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  1. What to Consider About Events: A Survey on the Ontology of Occurrents.Fabrício Henrique Rodrigues & Mara Abel - forthcoming - Applied Ontology:1-36.
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  • Layers: A New Approach to Locating Objects in Space.Maureen Donnelly & Barry Smith - 2003 - In W. Kuhn M. F. Worboys & S. Timpf (eds.), Spatial Information Theory: Foundations of Geographic Informa­tion Science. Springer. pp. 50-65.
    Standard theories in mereotopology focus on relations of parthood and connection among spatial or spatio-temporal regions. Objects or processes which might be located in such regions are not normally directly treated in such theories. At best, they are simulated via appeal to distributions of attributes across the regions occupied or by functions from times to regions. The present paper offers a richer framework, in which it is possible to represent directly the relations between entities of various types at different levels, (...)
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  • 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 these are (...)
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  • Persistence and Ontological Pluralism.Pierre Grenon & Barry Smith - 2008 - In Christian Kanzian (ed.), Persistence. Ontos. pp. 33-48.
    We aim to provide the ontological grounds for an adequate account of persistence. We defend a perspectivalist, or moderate pluralist, position, according to which some aspects of reality can be accounted for in ontological terms only via partial and mutually complementary ontologies, each one of which captures some relevant aspect of reality. Our thesis here is that this is precisely the sort of ontological account that is needed for the understanding of persistence, specifically an account involving two independent ontologies, one (...)
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  • Bradley's Reductio of Relations and Formal Ontological Relations.Jani Hakkarainen & Markku Keinänen - 2016 - In Hemmo Laiho & Arto Repo (eds.), DE NATURA RERUM - Scripta in honorem professoris Olli Koistinen sexagesimum annum complentis. University of Turku. pp. 246-261.
    In this paper, we argue that formal ontological relations avoid Bradley's reductio of relations, including his famous relation regress.
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  • The Ontological Form of Tropes - Refuting Douglas Ehring’s Main Argument Against Standard Trope Nominalism.Jani Hakkarainen & Markku Keinänen - 2017 - Philosophia 45 (2):647-658.
    According to standard trope nominalism, there are simple tropes that do not have parts or multiply distinct aspects. Douglas Ehring’s reductio ad absurdum against this standard view concludes that there are no simple tropes. In this paper, we provide a response to Ehring defending the standard view. Ehring’s argument may be refuted by (1) distinguishing the ontological form of tropes from their contribution to the ontological content of the world, and (2) construing tropes as having primitive identity. At the same (...)
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  • Applied Ontology: An Introduction.Katherine Munn & Barry Smith (eds.) - 2008 - Frankfurt: ontos.
    Ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. This is exactly what information scientists aim for in creating structured, automated representations, called 'ontologies,' for managing information in fields such as science, government, industry, and healthcare. Currently, these systems are designed in a variety of different ways, so they cannot share data with one another. They are often idiosyncratically structured, accessible only to those who (...)
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  • Interdisciplinary Perspectives on the Development, Integration and Application of Cognitive Ontologies.Janna Hastings, Gwen Alexandra Frishkoff, Barry Smith, Mark Jensen, Russell Poldrack, Jessica Turner, Jane Lomax, Anita Bandrowski, Fahim Imam, Jessica A. Turner & Maryann E. Martone - 2014 - Frontiers in Neuroinformatics 8 (62):1-7.
    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 mark-up and interpretation of multi-modal data. Finally, Challenge (...)
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  • Speech Acts and Medical Records: The Ontological Nexus.Lowell Vizenor & Barry Smith - 2004 - In Proceedings of the International Joint Meeting EuroMISE.
    Despite the recent advances in information and communication technology that have increased our ability to store and circulate information, the task of ensuring that the right sorts of information gets to the right sorts of people remains. We argue that the many efforts underway to develop efficient means for sharing information across healthcare systems and organizations would benefit from a careful analysis of human action in healthcare organizations. This in turn requires that the management of information and knowledge within healthcare (...)
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  • Molecular Interactions. On the Ambiguity of Ordinary Statements in Biomedical Literature.Stefan Schulz & Ludger Jansen - 2009 - Applied Ontology (4):21-34.
    Statements about the behavior of biochemical entities (e.g., about the interaction between two proteins) abound in the literature on molecular biology and are increasingly becoming the targets of information extraction and text mining techniques. We show that an accurate analysis of the semantics of such statements reveals a number of ambiguities that have to be taken into account in the practice of biomedical ontology engineering: Such statements can not only be understood as event reporting statements, but also as ascriptions of (...)
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  • Bridging the Gap Between Medical and Bioinformatics: An Ontological Case Study in Colon Carcinoma.Anand Kumar, Yum Lina Yip, Barry Smith & Pierre Grenon - 2006 - Computers in Biology and Medicine 36 (7):694--711.
