Results for 'biomedical ontology'

1000+ found
Order:
See also
  1. Putting Biomedical Ontologies to Work.Barry Smith & Mathias Brochhausen - 2010 - Methods of Information in Medicine 49 (2):135-40.
    Biomedical ontologies exist to serve integration of clinical and experimental data, and it is critical to their success that they be put to widespread use in the annotation of data. How, then, can ontologies achieve the sort of user-friendliness, reliability, cost-effectiveness, and breadth of coverage that is necessary to ensure extensive usage? Methods: Our focus here is on two different sets of answers to these questions that have been proposed, on the one hand in medicine, by the SNOMED CT (...)
    Direct download (2 more)  
     
    Export citation  
     
    Bookmark   2 citations  
  2. 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.
    Direct download (2 more)  
    Translate
     
     
    Export citation  
     
    Bookmark   86 citations  
  3. National Center for Biomedical Ontology: Advancing Biomedicine Through Structured Organization of Scientific Knowledge.Daniel L. Rubin, Suzanna E. Lewis, Chris J. Mungall, Misra Sima, Westerfield Monte, Ashburner Michael, Christopher G. Chute, Ida Sim, Harold Solbrig, M. A. Storey, Barry Smith, John D. Richter, Natasha Noy & Mark A. Musen - 2006 - Omics: A Journal of Integrative Biology 10 (2):185-198.
    The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use (...)
    Direct download  
     
    Export citation  
     
    Bookmark   4 citations  
  4. The National Center for Biomedical Ontology.Mark A. Musen, Natalya F. Noy, Nigam H. Shah, Patricia L. Whetzel, Christopher G. Chute, Margaret-Anne Story & Barry Smith - 2012 - Journal of the American Medical Informatics Association 19 (2):190-195.
    The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of (...)
    Direct download (2 more)  
     
    Export citation  
     
    Bookmark   2 citations  
  5.  19
    Open Biomedical Ontologies Applied to Prostate Cancer.James A. Overton, Cesare Romagnoli & Rethy Chhem - 2011 - Applied Ontology 6 (1):35-51.
  6. Classificatory Theory in Data-Intensive Science: The Case of Open Biomedical Ontologies.Sabina Leonelli - 2012 - International Studies in the Philosophy of Science 26 (1):47 - 65.
    Knowledge-making practices in biology are being strongly affected by the availability of data on an unprecedented scale, the insistence on systemic approaches and growing reliance on bioinformatics and digital infrastructures. What role does theory play within data-intensive science, and what does that tell us about scientific theories in general? To answer these questions, I focus on Open Biomedical Ontologies, digital classification tools that have become crucial to sharing results across research contexts in the biological and biomedical sciences, and (...)
    Direct download (6 more)  
     
    Export citation  
     
    Bookmark   19 citations  
  7. Clonal Complexes in Biomedical Ontologies.Albert Goldfain, Lindsay Cowell & Barry Smith - 2009 - In ICBO 2009: Proceedings of the First International Conference on Biomedical Ontology. pp. 168.
    An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Sequence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies.
    Direct download  
     
    Export citation  
     
    Bookmark   1 citation  
  8.  29
    Teaching Good Biomedical Ontology Design.D. Seddig-Raufie, M. Boeker, S. Schulz, N. Grewe, J. Röhl, L. Jansen & D. Schober - 2012 - In Ronald Cornet & Robert Stevens (eds.), International Conference for Biomedical Ontologies (ICBO 2012), KR-MED Series, Graz, Austria July 21-25, 2012.
    Background: In order to improve ontology quality, tool- and language-related tutorials are not sufficient. Care must be taken to provide optimized curricula for teaching the representational language in the context of a semantically rich upper level ontology. The constraints provided by rigid top and upper level models assure that the ontologies built are not only logically consistent but also adequately represent the domain of discourse and align to explicitly outlined ontological principles. Finally such a curriculum must take into (...)
    Direct download  
    Translate
     
     
    Export citation  
     
    Bookmark   1 citation  
  9. A Realism-Based Approach to the Evolution of Biomedical Ontologies.Barry Smith - 2006 - In Proceedings of the Annual AMIA Symposium. Washington, DC: American Medical Informatics Association. pp. 121-125.
    We present a novel methodology for calculating the improvements obtained in successive versions of biomedical ontologies. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous (...)
    Direct download (2 more)  
     
