Results for 'Formal Ontology'

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  1. A Formal Ontology of Artefacts.Gilles Kassel - 2010 - Applied Ontology 5 (3):223-246.
    This article presents a formal ontology which accounts for the general nature of artefacts. The objective is to help structure application ontologies in areas where specific artefacts are present - in other words, virtually any area of activity. The conceptualization relies on recent philosophical and psychological research on artefacts, having resulted in a largely consensual theoretical basis. Furthermore, this ontology of artefacts extends the foundational DOLCE ontology and supplements its axiomatization. The conceptual primitives are as follows: (...)
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  2. Formal Ontology for Natural Language Processing and the Integration of Biomedical Databases.Jonathan Simon, James M. Fielding, Mariana C. Dos Santos & Barry Smith - 2005 - International Journal of Medical Informatics 75 (3-4):224-231.
    The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end r®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this project we (...)
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  3. Formal Ontology, Common Sense, and Cognitive Science.Barry Smith - 1995 - International Journal of Human-Computer Studies 43 (5-6):641–667.
    Common sense is on the one hand a certain set of processes of natural cognition - of speaking, reasoning, seeing, and so on. On the other hand common sense is a system of beliefs (of folk physics, folk psychology and so on). Over against both of these is the world of common sense, the world of objects to which the processes of natural cognition and the corresponding belief-contents standardly relate. What are the structures of this world? How does the scientific (...)
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  4. Functions in Basic Formal Ontology.Andrew D. Spear, Werner Ceusters & Barry Smith - 2016 - Applied ontology 11 (2):103-128.
    The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of (...)
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  5. Framework for Formal Ontology.Barry Smith & Kevin Mulligan - 1983 - Topoi 2 (1):73-85.
    The discussions which follow rest on a distinction, first expounded by Husserl, between formal logic and formal ontology. The former concerns itself with (formal) meaning-structures; the latter with formal structures amongst objects and their parts. The paper attempts to show how, when formal ontological considerations are brought into play, contemporary extensionalist theories of part and whole, and above all the mereology of Leniewski, can be generalised to embrace not only relations between concrete objects and (...)
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  6. Logic and Formal Ontology.Barry Smith - 2000 - Manuscrito 23 (2):275-323.
    Revised version of chapter in J. N. Mohanty and W. McKenna (eds.), Husserl’s Phenomenology: A Textbook, Lanham: University Press of America, 1989, 29–67. -/- Logic for Husserl is a science of science, a science of what all sciences have in common in their modes of validation. Thus logic deals with universal laws relating to truth, to deduction, to verification and falsification, and with laws relating to theory as such, and to what makes for theoretical unity, both on the side of (...)
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  7. Basic Concepts of Formal Ontology.Barry Smith - 1998 - In Nicola Guarino (ed.), Formal Ontology in Information Systems. IOS Press. pp. 19-28.
    The term ‘formal ontology’ was first used by the philosopher Edmund Husserl in his Logical Investigations to signify the study of those formal structures and relations – above all relations of part and whole – which are exemplified in the subject-matters of the different material sciences. We follow Husserl in presenting the basic concepts of formal ontology as falling into three groups: the theory of part and whole, the theory of dependence, and the theory of (...)
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  8. An Essay in Formal Ontology.Barry Smith - 1978 - Grazer Philosophische Studien 6 (1):39-62.
    As conceived by analytic philosophers ontology consists in the application of the methods of mathematical logic to the analysis of ontological discourse. As conceived by realist philosophers such as Meinong and the early Husserl, Reinach and Ingarden, it consists in the investigation of the forms of entities of various types. The suggestion is that formal methods be employed by phenomenological ontologists, and that phenomenological insights may contribute to the construction of adequate formal-ontological languages. The paper sketches an (...)
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  9.  97
    The Formal Ontology of Boundaries.Barry Smith & Achille C. Varzi - 1997 - Electronic Journal of Analytic Philosophy 5 (5).
    Revised version published as Barry Smith and Achille Varzi, “Fiat and Bona Fide Boundaries”, Philosophy and Phenomenological Research, 60: 2 (March 2000), 401–420.
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  10. An Axiomatisation of Basic Formal Ontology with Projection Functions.Kerry Trentelman, Alan Ruttenberg & Barry Smith - 2010 - In Kerry Taylor (ed.), Advances in Ontologies, Proceedings of the Sixth Australasian Ontology Workshop. University of Adelaide. pp. 71-80.
