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253Tracking Referents in Electronic Health RecordsStudies in Health Technology and Informatics 116. 2005.Electronic Health Records (EHRs) are organized around two kinds of statements: those reporting observations made, and those reporting acts performed. In neither case does the record involve any direct reference to what such statements are actually about. They record not: what is happening on the side of the patient, but rather: what is said about what is happening. While the need for a unique patient identifier is generally recognized, we argue that we should now move to an EHR regime in which a…Read more
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252Philosophie und biomedizinische ForschungAllgemeine Zeitschrift für Philosophie 30 (1). 2005.Die bahnbrechenden wissenschaftlichen Ergebnisse der letzten Jahre erzwingen eine neue philosophische Auseinandersetzung mit den Grundkategorien der Biologie und der benachbarten Disziplinen. Insbesondere die Anwendung neuer informationstechnischer Mittel in der biomedizinischen Forschung und die damit verbundene, kontinuierlich zunehmende Datenflut sowie die Notwendigkeit, ihrer Herr zu werden, erfordern ein konsequentes Nachdenken darüber, wie biologische Daten systematisiert und klassifizier…Read more
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252The Ontology of Reference: Studies in Logic and PhenomenologyDissertation, Manchester. 1976.Abstract: We propose a dichotomy between object-entities and meaning-entities. The former are entities such as molecules, cells, organisms, organizations, numbers, shapes, and so forth. The latter are entities such as concepts, propositions, and theories belonging to the realm of logic. Frege distinguished analogously between a ‘realm of reference’ and a ‘realm of sense’, which he presented in some passages as mutually exclusive. This however contradicts his assumption elsewhere that every entit…Read more
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251On carcinomas and other pathological entitiesComparative and Functional Genomics 6 (7/8). 2005.Tumors, abscesses, cysts, scars, fractures are familiar types of what we shall call pathological continuant entities. The instances of such types exist always in or on anatomical structures, which thereby become transformed into pathological anatomical structures of corresponding types: a fractured tibia, a blistered thumb, a carcinomatous colon. In previous work on biomedical ontologies we showed how the provision of formal definitions for relations such as is_a, part_of and transform…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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250Austria and the rise of scientific philosophyIn Arkadiusz Chrudzimski & Wolfgang Huemer (eds.), Phenomenology and analysis: essays on Central European philosophy, Ontos. pp. 33-56. 2004.The term ‘Continental philosophy’ designates not philosophy on the continent of Europe as a whole, but rather a selective slice of Franco-German philosophy. Through a critical analysis of the arguments advanced by Otto Neurath, the paper addresses the issue of why Austrian philosophers in particular are not counted in the pantheon of Continental philosophers. Austrian philosophy is marked by the predominance of philosophical analysis and of the philosophy of science. The paper concludes that it …Read more
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249OBCS: 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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249We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes (occurrents) and the enduring entities (continuants) that participate in such processes. For this purpose we distinguish between meta-ontology and token ontologies. Token ontologies fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and result in distinct though compatible systems of categories. The…Read more
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248The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of the…Read more
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248Using ontology in query answering systems: Scenarios, requirements and challengesIn R. Bernardi & M. Moortgat (eds.), Questions and Answers: Theoretical and Applied Perspectives, Proceedings of the 2nd CoLogNET-Elsnet Symposium, December 2003, . pp. 5-15. 2003.Equipped with the ultimate query answering system, computers would finally be in a position to address all our information needs in a natural way. In this paper, we describe how Language and Computing nv (L&C), a developer of ontology-based natural language understanding systems for the healthcare domain, is working towards the ultimate Question Answering (QA) System for healthcare workers. L&C’s company strategy in this area is to design in a step-by-step fashion the essential components of suc…Read more
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248Bela 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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247Ontological relationsIn Katherine Munn & Barry Smith (eds.), Applied Ontology, Walter De Gruyter. pp. 219-234. 2008.
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246What follows is a summary of basic principles pertaining to the definitions used in constructing an ontology. A definition is a statement of necessary and sufficient conditions. What this means in the simplest case can be understood as follows. To say that ɸ‐ing is a necessary condition for being an A is just another way of saying that every A ɸ’s; to say that ɸ‐ing is a sufficient condition for being an A is just another way of saying that everything that ɸ’s is an A. The goal in writing a defi…Read more
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245On the ontology of functionsApplied ontology 6 (2): 99-104. 2011.This special issue of Applied Ontology is devoted to the foundation, the comparison and the application of functional theories in all areas, with particular attention to the biological and engineering domains. It includes theoretical and technical contributions related to the description, characterization, and application of functions.