    Export citation  
     
    Bookmark   17 citations  
  10. Biomedical Ontology Alignment: An Approach Based on Representation Learning.Prodromos Kolyvakis, Alexandros Kalousis, Barry Smith & Dimitris Kiritsis - 2018 - Journal of Biomedical Semantics 9 (21).
    While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through (...)
    Direct download  
     
    Export citation  
     
    Bookmark  
  11. The Role of Foundational Relations in the Alignment of Biomedical Ontologies.Barry Smith & Cornelius Rosse - 2004 - In M. Fieschi, E. Coiera & Y.-C. J. Li (eds.), Medinfo. IOS Press. pp. 444-448.
    The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities that is designed to serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems. We diagnose certain characteristic errors in the treatment (...)
    Direct download (2 more)  
     
    Export citation  
     
    Bookmark   26 citations  
  12.  31
    Reference Ontologies for Biomedical Ontology Integration and Natural Language Processing.Jonathan Simon, James Fielding, Mariana Dos Santos & Barry Smith - 2004 - In Proceedings of the International Joint Meeting EuroMISE 2004. pp. 62-72.
    The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies.[1] To this end LinKBase®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO).[2] With this project we aim to move (...)
    Direct download  
     
    Export citation  
     
    Bookmark   2 citations  
  13. 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. (...)
    Direct download  
     
    Export citation  
     
    Bookmark   9 citations  
  14. A Strategy for Improving and Integrating Biomedical Ontologies.Cornelius Rosse, Anand Kumar, Jose L. V. Mejino, Daniel L. Cook, Landon T. Detwiler & Barry Smith - 2005 - In Proceedings of the Annual Symposium of the American Medical Informatics Association. AMIA. pp. 639-643.
    The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries (...)
    Direct download (3 more)  
    Translate
     
     
    Export citation  
     
    Bookmark   6 citations  
  15. The Ontology for Biomedical Investigations.Anita Bandrowski, Ryan Brinkman, Mathias Brochhausen, Matthew H. Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Frank Gibson, Alejandra Gonzalez-Beltran, Melissa A. Haendel, Yongqun He, Mervi Heiskanen, Tina Hernandez-Boussard, Mark Jensen, Yu Lin, Allyson L. Lister, Phillip Lord, James Malone, Elisabetta Manduchi, Monnie McGee, Norman Morrison, James A. Overton, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Daniel Schober, Barry Smith, Larisa N. Soldatova, Christian J. Stoeckert, Chris F. Taylor, Carlo Torniai, Jessica A. Turner, Randi Vita, Patricia L. Whetzel & Jie Zheng - 2016 - PLoS ONE 11 (4):e0154556.
    The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such (...)
    Direct download (11 more)  
     
    Export citation  
     
    Bookmark   18 citations  
  16.  49
    The Logic of Biological Classification and the Foundations of Biomedical Ontology.Barry Smith - 2005 - In Dag Westerståhl (ed.), Logic, Methodology and Philosophy of Science. Proceedings of the 12th International Conference. King's College Publication. pp. 505-520.
    Biomedical research is increasingly a matter of the navigation through large computerized information resources deriving from functional genomics or from the biochemistry of disease pathways. To make such navigation possible, controlled vocabularies are needed in terms of which data from different sources can be unified. One of the most influential developments in this regard is the so-called Gene Ontology, which consists of controlled vocabularies of terms used by biologists to describe cellular constituents, biological processes and molecular functions, organized (...)
    Direct download  
     
    Export citation  
     
    Bookmark   11 citations  
  17.  7
    Rezension: Biomedical Ontology and the Metaphysics of Composite Substances 1540–1670 von Andreas Blank.Georg Toepfer - 2012 - Berichte Zur Wissenschaftsgeschichte 35 (2):163-165.
    No categories
    Direct download (3 more)  
    Translate
     