    Ontological principles are needed in order to bridge the gap between medical and biological information in a robust and computable fashion. This is essential in order to draw inferences across the levels of granularity which span medicine and biology, an example of which include the understanding of the roles of tumor markers in the development and progress of carcinoma. Such information integration is also important for the integration of genomics information with the information contained in the electronic patient records in (...)
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  • 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 maximize reasoning (...)
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  • 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, and dispositions, (...)
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  • Interdyscyplinarne Perspektywy Rozwoju, Integracji I Zastosowań Ontologii Poznawczych.Joanna Hastings, Gwen A. Frishkoff, Barry Smith, Mark Jensen, Russell A. Poldrack, Jane Lomax, Anita Bandrowski, Fahim Imam, Jessica A. Turner & Maryann E. Martone - 2016 - Avant: Trends in Interdisciplinary Studies 7 (3):101-117.
    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 mark-up and interpretation of multi-modal data. Finally, Challenge (...)
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  • Causality and the Ontology of Disease.Robert J. Rovetto & Riichiro Mizoguchi - 2015 - Applied Ontology 10 (2):79-105.
    The goal of this paper is two-fold: first, to emphasize causality in disease ontology and knowledge representation, presenting a general and cursory discussion of causality and causal chains; and second, to clarify and develop the River Flow Model of Diseases (RFM). The RFM is an ontological account of disease, representing the causal structure of pathology. It applies general knowledge of causality using the concept of causal chains. The river analogy of disease is explained, formal descriptions are offered, and the RFM (...)
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  • A Spatio-Temporal Ontology for Geographic Information Integration.Thomas Bittner & Barry Smith - 2009 - International Journal for Geographical Information Science 23 (6):765-798.
    This paper presents an axiomatic formalization of a theory of top-level relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the sub-universal relation among universals and the parthood relation among individuals, as well as cross-categorial relations such as instantiation and membership. We show that an adequate understanding of the formal properties of such relations – in particular their behavior with respect to time – is critical for (...)
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  • The Ontology of Processes and Functions: A Study of the International Classification of Functioning, Disability and Health.Anand Kumar & Barry Smith - 2007 - In Sharing Knowledge through the ICF: 13th Annual North American WHO Collaborating Center Conference on the ICF, Niagara Falls, June 7, 2007. North American WHO Collaborating Center.
    The International Classification of Functioning, Disability and Health provides a classification of human bodily functions, which, while exhibiting non-conformance to many formal ontological principles, provides an insight into which basic functions such a classification should include. Its evaluation is an important first step towards such an adequate ontology of this domain. Presented at the 13th Annual North American WHO Collaborating Center Conference on the ICF, 2007.
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  • Introduction: What is Ontology For.Katherine Munn - 2008 - In Munn Katherine & Smith Barry (eds.), Applied Ontology: An Introduction. Walter de Gruyter. pp. 7-19.
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  • DE NATURA RERUM - Scripta in Honorem Professoris Olli Koistinen Sexagesimum Annum Complentis.Hemmo Laiho & Arto Repo (eds.) - 2016 - University of Turku.
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  • Lmn-2 Interacts with Elf-2. On the Meaning of Common Statements in Biomedical Literature.Stefan Schulz & Ludger Jansen - 2006 - In KR-MED 2006 – Biomedical Ontology in Action. Proceedings of the 2nd International Workshop on Formal Knowledge Representation. MD. pp. 37-45.
    Statements about the behavior of biological entities, e.g. about the interaction between two proteins, abound in the literature on molecular biology and are increasingly becoming the targets of information extraction and text mining techniques. We show that an accurate analysis of the semantics of such statements reveals a number of ambiguities that is necessary to take into account in the practice of biomedical ontology engineering. Several concurring formalizations are proposed. Emphasis is laid on the discussion of biological dispositions.
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  • Temporal Phenomenology in Roentgen Semiotics.Robert M. Cantor - 2010 - Semiotica 2010 (182):69-79.
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  • On the Role of Thematic Roles in a Historical Event Ontology.Anna Goy, Diego Magro & Marco Rovera - 2018 - Applied Ontology 13 (1):19-39.
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  • Formal Ontology of Space, Time, and Physical Entities in Classical Mechanics.Thomas Bittner - 2018 - Applied Ontology 13 (2):135-179.
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  • Foundations of an Ontology of Philosophy.Pierre Grenon & Barry Smith - 2011 - Synthese 182 (2):185-204.
    We describe an ontology of philosophy that is designed to aid navigation through philosophical literature, including literature in the form of encyclopedia articles and textbooks and in both printed and digital forms. The ontology is designed also to serve integration and structuring of data pertaining to the philosophical literature, and in the long term also to support reasoning about the provenance and contents of such literature, by providing a representation of the philosophical domain that is oriented around what philosophical literature (...)
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