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  1. Oncology Ontology in the NCI Thesaurus.Anand Kumar & Barry Smith - 2005 - Artificial Intelligence in Medicine:213-220.
    The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of the kinds of (...)
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  • Open Biomedical Ontologies Applied to Prostate Cancer.James A. Overton, Cesare Romagnoli & Rethy Chhem - 2011 - Applied Ontology 6 (1):35-51.
  • 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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  • Representing the NCI Thesaurus in OWL DL: Modeling Tools Help Modeling Languages.Natalya F. Noy, Sherri de Coronado, Harold Solbrig, Gilberto Fragoso, Frank W. Hartel & Mark A. Musen - 2008 - Applied Ontology 3 (3):173-190.
  • 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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  • Special Issue: Biomedical Ontology in Action.Olivier Bodenreider - 2009 - Applied Ontology 4 (1):1-4.
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  • Ontologies and Terminologies: Continuum or Dichotomy?Natalia Grabar, Thierry Hamon & Olivier Bodenreider - 2012 - Applied Ontology 7 (4):375-386.
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  • Switching Partners: Dancing with the Ontological Engineers.Werner Ceusters & Barry Smith - 2011 - In Thomas Batcherer & Roderick Coover (eds.), Switching Codes: Thinking through Digital Technology in the Humanities and the Arts. University of Chicago Press. pp. 103--124.
    Ontologies are today being applied in almost every field to support the alignment and retrieval of data of distributed provenance. Here we focus on new ontological work on dance and on related cultural phenomena belonging to what UNESCO calls the “intangible heritage.” Currently data and information about dance, including video data, are stored in an uncontrolled variety of ad hoc ways. This serves not only to prevent retrieval, comparison and analysis of the data, but may also impinge on our ability (...)
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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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  • Applications of the ACGT Master Ontology on Cancer.Mathias Brochhausen, Gabriele Weiler, Luis Martín, Cristian Cocos, Holger Stenzhorn, Norbert Graf, Martin Dörr, Manolis Tsiknakis & Barry Smith - 2008 - In R. Meersman & P. Herrero (eds.), Proceedings of 4th International IFIP Workshop On Semantic Web and Web Semantics (OTM 2008: Workshops), LNCS 5333. pp. 1046–1055.
    In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the ontology within (...)
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  • Review of Sabina Leonelli’s Data-Centric Biology: A Philosophical Study. [REVIEW]Beckett Sterner - 2018 - Philosophy of Science 85 (3):540-550.
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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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  • Establishing and Harmonizing Ontologies in an Interdisciplinary Health Care and Clinical Research Environment.Barry Smith & Mathias Brochhausen - 2008 - Studies in Health, Technology and Informatics 134:219-234.
    Ontologies are being ever more commonly used in biomedical informatics and we provide a survey of some of these uses, and of the relations between ontologies and other terminology resources. In order for ontologies to become truly useful, two objectives must be met. First, ways must be found for the transparent evaluation of ontologies. Second, existing ontologies need to be harmonised. We argue that one key foundation for both ontology evaluation and harmonisation is the adoption of a realist paradigm in (...)
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  • Effects of Guideline-Based Training on the Quality of Formal Ontologies: A Randomized Controlled Trial.M. Boeker, L. Jansen, J. Röhl, N. Grewe, D. Seddig-Raufie & S. Schulz - 2013 - PLoS ONE 1.
    BACKGROUND -/- The importance of ontologies in the biomedical domain is generally recognized. However, their quality is often too poor for large-scale use in critical applications, at least partially due to insufficient training of ontology developers. -/- OBJECTIVE -/- To show the efficacy of guideline-based ontology development training on the performance of ontology developers. The hypothesis was that students who received training on top-level ontologies and design patterns perform better than those who only received training in the basic principles of (...)
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