Results for 'Ian A. Smith'

999 found
Order:
See also
Ian Smith
Washburn University
Ian A. Smith
Washburn University
  1. A Semantic Approach for Knowledge Capture of microRNA-Target Gene Interactions.Jingshan Huang, Fernando Gutierrez, Dejing Dou, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Barry Smith, Yu Lin, Xiaowei Wang & Zixing Liu - 2015 - In IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2015),. pp. 975-982.
    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, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...)
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  2.  41
    A General Framework for Implementation of Clinical Guidelines by Healthcare Organizations.A. Kumar, Barry Smith, D. M. Pisanelli, A. Gangemi & M. Stefanelli - 2003 - In D. M. Pisanelli (ed.), Ontologies in Medicine: Proceedings of the Workshop on Medical Ontologies (Rome October 2003). Amsterdam: IOS Press. pp. 95-107.
    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 (...)
    Download  
     
    Export citation  
     
    Bookmark  
  3.  38
    OmniSearch: A Semantic Search System Based on the Ontology for MIcroRNA Target for microRNA-Target Gene Interaction Data.Huang Jingshan, Gutierrez Fernando, J. Strachan Harrison, Dou Dejing, Huang Weili, A. Blake Judith, Barry Smith, Eilbeck Karen, A. Natale Darren & Lin Yu - 2016 - Journal of Biomedical Semantics 7 (1):1.
    In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...)
    Download  
     
    Export citation  
     
    Bookmark  
  4. The Protein Ontology: A Structured Representation of Protein Forms and Complexes.Darren Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D’Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Barry Smith, Jian Zhang & Cathy H. Wu - 2011 - Nucleic Acids Research 39 (1):D539-D545.
    The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...)
    Download  
     
    Export citation  
     
    Bookmark   8 citations  
  5. The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses.Laurel Cooper, Ramona Walls, Justin Elser, Maria A. Gandolfo, Dennis W. Stevenson, Barry Smith & Others - 2013 - Plant and Cell Physiology 54 (2):1-23..
    The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...)
    Download  
     
    Export citation  
     
    Bookmark   3 citations  
  6.  22
    An Improved Ontological Representation of Dendritic Cells as a Paradigm for All Cell Types.Masci Anna Maria, N. Arighi Cecilia, D. Diehl Alexander, E. Lieberman Anne, Mungall Chris, H. Scheuermann Richard, Barry Smith & G. Cowell Lindsay - 2009 - BMC Bioinformatics 10 (1):70.
    The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...)
    Download  
     
    Export citation  
     
    Bookmark   2 citations  
  7. Framework for a Protein Ontology.Darren A. Natale, Cecilia N. Arighi, Winona Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith & Cathy H. Wu - 2007 - BMC Bioinformatics 8 (Suppl 9):S1.
    Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...)
    Download  
    Translate
     
     
    Export citation  
     
    Bookmark   8 citations  
  8.  98
    A Domain Ontology for the Non-Coding RNA Field.Jingshan Huang, Karen Eilbeck, Judith A. Blake, Dejing Dou, Darren A. Natale, Alan Ruttenberg, Barry Smith, Michael T. Zimmermann, Guoqian Jiang & Yu Lin - 2015 - In IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2015). pp. 621-624.
    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 of ncRNA biology.
    Download  
     
    Export citation  
     
    Bookmark  
  9.  99
    Protein Ontology: A Controlled Structured Network of Protein Entities.A. Natale Darren, N. Arighi Cecilia, A. Blake Judith, J. Bult Carol, R. Christie Karen, Cowart Julie, D’Eustachio Peter, D. Diehl Alexander, J. Drabkin Harold, Helfer Olivia, Barry Smith & Others - 2013 - Nucleic Acids Research 42 (1):D415-21..
    The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...)
    Download  
     
