62 found
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  1. Wüsteria.Barry Smith, Werner Ceusters & Rita Temmerman - 2005 - Studies in Health Technology and Informatics 116:647-652.
    The last two decades have seen considerable efforts directed towards making Electronic Health Records interoperable through improvements in medical ontologies, terminologies and coding systems. Unfortunately, these efforts have been hampered by a number of influential ideas inherited from the work of Eugen Wüster, the father of terminology standardization and the founder of ISO TC 37. We here survey Wüster’s ideas – which see terminology work as being focused on the classification of concepts in people’s minds – and we argue that (...)
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  2. Diagnostic Criteria for Temporomandibular Disorders (DC/TMD) for Clinical and Research Applications.Eric Schiffman, Richard Ohrbach, E. Truelove, Edmond Truelove, John Look, Gary Anderson, Werner Ceusters, Barry Smith & Others - 2014 - Journal of Oral and Facial Pain and Headache 28 (1):6-27.
    Aims: The Research Diagnostic Criteria for Temporomandi¬bular Disorders (RDC/TMD) Axis I diagnostic algorithms were demonstrated to be reliable but below target sensitivity and specificity. Empirical data supported Axis I algorithm revisions that were valid. Axis II instruments were shown to be both reliable and valid. An international consensus workshop was convened to obtain recommendations and finalization of new Axis I diagnostic algorithms and new Axis II instruments. Methods: A comprehensive search of published TMD diagnostic literature was followed by review and (...)
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  3.  92
    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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  4. The Evaluation of Ontologies: Toward Improved Semantic Interoperability.Leo Obrst, Werner Ceusters, Inderjeet Mani, Steve Ray & Barry Smith - 2006 - In Chris Baker & Kei H. Cheung (eds.), Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences. Springer. pp. 139-158.
    Recent years have seen rapid progress in the development of ontologies as semantic models intended to capture and represent aspects of the real world. There is, however, great variation in the quality of ontologies. If ontologies are to become progressively better in the future, more rigorously developed, and more appropriately compared, then a systematic discipline of ontology evaluation must be created to ensure quality of content and methodology. Systematic methods for ontology evaluation will take into account representation of individual ontologies, (...)
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  5.  82
    Malaria Diagnosis and the Plasmodium Life Cycle: The BFO Perspective.Werner Ceusters & Barry Smith - 2010 - In Interdisciplinary Ontology. Proceedings of the Third Interdisciplinary Ontology Meeting. Tokyo: Keio University Press. pp. 25-34.
    Definitive diagnosis of malaria requires the demonstration through laboratory tests of the presence within the patient of malaria parasites or their components. Since malaria parasites can be present even in the absence of malaria manifestations, and since symptoms of malaria can be manifested even in the absence of malaria parasites, malaria diagnosis raises important issues for the adequate understanding of disease, etiology and diagnosis. One approach to the resolution of these issues adopts a realist view, according to which the needed (...)
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  6. HL7 RIM: An Incoherent Standard.Barry Smith & Werner Ceusters - 2006 - Studies in Health Technology and Informatics 124 (Proceedings of MIE 2006):133–138.
    The Health Level 7 Reference Information Model (HL7 RIM) is lauded by its authors as ‘the foundation of healthcare interoperability’. Yet even after some 10 years of development work, the RIM is still subject to a variety of logical and ontological flaws which have placed severe obstacles in the way of those who are called upon to develop implementations. We offer evidence that these obstacles are insurmountable and that the time has come to abandon an unworkable paradigm.
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  7. Functions in Basic Formal Ontology.Andrew Spear, Werner Ceusters & Barry Smith - 2016 - Applied Ontology 11 (2):103-128.
    The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories identified (...)
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  8. Towards an Ontology of Pain.Barry Smith, Werner Ceusters, Louis J. Goldberg & Richard Ohrbach - 2011 - In Proceedings of the Conference on Ontology and Analytical Metaphysics. Keio University Press.
    We present an ontology of pain and of other pain-related phenomena, building on the definition of pain provided by the International Association for the Study of Pain (IASP). Our strategy is to identify an evolutionarily basic canonical pain phenomenon, involving unpleasant sensory and emotional experience based causally in localized tissue damage that is concordant with that experience. We then show how different variant cases of this canonical pain phenomenon can be distinguished, including pain that is elevated relative to peripheral trauma, (...)