    This paper proposes a reformulation of the treatment of boundaries, at parts and aggregates of entities in Basic Formal Ontology. These are currently treated as mutually exclusive, which is inadequate for biological representation since some entities may simultaneously be at parts, boundaries and/or aggregates. We introduce functions which map entities to their boundaries, at parts or aggregations. We make use of time, space and spacetime projection functions which, along the way, allow us to develop a simple temporal theory.
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  11. On Classifying Material Entities in Basic Formal Ontology.Barry Smith - 2012 - In Interdisciplinary Ontology: Proceedings of the Third Interdisciplinary Ontology Meeting. Keio University Press. pp. 1-13.
    Basic Formal Ontology was created in 2002 as an upper-level ontology to support the creation of consistent lower-level ontologies, initially in the subdomains of biomedical research, now also in other areas, including defense and security. BFO is currently undergoing revisions in preparation for the release of BFO version 2.0. We summarize some of the proposed revisions in what follows, focusing on BFO’s treatment of material entities, and specifically of the category object.
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  12. Function, Role and Disposition in Basic Formal Ontology.Robert Arp & Barry Smith - 2008 - Proceedings of Bio-Ontologies Workshop, Intelligent Systems for Molecular Biology (ISMB), Toronto.
    Numerous research groups are now utilizing Basic Formal Ontology as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three existing BFO subcategories of realizable entity, namely function, role, and disposition. It proposes one further sub-category of tendency, and considers the merits of recognizing two sub-categories of function for domain ontologies, namely, artifactual and biological function. The motivation is to help advance the coherent ontological treatment of functions, roles, (...)
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  13. Parts and Moments. Studies in Logic and Formal Ontology.Barry Smith (ed.) - 1982 - Philosophia Verlag.
    A collection of material on Husserl's Logical Investigations, and specifically on Husserl's formal theory of parts, wholes and dependence and its influence in ontology, logic and psychology. Includes translations of classic works by Adolf Reinach and Eugenie Ginsberg, as well as original contributions by Wolfgang Künne, Kevin Mulligan, Gilbert Null, Barry Smith, Peter M. Simons, Roger A. Simons and Dallas Willard. Documents work on Husserl's ontology arising out of early meetings of the Seminar for Austro-German Philosophy.
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  14. Logic and Formal Ontology.B. Smith - 1989 - In J. N. Mohanty & W. McKenna (eds.), Husserl’s Phenomenology: A Textbook. Lanham: University Press of America. pp. 29-67.
    The current resurgence of interest in cognition and in the nature of cognitive processing has brought with it also a renewed interest in the early work of Husserl, which contains one of the most sustained attempts to come to grips with the problems of logic from a cognitive point of view. Logic, for Husserl, is a theory of science; but it is a theory which takes seriously the idea that scientific theories are constituted by the mental acts of cognitive subjects. (...)
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  15. Formal Ontology as an Operative Tool in the Theories of the Objects of the Life-World.Horacio Banega - 2012 - Symposium 16 (2):64-88.
    Formal ontology as it is presented in Husserl`s Third Logical Investigation can be interpreted as a fundamental tool to describe objects in a formal sense. It is presented one of the main sources: chapter five of Carl Stumpf`s Ûber den psycholoogischen Ursprung der Raumovorstellung (1873), and then it is described how Husserlian Formal Ontology is applied in Fifth Logical Investigation. Finally, it is applied to dramatic structures, in the spirit of Roman Ingarden.
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  16.  90
    Formal Ontology for Biomedical Knowledge Systems Integration.J. M. Fielding, J. Simon & Barry Smith - 2004 - Proceedings of Euromise:12-17.
    The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology will greatly benefit software application ontologies. To this end LinKBase®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this, (...)
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  17. Basic Formal Ontology for Bioinformatics.Barry Smith, Anand Kumar & Thomas Bittner - 2005 - IFOMIS Reports.
    Two senses of ‘ontology’ can be distinguished in the current literature. First is the sense favored by information scientists, who view ontologies as software implementations designed to capture in some formal way the consensus conceptualization shared by those working on information systems or databases in a given domain. [Gruber 1993] Second is the sense favored by philosophers, who regard ontologies as theories of different types of entities (objects, processes, relations, functions) [Smith 2003]. Where information systems ontologists seek to (...)
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  18. Normalizing Medical Ontologies Using Basic Formal Ontology.Thomas Bittner & Barry Smith - 2004 - In K. Versorgung & V. Forschung (eds.), Ubiquitäre Information (Proceedings of GMDS 2004). Videel OHG. pp. 199-201.
