-
224Acts 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
-
239Abstract: 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
-
174A 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
-
528A 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
-
495A 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
-
489A 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
-
411A 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
-
481A 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.
-
178A 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
-
223A 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
-
287Palaeontological 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.
-
258The 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
-
689Un'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
-
280Zur 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
-
208Would 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
-
197What do identifiers in HL7 identify? An essay in the ontology of identityIn Ceusters Werner & Barry Smith (eds.), Proceedings of InterOntology (Tokyo, Japan, February 27-March 1, 2009), Keio University Press. pp. 77-86. 2009.Health Level 7 (HL7) is an organization seeking to provide universal standards for the exchange of healthcare information. In a document entitled ‘HL7 Version 3 Standard: Data Types’, the HL7 organization advances descriptions of data types recom- mended for use as identifiers. We will argue that the descriptions supplied provide insufficient guidance as to what exactly the entities are which these data types uniquely identify. Are they real things, such as persons or pieces of equipment? Or are…Read more
-
233Using philosophy to improve the coherence and interoperability of applications ontologies: A field report on the collaboration of IFOMIS and L&CIn Gregor Büchel, Bertin Klein & Thomas Roth-Berghofer (eds.), Proceedings of the First Workshop on Philosophy and Informatics. Deutsches Forschungszentrum für künstliche Intelligenz, Cologne: 2004 (CEUR Workshop Proceedings 112), . pp. 65-72. 2004.The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into …Read more
-
476Vital Sign OntologyIn Goldfain Albert, Smith Barry, Arabandi Sivaram, Brochhausen Mathias & Hogan William R. (eds.), Proceedings of the Workshop on Bio-Ontologies, ISMB, Vienna, June 2011, . pp. 71-74. 2011.We introduce the Vital Sign Ontology (VSO), an extension of the Ontology for General Medical Science (OGMS) that covers the consensus human vital signs: blood pressure, body temperature, respiratory rate, and pulse rate. VSO provides a controlled structured vocabulary for describing vital sign measurement data, the processes of measuring vital signs, and the anatomical entities participating in such measurements. VSO is implemented in OWL-DL and follows OBO Foundry guidelines and best practices.…Read more
-
255Using 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
-
519Truthmakers, Truthbearers and the Objectivity of TruthIn Jaako Hintikka (ed.), Philosophy and Logic: In Search of the Polish Tradition, Kluwer. pp. 229-268. 2003.The aim of this paper is to show that the account of objective truth taken for granted by logicians at least since the publication in 1933 of Tarski’s “The Concept of Truth in Formalized Languages” arose out of a tradition of philosophical thinking initiated by Bolzano and Brentano. The paper shows more specifically that certain investigations of states of affairs and other objectual correlates of judging acts, investigations carried out by Austrian and Polish philosophers around the turn of the…Read more
-
276Each annual Ontology Summit initiative makes a statement appropriate to each Summits theme as part of our general advocacy designed to bring ontology science and engineering into the mainstream. The theme this year is "Towards an Open Ontology Repository". This communiqué represents the joint position of those who were engaged in the year's summit discourse on an Open Ontology Repository (OOR) and of those who endorse below. In this discussion, we have agreed that an "ontology repository is a f…Read more
-
263Deskriptive Psychologie by Franz Brentano (review)Philosophy and Phenomenological Research 45 (4): 627-644. 1985.We provide a detailed exposition of Brentano’s descriptive psychology, focusing on the unity of consciousness, the modes of connection and the types of part, including separable parts, distinctive parts, logical parts and what Brentano calls modificational quasi-parts. We also deal with Brentano’s account of the objects of sensation and the experience of time.
-
269Kurt Lewin, Wissenschaftstheorie I (review)History and Philosophy of Logic 4 (2): 235-238. 1983.
-
336La verità trionfa: Da T. G. Masaryk a Jan PatočkaDiscipline Filosofiche 2. 1991.Thomas Garrigue Masaryk, later founder and President of the Republic of Czechoslovakia, studied philosophy in the University of Vienna from 1872 to 1876, where he came under the powerful influence of Franz Brentano. We survey the role of Brentano’s philosophy, and especially of his ethics, in Masaryk’s life and work.
-
315Towards an ontology of common senseIn Jaakko Hintikka (ed.), The British Tradition in Twentieth-Century Philosophy, Vienna: Hölder-pichler-tempsky. pp. 300--309. 1995.Philosophers from Plotinus to Paul Churchland have yielded to the temptation to embrace doctrines which contradict the core beliefs of common sense. Philosophical realists have on the other hand sought to counter this temptation and to vindicate those core beliefs. The remarks which follow are to be understood as a further twist of the wheel in this never-ending battle. They pertain to the core beliefs of common sense concerning the external reality that is given in everyday experience -the beli…Read more
-
389that can serve as a foundation for more refined ontologies in the field of proteomics. Standard data sources classify proteins in terms of just one or two specific aspects. Thus SCOP (Structural Classification of Proteins) is described as classifying proteins on the basis of structural features; SWISSPROT annotates proteins on the basis of their structure and of parameters like post-translational modifications. Such data sources are connected to each other by pairwise term-to-term mappings. Howe…Read more
-
231Towards a Body Fluids Ontology: A unified application ontology for basic and translational scienceSecond International Conference on Biomedical Ontology , Buffalo, Ny 833 227-229. 2011.We describe the rationale for an application ontology covering the domain of human body fluids that is designed to facilitate representation, reuse, sharing and integration of diagnostic, physiological, and biochemical data, We briefly review the Blood Ontology (BLO), Saliva Ontology (SALO) and Kidney and Urinary Pathway Ontology (KUPO) initiatives. We discuss the methods employed in each, and address the project of using them as starting point for a unified body fluids ontology resource. We con…Read more
-
263This paper takes the form of a series of sketches of 19th century Austrian political and intellectual history, allied with a number of more general reflections designed to contribute to our understanding of some of the peculiar characteristics of Austrian thought, particularly Austrian philosophy and economics, in the period in question.
-
340The Plant Ontology: A common reference ontology for plantsIn Walls Ramona L., Cooper Laurel D., Justin Elser, Stevenson Dennis W., Smith Barry, Chris Mungall, Gandolfo Maria A. & Pankaj Jaiswal (eds.), Proceedings of the Workshop on Bio-Ontologies, ISMB, Boston, July, 2010, . 2010.The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical stru…Read more
-
308The significance of SNODENTMedical Informatics Europe 2005. 2005.SNODENT is a dental diagnostic vocabulary incompletely integrated in SNOMED-CT. Nevertheless, SNODENT could become the de facto standard for dental diagnostic coding. SNODENT's manageable size, the fact that it is administratively self-contained, and relates to a well-understood domain provides valuable opportunities to formulate and test, in controlled experiments, a series of hypothesis concerning diagnostic systems. Of particular interest are questions related to establishing appropriate qual…Read more
Barry Smith
University at Buffalo
National Center for Ontological Research
-
University at BuffaloDepartment of Philosophy
Biomedical Informatics
Neurology
Computer Science and EngineeringDistinguished Professor, Julian Park Chair -
National Center for Ontological ResearchAdministrator
-
APA Eastern Division
Buffalo, New York, United States of America
Areas of Specialization
Metaphysics |
Ontology |
Philosophy of Artificial Intelligence |
Philosophy of Biology |