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  9. 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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  10. 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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  11.  13
    Referent Tracking of Portions of Reality. Docket No. 1097.015A (USPA 2009055437).Werner Ceusters, Shahid Manzoor & Barry Smith - 2008 - In U.S. Patent Application. US Patent Office.
    Management of information is facilitated by unambiguously tracking portions of reality over time. To track the portions of reality, a referent tracking system is used. The referent tracking system is able to communicate with other tracking systems and/or tradition information systems. Errors in the referent tracking system are detected and corrected to maintain actual representations of the portions of reality.
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  12.  38
    The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration.Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J. Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J. Mungall, Neocles Leontis & Others - 2007 - Nature Biotechnology 25 (11):1251-1255.
    The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...)
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  13.  59
    Ontology-Based Error Detection in SNOMED-CT.Werner Ceusters, Barry Smith, Anand Kumar & Christoffel Dhaen - 2004 - Proceedings of Medinfo 2004:482-6.
    Quality assurance in large terminologies is a difficult issue. We present two algorithms that can help terminology developers and users to identify potential mistakes. We demon­strate the methodology by outlining the different types of mistakes that are found when the algorithms are applied to SNOMED-CT. On the basis of the results, we argue that both formal logical and linguistic tools should be used in the development and quality-assurance process of large terminologies.
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  14.  52
    Ontology and Medical Terminology: Why Description Logics Are Not Enough.Werner Ceusters, Barry Smith & Jim Flanagan - 2003 - In Proceedings of the Conference: Towards an Electronic Patient Record (TEPR 2003). Boston, MA: Medical Records Institute.
    Ontology is currently perceived as the solution of first resort for all problems related to biomedical terminology, and the use of description logics is seen as a minimal requirement on adequate ontology-based systems. Contrary to common conceptions, however, description logics alone are not able to prevent incorrect representations; this is because they do not come with a theory indicating what is computed by using them, just as classical arithmetic does not tell us anything about the entities that are added or (...)
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  15. The Emotion Ontology: Enabling Interdisciplinary Research in the Affective Sciences.Janna Hastings, Werner Ceusters, Barry Smith & Kevin Mulligan - 2011 - In M. Beigl, H. Christiansen, T. Roth-Berghofer, A. Kofod-Petersen, K. R. Coventry & H. R. Schmidtke (eds.), CONTEXT, The Seventh International and Interdisciplinary Conference on Modeling and Using Context. Springer. pp. 119--123.
    Affective science conducts interdisciplinary research into the emotions and other affective phenomena. Currently, such research is hampered by the lack of common definitions of terms used to describe, categorise and report both individual emotional experiences and the results of scientific investigations of such experiences. High quality ontologies provide formal definitions for types of entities in reality and for the relationships between such entities, definitions which can be used to disambiguate and unify data across different disciplines. Heretofore, there has been little (...)
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  16. Biomarkers in the Ontology for General Medical Science.Werner Ceusters & Barry Smith - 2015 - In Ronald Cornet (ed.), Digital Healthcare Empowering Europeans. IOS Press. pp. 155-159.
    Based on the Ontology for General Medical Science, we propose definitions for biomarkers of various types of. These definitions provide not only a complete formal representation of what biomarkers are according to the Institute of Medicine (IOM), but also remove the ambiguities and inconsistencies encountered in the documentation provided by the IOM.
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  17. Dispositions and Processes in the Emotion Ontology.Janna Hastings, Werner Ceusters, Barry Smith & Kevin Mulligan - 2011 - In Proceedings of the 2nd International Conference on Biomedical Ontology. CEUR Workshop Proceedings. pp. 71-78.
    Affective science conducts interdisciplinary research into the emotions and other affective phenomena. Currently, such research is hampered by the lack of common definitions of te rms used to describe, categorise and report both individual emotional experiences and the results of scientific investigations of such experiences. High quality ontologies provide formal definitions for types of entities in reality and for the relationships between such entities, definitions which can be used to disambiguate and unify data across different disciplines. Heretofore, there has been (...)
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  18. Towards Industrial Strength Philosophy: How Analytical Ontology Can Help Medical Informatics.Barry Smith & Werner Ceusters - 2003 - Interdisciplinary Science Reviews 28 (2):106–111.
    Initially the problems of data integration, for example in the field of medicine, were resolved in case by case fashion. Pairs of databases were cross-calibrated by hand, rather as if one were translating from French into Hebrew. As the numbers and complexity of database systems increased, the idea arose of streamlining these efforts by constructing one single benchmark taxonomy, as it were a central switchboard, into which all of the various classification systems would need to be translated only once. By (...)
