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212Enhancing GO for the sake of clinical bioinformaticsProceedings of the Bio-Ontologies Workshop , Glasgow 133. 2004.Recent work on the quality assurance of the Gene Ontology (GO, Gene Ontology Consortium 2004) from the perspective of both linguistic and ontological organization has made it clear that GO lacks the kind of formalism needed to support logic-based reasoning. At the same time it is no less clear that GO has proven itself to be an excellent terminological resource that can serve to combine together a variety of biomedical database and information systems. Given the strengths of GO, it is worth inve…Read more
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308Environmental MetaphysicsIn Uwe Meixner (ed.), Metaphysics in the post-metaphysical age, . pp. 231-242. 2001.We propose the beginnings of a general theory of environments, of the parts or regions of space in which organisms live and move. We draw on two sources: on the one hand on recent work on the ontology of space; and on the other hand on work by ecological scientists on concepts such as territory, habitat, and niche. An environment is in first approximation a volume of space; it is a specific habitat, location, or site that is suitable or adequate for given purposes (of foraging, resting, hunti…Read more
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250Dependence relationships between Gene Ontology terms based on TIGR gene product annotationsProceedings of the 3rd International Workshop on Computational Terminology 2004 31-38. 2004.The Gene Ontology is an important tool for the representation and processing of information about gene products and functions. It provides controlled vocabularies for the designations of cellular components, molecular functions, and biological processes used in the annotation of genes and gene products. These constitute three separate ontologies, of cellular components), molecular functions and biological processes, respectively. The question we address here is: how are the terms in these three …Read more
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246Clinical data wrangling using Ontological Realism and Referent TrackingIn Ceusters Werner, Hsu Chiun Yu & Smith Barry (eds.), Proceedings of the Fifth International Conference on Biomedical Ontology (ICBO), Houston, 2014, (CEUR, 1327), . pp. 27-32. 2014.Ontological realism aims at the development of high quality ontologies that faithfully represent what is general in reality and to use these ontologies to render heterogeneous data collections comparable. To achieve this second goal for clinical research datasets presupposes not merely (1) that the requisite ontologies already exist, but also (2) that the datasets in question are faithful to reality in the dual sense that (a) they denote only particulars and relationships between particulars tha…Read more
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371Clonal complexes in biomedical ontologiesIn Barry Smith (ed.), ICBO 2009: Proceedings of the First International Conference on Biomedical Ontology, Ncor. pp. 168. 2009.An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Sequence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms …Read more
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792Common senseIn Barry Smith & David Woodruff Smith (eds.), The Cambridge companion to Husserl, Cambridge University Press. pp. 394-437. 1995.Can there be a theory-free experience? And what would be the object of such an experience. Drawing on ideas set out by Husserl in the “Crisis” and in the second book of his “Ideas”, the paper presents answers to these questions in such a way as to provide a systematic survey of the content and ontology of common sense. In the second part of the paper Husserl’s ideas on the relationship between the common-sense world (what he called the ‘life-world’) and the world of physical theory are subjected…Read more
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184Command and Control OntologyInternational Journal of Intelligent Defence Support Systems (Special Issue) 4 (3). 2011.Intelligent defence support systems are confronted with the need to manage ever-increasing floods of data in a way that raises significant challenges because the data are described and presented using different terminologies and formats. How, on this basis, is it possible to reach a common understanding of the information content of these data among people and software agents? How is it possible to ensure that domain knowledge is reused in consistent fashion in a way that makes this information …Read more
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269Clinical ontologies interfacing the real worldIn Schulz Stefan, Stenzhorn Holger, Boeker Martin, Klar Rüdiger & Smith Barry (eds.), Third International Conference on Semantic Technologies (i-semantics 2007), Graz, Austria, . 2007.The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. T…Read more
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252Biomedizinische Ontologien für die PraxisEuropean Journal for Biomedical Informatics 1. 2009.Hintergrund: Biomedizinische Ontologien existieren unter anderem zur Integration von klinischen und experimentellen Daten. Um dies zu erreichen ist es erforderlich, dass die fraglichen Ontologien von einer großen Zahl von Benutzern zur Annotation von Daten verwendet werden. Wie können Ontologien das erforderliche Maß an Benutzerfreundlichkeit, Zuverlässigkeit, Kosteneffektivität und Domänenabdeckung erreichen, um weitreichende Akzeptanz herbeizuführen? Material und Methoden: Wir konzentrieren un…Read more
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354Bioportal: 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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253Biomedical Terminologies and Ontologies: Enabling Biomedical Semantic Interoperability and Standards in EuropeIn Bernard de Bono, Mathias Brochhausen, Sybo Dijkstra, Dipak Kalra, Stephan Keifer & Barry Smith (eds.), European Large-Scale Action on Electronic Health, . 2009.In the management of biomedical data, vocabularies such as ontologies and terminologies (O/Ts) are used for (i) domain knowledge representation and (ii) interoperability. The knowledge representation role supports the automated reasoning on, and analysis of, data annotated with O/Ts. At an interoperability level, the use of a communal vocabulary standard for a particular domain is essential for large data repositories and information management systems to communicate consistently with one other.…Read more
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350Applications of the ACGT Master Ontology on CancerIn Meersman R. & Herrero P. (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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170An ontology-based methodology for the migration of biomedical terminologies to electronic health recordsIn Smith Barry & Ceusters Werner (eds.), Proceedings of AMIA Symposium 2005, Washington DC,, Amia. 2005.Biomedical terminologies are focused on what is general, Electronic Health Records (EHRs) on what is particular, and it is commonly assumed that the step from the one to the other is unproblematic. We argue that this is not so, and that, if the EHR of the future is to fulfill its promise, then the foundations of both EHR architectures and biomedical terminologies need to be reconceived. We accordingly describe a new framework for the treatment of both generals and particulars in biomedical infor…Read more
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256Adolf 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
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335Adolf Reinach e la fondazione della fenomenologia realistica. Seconda parte: Giudizi e stati di coseParadigmi 5 (15): 485-507. 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
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197An evolutionary approach to the representation of adverse eventsStudies in Health Technology and Informatics 150 537-541. 2009.One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.