     
    Export citation  
     
    Bookmark  
  18.  14
    Biomedical Ontology and the Metaphysics of Composite Substances 1540–1670.Karin Ekholm - 2012 - British Journal for the History of Philosophy 20 (5):1048-1052.
    British Journal for the History of Philosophy, Volume 0, Issue 0, Page 1-4, Ahead of Print.
    Direct download (3 more)  
     
    Export citation  
     
    Bookmark  
  19.  44
    On the Proper Treatment of Pathologies in Biomedical Ontologies.Barry Smith & Anand Kumar - 2005 - In Proceedings of the Bio-Ontologies Workshop, Intelligent Systems for Molecular Biology (ISMB 2005). Detroit: pp. 22-23.
    In previous work on biomedical ontologies we showed how the provision of formal definitions for relations such as is_a and part_of can support new types of auto-mated reasoning about biomedical phenomena. We here extend this approach to the transformation_of characteristic of pathologies.
    Direct download  
     
    Export citation  
     
    Bookmark   1 citation  
  20.  28
    Grains, Components and Mixtures in Biomedical Ontologies.Ludger Jansen & Schulz Stefan - 2011 - Journal of Biomedical Semantics 2 (4).
    BACKGROUND -/- In biomedical ontologies, mereological relations have always been subject to special interest due to their high relevance in structural descriptions of anatomical entities, cells, and biomolecules. This paper investigates two important subrelations of has_proper_part, viz. the relation has_grain, which relates a collective entity to its multiply occurring uniform parts (e.g., water molecules in a portion of water), and the relation has_component, which relates a compound to its constituents (e.g., molecules to the atoms they consist of). -/- METHOD (...)
    Direct download  
    Translate
     
     
    Export citation  
     
    Bookmark   1 citation  
  21.  46
    Towards Interoperability of Biomedical Ontologies - Report Number 07132.Mark Musen, Michael Schroeder & Barry Smith - 2008 - In Towards Interoperability of Biomedical Ontologies. Schloss Dagstuhl-Leibniz-Zentrum Fuer Informatik.
    The meeting focused on uses of ontologies, with a special focus on spatial ontologies, in addressing the ever increasing needs faced by biology and medicine to cope with ever expanding quantities of data. To provide effective solutions computers need to integrate data deriving from myriad heterogeneous sources by bringing the data together within a single framework. The meeting brought together leaders in the field of what are called "top-level ontologies" to address this issue, and to establish strategies among leaders in (...)
    Direct download  
     
    Export citation  
     
    Bookmark  
  22.  60
    Towards Interoperability of Biomedical Ontologies.Musen Mark, A. Schroeder, Michael Smith & Barry - 2008 - Schloss Dagstuhl: Leibniz-Zentrum für Informatik.
    Report on Dagstuhl Seminar 07132, Schloss Dagstuhl, March 27-30 , 2007.
    Direct download (2 more)  
     
    Export citation  
     
    Bookmark  
  23. International Conference for Biomedical Ontologies (ICBO 2012), KR-MED Series, Graz, Austria July 21-25, 2012.Ronald Cornet & Robert Stevens (eds.) - 2012
    Translate
     
     
    Export citation  
     
    Bookmark  
  24.  66
    Special Issue: Biomedical Ontology in Action.Olivier Bodenreider - 2009 - Applied Ontology 4 (1):1-4.
    Direct download (2 more)  
     
    Export citation  
     
    Bookmark  
  25. Biodynamic Ontology: Applying BFO in the Biomedical Domain.Barry Smith, Pierre Grenon & Louis Goldberg - 2004 - Studies in Health and Technology Informatics 102:20–38.
    Current approaches to formal representation in biomedicine are characterized by their focus on either the static or the dynamic aspects of biological reality. We here outline a theory that combines both perspectives and at the same time tackles the by no means trivial issue of their coherent integration. Our position is that a good ontology must be capable of accounting for reality both synchronically (as it exists at a time) and diachronically (as it unfolds through time), but that these (...)
    Direct download (2 more)  
     