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  19.  24
    Ontology-Assisted Database Integration to Support Natural Language Processing and Biomedical Data-Mining.Jean-Luc Verschelde, Marianna C. Santos, Tom Deray, Barry Smith & Werner Ceusters - 2004 - Journal of Integrative Bioinformatics. Repr. In: Yearbook of Bioinformatics , 39–48 1:1-10.
    Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes of (...)
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  20.  57
    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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  21.  22
    Mistakes in Medical Ontologies: Where Do They Come From and How Can They Be Detected?Werner Ceusters, Barry Smith, Anand Kumar & Christoffel Dhaen - 2004 - Studies in Health and Technology Informatics 102:145-164.
    We present the details of a methodology for quality assurance in large medical terminologies and describe three algorithms that can help terminology developers and users to identify potential mistakes. The methodology is based in part on linguistic criteria and in part on logical and ontological principles governing sound classifications. We conclude by outlining the results of applying the methodology in the form of a taxonomy different types of errors and potential errors detected in SNOMED-CT.
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  22. Ontological Theory for Ontological Engineering: Biomedical Systems Information Integration.James M. Fielding, Jonathan Simon, Werner Ceusters & Barry Smith - 2004 - In Proceedings of the Ninth International Conference on the Principles of Knowledge Representation and Reasoning. AMIA.
    Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...)
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  23. Referent Tracking for Command and Control Messaging Systems.Shahid Manzoor, Werner Ceusters & Barry Smith - 2009 - CEUR, Volume 555.
    The Joint Battle Management Language (JBML) is an XML-based language designed to allow Command and Control (C2) systems to interface easily with Modeling and Simulation (M&S) systems. While some of the XML-tags defined in this language correspond to types of entities that exist in reality, others are mere syntactic artifacts used to structure the messages themselves. Because these two kinds of tags are not formally distinguishable, JBML messages in effect confuse data with what the data represent. In this paper we (...)
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  24.  17
    Clinical Data Wrangling Using Ontological Realism and Referent Tracking.Werner Ceusters, Chiun Yu Hsu & Barry Smith - 2014 - In Proceedings of the Fifth International Conference on Biomedical Ontology (ICBO), Houston, 2014, (CEUR, 1327). pp. 27-32.
    Ontological realism aims at the development of high quality ontologies that faithfully represent what is general in reality and to use these ontologies to render heterogeneous data collections comparable. To achieve this second goal for clinical research datasets presupposes not merely (1) that the requisite ontologies already exist, but also (2) that the datasets in question are faithful to reality in the dual sense that (a) they denote only particulars and relationships between particulars that do in fact exist and (b) (...)
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  25.  18
    Using Ontology in Query Answering Systems: Scenarios, Requirements and Challenges.Werner Ceusters, Barry Smith & Maarten Van Mol - 2003 - In R. Bernardi & M. Moortgat (eds.), Questions and Answers: Theoretical and Applied Perspectives, Proceedings of the 2nd CoLogNET-Elsnet Symposium, December 2003. Amsterdam: pp. 5-15.
    Equipped with the ultimate query answering system, computers would finally be in a position to address all our information needs in a natural way. In this paper, we describe how Language and Computing nv (L&C), a developer of ontology-based natural language understanding systems for the healthcare domain, is working towards the ultimate Question Answering (QA) System for healthcare workers. L&C’s company strategy in this area is to design in a step-by-step fashion the essential components of such a system, each component (...)
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  26.  19
    Was Die Philosophische Ontologie Zur Biomedizinischen Informatik Beitragen Kann.Barry Smith, Dirk Siebert & Werner Ceusters - 2004 - Information: Wissenschaft Und Praxis 55 (3):143-146.
    Die biomedizinische Forschung hat ein Kommunikationsproblem. Um die Ergebnisse ihrer Arbeit darzustellen, greifen einzelne Forschergruppen auf unterschiedliche und oft inkompatible Terminologien zurück. Für den Fortschritt der modernen Biomedizin ist die Integration dieser Ergebnisse jedoch unabdingbar.
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  27.  18
    ARGOS Policy Brief on Semantic Interoperability.Dipak Kalra, Mark Musen, Barry Smith & Werner Ceusters - 2011 - Studies in Health Technology and Informatics 170 (1):1-15.