    Description Logics are nowadays widely accepted as formalisms which provide reasoning facilities which allow us to discover inconsistencies in ontologies in an automatic fashion. Where ontologies are developed in modular fashion, they allow changes in one module to propogated through the system of ontologies automatically in a way which helps to maintain consistency and stability. For this feature to be utilized effectively, however, requires that domain ontologies be represented in a normalized form.
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  19. 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 (...)
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  20. 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 (...) descending from BFO. The axiomatization is designed to capture the meanings of terms commonly used in manufacturing and is designed to serve as starting point for the construction of the IOF ontology suite. (shrink)
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  21. Applying the Realism-Based Ontology-Versioning Method for Tracking Changes in the Basic Formal Ontology.Selja Seppälä, Barry Smith & Werner Ceusters - 2014 - In P. Garbacz & O. Kutz (eds.), Formal Ontology in Information Systems (FOIS 2014). IOS Press. pp. 227-240.
    Changes in an upper level ontology have obvious conse-quences for the domain ontologies that use it at lower levels. It is therefore crucial to document the changes made between successive versions of ontologies of this kind. We describe and apply a method for tracking, explaining and measuring changes between successive versions of upper level ontologies such as the Basic Formal Ontology (BFO). The proposed change-tracking method extends earlier work on Realism-Based Ontology Versioning (RBOV) and Evolutionary Terminology (...)
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  22. Wholistic Reference, Truth-Values, Universes of Discourse, and Formal Ontology: Tréplica to Oswaldo Chateaubriand.John Corcoran - 2005 - Manuscrito 28 (1):143-167.
    ABSTRACT: In its strongest unqualified form, the principle of wholistic reference is that in any given discourse, each proposition refers to the whole universe of that discourse, regardless of how limited the referents of its non-logical or content terms. According to this principle every proposition of number theory, even an equation such as "5 + 7 = 12", refers not only to the individual numbers that it happens to mention but to the whole universe of numbers. This principle, its history, (...)
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  23. Facts, Formal Objects and Ontology.Kevin Mulligan - 2009 - Swiss Philosophical Preprints.
    What is a fact ? Are there such things ?
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  24.  80
    An Overview of the BFO - Basic Formal Ontology - and Its Applicability for Satellite Systems.Adolfo Americano Brandão & Geilson Loureiro - 2020 - In Franciele Braga Machado Tullio & Lucio Mauro Braga Machado (eds.), Ampliação e Aprofundamento de Conhecimentos nas Áreas das Engenharias,. Ponta Grossa, Brazil: Atena Editora. pp. 30-38.
    This work aims to present an overview of the top-level ontology BFO - Basic Formal Ontology - and its applicability for Satellite Systems. As an upper level ontology, the BFO was designed to be extended, providing the basis for the specification of detailed representational artifacts about scientific information domains. These aspects and the challenges of satellite systems complexity and large size compose a suitable scenario for the creation of a specialized dialect to improve efficiency and accuracy (...)
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  25. 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 (...)
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  26. Biodynamic Ontology: Applying BFO in the Biomedical Domain.Barry Smith, Pierre Grenon & Louis Goldberg - 2004 - Studies in Health and Technology Informatics 102:20–38.
    Current approaches to formal representation in biomedicine are characterized by their focus on either the static or the dynamic aspects of biological reality. We here outline a theory that combines both perspectives and at the same time tackles the by no means trivial issue of their coherent integration. Our position is that a good ontology must be capable of accounting for reality both synchronically (as it exists at a time) and diachronically (as it unfolds through time), but that (...)
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  27. The Ontology for Biomedical Investigations.Anita Bandrowski, Ryan Brinkman, Mathias Brochhausen, Matthew H. Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Frank Gibson, Alejandra Gonzalez-Beltran, Melissa A. Haendel, Yongqun He, Mervi Heiskanen, Tina Hernandez-Boussard, Mark Jensen, Yu Lin, Allyson L. Lister, Phillip Lord, James Malone, Elisabetta Manduchi, Monnie McGee, Norman Morrison, James A. Overton, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Daniel Schober, Barry Smith, Larisa N. Soldatova, Christian J. Stoeckert, Chris F. Taylor, Carlo Torniai, Jessica A. Turner, Randi Vita, Patricia L. Whetzel & Jie Zheng - 2016 - PLoS ONE 11 (4):e0154556.
    The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic (...)
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  28. Ontology-Based Fusion of Sensor Data and Natural Language.Erik Thomsen & Barry Smith - 2018 - Applied Ontology 13 (4):295-333.
