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A realism-based approach to the evolution of biomedical ontologies

In Proceedings of the Annual AMIA Symposium. Washington, DC: American Medical Informatics Association. pp. 121-125 (2006)

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  1. 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. (...)
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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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  • Health as a Clinic-Epidemiological Concept.Marco Antonio Azevedo - 2015 - Journal of Evaluation in Clinical Practice 21 (3):365-373.
    I propose a clinic-epidemiological concept of health as the best description of what physicians actually think about health within medical practice. Its aim is to be an alternative to the best approach in the philosophy of medicine about health, Christopher Boorse’s biostatistical theory. Contrary to Boorse’s ‘theoretical’ approach, I propose to take health as a practical clinical concept. In the first two parts of the paper, I will present my complaints against Boorse’s view that health is a theoretical concept, a (...)
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  • Modelling Empty Representations: The Case of Computational Models of Hallucination.Marcin Miłkowski - 2017 - In Gordana Dodig-Crnkovic & Raffaela Giovagnoli (eds.), Representation and Reality in Humans, Other Living Organisms and Intelligent Machines. Springer, Cham. pp. 17--32.
    I argue that there are no plausible non-representational explanations of episodes of hallucination. To make the discussion more specific, I focus on visual hallucinations in Charles Bonnet syndrome. I claim that the character of such hallucinatory experiences cannot be explained away non-representationally, for they cannot be taken as simple failures of cognizing or as failures of contact with external reality—such failures being the only genuinely non-representational explanations of hallucinations and cognitive errors in general. I briefly introduce a recent computational model (...)
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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 Benefits of Realism: A Realist Logic with Applications.Barry Smith - 2008 - In Katherine Munn & Barry Smith (eds.), Applied Ontology: An Introduction. Ontos. pp. 109-124.
    We propose a formalization of a realist ontology using first order logic with identity and allowing quantification over terms representing both individuals and universals. In addition to identity, the ontology includes also relational predicates such as subtype, instantiation, parthood, location, and inherence. Inspired in part by Davidson’s treatment of events, the ontology includes also various relations linking events to their participants and to the times at which they occur.
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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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  • 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 Auditing (ETA). We describe (...)
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  • Aboutness: Towards Foundations for the Information Artifact Ontology.Werner Ceusters & Barry Smith - 2015 - In Proceedings of the Sixth International Conference on Biomedical Ontology (ICBO). CEUR vol. 1515. pp. 1-5.
    The Information Artifact Ontology (IAO) was created to serve as a domain‐neutral resource for the representation of types of information content entities (ICEs) such as documents, data‐bases, and digital im‐ages. We identify a series of problems with the current version of the IAO and suggest solutions designed to advance our understanding of the relations between ICEs and associated cognitive representations in the minds of human subjects. This requires embedding IAO in a larger framework of ontologies, including most importantly the Mental (...)
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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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  • 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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  • From Encyclopedia to Ontology: Toward Dynamic Representation of the Discipline of Philosophy.Cameron Buckner, Mathias Niepert & Colin Allen - 2011 - Synthese 182 (2):205-233.
    The application of digital humanities techniques to philosophy is changing the way scholars approach the discipline. This paper seeks to open a discussion about the difficulties, methods, opportunities, and dangers of creating and utilizing a formal representation of the discipline of philosophy. We review our current project, the Indiana Philosophy Ontology (InPhO) project, which uses a combination of automated methods and expert feedback to create a dynamic computational ontology for the discipline of philosophy. We argue that our distributed, expert-based approach (...)
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  • Consolidating SNOMED CT's Ontological Commitment.Stefan Schulz, Ronald Cornet & Kent Spackman - 2011 - Applied Ontology 6 (1):1-11.
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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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  • 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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  • Would SNOMED CT Benefit From Realism-Based Ontology Evolution?Werner Ceusters, Kent Spackman & Barry Smith - 2007 - AMIA Annual Symposium Proceedings 2007:105-109.
    If SNOMED CT is to serve as a biomedical reference terminology, then steps must be taken to ensure comparability of information formulated using successive versions. New releases are therefore shipped with a history mechanism. We assessed the adequacy of this mechanism for its treatment of the distinction between changes occurring on the side of entities in reality and changes in our understanding thereof. We found that these two types are only partially distinguished and that a more detailed study is required (...)
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