    Export citation  
     
    Bookmark  
  10. Adam Smith's Political Philosophy: The Invisible Hand and Spontaneous Order.Craig Smith - 2006 - Routledge.
    When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...)
    Download  
     
    Export citation  
     
    Bookmark   4 citations  
  11.  93
    Developing the Quantitative Histopathology Image Ontology : A Case Study Using the Hot Spot Detection Problem.Metin Gurcan, Tomaszewski N., Overton John, A. James, Scott Doyle, Alan Ruttenberg & Barry Smith - 2017 - Journal of Biomedical Informatics 66:129-135.
    Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with (...)
    Download  
     
    Export citation  
     
    Bookmark  
  12.  47
    The Plant Ontology: A Common Reference Ontology for Plants.L. Walls Ramona, D. Cooper Laurel, Elser Justin, W. Stevenson Dennis, Barry Smith, Mungall Chris, A. Gandolfo Maria & Jaiswal Pankaj - 2010 - In Proceedings of the Workshop on Bio-Ontologies, ISMB, Boston, July, 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 structures as well as growth and developmental stages (...)
    Download  
     
    Export citation  
     
    Bookmark  
  13.  46
    The Non-Coding RNA Ontology : A Comprehensive Resource for the Unification of Non-Coding RNA Biology.Huang Jingshan, Eilbeck Karen, Barry Smith, A. Blake Judith, Dou Dejing, Huang Weili, A. Natale Darren, Ruttenberg Alan, Huan Jun & T. Zimmermann Michael - 2016 - Journal of Biomedical Semantics 7 (1).
    In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...)
    Download  
     
    Export citation  
     
    Bookmark  
  14. Practical Knowledge: Outlines of a Theory of Traditions and Skills.J. C. Nyíri & Barry Smith (eds.) - 1988 - Croom Helm.
    A series of papers on different aspects of practical knowledge by Roderick Chisholm, Rudolf Haller, J. C. Nyiri, Eva Picardi, Joachim Schulte Roger Scruton, Barry Smith and Johan Wrede.
    Download  
    Translate
     
     
    Export citation  
     
    Bookmark   4 citations  
  15. A Product Life Cycle Ontology for Additive Manufacturing.Munira Mohd Ali, Rahul Rai, J. Neil Otte & Barry Smith - 2019 - Computers in Industry 105:191-203.
    The manufacturing industry is evolving rapidly, becoming more complex, more interconnected, and more geographically distributed. Competitive pressure and diversity of consumer demand are driving manufacturing companies to rely more and more on improved knowledge management practices. As a result, multiple software systems are being created to support the integration of data across the product life cycle. Unfortunately, these systems manifest a low degree of interoperability, and this creates problems, for instance when different enterprises or different branches of an enterprise interact. (...)
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  16. Interoperability of Disparate Engineering Domain Ontologies Using Basic Formal Ontology.Thomas J. Hagedorn, Barry Smith, Sundar Krishnamurty & Ian R. Grosse - 2019 - Journal of Engineering Design 31.
    As engineering applications require management of ever larger volumes of data, ontologies offer the potential to capture, manage, and augment data with the capability for automated reasoning and semantic querying. Unfortunately, considerable barriers hinder wider deployment of ontologies in engineering. Key among these is lack of a shared top-level ontology to unify and organise disparate aspects of the field and coordinate co-development of orthogonal ontologies. As a result, many engineering ontologies are limited to their scope, and functionally difficult to extend (...)
    Download  
     
    Export citation  
     
    Bookmark  
  17. The Connectionist Mind: A Study of Hayekian Psychology.Barry Smith - 1997 - In Stephen F. Frowen (ed.), Hayek: Economist and Social Philosopher: A Critical Retrospect. London: St. Martin's Press. pp. 9-29.
    In his book The Sensory Order, Hayek anticipates many of the central ideas behind what we now call the connectionist paradigm, and develops on this basis a theory of the workings of the human mind that extends the thinking of Hume and Mach. He shows that the idea of neural networks is can be applied not only in psychology and neurology but also in the sphere of economics. For the mind, from the perspective of The Sensory Order, is a dynamic, (...)
    Download  
     