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245Controlled and uncontrolled English for ontology editingSemantic Technology for Intelligence, Defense and Security 1523 74-81. 2015.Ontologies formally represent reality in a way that limits ambiguity and facilitates automated reasoning and data fusion, but is often daunting to the non-technical user. Thus, many researchers have endeavored to hide the formal syntax and semantics of ontologies behind the constructs of Controlled Natural Languages (CNLs), which retain the formal properties of ontologies while simultaneously presenting that information in a comprehensible natural language format. In this paper, we build upon pr…Read more
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244Switching Partners: Dancing with the Ontological EngineersIn Thomas Batcherer & Roderick Coover (eds.), Switching Codes: Thinking through Digital Technology in the Humanities and the Arts, University of Chicago Press. pp. 103--124. 2011.Ontologies are today being applied in almost every field to support the alignment and retrieval of data of distributed provenance. Here we focus on new ontological work on dance and on related cultural phenomena belonging to what UNESCO calls the “intangible heritage.” Currently data and information about dance, including video data, are stored in an uncontrolled variety of ad hoc ways. This serves not only to prevent retrieval, comparison and analysis of the data, but may also impinge on our ab…Read more
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242The future of ontologiesIn Terminology, Ontology and their Implementations, Springer Nature. 2023.We have now reached the point at which cloud computing and other types of advanced infrastructure are bringing about a situation in which knowledge objects can be delivered in an efficient manner to hose who need to consume them. And just as highways were the infrastructure necessary for a manufacturing economy, serving as the arteries along which raw materials and manufactured goods coming in from all directions could flow, so we believe that ontologies will in the future provide an important p…Read more
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242Formalisms 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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241Representing 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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240Realitätsrepräsentation: Das Ziel der OntologieIn Ludger Jansen & Barry Smith (eds.), Biomedizinische Ontologie. Philosophie – Lebenswissenschaften - Informationstechnik, Vdf (utb Forum). pp. 31-46. 2008.The development of ontologies for the purposes of data curation is an important element in modern-day data and information sciences. Unfortunately, much of the work on these applied ontologies is associated with a relativist or conceptualist point of view, according to which ontologies represent (for example) the concepts in the minds of human beings. The paper describes a series of problems with such views, and defends an alternative realist interpretation.
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240Biomedizinische Ontologie: Wissen strukturieren für den Informatik-Einsatz (edited book)Vdf Hochschulverlag. 2008.Dieses Buch betritt Neuland. Es ist eine Einführung in das neue Gebiet der angewandten Ontologie, jenem multidisziplinären Arbeitsgebiet, in dem Philosophen gemeinsam mit Informatikern und Vertretern der jeweils thematischen Wissenschaftsbereiche, in unserem Fall mit Biologen und Medizinern, daran arbeiten, wissenschaftliches Wissen informationstechnisch zu repräsentieren. Es zeigt, wie Philosophie eine praktische Anwendung findet, die von zunehmender Wichtigkeit nicht nur in den heutigen Lebens…Read more
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239Six questions on the construction of ontologies in biomedicineReport of the AMIA Working Group on Formal Biomedical Knowledge Representation 1. 2005.(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these exper…Read more
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239ItIn Rudolf Haller & Wolfgang Grassl (eds.), Language, Logic and Philosophy, Reidel. 1980.A brief study of the logical, linguistic, psychological and ontological problem of ‘impersonalia’, which is to say of assertions such as ‘it’s raining’ or ‘es blitzt’ which seem to have no subject. Such assertions cause problems not only for defenders of traditional subject-predicate views of assertive sentences, but also for those, such as Frege, who defended a view in terms of functions and arguments.
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239The Ontology of Processes and Functions: A Study of the International Classification of Functioning, Disability and HealthIn Sharing Knowledge through the ICF: 13th Annual North American WHO Collaborating Center Conference on the ICF, Niagara Falls, June 7, 2007, North American Who Collaborating Center. 2007.The International Classification of Functioning, Disability and Health provides a classification of human bodily functions, which, while exhibiting non-conformance to many formal ontological principles, provides an insight into which basic functions such a classification should include. Its evaluation is an important first step towards such an adequate ontology of this domain. Presented at the 13th Annual North American WHO Collaborating Center Conference on the ICF, 2007.
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239Ontology as the core discipline of biomedical informatics: Legacies of the past and recommendations for the future direction of researchIn Gordana Dodig Crnkovic & Susan Stuart (eds.), Computation, Information, Cognition: The Nexus and the Liminal, Cambridge Scholars Publishing. pp. 104-122. 2007.The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on a…Read more
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238Referent Tracking of Portions of Reality. Docket No. 1097.015A (USPA 2009055437)In U.S. Patent Application, Us Patent Office. 2008.Management of information is facilitated by unambiguously tracking portions of reality over time. To track the portions of reality, a referent tracking system is used. The referent tracking system is able to communicate with other tracking systems and/or tradition information systems. Errors in the referent tracking system are detected and corrected to maintain actual representations of the portions of reality.
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238Dalla metafisica classica all'informatica medicaIn Smith Barry (ed.), Ontologia, , 154--158, Naples: Guida. pp. 154-159. 2003.In un articolo comparso sul Wall Street Journal del 13 novembre 2oi:n viene descritto il modo in cui i computer potrebbero essere utilizzati al fine di allertare i responsabili della salute pubblica in relazione ad eventuali problemi provocati dal bioterrorismo. L'autore nota come gli attacchi biologici sarebbero probabilmente contraddistinti da picchi statistici negli acquisti senza ricetta medica di rimedi per specifici disturbi di tipo comune e come i dati che riguardano tali acquisti possano…Read more
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237Abstract: We propose a view of vagueness as a semantic property of names and predicates. All entities are crisp, on this semantic view, but there are, for each vague name, multiple portions of reality that are equally good candidates for being its referent, and, for each vague predicate, multiple classes of objects that are equally good candidates for being its extension. We provide a new formulation of these ideas in terms of a theory of granular partitions. We show that this theory provides a …Read more
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235A new framework for host-pathogen interaction researchFrontiers in Immunology 13. 2022.COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host…Read more
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233Adolf Reinach e la fondazione della fenomenologia realistica. Prima parte: Nomi e oggettiParadigmi 5 (14): 229-241. 1987.The theory of speech acts put forward by Adolf Reinach in his "The A Priori Foundations of the Civil Law" of 1913 rests on a systematic account of the ontological structures associated with various different sorts of language use. One of the most original features of Reinach's account lies in hIs demonstration of how the ontological structure of, say, an action of promising or of commanding, may be modified in different ways, yielding different sorts of non-standard instances of the correspondin…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 |