical artifacts they are characterized by a continuous flow and exchange of matter. A closer analysis of the spatial relations in biological organisms reveals that the decision as to whether a given particular is part-of a second particular or whether it is only contained-in the second particular is often controversial. …Read more
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208Ontology-based integration of medical coding systems and electronic patient recordsIFOMIS Reports. 2004.In the last two decades we have witnessed considerable efforts directed towards making electronic healthcare records comparable and interoperable through advances in record architectures and (bio)medical terminologies and coding systems. Deep semantic issues in general, and ontology in particular, have received some interest from the research communities. However, with the exception of work on so-called ‘controlled vocabularies’, ontology has thus far played little role in work on standardizatio…Read more
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208Ontological representation of CDC Active Bacterial Core Surveillance Case ReportsProceedings of the Fifth International Conference on Biomedical Ontology 1327 74-77. 2014.The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excell…Read more
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206Information may be defined as the conceptual or communicable part of the content of mental acts. The content of mental acts includes sensory data as well as concepts, particular as well as general information. An information system is an external (non-mental) system designed to store such content. Information systems afford indirect transmission of content between people, some of whom may put information into the system and others who are among those who use the system. In order for communicatio…Read more
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206VérifacteursEtudes de Philosophie 9 104-138. 2008-2011.French translation of "Truth-Makers" (1984). A realist theory of truth for a class of sentence holds that there are entities in virtue of which these sentences are true or false. We call such entities ‘truthmakers’ and contend that those for a wide range of sentences about the real world are moments (dependent particulars). Since moments are unfamiliar we provide a definition and a brief philosophical history, anchoring them in our ontology by showing that they are objects of perception. The co…Read more
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206Il significato della vita: come valurare una civiltàIn Philippe Nemo & Jean Petitot (eds.), Storia del liberalismo in Europa, Rubbettino. 2013.In what respects is Western civilization superior or inferior to its rivals? In raising this question we are addressing a particularly strong form of the problem of relativism. For in order to compare civilizations one with another we would need to be in possession of a framework based on principles of evaluation which would be acceptable, in principle, to all human beings. Morality will surely provide one axis of such a framework (and we note in passing that believers in Islam might quite reaso…Read more
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205Formal ontology for biomedical knowledge systems integrationProceedings of Euromise 12-17. 2004.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 will greatly benefit software application ontologies. To this end LinKBase®, 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 F…Read more
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205The Ecological Approach to Information ProcessingIn Kristóf Nyíri (ed.), Mobile Learning: Essays on Philosophy, Psychology and Education, Passagen Verlag. pp. 17--24. 2003.Imagine a 5-stone weakling whose brain has been loaded with all the knowledge of a champion tennis player. He goes to serve in his first match – Wham! – His arm falls off. The 5-stone weakling just doesn’t have the bone structure or muscular development to serve that hard. There are, clearly, different types of knowledge/ability/skill, only some of which are a matter of what can be transferred simply by passing signals down a wire from one brain (or computer) to another. Sometimes it is the body…Read more
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204A unified framework for building ontological theories with application and testing in the field of clinical trialsIn IFOMIS Reports, University of Leipzig. 2001.The objective of this research programme is to contribute to the establishment of the emerging science of Formal Ontology in Information Systems via a collaborative project involving researchers from a range of disciplines including philosophy, logic, computer science, linguistics, and the medical sciences. The researchers will work together on the construction of a unified formal ontology, which means: a general framework for the construction of ontological theories in specific domains. The f…Read more
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202If we are to develop efficient, reliable and secure means for sharing information across healthcare systems and organizations, then a careful analysis of human actions will be needed. To address this need, the HL7 organization has proposed its Reference Information Model (RIM), which is designed to provide a comprehensive representation of the entire domain of healthcare centered around the phenomenon of human action. Taking the Basic Formal Ontology as our starting point, we examine the RIM fro…Read more
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201Groups, sets, and wholesRivista di Estetica 43 (24): 126-127. 2003.As he recalls in his book Naive Physics, Paolo Bozzi’s experiments on naïve or phenomenological physics were partly inspired by Aristotle’s spokesman Simplicio in Galileo’s Dialogue. Aristotle’s ‘naïve’ views of physical reality reflect the ways in which we are disposed perceptually to organize the physical reality we see. In what follows I want to apply this idea to the notion of a group, a term which I shall apply as an umbrella expression embracing ordinary visible collections (of pieces of f…Read more