    Export citation  
     
    Bookmark   5 citations  
  18.  23
    Dwa Oblicza Idealizmu: Lask a Husserl.Karl Schuhmann & Barry Smith - 2002 - In Andrjez J. Noras & Dariusz Kubok (eds.), Miedzy Kantyzmem a Neokantyzmem. Katowice: Wydawnictwo Uniwersyteto Slaskiego. pp. 130-156.
    Neo-Kantianism is common conceived as a philosophy ‘from above’, excelling in speculative constructions – as opposed to the attitude of patient description which is exemplified by the phenomenological turn ‘to the things themselves’. When we study the work of Emil Lask in its relation to that of Husserl and the phenomenologists, however, and when we examine the influences moving in both directions, then we discover that this idea of a radical opposition is misconceived. Lask himself was influenced especially by Husserl’s (...)
    Download  
    Translate
     
     
    Export citation  
     
    Bookmark  
  19.  52
    Foundation for a Realist Ontology of Cognitive Processes.David Kasmier, David Limbaugh & Barry Smith - 2019 - In Proceedings of the International Conference on Biomedical Ontology (ICBO), University at Buffalo, NY.
    What follows is a first step towards an ontology of conscious mental processes. We provide a theoretical foundation and characterization of conscious mental processes based on a realist theory of intentionality and using BFO as our top-level ontology. We distinguish three components of intentional mental process: character, directedness, and objective referent, and describe several features of the process character and directedness significant to defining and classifying mental processes. We arrive at the definition of representational mental process as a process that (...)
    Download  
     
    Export citation  
     
    Bookmark  
  20.  58
    A First-Order Logic Formalization of the Industrial Ontology Foundry Signature Using Basic Formal Ontology.Barry Smith, Farhad Ameri, Hyunmin Cheong, Dimitris Kiritsis, Dusan Sormaz, Chris Will & J. Neil Otte - 2019 - In Proceedings of the Joint Ontology Workshops (JOWO), Graz.
    Basic Formal Ontology (BFO) is a top-level ontology used in hundreds of active projects in scientific and other domains. BFO has been selected to serve as top-level ontology in the Industrial Ontologies Foundry (IOF), an initiative to create a suite of ontologies to support digital manufacturing on the part of representatives from a number of branches of the advanced manufacturing industries. We here present a first draft set of axioms and definitions of an IOF upper ontology descending from BFO. The (...)
    Download  
     
    Export citation  
     
    Bookmark  
  21. A Generalised Lottery Paradox for Infinite Probability Spaces.Martin Smith - 2010 - British Journal for the Philosophy of Science 61 (4):821-831.
    Many epistemologists have responded to the lottery paradox by proposing formal rules according to which high probability defeasibly warrants acceptance. Douven and Williamson present an ingenious argument purporting to show that such rules invariably trivialise, in that they reduce to the claim that a probability of 1 warrants acceptance. Douven and Williamson’s argument does, however, rest upon significant assumptions – amongst them a relatively strong structural assumption to the effect that the underlying probability space is both finite and uniform. In (...)
    Download  
     
    Export citation  
     
    Bookmark   12 citations  
  22. Flow, Code and Stock: A Note on Deleuze's Political Philosophy.Daniel W. Smith - 2011 - Deleuze and Guatarri Studies 5 (Suppl):36-55.
    In Anti-Oedipus, Deleuze and Guattari claim that a general theory of society must be a generalised theory of flows. This is hardly a straightforward claim, and this paper attempts to examine the grounds for it. Why should socio-political theory be based on a theory of flows rather than, say, a theory of the social contract, or a theory of the State, or the questions of legitimation or revolution, or numerous other possible candidates? The concept of flow (and the related notions (...)
    Download  
     
