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365Clonal 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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782Common 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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180Command 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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257Clinical 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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246Biomedizinische 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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349Bioportal: 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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215Biomedical 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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346Applications of the ACGT Master Ontology on CancerIn R. Meersman & P. Herrero (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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166An 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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241Adolf 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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324Adolf 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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192An 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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684Adolf 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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329An 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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242A 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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237Acts 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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254Abstract: 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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181A 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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543A 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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534A 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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502A 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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443A 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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493A multi-INT semantic reasoning framework for intelligence analysis supportIn L. Obrst, Terry Janssen & 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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191A 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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230A 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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310Palaeontological 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.
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266The 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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709Un'aporia nella costruzione della realtà sociale: Naturalismo e realismo in John R. SearleIn Paolo Di Lucia (ed.), Ontologia Sociale, Quodlibet. pp. 137-152. 2003.We provide an overview of Searle's contributions to speech act theory and the ontology of social reality, focusing on his theory of constitutive rules. In early versions of this theory, Searle proposed that all such rules have the form 'X counts as Y in context C' formula – as for example when Barack Obama (X) counts as President of the United States (Y) in the context of US political affairs. Crucially, the X and the Y terms are here identical. A problem arises for this theory for cases involvi…Read more
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292Zur Kognition räumlicher Grenzen: Eine mereotopologische UntersuchungKognitionswissenschaft 4 177-184. 1995.The perception of spatial bodies is at least in part a perception of bodily boundaries or surfaces. The usual mathematical conception of boundaries as abstract constructions is, however, of little use for cognitive science purposes. The essay therefore seeks a more adequate conception of the ontology of boundaries building on ideas in Aristotle and Brentano on what we may call the coincidence of boundaries. It presents a formal theory of boundaries and of the continua to which they belong, of a …Read more
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221Would 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
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 |