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200Historicity, 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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200An 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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199Zeno’s paradox for coloursIn O. K. Wiegand, R. J. Dostal, L. Embree, J. Kockelmans & J. N. Mohanty (eds.), Phenomenology of German Idealism, Hermeneutics, and Logic, Dordrecht. pp. 201-207. 2000.We outline Brentano’s theory of boundaries, for instance between two neighboring subregions within a larger region of space. Does every such pair of regions contain points in common where they meet? Or is the boundary at which they meet somehow pointless? On Brentano’s view, two such subregions do not overlap; rather, along the line where they meet there are two sets of points which are not identical but rather spatially coincident. We outline Brentano’s theory of coincidence, and show how he us…Read more
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199On the Phases of ReismIn Arkadiusz Chrudzimski & Dariusz Łukasiewicz (eds.), Actions, products, and things: Brentano and Polish philosophy, Ontos. pp. 137--183. 2006.Kotarbiński is one of the leading figures in the Lvov-Warsaw school of Polish philosophy. We summarize the development of Kotarbiński’s thought from his early nominalism and ‘pansomatistic reism’ to the later doctrine of ‘temporal phases’. We show that the surface clarity and simplicity of Kotarbiński’s writings mask a number of profound philosophical difficulties, connected above all with the problem of giving an adequate account of the truth of contingent (tensed) predications. The paper will …Read more
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198Aristoteles 2002In T. Buchheim (ed.), Kann man heute noch etwas anfangen mit Aristoteles?, Meiner. pp. 3-38. 2003.The essay surveys recent developments in ontology and defends a strategy for improvement of ontologies based on ontological realism. As a thought experiment, we consider central theses of Aristotelian metaphysics, and show how they fall short of what we believe to be the requirements of ontology today. Above all, Aristotle provides us with no strategy for the reconciliation of common-sense realism and scientific realism where these diverge. We focus specifically on shortfalls in Aristotle’s trea…Read more
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198Would SNOMED CT benefit from realism-based ontology evolution?AMIA Annual Symposium Proceedings 2007 105-109. 2007.If SNOMED CT is to serve as a biomedical reference terminology, then steps must be taken to ensure comparability of information formulated using successive versions. New releases are therefore shipped with a history mechanism. We assessed the adequacy of this mechanism for its treatment of the distinction between changes occurring on the side of entities in reality and changes in our understanding thereof. We found that these two types are only partially distinguished and that a more detailed st…Read more
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197Zalai 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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197Adolf Reinach: An annotated bibliographyIn Kevin Mulligan (ed.), Speech Act and Sachverhalt. Reinach and the Foundations of Realist Phenomenology, Reidel. pp. 299-332. 1987.Reinach is principally known for his anticipation in 1913 of many ideas subsequently developed by Austin, Searle and others under the heading of 'speech act theory'. This bibliography of primary and secondary literature by and on Reinach shows that his influenced extended more broadly into areas such as the theory of judgment, the ontology of states of affairs, and the philosophy of law.
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195A Unified Framework for Biomedical Terminologies and OntologiesStudies in Health Technology and Informatics 160 1050-1054. 2010.The goal of the OBO (Open Biomedical Ontologies) Foundry initiative is to create and maintain an evolving collection of non-overlapping interoperable ontologies that will offer unambiguous representations of the types of entities in biological and biomedical reality. These ontologies are designed to serve non-redundant annotation of data and scientific text. To achieve these ends, the Foundry imposes strict requirements upon the ontologies eligible for inclusion. While these requirements are not…Read more
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194Despite 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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194Logica KirchbergensisIn Peter Klein (ed.), Praktische Logik. Traditionen und Tendenzen, Vandenhoeck & Ruprecht. pp. 123-145. 1989.In der klassischen Logik von Aristoteles bis Wolff findet sich eine durchgängige Parallelität von logischen (einschließlich grammatikalischen und psychologischen) und ontologischen Gebilden. Der Logiker beschäftigt sich mit Subjekt und Prädikat, aber gleichzeitig auch z.B. mit Substanz und Akzidenz als Entitäten in der Welt. Nach Kant begann für die Logik eine Phase, in der diese ontologische oder objektbezogene Seite verloren ging. Gegen Ende des 19. Jahrhunderts beginnt man dann aber wieder üb…Read more
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194On Forms of Communication In PhilosophyThe Proceedings of the Twentieth World Congress of Philosophy 12 73-82. 2001.In previous work, I have drawn attention to certain systematic differences among philosophical traditions as regards to the literary forms that are prevalent in each. In this paper, however, I focus on the commentary form. I raise the question of why the use of commentaries abounds in most traditions except those transmitted in the English language and suggest that problems of translation are central to this issue. I argue that the appearance of commentaries in a philosophical tradition is a cri…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 |