    Export citation  
     
    Bookmark  
  23.  79
    Ontological Realism: A Methodology for Coordinated Evolution of Scientific Ontologies.Barry Smith & Werner Ceusters - 2010 - Applied Ontology 5 (3):139-188.
    Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...)
    Download  
     
    Export citation  
     
    Bookmark   25 citations  
  24.  76
    A Theory of Granular Partitions.Thomas Bittner & Barry Smith - 2003 - In M. Duckham, M. F. Goodchild & M. F. Worboys (eds.), Foundations of Geographic Information Science. London: Taylor & Francis. pp. 117-151.
    We have a variety of different ways of dividing up, classifying, mapping, sorting and listing the objects in reality. The theory of granular partitions presented here seeks to provide a general and unified basis for understanding such phenomena in formal terms that is more realistic than existing alternatives. Our theory has two orthogonal parts: the first is a theory of classification; it provides an account of partitions as cells and subcells; the second is a theory of reference or intentionality; it (...)
    Download  
     
    Export citation  
     
    Bookmark   39 citations  
  25. Measuring the Consequences of Rules: Holly M. Smith.Holly M. Smith - 2010 - Utilitas 22 (4):413-433.
    Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism, while Michael Ridge advocates variable-rate rule-utilitarianism. I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two fatal (...)
    Download  
     
    Export citation  
     
    Bookmark   11 citations  
  26. The Cost of Treating Knowledge as a Mental State.Martin Smith - forthcoming - In A. Carter, E. Gordon & B. Jarvis (eds.), Knowledge First, Approaches to Epistemology and Mind. Oxford University Press.
    My concern in this paper is with the claim that knowledge is a mental state – a claim that Williamson places front and centre in Knowledge and Its Limits. While I am not by any means convinced that the claim is false, I do think it carries certain costs that have not been widely appreciated. One source of resistance to this claim derives from internalism about the mental – the view, roughly speaking, that one’s mental states are determined by one’s (...)
    Download  
     
    Export citation  
     
    Bookmark  
  27.  87
    Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain.Barry Smith, Waclaw Kusnierczyk, Daniel Schober, & Werner Ceusters - 2006 - In Proceedings of KR-MED, CEUR, vol. 222. pp. 57-65.
    Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance a (...)
    Download  
    Translate
     
     
    Export citation  
     
    Bookmark   27 citations  
  28.  68
    Review of Harald Delius, Self-Awareness: A Semantical Inquiry. [REVIEW]Barry Smith - 1985 - Philosophy and Phenomenological Research 46:170--173.
    The thesis of Delius's book is that statements of self-awareness such as "I am aware that I see a cat" possess what he calls 'Cartesian characteristics' of indubitability or absolute self-evidence. He argues that this is the case in virtue of the fact that such statements are not about anything independent of themselves. The book is described as a 'semantical inquiry', but it is not by any means a contribution to the philosophy of language of the predictable sort. Statements of (...)
    Download  
     
    Export citation  
     
    Bookmark  
  29. On the Application of Formal Principles to Life Science Data: A Case Study in the Gene Ontology.Jacob Köhler, Anand Kumar & Barry Smith - 2004 - In Proceedings of DILS 2004 (Data Integration in the Life Sciences), (Lecture Notes in Bioinformatics 2994). Berlin: Springer. pp. 79-94.
    Formal principles governing best practices in classification and definition have for too long been neglected in the construction of biomedical ontologies, in ways which have important negative consequences for data integration and ontology alignment. We argue that the use of such principles in ontology construction can serve as a valuable tool in error-detection and also in supporting reliable manual curation. We argue also that such principles are a prerequisite for the successful application of advanced data integration techniques such as ontology-based (...)
    Download  
     