    We describe a prototype ontology-driven information system (ODIS) that exploits what we call Portion of Reality (POR) representations. The system takes both sensor data and natural language text as inputs and composes on this basis logically structured POR assertions. The goal of our prototype is to represent both natural language and sensor data within a single framework that is able to support both axiomatic reasoning and computation. In addition, the framework should be capable of discovering and representing new kinds (...)
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  29. Strengths and Limitations of Formal Ontologies in the Biomedical Domain.Barry Smith - 2009 - Electronic Journal of Communication, Information and Innovation in Health 3 (1):31-45.
    We propose a typology of representational artifacts for health care and life sciences domains and associate this typology with different kinds of formal ontology and logic, drawing conclusions as to the strengths and limitations for ontology in a description logics framework. The four types of domain representation we consider are: (i) lexico-semantic representation, (ii) representation of types of entities, (iii) representations of background knowledge, and (iv) representation of individuals. We advocate a clear distinction of the four kinds (...)
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  30. Ontology and the Logistic Analysis of Reality.Barry Smith - 1993 - In Nicola Guarino & Roberto Poli (eds.), Proceedings of the International Workshop on Formal Ontology in Conceptual Analysis and Knowledge Representation. Italian National Research Council. pp. 51-68.
    I shall attempt in what follows to show how mereology, taken together with certain topological notions, can yield the basis for future investigations in formal ontology. I shall attempt to show also how the mereological framework here advanced can allow the direct and natural formulation of a series of theses – for example pertaining to the concept of boundary – which can be formulated only indirectly (if at all) in set-theoretic terms.
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  31. Duality and Ontology.Baptiste Le Bihan & James Read - 2018 - Philosophy Compass 13 (12):e12555.
    A ‘duality’ is a formal mapping between the spaces of solutions of two empirically equivalent theories. In recent times, dualities have been found to be pervasive in string theory and quantum field theory. Naïvely interpreted, duality-related theories appear to make very different ontological claims about the world—differing in e.g. space-time structure, fundamental ontology, and mereological structure. In light of this, duality-related theories raise questions familiar from discussions of underdetermination in the philosophy of science: in the presence of dual (...)
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  32. 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 (...)
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  33. The Ontology of Collective Action.Kirk Ludwig - 2014 - In Sara Chant Frank Hindriks & Gerhard Preyer (eds.), From Individual to Collective Intentionality: New Essays. Oxford University Press.
    What is the ontology of collective action? I have in mind three connected questions. 1. Do the truth conditions of action sentences about groups require there to be group agents over and above individual agents? 2. Is there a difference, in this connection, between action sentences about informal groups that use plural noun phrases, such as ‘We pushed the car’ and ‘The women left the party early’, and action sentences about formal or institutional groups that use singular noun (...)
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  34. 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 (...)
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  35. Parts: A Study in Ontology.Peter Simons - 1987 - Oxford University Press.
    Although the relationship of part to whole is one of the most fundamental there is, this is the first full-length study of this key concept. Showing that mereology, or the formal theory of part and whole, is essential to ontology, Simons surveys and critiques previous theories--especially the standard extensional view--and proposes a new account that encompasses both temporal and modal considerations. Simons's revised theory not only allows him to offer fresh solutions to long-standing problems, but also has far-reaching (...)
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  36. Classifying Processes: An Essay in Applied Ontology.Barry Smith - 2012 - Ratio 25 (4):463-488.
    We begin by describing recent developments in the burgeoning discipline of applied ontology, focusing especially on the ways ontologies are providing a means for the consistent representation of scientific data. We then introduce Basic Formal Ontology (BFO), a top-level ontology that is serving as domain-neutral framework for the development of lower level ontologies in many specialist disciplines, above all in biology and medicine. BFO is a bicategorial ontology, embracing both three-dimensionalist (continuant) and four-dimensionalist (occurrent) perspectives (...)
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  37. 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 (...)
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  38. Ontology with Human Subjects Testing: An Empirical Investigation of Geographic Categories.Barry Smith & David M. Mark - 1998 - American Journal of Economics and Sociology 58 (2):245–272.
    Ontology, since Aristotle, has been conceived as a sort of highly general physics, a science of the types of entities in reality, of the objects, properties, categories and relations which make up the world. At the same time ontology has been for some two thousand years a speculative enterprise. It has rested methodologically on introspection and on the construction and analysis of elaborate world-models and of abstract formal-ontological theories. In the work of Quine and others this ontological (...)
