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Beyond concepts: Ontology as reality representation

In Achille C. Varzi & Laure Vieu (eds.), Formal Ontology in Information Systems (FOIS). pp. 1-12 (2004)

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  1. 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 (...)
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  • Alternatives to Realist Consensus in Bio-Ontologies: Taxonomic Classification as a Basis for Data Discovery and Integration.Beckett Sterner, Joeri Witteveen & Nico Franz - unknown
    Big data is opening new angles on old questions about scientific progress. Is scientific knowledge cumulative? If yes, how does it make progress? In the life sciences, what we call the Consensus Principle has dominated the design of data discovery and integration tools: the design of a formal classificatory system for expressing a body of data should be grounded in consensus. Based on current approaches in biomedicine and systematic biology, we formulate and compare three types of the Consensus Principle: realist, (...)
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  • Referent Tracking for Digital Rights Management.Werner Ceusters & Barry Smith - 2007 - International Journal of Metadata, Semantics and Ontologies 2 (1):45-53.
    Digital Rights Management (DRM) covers the description, identification, trading, protection, monitoring and tracking of all forms of rights over both tangible and intangible assets. The Digital Object Identifier (DOI) system provides a framework for the persistent identification of entities involved in this domain. Although the system has been very well designed to manage object identifiers, some important questions relating to the creation and assignment of identifiers are left open. The paradigm of a Referent Tracking System (RTS) recently advanced in the (...)
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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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  • Referent Tracking for Corporate Memories.Werner Ceusters & Barry Smith - 2007 - In Peter Rittgen (ed.), Handbook of Ontologies for Business Interaction. Idea Group Publishing. pp. 34-46.
    For corporate memory and enterprise ontology systems to be maximally useful, they must be freed from certain barriers placed around them by traditional knowledge management paradigms. This means, above all, that they must mirror more faithfully those portions of reality which are salient to the workings of the enterprise, including the changes that occur with the passage of time. The purpose of this chapter is to demonstrate how theories based on philosophical realism can contribute to this objective. We discuss how (...)
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  • 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 (...)
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  • Referent Tracking and its Applications.Werner Ceusters & Barry Smith - 2007 - In Proceedings of the Workshop WWW2007 Workshop i3: Identity, Identifiers, Identification (Workshop on Entity-Centric Approaches to Information and Knowledge Management on the Web), Banff, Canada. CEUR.
    Referent tracking (RT) is a new paradigm, based on unique identification, for representing and keeping track of particulars. It was first introduced to support the entry and retrieval of data in electronic health records (EHRs). Its purpose is to avoid the ambiguity that arises when statements in an EHR refer to disorders or other entities on the side of the patient exclusively by means of compound descriptions utilizing general terms such as ‘pimple on nose’ or ‘small left breast tumor’. In (...)
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  • An Ontology-Based Methodology for the Migration of Biomedical Terminologies to Electronic Health Records.Barry Smith & Werner Ceusters - 2005 - In Proceedings of AMIA Symposium 2005, Washington DC,. Washington, DC: AMIA. pp. 704-708.
    Biomedical terminologies are focused on what is general, Electronic Health Records (EHRs) on what is particular, and it is commonly assumed that the step from the one to the other is unproblematic. We argue that this is not so, and that, if the EHR of the future is to fulfill its promise, then the foundations of both EHR architectures and biomedical terminologies need to be reconceived. We accordingly describe a new framework for the treatment of both generals and particulars in (...)
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  • Aproximaciones a la Ontología Del Arte [Approaches to the Ontology of Art].Paulo Vélez León - 2006 - Analysis. Documentos de Investigación 9 (1):1-21.
    El presenta trabajo describe y caracteriza de manera breve y concisa lo que podría ser una ontología del arte. En la primera sección se presentan las dificultades actuales, así como las nociones y preguntas principales de la ontología. En la sección segunda, se bosquejan las definiciones y caracterizaciones actuales de la ontología, se hace especial hincapié, en la ontología aplicada. En la tercera, cuarta y quinta sección se caracteriza y configura lo que podría ser una ontología del arte, se evidencian (...)
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  • The Philosophy of Computer Science.Raymond Turner - 2013 - Stanford Encyclopedia of Philosophy.
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  • Continua in Biological Systems.Ingvar Johansson - 2007 - The Monist 90 (4):499-522.
    We defend the fundamental ontological-pragmatic principle that where there are continua in reality science is often forced to make partly fiat terminological delimitations. In particular, this principle applies when it comes to describing biological organisms, their parts, properties, and relations. Human-made fiat delimitations are indispensable at the level of both individuals and the natural kinds which they instantiate. The kinds of pragmatically based ‘fiatness’ that we describe can create incompatibilities and lack of interoperability even between properly designed ontologies, if not (...)