    Export citation  
     
    Bookmark   23 citations  
  30.  96
    Mereotopology: A Theory of Parts and Boundaries.Barry Smith - 1996 - Data and Knowledge Engineering 20 (3):287–303.
    The paper is a contribution to formal ontology. It seeks to use topological means in order to derive ontological laws pertaining to the boundaries and interiors of wholes, to relations of contact and connectedness, to the concepts of surface, point, neighbourhood, and so on. The basis of the theory is mereology, the formal theory of part and whole, a theory which is shown to have a number of advantages, for ontological purposes, over standard treatments of topology in set-theoretic terms. One (...)
    Download  
     
    Export citation  
     
    Bookmark   46 citations  
  31. Ontology: Towards a New Synthesis.Barry Smith & Chris Welty - 2001 - In Formal Ontology in Information Systems. New York: ACM Press.
    This introduction to the second international conference on Formal Ontology and Information Systems presents a brief history of ontology as a discipline spanning the boundaries of philosophy and information science. We sketch some of the reasons for the growth of ontology in the information science field, and offer a preliminary stocktaking of how the term ‘ontology’ is currently used. We conclude by suggesting some grounds for optimism as concerns the future collaboration between philosophical ontologists and information scientists.
    Download  
     
    Export citation  
     
    Bookmark   2 citations  
  32. Kafka and Brentano: A Study in Descriptive Psychology.Barry Smith - 1981 - In Structure and Gestalt: Philosophy and Literature in Austria-Hungary and Her Successor States. Amsterdam: John Benjamins. pp. 113-144.
    There is a narrow thread in the vast literature on Kafka which pertains to Kafka’s knowledge of philosophy, and more precisely to Kafka’s use in his fictional writings of some of the main ideas of Franz Brentano. Kafka attended courses in philosophy at the Charles University given by Brentano’s students Anton Marty and Christian von Ehrenfels, and was for several years a member of a discussion-group organized by orthodox adherents of the Brentanian philosophy in Prague. The present essay summarizes what (...)
    Download  
     
    Export citation  
     
    Bookmark   9 citations  
  33. Development of a Manufacturing Ontology for Functionally Graded Materials.Francesco Furini, Rahul Rai, Barry Smith, Georgio Colombo & Venkat Krovi - 2016 - In Proceedings of International Design Engineering Technical Conferences & Computers and Information in Engineering Conference (IDETC/CIE).
    The development of manufacturing technologies for new materials involves the generation of a large and continually evolving volume of information. The analysis, integration and management of such large volumes of data, typically stored in multiple independently developed databases, creates significant challenges for practitioners. There is a critical need especially for open-sharing of data pertaining to engineering design which together with effective decision support tools can enable innovation. We believe that ontology applied to engineering (OE) represents a viable strategy for the (...)
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  34. A Unified Theory of Truth and Reference.Barry Smith & Berit Brogaard - 2000 - Logique Et Analyse 43 (169-170):49–93.
    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. (...)
    Download  
     
    Export citation  
     
    Bookmark   30 citations  
  35. Negative Findings in Electronic Health Records and Biomedical Ontologies: A Realist Approach.Werner Ceusters, Peter Elkin & Barry Smith - 2007 - International Journal of Medical Informatics 76 (3):S326-S333.
    PURPOSE—A substantial fraction of the observations made by clinicians and entered into patient records are expressed by means of negation or by using terms which contain negative qualifiers (as in “absence of pulse” or “surgical procedure not performed”). This seems at first sight to present problems for ontologies, terminologies and data repositories that adhere to a realist view and thus reject any reference to putative non-existing entities. Basic Formal Ontology (BFO) and Referent Tracking (RT) are examples of such paradigms. The (...)
    Download  
     
    Export citation  
     
    Bookmark   7 citations  
  36. A Relational Theory of the Act.Kevin Mulligan & Barry Smith - 1986 - Topoi 5 (2):115-130.
    ‘What is characteristic of every mental activity’, according to Brentano, is ‘the reference to something as an object. In this respect every mental activity seems to be something relational.’ But what sort of a relation, if any, is our cognitive access to the world? This question – which we shall call Brentano’s question – throws a new light on many of the traditional problems of epistemology. The paper defends a view of perceptual acts as real relations of a subject to (...)
    Download  
     