    Export citation  
     
    Bookmark   27 citations  
  26. Biomedical Imaging Ontologies: A Survey and Proposal for Future Work.Barry Smith, Sivaram Arabandi, Mathias Brochhausen, Michael Calhoun, Paolo Ciccarese, Scott Doyle, Bernard Gibaud, Ilya Goldberg, Charles E. Kahn Jr, James Overton, John Tomaszewski & Metin Gurcan - 2015 - Journal of Pathology Informatics 6 (37):37.
    Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged (...)
    Direct download (2 more)  
     
    Export citation  
     
    Bookmark   1 citation  
  27. ICBO 2009: Proceedings of the First International Conference on Biomedical Ontology.Barry Smith (ed.) - 2009 - Buffalo: NCOR.
  28. 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 (...)
    Direct download  
     
    Export citation  
     
    Bookmark   2 citations  
  29. 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. AMIA. 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 (...)
    Direct download (2 more)  
     
    Export citation  
     
    Bookmark   3 citations  
  30.  77
    A Unified Framework for Biomedical Terminologies and Ontologies.Werner Ceusters & Barry Smith - 2010 - Studies in Health Technology and Informatics 160:1050-1054.
    The goal of the OBO (Open Biomedical Ontologies) Foundry initiative is to create and maintain an evolving collection of non-overlapping interoperable ontologies that will offer unambiguous representations of the types of entities in biological and biomedical reality. These ontologies are designed to serve non-redundant annotation of data and scientific text. To achieve these ends, the Foundry imposes strict requirements upon the ontologies eligible for inclusion. While these requirements are not met by most existing biomedical terminologies, the latter (...)
    Direct download (3 more)  
    Translate
     
     
    Export citation  
     
    Bookmark   5 citations  
  31.  67
    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 (...)
    Direct download  
     
    Export citation  
     
    Bookmark   5 citations  
  32. Formal Ontology for Natural Language Processing and the Integration of Biomedical Databases.Jonathan Simon, James M. Fielding, Mariana C. Dos Santos & Barry Smith - 2005 - International Journal of Medical Informatics 75 (3-4):224-231.
    The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end r®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this project we aim to move (...)
    Direct download (2 more)  
     
    Export citation  
     
    Bookmark   3 citations  
  33.  74
    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. (...)
    Direct download  
     
    Export citation  
     
    Bookmark   110 citations  
  34.  7
    Orienteering Tools: Biomedical Research with Ontologies.Federico Boem - 2016 - Humana Mente 9 (30).
    Biomedical ontologies are considered a serious innovation for biomedical research and clinical practice. They promise to integrate information coming from different biological databases thus creating a common ground for the representation of knowledge in all the life sciences. Such a tool has potentially many implications for both basic biomedical research and clinical practice. Here I discuss how this tool has been generated and thought. Due to the analysis of some empirical cases I try to elaborate how (...) ontologies constitute a novelty also from an epistemological point of view. (shrink)
    No categories
    Direct download (2 more)  
     
    Export citation  
     
    Bookmark   2 citations  
  35. Proceedings of the Second International Conference on Biomedical Ontology, Buffalo, NY, July 28-30, 2011 (CEUR 883).Barcellos Almeida Mauricio, Carneiro Proietti Anna Barbara de Freitas, Jiye Ai & Smith Barry - 2011
    No categories
     
    Export citation  
     
    Bookmark  
  36. Proceeedings of the Third International Conference on Biomedical Ontology (CEUR 897).Walls Ramona, Smith Barry, Justin Elser, Albert Goldfain & W. Stevenson Dennis - 2012
    No categories
     
    Export citation  
     
    Bookmark  
  37. Proceedings of the 2nd International Conference on Biomedical Ontology, Buffalo, NY.L. Whetzel Patricia, H. Shah Nigam, F. Noy Natalya, Benjamin Dai, Michael Dorf, Nicholas Griffith, Clement Jonquet, Cherie Youn, Chris Callendar, Adrien Coulet, Smith Barry, Chute Chris & Musen Mark - 2011
    No categories
     
    Export citation  
     
    Bookmark  
  38. Proceedings of the Fifth International Conference on Biomedical Ontology (ICBO), Houston, 2014, (CEUR, 1327).Ceusters Werner, Hsu Chiun Yu & Smith Barry - 2014
    No categories
     