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701Adolf Reinach: An Intellectual BiographyIn Kevin Mulligan (ed.), Speech Act and Sachverhalt: Reinach and the Foundations of Realist Phenomenology, Reidel. pp. 1-27. 1987.The essay provides an account of the development of Reinach’s philosophy of “Sachverhalte” (states of affairs) and on problems in the philosophy of law, leading up to his discovery of the theory of speech acts in 1913. Reinach’s relations to Edmund Husserl and to the Munich phenomenologists are also dealt with.
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335An evolutionary approach to realism-based adverse event representationsMethods of Information in Medicine 50 (1): 62-73. 2011.One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.
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284A unified framework for building ontological theories with application and testing in the field of clinical trialsIn Vizenor Lowell, Smith Barry & Ceusters Werner (eds.), Ifomis Reports, Ifomis. 2004.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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251Acts and their objectsIn Epistemology and Philosophy of Science, Vienna: Hölder-pichler-tempsky. pp. 85--88. 1983.I shall begin with the assumption that there are, among our mental acts. some which stand in direct contact with ohjects in the material world. The aim of this paper will he to clarify and to draw out certain implications of this somewhat trivial assumption, and ultimately to say something about the ontological structure of those of our acts which effect the function of bringing us into contact with material acts which serve. as we might say, as the most external points of consciousness which to…Read more
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261A unified theory of granularity, vagueness and approximationIn Bittner Thomas & Smith Barry (eds.), COSIT Workshop on Spatial Vagueness, Uncertainty and Granularity, . pp. 39. 2001.Abstract: 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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185A user profiling component with the aid of user ontologiesIn Nébel István-Tibor, Barry Smith & Paschke Ralf (eds.), Learning – Teaching – Knowledge – Adaptivity (LLWA), University of Karlsruhe (2003)., . 2003.Abstract: What follows is a contribution to the field of user modeling for adaptive teaching and learning programs especially in the medical field. The paper outlines existing approaches to the problem of extracting user information in a form that can be exploited by adaptive software. We focus initially on the so-called stereotyping method, which allocates users into classes adaptively, reflecting characteristics such as physical data, social background, and computer experience. The user classi…Read more
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508A unified theory of truth and referenceLogique Et Analyse 43 (169-170). 2000.The truthmaker theory rests on the thesis that the link between a true judgment and that in the world to which it corresponds is not a one-to-one but rather a one-to-many relation. An analogous thesis in relation to the link between a singular term and that in the world to which it refers is already widely accepted. This is the thesis to the effect that singular reference is marked by vagueness of a sort that is best understood in supervaluationist terms. In what follows we show that the superva…Read more
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575A semantic approach for knowledge capture of microRNA-target gene interactionsIn Jingshan Huang, Fernando Gutierrez, Dejing Dou, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Barry Smith, Yu Lin, Xiaowei Wang & Zixing Liu (eds.), IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2015),, . pp. 975-982. 2015.Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, sema…Read more
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508A domain ontology for the non-coding RNA fieldIn Huang Jingshan, Eilbeck Karen, Blake Judith A., Dou Dejing, Natale Darren A., Ruttenberg Alan, Smith Barry, Zimmermann Michael T., Jiang Guoqian & Lin Yu (eds.), IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2015), . pp. 621-624. 2015.Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification o…Read more
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452A plant disease extension of the Infectious Disease OntologyIn Walls Ramona, Smith Barry, Justin Elser, Albert Goldfain & Stevenson Dennis W. (eds.), Proceeedings of the Third International Conference on Biomedical Ontology (CEUR 897), . pp. 1-5. 2012.Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phen…Read more
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507A multi-INT semantic reasoning framework for intelligence analysis supportIn L. Obrst, Janssen Terry & W. Ceusters (eds.), Ontologies and Semantic Technologies for the Intelligence Community, Ios Press. pp. 57-69. 2010.Lockheed Martin Corp. has funded research to generate a framework and methodology for developing semantic reasoning applications to support the discipline oflntelligence Analysis. This chapter outlines that framework, discusses how it may be used to advance the information sharing and integrated analytic needs of the Intelligence Community, and suggests a system I software architecture for such applications.
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200A framework for protein classificationIn Anand Kumar & Barry Smith (eds.), Proceedings of the 2003 German Conference on Bioinformatics, Vol. II, . pp. 55-57. 2003.It is widely understood that protein functions can be exhaustively described in terms of no single parameter, whether this be amino acid sequence or the three-dimensional structure of the underlying protein molecule. This means that a number of different attributes must be used to create an ontology of protein functions. Certainly much of the required information is already stored in databases such as Swiss-Prot, Protein Data Bank, SCOP and MIPS. But the latter have been developed for different …Read more
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235A 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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328Palaeontological reflections on the TractatusSAGP Reports. 1978.A collection of discussions of possible influences on Wittgenstein when he was writing the Tractatus, includes treatments of Reinach and Meinong.
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 |