    Export citation  
     
    Bookmark   26 citations  
  37.  76
    Foundations for a Realist Ontology of Mental Disease.Werner Ceusters & Barry Smith - 2010 - Journal of Biomedical Semantics 1 (10):1-23.
    While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the patient. (...)
    Download  
     
    Export citation  
     
    Bookmark   11 citations  
  38.  99
    On Drawing Lines on a Map.Barry Smith - 1995 - In A. U. Frank, W. Kuhn & D. M. Mark (eds.), Spatial Information Theory: Proceedings of COSIT '95. New York: Springer. pp. 475-484.
    The paper is an exercise in descriptive ontology, with specific applications to problems in the geographical sphere. It presents a general typology of spatial boundaries, based in particular on an opposition between bona fide or physical boundaries on the one hand, and fiat or human-demarcation-induced boundaries on the other. Cross-cutting this opposition are further oppositions in the realm of boundaries, for example between: crisp and indeterminate, complete and incomplete, enduring and transient, symmetrical and asymmetrical. The resulting typology generates a corresponding (...)
    Download  
     
    Export citation  
     
    Bookmark   29 citations  
  39. Biomedical Imaging Ontologies: A Survey and Proposal for Future Work.Barry Smith, Sivaram Arabandi, Mathias Brochhausen, Michael Calhoun, Paolo Ciccarese, Scott Doyle, Bernard Gibaud, Ilya Goldberg, Charles E. Kahn Jr, James Overton, John Tomaszewski & Metin Gurcan - 2015 - Journal of Pathology Informatics 6 (37):37.
    Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This (...)
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  40. What Particulars Are Referred to in EHR Data? A Case Study in Integrating Referent Tracking Into an Electronic Health Record Application.Ron Rudnicki, Werner Ceusters, Shaid Manzoo & Barry Smith - 2007 - In Proceedings of the Annual Symposium of the American Medical Informatics Association, Chicago, IL. Washington, DC: AMIA. pp. 630-634.
    Referent Tracking (RT) advocates the use of instance unique identifiers to refer to the entities comprising the subject matter of patient health records. RT promises many benefits to those who use health record data to improve patient care. To further the adoption of the paradigm we provide an illustration of how data from an EHR application needs to be decomposed in order to make it accord with the tenets of RT. We describe the ontological principles on which this decomposition is (...)
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  41. A Realism-Based Approach to the Evolution of Biomedical Ontologies.Barry Smith - 2006 - In Proceedings of the Annual AMIA Symposium. Washington, DC: American Medical Informatics Association. pp. 121-125.
    We present a novel methodology for calculating the improvements obtained in successive versions of biomedical ontologies. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to those that (...)
    Download  
     
    Export citation  
     
    Bookmark   12 citations  
  42. Joint Doctrine Ontology: A Benchmark for Military Information Systems Interoperability.Peter Morosoff, Ron Rudnicki, Jason Bryant, Robert Farrell & Barry Smith - 2015 - In Semantic Technology for Intelligence, Defense and Security (STIDS). CEUR vol. 1325. pp. 2-9.
    When the U.S. conducts warfare, elements of a force are drawn from different services and work together as a single team to accomplish an assigned mission. To achieve such unified action, it is necessary that the doctrines governing the actions of members of specific services be both consistent with and subservient to joint Doctrine. Because warfighting today increasingly involves not only live forces but also automated systems, unified action requires that information technology that is used in joint warfare must be (...)
    Download  
     
