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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. 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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  • 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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  • Electronic Healthcare Ontologies : Philosophy, the Real World and IT Structures.Martin Berzell - 2010 - Dissertation, Linköping University
    The thesis investigates how the notion of ‘ontology’ has been used in the field of medical informatics and knowledge representation. Partly to investigate what an ‘ontology’ can be said to represent and what requirements we can have on a good ‘ontology’. The author studies the already existing medical terminologies and ‘ontologies’ to elucidate what theories they are based on. The terminological theories of Eugen Wüster and his legacy in medical informatics are studied. It is noted that terminological theories handling linguistic (...)
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  • 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 (...)
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  • Ontological Realism: Methodology or Misdirection?Gary H. Merrill - 2010 - Applied Ontology 5 (2):79-108.
    In a series of papers over a period of several years Barry Smith andWerner Ceusters have offered a number of cogent criticisms of historical approaches to creating, maintaining, and applying biomedical terminologies and ontologies. And they have urged the adoption of what they refer to as a “realism-based” approach. Indeed, at times they insist that the realism-based approach not only offers clear advantages and a well-founded methodological basis for ontology development and evaluation, but that such a realist perspective is in (...)
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  • Coordination Instead of Consensus Classification: Insights From Systematics for Bio-Ontologies.Beckett Sterner, Joeri Witteveen & Nico Franz - forthcoming - History and Philosophy of the Life Sciences.
    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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  • 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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  • 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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  • The Philosophy of Computer Science.Raymond Turner - 2013 - Stanford Encyclopedia of Philosophy.
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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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  • Barry Smith an Sich.Gerald J. Erion & Gloria Zúñiga Y. Postigo (eds.) - 2017 - Cosmos + Taxis.
    Festschrift in Honor of Barry Smith on the occasion of his 65th Birthday. Published as issue 4:4 of the journal Cosmos + Taxis: Studies in Emergent Order and Organization. Includes contributions by Wolfgang Grassl, Nicola Guarino, John T. Kearns, Rudolf Lüthe, Luc Schneider, Peter Simons, Wojciech Żełaniec, and Jan Woleński.
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  • Signs and Meanings.Barry Smith - 2009 - In Peer Bundgaard & Frederik Stjernfelt (eds.), Signs and Meanings: Five Questions. Automatic Press. pp. 199--206.
    A background piece on the role of ontology in technology research, focusing especially on the use-mention confusion.
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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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  • 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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  • Four Rules for Classifying Social Entities.Ludger Jansen - forthcoming - In Ruth Hagengruber (ed.), Philosophy’s Relevance for Information Science.
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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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  • Aristotle’s Categories.Ludger Jansen - 2007 - Topoi 26 (1):153-158.
    Being an "untimely review", this paper reviews Aristotle's 'Categories' as if they were published today, in the era of computerised information, where categorisation becomes more and more essential for information retrieval. I suggest a systematic ordering of Aristotle's list of categories and argue that Aristotle's discussion of ontological dependency and his focus on concrete entities are still a source of new insight and can indeed be read as a contribution to the emerging field of applied ontology and ontological engineering.
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  • Relationships and Relata in Ontologies and Thesauri: Differences and Similarities.Daniel Kless, Simon Milton & Edmund Kazmierczak - 2012 - Applied Ontology 7 (4):401-428.
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  • 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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  • 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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  • 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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  • 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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  • 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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