    Semantic interoperability requires the use of standards, not only for Electronic Health Record (EHR) data to be transferred and structurally mapped into a receiving repository, but also for the clinical content of the EHR to be interpreted in conformity with the original meanings intended by its authors. Accurate and complete clinical documentation, faithful to the patient’s situation, and interoperability between systems, require widespread and dependable access to published and maintained collections of coherent and quality-assured semantic resources, including models such as (...)
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  28. Wanting What We Don't Want to Want: Representing Addiction in Interoperable Bio-Ontologies.Janna Hastings, Nicolas Le Novère, Werner Ceusters, Kevin Mulligan & Barry Smith - 2012 - In Ronald Cornet & Robert Stevens (eds.), Proceeedings of the Third International Conference on Biomedical Ontology. CEUR. pp. 56-60.
    Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most pressing public health challenges. Primary research across multiple disciplines such as psychology, psychiatry, biology, neuroscience and pharmacology (...)
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  29.  46
    Annotating Affective Neuroscience Data with the Emotion Ontology.Janna Hastings, Werner Ceusters, Kevin Mulligan & Barry Smith - 2012 - In Third International Conference on Biomedical Ontology. ICBO. pp. 1-5.
    The Emotion Ontology is an ontology covering all aspects of emotional and affective mental functioning. It is being developed following the principles of the OBO Foundry and Ontological Realism. This means that in compiling the ontology, we emphasize the importance of the nature of the entities in reality that the ontology is describing. One of the ways in which realism-based ontologies are being successfully used within biomedical science is in the annotation of scientific research results in publicly available databases. Such (...)
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  30.  15
    Semantic Interoperability in Healthcare. State of the Art in the US. A Position Paper with Background Materials.Werner Ceusters & Barry Smith - 2010 - In European Union ARGOS Project: Transatlantic Observatory for Meeting Global Health Policy Challenges through ICT-Enabled Solution.
    Semantic interoperability can be defined as the ability of two or more computer systems to exchange information in such a way that the meaning of that information can be automatically interpreted by the receiving system accurately enough to produce useful results to the end users of both systems. Several activities are currently being performed by a variety of stakeholders to achieve semantic interoperability in healthcare. Many of these activities are not beneficial, because they place too great a focus on business (...)
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  31.  14
    The Significance of SNODENT.Louis Goldberg, Werner Ceusters, John Eisner & Barry Smith - 2005 - Medical Informatics Europe 2005: 737-742.
    SNODENT is a dental diagnostic vocabulary incompletely integrated in SNOMED-CT. Nevertheless, SNODENT could become the de facto standard for dental diagnostic coding. SNODENT's manageable size, the fact that it is administratively self-contained, and relates to a well-understood domain provides valuable opportunities to formulate and test, in controlled experiments, a series of hypothesis concerning diagnostic systems. Of particular interest are questions related to establishing appropriate quality assurance methods for its optimal level of detail in content, its ontological structure, its construction and (...)
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  32.  26
    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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  33.  47
    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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  34.  14
    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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  35.  14
    Ontology as the Core Discipline of Biomedical Informatics: Legacies of the Past and Recommendations for the Future Direction of Research.Barry Smith & Werner Ceusters - 2007 - In Gordana Dodig Crnkovic & Susan Stuart (eds.), Computation, Information, Cognition: The Nexus and the Liminal. Cambridge Scholars Publishing. pp. 104-122.
    The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on all occasions of use. In the (...)
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  36.  12
    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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  37.  12
    What Particulars Are Referred to in EHR Data? A Case Study in Integrating Referent Tracking Into an Electronic Health Record Application.Ron Rudnicki, Werner Ceusters, Shaid Manzoo & Barry Smith - 2007 - In Proceedings of the Annual Symposium of the American Medical Informatics Association, Chicago, IL. Washington, DC: pp. 630-634.
    Referent Tracking (RT) advocates the use of instance unique identifiers to refer to the entities comprising the subject matter of patient health records. RT promises many benefits to those who use health record data to improve patient care. To further the adoption of the paradigm we provide an illustration of how data from an EHR application needs to be decomposed in order to make it accord with the tenets of RT. We describe the ontological principles on which this decomposition is (...)
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  38.  17
    Relations in Biomedical Ontologies.Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kuma, Jane Lomax, Chris Mungall, , Fabian Neuhaus, Alan Rector & Cornelius Rosse - 2005 - Genome Biology 6 (5):R46.
    To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.