    Export citation  
     
    Bookmark  
  43.  50
    Pieces of a Theory.Barry Smith & Kevin Mulligan - 1982 - In Parts and Moments: Studies in Logic and Formal Ontology. Munich: Philosophia Verlag. pp. 15-109.
    A survey of theories of part, whole and dependence from Aristotle to the Gestalt psychologists, with special attention to Husserl’s Third Logical Investigation “On the Theory of Parts and Wholes”.
    Download  
     
    Export citation  
     
    Bookmark   36 citations  
  44. A Course in Metaphilosophy for Undergraduates.Renée Smith - 2017 - Teaching Philosophy 40 (1):57-85.
    This paper describes an undergraduate course in metaphilosophy for philosophy majors and argues that there are four potential benefits to students; namely that doing metaphilosophy allows students to draw their own conclusions about what philosophy is, develops students’ metacognitive skills to promote learning, establishes students as members of the philosophical community, and disposes students to live lives that reflect their philosophical education. It describes issues of transparency of course design and the particulars of the course, including course content, and provides (...)
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  45.  62
    The Ontology-Epistemology Divide: A Case Study in Medical Terminology.OIivier Bodenreider, Barry Smith & Anita Burgun - 2004 - In Achille Varzi & Laure Vieu (eds.), Formal Ontology in Information Systems. Proceedings of the Third International Conference (FOIS 2004). IOS Press.
    Medical terminology collects and organizes the many different kinds of terms employed in the biomedical domain both by practitioners and also in the course of biomedical research. In addition to serving as labels for biomedical classes, these names reflect the organizational principles of biomedical vocabularies and ontologies. Some names represent invariant features (classes, universals) of biomedical reality (i.e., they are a matter for ontology). Other names, however, convey also how this reality is perceived, measured, and understood by health professionals (i.e., (...)
    Download  
    Translate
     
     
    Export citation  
     
    Bookmark   13 citations  
  46. Saliva Ontology: An Ontology-Based Framework for a Salivaomics Knowledge Base.Jiye Ai, Barry Smith & David Wong - 2010 - BMC Bioinformatics 11 (1):302.
    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-based controlled vocabulary of terms and relations dedicated to the salivaomics (...)
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  47. Controlled Vocabularies in Bioinformatics: A Case Study in the Gene Ontology.Barry Smith & Anand Kumar - 2004 - Drug Discovery Today: Biosilico 2 (6):246-252.
    The automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is rapidly acquiring the (...)
    Download  
     
    Export citation  
     
    Bookmark   3 citations  
  48.  46
    Investigating Subsumption in DL-Based Terminologies: A Case Study in SNOMED CT.Olivier Bodenreider, Barry Smith, Anand Kumar & Anita Burgun - 2004 - In Proceedings of the First International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2004). pp. 12-20.
    Formalisms 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. Our major results are: 31% of (...)
    Download  
     
    Export citation  
     
    Bookmark   9 citations  
  49. Scepticism by a Thousand Cuts.Martin Smith - 2016 - International Journal for the Study of Skepticism 6 (1):44-52.
    _ Source: _Page Count 9 Global sceptical arguments seek to undermine vast swathes of our putative knowledge by deploying hypotheses that posit massive deception or error. Local sceptical arguments seek to undermine just a small region of putative knowledge, using hypotheses that posit deception or error of a more mundane kind. Those epistemologists who have devised anti-sceptical strategies have tended to have global sceptical arguments firmly in their sights. I argue here that local sceptical arguments, while less dramatic, ultimately pose (...)
    Download  
     
    Export citation  
     
    Bookmark  
  50. A Multi-INT Semantic Reasoning Framework for Intelligence Analysis Support.Janssen Terry, Basik Herbert, Dean Mike & Barry Smith - 2010 - In L. Obrst, Terry Janssen & W. Ceusters (eds.), Ontologies and Semantic Technologies for the Intelligence Community. Amsterdam, The Netherlands: IOS Press. pp. 57-69.
    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.
    Download  
     
    Export citation  
     
    Bookmark  
1 — 50 / 999