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  • Blockchain Design and Modelling.Nicolae Sfetcu - manuscript
    Ontology engineering, along with semantic Web technologies, allow the semantic development and modeling of the operational flow required for blockchain design. The semantic Web, in accordance with W3C, "provides a common framework that allows data to be shared and reused across application, enterprise, and community boundaries" and can be seen as an integrator for various content, applications and information systems. The most widely used blockchain modelling system, by abstract representation, description and definition of structure, processes, information and resources, is the (...)
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  • Concepts and Synonymy in the UMLS Metathesaurus.Gary H. Merrill - 2009 - Journal of Biomedical Discovery and Collaboration 4 (7).
    This paper advances a detailed exploration of the complex relationships among terms, concepts, and synonymy in the UMLS Metathesaurus, and proposes the study and understanding of the Metathesaurus from a model-theoretic perspective. Initial sections provide the background and motivation for such an approach, and a careful informal treatment of these notions is offered as a context and basis for the formal analysis. What emerges from this is a set of puzzles and confusions in the Metathesaurus and its literature pertaining to (...)
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  • From Concepts to Clinical Reality: An Essay on the Benchmarking of Biomedical Terminologies.Barry Smith - 2006 - Journal of Biomedical Informatics 39 (3):288-298.
    It is only by fixing on agreed meanings of terms in biomedical terminologies that we will be in a position to achieve that accumulation and integration of knowledge that is indispensable to progress at the frontiers of biomedicine. Standardly, the goal of fixing meanings is seen as being realized through the alignment of terms on what are called ‘concepts’. Part I addresses three versions of the concept-based approach – by Cimino, by Wüster, and by Campbell and associates – and surveys (...)
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  • Strategies for Referent Tracking in Electronic Health Records.Werner Ceusters & Barry Smith - 2006 - Journal of Biomedical Informatics 39 (3):362-378.
    The goal of referent tracking is to create an ever-growing pool of data relating to the entities existing in concrete spatiotemporal reality. In the context of Electronic Healthcare Records (EHRs) the relevant concrete entities are not only particular patients but also their parts, diseases, therapies, lesions, and so forth, insofar as these are salient to diagnosis and treatment. Within a referent tracking system, all such entities are referred to directly and explicitly, something which cannot be achieved when familiar concept-based systems (...)
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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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  • Against Fantology.Barry Smith - 2005 - In Johann C. Marek & Maria E. Reicher (eds.), Experience and Analysis. HPT&ÖBV. pp. 153-170.
    The analytical philosophy of the last hundred years has been heavily influenced by a doctrine to the effect that the key to the correct understanding of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of standard firstorder predicate logic. Here ‘F’ stands for what is general in reality and ‘a’ for what is individual. Hence “f(a)ntology”. Because predicate logic has exactly two syntactically different kinds of referring expressions—‘F’, ‘G’, ‘R’, etc., and ‘a’, ‘b’, (...)
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  • Aristotle’s Categories.Ludger Jansen - 2007 - Topoi 26 (1):153-158.
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  • Filosofia tehnologiei blockchain - Ontologii.Nicolae Sfetcu - manuscript
    Despre necesitatea şi utilitatea dezvoltării unei filosofii specifice tehnologiei blockchain, accentuând pe aspectele ontologice. După o Introducere în care evidenţiez principalele direcţii filosofice pentru această tehnologie emergentă, în Tehnologia blockchain explicitez modul de funcţionare al blockchain, punând în discuţie direcţiile ontologice de dezvoltare în Proiectarea şi Modelarea acestei tehnologii. Următoarea secţiune este dedicată principalei aplicaţii a tehnologiei blockchain, Bitcoin, cu implicaţiile sociale ale acestei criptovalute. Urmează o secţiune de Filosofie în care identific tehnologia blockchain cu conceptul de heterotopie dezvoltat de (...)
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  • Domain Modelling and NLP: Formal Ontologies? Lexica? Or a Bit of Both?Massimo Poesio - 2005 - Applied Ontology 1 (1):27-33.
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  • Legal Concepts as Inferential Nodes and Ontological Categories.Giovanni Sartor - 2009 - Artificial Intelligence and Law 17 (3):217-251.
    I shall compare two views of legal concepts: as nodes in inferential nets and as categories in an ontology (a conceptual architecture). Firstly, I shall introduce the inferential approach, consider its implications, and distinguish the mere possession of an inferentially defined concept from the belief in the concept’s applicability, which also involves the acceptance of the concept’s constitutive inferences. For making this distinction, the inferential and eliminative analysis of legal concepts proposed by Alf Ross will be connected to the views (...)
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  • Ontology, Ontologies, and Science.Gary H. Merrill - 2011 - Topoi (1):71-83.
    Philosophers frequently struggle with the relation of metaphysics to the everyday world, with its practical value, and with its relation to empirical science. This paper distinguishes several different models of the relation between philosophical ontology and applied (scientific) ontology that have been advanced in the history of philosopy. Adoption of a strong participation model for the philosophical ontologist in science is urged, and requirements and consequences of the participation model are explored. This approach provides both a principled view and justification (...)
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