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  39. SNAP and SPAN: Towards Dynamic Spatial Ontology.Pierre Grenon & Barry Smith - 2004 - Spatial Cognition and Computation 4 (1):69–103.
    We propose a modular ontology of the dynamic features of reality. This amounts, on the one hand, to a purely spatial ontology supporting snapshot views of the world at successive instants of time and, on the other hand, to a purely spatiotemporal ontology of change and process. We argue that dynamic spatial ontology must combine these two distinct types of inventory of the entities and relationships in reality, and we provide characterizations of spatiotemporal reasoning in the (...)
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  40.  89
    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 (...)
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  41. The Ontology of Impossible Worlds.David A. Vander Laan - 1997 - Notre Dame Journal of Formal Logic 38 (4):597-620.
    The best arguments for possible worlds as states of affairs furnish us with equally good arguments for impossible worlds of the same sort. I argue for a theory of impossible worlds on which the impossible worlds correspond to maximal inconsistent classes of propositions. Three objections are rejected. In the final part of the paper, I present a menu of impossible worlds and explore some of their interesting formal properties.
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  42. Ontology for the Intelligence Analyst.Barry Smith - 2012 - CrossTalk 14 (Nov/Dec):18-25.
    As available intelligence data and information expand in both quantity and variety, new techniques must be deployed for search and analytics. One technique involves the semantic enhancement of data through the creation of what are called ‘ontologies’ or ‘controlled vocabularies.’ When multiple different bodies of heterogeneous data are tagged by means of terms from common ontologies, then these data become linked together in ways which allow more effective retrieval and integration. We describe a simple case study to show how these (...)
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  43.  44
    Applied Ontology: Focusing on Content.Nicola Guarino & Mark A. Musen - 2005 - Applied ontology 1 (1):1-5.
    In a world that is overflowing with journals and other outlets for scientific publication, the appearance of any new periodical requires some justification. There are already more journals than we can read and more conferences than we can attend. In the case of applied Ontology, we believe that the creation of anew journal not only is completely justifiable, it is downright exciting. For too long, workers in computer science have assumed that content comes for free. “Theory” in computer science (...)
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  44. A Formal Theory of Substances, Qualities, and Universals.Fabian Neuhaus, Pierre Grenon & Barry Smith - 2004 - In Achille Varzi & Laure Vieu (eds.), Formal Ontology in Information Systems. Proceedings of the Third International Conference. IOS Press.
    One of the tasks of ontology in information science is to support the classification of entities according to their kinds and qualities. We hold that to realize this task as far as entities such as material objects are concerned we need to distinguish four kinds of entities: substance particulars, quality particulars, substance universals, and quality universals. These form, so to speak, an ontological square. We present a formal theory of classification based on this idea, including both a semantics (...)
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  45.  86
    Formal Ontologies of Space and Time. IFOMIS Report.Thomas Bittner & Barry Smith - 2003 - In IFOMIS Report.
    We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes (occurrents) and the enduring entities (continuants) that participate in such processes. For this purpose we distinguish between meta-ontology and token ontologies. Token ontologies fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and result in distinct though compatible systems of categories. The meta-ontological level then describes the relationships between the different token ontologies. (...)
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  46. Beyond Concepts: Ontology as Reality Representation.Barry Smith - 2004 - In Achille C. Varzi & Laure Vieu (eds.), Formal Ontology in Information Systems (FOIS). pp. 1-12.
    The present essay is devoted to the application of ontology in support of research in the natural sciences. It defends the thesis that ontologies developed for such purposes should be understood as having as their subject matter, not concepts, but rather the universals and particulars which exist in reality and are captured in scientific laws. We outline the benefits of a view along these lines by showing how it yields rigorous formal definitions of the foundational relations used in (...)
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  47. 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 (...)
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  48. 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 (...)
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  49. Ontology-Based Error Detection in SNOMED-CT.Werner Ceusters, Barry Smith, Anand Kumar & Christoffel Dhaen - 2004 - Proceedings of Medinfo 2004:482-6.
    Quality assurance in large terminologies is a difficult issue. We present two algorithms that can help terminology developers and users to identify potential mistakes. We demon­strate the methodology by outlining the different types of mistakes that are found when the algorithms are applied to SNOMED-CT. On the basis of the results, we argue that both formal logical and linguistic tools should be used in the development and quality-assurance process of large terminologies.
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  50. Infectious Disease Ontology.Lindsay Grey Cowell & Barry Smith - 2009 - In Infectious Disease Informatics. New York: Springer New York. pp. 373-395.
    Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and (...)
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