    Export citation  
     
    Bookmark  
  39. Proceedings of the 2nd International Conference on Biomedical Ontology.Landgrebe Jobst & Smith Barry - 2011 - CEUR, vol. 833.
    No categories
     
    Export citation  
     
    Bookmark  
  40.  6
    Von Leibniz'Metaphysik (2001), Leibniz: Metaphilosophy and Metaphysics, 1666–1686 (2005), and Biomedical Ontology and the Metaphysics of Composite Substances, 1540–1670 (2010). Martin Campbell-Kelly is Emeritus Professor in the Department of Com-Puter Science at the University of Warwick, Where He Specializes in The. [REVIEW]J. L. Heilbron & Helge Kragh - 2013 - Perspectives on Science 21 (3).
    Direct download  
     
    Export citation  
     
    Bookmark  
  41. Proceeedings of the Third International Conference on Biomedical Ontology (CEUR 897).Goldfain Albert, G. Cowell Lindsay & Smith Barry - 2012
    No categories
     
    Export citation  
     
    Bookmark  
  42. Proceedings of the Fourth International Conference on Biomedical Ontology (ICBO).Albert Goldfain, Min Xu, Jonathan Bona & Smith Barry - 2013
    No categories
     
    Export citation  
     
    Bookmark  
  43. International Workshop on Definitions in Ontologies, Organized in Conjunction with the Fourth International Conference on Biomedical Ontology (ICBO), Montreal, July 7, 2013, (CEUR, 1061).Smith Barry - 2013
    No categories
     
    Export citation  
     
    Bookmark  
  44.  36
    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 (...)
    Direct download  
     
    Export citation  
     
    Bookmark   1 citation  
  45. 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. (...)
    Direct download (2 more)  
    Translate
     
     
    Export citation  
     
    Bookmark   29 citations  
  46. Building Ontologies with Basic Formal Ontology.Robert Arp, Barry Smith & Andrew D. Spear - 2015 - Cambridge, MA: MIT Press.
    In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology (...)
    Direct download (3 more)  
     
    Export citation  
     
    Bookmark   38 citations  
  47.  65
    Biomedical Terminologies and Ontologies: Enabling Biomedical Semantic Interoperability and Standards in Europe.Bernard de Bono, Mathias Brochhausen, Sybo Dijkstra, Dipak Kalra, Stephan Keifer & Barry Smith - 2009 - In European Large-Scale Action on Electronic Health.
    In the management of biomedical data, vocabularies such as ontologies and terminologies (O/Ts) are used for (i) domain knowledge representation and (ii) interoperability. The knowledge representation role supports the automated reasoning on, and analysis of, data annotated with O/Ts. At an interoperability level, the use of a communal vocabulary standard for a particular domain is essential for large data repositories and information management systems to communicate consistently with one other. Consequently, the interoperability benefit of selecting a particular O/T as (...)
    Direct download  
     
    Export citation  
     
    Bookmark  
  48. The Environment Ontology: Contextualising Biological and Biomedical Entities.Pier Luigi Buttigieg, Norman Morrison, Barry Smith, Christopher J. Mungall & Suzanna E. Lewis - 2013 - Journal of Biomedical Semantics 4 (43):1-9.
    As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This (...)
    Direct download (2 more)  
     
    Export citation  
     
    Bookmark   2 citations  
  49.  9
    Formal Ontologies in Biomedical Knowledge Representation.S. Schulz & L. Jansen - 2013 - In M.-C. Jaulent, C. U. Lehmann & B. Séroussi (eds.), Yearbook of Medical Informatics 8. pp. 132-146.
    Objectives: Medical decision support and other intelligent applications in the life sciences depend on increasing amounts of digital information. Knowledge bases as well as formal ontologies are being used to organize biomedical knowledge and data. However, these two kinds of artefacts are not always clearly distinguished. Whereas the popular RDF(S) standard provides an intuitive triple-based representation, it is semantically weak. Description logics based ontology languages like OWL-DL carry a clear-cut semantics, but they are computationally expensive, and they are (...)
    Direct download  
     
    Export citation  
     
    Bookmark  
  50. 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 (...)
    Direct download (3 more)  
     
    Export citation  
     
    Bookmark   8 citations  
1 — 50 / 1000