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  39.  72
    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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  40.  10
    Ontological Theory for Ontological Engineering: Biomedical Systems Information Integration.James M. Fielding, Jonathan Simon, Werner Ceusters & Barry Smith - 2004 - In Proceedings of the Ninth International Conference on the Principles of Knowledge Representation and Reasoning (KR2004), Whistler, BC, 2-5 June 2004. pp. 114–120.
    Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...)
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  41.  10
    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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  42.  9
    What Do Identifiers in HL7 Identify? An Essay in the Ontology of Identity.Werner Ceusters & Barry Smith - 2009 - In Proceedings of InterOntology (Tokyo, Japan, February 27-March 1, 2009). Tokyo: Keio University Press. pp. 77-86.
    Health Level 7 (HL7) is an organization seeking to provide universal standards for the exchange of healthcare information. In a document entitled ‘HL7 Version 3 Standard: Data Types’, the HL7 organization advances descriptions of data types recom- mended for use as identifiers. We will argue that the descriptions supplied provide insufficient guidance as to what exactly the entities are which these data types uniquely identify. Are they real things, such as persons or pieces of equipment? Or are they representations of (...)
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  43.  12
    Using Cross-Lingual Information to Cope with Underspecification in Formal Ontologies.Werner Ceusters, Ignace Desimpel, Barry Smith & Stefan Schulz - 2003 - Studies in Health Technology and Informatics 95:391-396.
    Description logics and other formal devices are frequently used as means for preventing or detecting mistakes in ontologies. Some of these devices are also capable of inferring the existence of inter-concept relationships that have not been explicitly entered into an ontology. A prerequisite, however, is that this information can be derived from those formal definitions of concepts and relationships which are included within the ontology. In this paper, we present a novel algorithm that is able to suggest relationships among existing (...)
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  44.  8
    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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  45.  9
    Verso una filosofia al servizio dell' industria: l'utilità dell' ontologia analitica per l'informatica medica.Barry Smith & Werner Ceusters - 2003 - Sistemi Intelligenti 15 (3):407-417.
    La ricerca medica è afflitta da un problema di comunicazione. Comunità distinte di ricercatori si servono di terminologie diverse e spesso incompatibili per esprimere i risultati del loro lavoro, generando in questo modo problemi di integrazione tra database ogniqualvolta si presenti la necessità di inserire i dati medici nei computer. In un primo momento i problemi di integrazione tra database venivano risolti caso per caso, in seguito si è fatta strada l’idea di realizzare un’unica tassonomia di riferimento in cui tradurre, (...)
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  46.  7
    An Evolutionary Approach to the Representation of Adverse Events.Werner Ceusters, Maria Capolupo, Barry Smith & Georges De Moor - 2009 - Studies in Health Technology and Informatics 150:537-541.
    One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.
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  47.  57
    Representing Mental Functioning: Ontologies for Mental Health and Disease.Janna Hastings, Werner Ceusters, Mark Jensen, Kevin Mulligan & Barry Smith - 2012 - In Towards an Ontology of Mental Functioning (ICBO Workshop), Proceeedings of the Third International Conference on Biomedical Ontology.
    Mental and behavioral disorders represent a significant portion of the public health burden in all countries. The human cost of these disorders is immense, yet treatment options for sufferers are currently limited, with many patients failing to respond sufficiently to available interventions and drugs. High quality ontologies facilitate data aggregation and comparison across different disciplines, and may therefore speed up the translation of primary research into novel therapeutics. Realism-based ontologies describe entities in reality and the relationships between them in such (...)
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  48.  7
    An Evolutionary Approach to Realism-Based Adverse Event Representations.Werner Ceusters, Maria Capolupo, G. De Moor, J. Devlies & Barry Smith - 2011 - Methods of Information in Medicine 50 (1):62-73.
    One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.
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  49.  50
    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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  50.  42
    LinkSuite™: Software Tools for Formally Robust Ontology-Based Data and Information Integration.Werner Ceusters, Barry Smith & James Matthew Fielding - 2004 - In Proceedings of DILS 2004 (Data Integration in the Life Sciences), (Lecture Notes in Bioinformatics, 2994). Springer. pp. 1-16.
    The integration of information resources in the life sciences is one of the most challenging problems facing bioinformatics today. We describe how Language and Computing nv, originally a developer of ontology-based natural language understanding systems for the healthcare domain, is developing a framework for the integration of structured data with unstructured information contained in natural language texts. L&C’s LinkSuite™ combines the flexibility of a modular software architecture with an ontology based on rigorous philosophical and logical principles that is designed to (...)
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