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359Referent Tracking for Command and Control Messaging SystemsCEUR, Volume 555. 2009.The Joint Battle Management Language (JBML) is an XML-based language designed to allow Command and Control (C2) systems to interface easily with Modeling and Simulation (M&S) systems. While some of the XML-tags defined in this language correspond to types of entities that exist in reality, others are mere syntactic artifacts used to structure the messages themselves. Because these two kinds of tags are not formally distinguishable, JBML messages in effect confuse data with what the data represen…Read more
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388The role of ontologies for sustainable, semantically interoperable and trustworthy EHR solutionsStudies in Health Technology and Informatics 150 953-957. 2009.As health systems around the world turn towards highly distributed, specialized and cooperative structures to increase quality and safety of care as well as efficiency and efficacy of delivery processes, there is a growing need for supporting communication and collaboration of all parties involved with advanced ICT solutions. The Electronic Health Record (EHR) provides the information platform which is maturing towards the eHealth core application. To meet the requirements for sustainable, seman…Read more
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180Letter to the Editor: Dealing with socially constructed concepts in an ontologyJournal of Empirical Research on Human Research Ethics 4 (2): 75-76. 2009.Response to the paper “The Biomedical Ethics Ontology Proposal: Excellent Aims, Questionable Methods" by James DuBois, published in the Journal of Empirical Research on Human Research Ethics
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463Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge BaseBMC Bioinformatics 11 (1): 302. 2010.The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO). We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/) as a consensus…Read more
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196More about ontology: ResponseJournal of the American Dental Association 142 (3): 252-254. 2011.Letter commenting on the paper Barry Smith, Louis J. Goldberg, Alan Ruttenberg & Michael Glick, "Ontology and the Future of Dental Research Informatics", Journal of the American Dental Association 141 2010;(10):1173-75 with responses by the authors of the paper.
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181Guest Editorial: Ontologies for clinical and translational researchJournal of Biomedical Informatics 44 (1): 3--7. 2011.
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268The representation of protein complexes in the Protein OntologyBMC Bioinformatics 12 (371): 1-11. 2011.Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consor…Read more
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234ARGOS policy brief on semantic interoperabilityStudies in Health Technology and Informatics 170 (1): 1-15. 2011.Semantic interoperability requires the use of standards, not only for Electronic Health Record (EHR) data to be transferred and structurally mapped into a receiving repository, but also for the clinical content of the EHR to be interpreted in conformity with the original meanings intended by its authors. Accurate and complete clinical documentation, faithful to the patient’s situation, and interoperability between systems, require widespread and dependable access to published and maintained coll…Read more
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427Wanting what we don't want to want: Representing Addiction in Interoperable Bio-OntologiesIn Janna Hastings, Werner Ceusters, Mark Jensen, Kevin Mulligan & Barry Smith (eds.), Towards an Ontology of Mental Functioning (ICBO Workshop), Ceur. pp. 56-60. 2012.Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most p…Read more
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362Bioinformatics advances in saliva diagnosticsInternational Journal of Oral Science 4 (2): 85--87. 2012.There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the in…Read more
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386Interdisciplinary perspectives on the development, integration and application of cognitive ontologiesFrontiers in Neuroinformatics 8 (62): 1-7. 2014.We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for…Read more
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441The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse…Read more
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507The development of non-coding RNA ontologyInternational Journal of Data Mining and Bioinformatics 15 (3): 214--232. 2016.Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semant…Read more
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457Une théorie unifiée de la vérité et de la référenceIn J. M. Monnoyer (ed.), La Structure du Monde: Objets, Propriétés, États du Choses, Vrin. pp. 141-184. 2004.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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595Aristotelianism, apriorism, essentialismIn Peter Boettke (ed.), The Elgar Companion to Austrian Economics, Edward Elgard. pp. 33-37. 1994.
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517A Taxonomy of Granular PartitionsIn Daniel Montello (ed.), Spatial Information Theory. Foundations of Geographic Information Science, Springer. pp. 28-43. 2001.In this paper we propose a formal theory of partitions (ways of dividing up or sorting or mapping reality) and we show how the theory can be applied in the geospatial domain. We characterize partitions at two levels: as systems of cells (theory A), and in terms of their projective relation to reality (theory B). We lay down conditions of well-formedness for partitions and we define what it means for partitions to project truly onto reality. We continue by classifying well-formed partitions along…Read more
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357Les objects sociauxPhilosophique 26 (2). 2002.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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685How to Do Things with DocumentsRivista di Estetica 50 179-198. 2012.This essay is a contribution to social ontology, drawing on the work of John Searle and of Hernando de Soto. At the center of the argument is the proposition advanced by de Soto in his Mystery of Capital to the effect that many of the entities which structure our contemporary social reality are entities which exist in virtue of the fact that there are (paper or digital) documents which support their existence. I here develop de Soto’s argument further, focusing specifically on the ontological pr…Read more
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173Wittgensteinian Philosophy and the Culture of the CommentaryIn Rudolf Haller & Johannes Brandl (eds.), Wittgenstein: Towards a Re-Evaluation, Volume 2, Hölder-pichler-tempsky. pp. 247-254. 1990.The object of the present paper is the philosophical commentary, a form of literature that once predominated in all major philosophical cultures from classical Greece to Renaissance Italy, but which has more recently fallen into comparative disuse. Commentaries on the writings of German thinkers such as Kant, Hegel, Marx and Heidegger have, certainly, kept the form alive to some extent in recent centuries; in the tradition of philosophy that was initiated by Descartes and Locke, however, and whi…Read more
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173Ingarden versus Meinong o logice fikcjiIn Z. Muszyński (ed.), Z badań nad prawdą i poznaniem, Wydawnictwo Umc-s. 1998.: For Meinong, familiarly, fictional entities are not created, but rather merely discovered (or picked out) from the inexhaustible realm of Aussersein (beyond being and non-being). The phenomenologist Roman Ingarden, in contrast, offers in his Literary Work of Art of 1931 a constructive ontology of fiction, which views fictional objects as entities which are created by the acts of an author (as laws, for example, are created by acts of parliament). We outline the logic of fiction which is implie…Read more
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505Modelling Principles and Methodologies: Relations in Anatomical OntologiesIn Albert Burger, Duncan Davidson & Richard Baldock (eds.), Anatomy Ontologies for Bioinformatics: Principles and Practice, Springer. pp. 289--306. 2008.It is now increasingly accepted that many existing biological and medical ontologies can be improved by adopting tools and methods that bring a greater degree of logical and ontological rigor. In this chapter we will focus on the merits of a logically sound approach to ontologies from a methodological point of view. As we shall see, one crucial feature of a logically sound approach is that we have clear and functional definitions of the relational expressions such as ‘is a’ and ‘part of ’.
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218VérifacteursEtudes 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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210On 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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55Surrounding SpaceTheory in Biosciences 121 (2): 139-162. 2002.The history of evolution is a history of development from less to more complex organisms. This growth in complexity of organisms goes hand in hand with a concurrent growth in complexity of environments and of organism-environment relations. It is a concern with this latter aspect of evolutionary development that motivates the present paper. We begin by outlining a theory of organism-environment relations. We then show that the theory can be applied to a range of different sorts of cases, both bi…Read more
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377Bodily Systems and the Modular Structure of the Human BodyArtificial Intelligence in Medicine (Lecture Notes on Artificial Intelligence 2780) 9 86-90. 2003.Medical science conceives the human body as a system comprised of many subsystems at a variety of levels. At the highest level are bodily systems proper, such as the endocrine system, which are central to our understanding of human anatomy, and play a key role in diagnosis and in dynamic modeling as well as in medical pedagogy and computer visualization. But there is no explicit definition of what a bodily system is; such informality is acceptable in documentation created for human beings, but f…Read more
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24Alexius Meinong, On Objects of Higher Order and Husserl's Phenomenology (review)Philosophical Quarterly 30 (120): 252. 1980.
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1796On Luck, Responsibility and the Meaning of LifePhilosophical Papers 34 (3): 443-458. 2005.A meaningful life, we shall argue, is a life upon which a certain sort of valuable pattern has been imposed by the person in question - a pattern which involves in serious ways the person having an effect upon the world. Meaningfulness is thus a special kind of value which a human life can bear. Two interrelated difficulties face ths proposal. One concerns responsiblity: how are we to account for the fact that a life that satisfies the above criteria can have more meaning than a life with the sa…Read more
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997HL7 RIM: An incoherent standardStudies in Health Technology and Informatics 124 (Proceedings of MIE 2006). 2006.The Health Level 7 Reference Information Model (HL7 RIM) is lauded by its authors as ‘the foundation of healthcare interoperability’. Yet even after some 10 years of development work, the RIM is still subject to a variety of logical and ontological flaws which have placed severe obstacles in the way of those who are called upon to develop implementations. We offer evidence that these obstacles are insurmountable and that the time has come to abandon an unworkable paradigm.
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1860Mach and Ehrenfels: The foundations of Gestalt TheoryIn Barry Smith (ed.), Foundations of Gestalt Theory, Philosophia Verlag. pp. 124-157. 1988.Ernst Mach's atomistic theory of sensation faces problems in doing justice to our ability to perceive and remember complex phenomena such as melodies and shapes. Christian von Ehrenfels attempted to solve these problems with his theory of "Gestalt qualities", which he sees as entities depending one-sidedly on the corresponding simple objects of sensation. We explore the theory of dependence relations advanced by Ehrenfels and show how it relates to the views on the objects of perception advanced…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 |