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  1. Olivier Bodenreider, Barry Smith, Anand Kumar & Anita Burgun (2007). Investigating Subsumption in SNOMED CT: An Exploration Into Large Description Logic-Based Biomedical Terminologies”,. Artificial Intelligence in Medicine 39:183-195.
    Formalisms based on one or other flavor of Description Logic (DL) are sometimes put forward as helping to ensure that terminologies and controlled vocabularies comply with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) does indeed comply with such principles. We defined seven ontological principles (for example: each class must have at least one parent, each class must differ from its parent) and examined the properties of SNOMED (...)
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  2. Anand Kumar & Barry Smith (2007). The Ontology of Processes and Functions: A Study of the International Classification of Functioning, Disability and Health. In Sharing Knowledge through the ICF: 13th Annual North American WHO Collaborating Center Conference on the ICF, Niagara Falls, June 7, 2007. North American WHO Collaborating Center.
    The International Classification of Functioning, Disability and Health provides a classification of human bodily functions, which, while exhibiting non-conformance to many formal ontological principles, provides an insight into which basic functions such a classification should include. Its evaluation is an important first step towards such an adequate ontology of this domain. Presented at the 13th Annual North American WHO Collaborating Center Conference on the ICF, 2007.
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  3. Anand Kumar & Barry Smith (2005). IFOMIS Reports.
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  4. Cornelius Rosse, Anand Kumar, Jose L. V. Mejino, Daniel L. Cook, Landon T. Detwiler & Barry Smith (2005). A Strategy for Improving and Integrating Biomedical Ontologies. In Proceedings of the Annual Symposium of the American Medical Informatics Association. AMIA.
    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 of domain ontologies (...)
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  5. Barry Smith, Anand Kumar, Werner Ceusters & Cornelius Rosse (2005). On Carcinomas and Other Pathological Entities. Comparative and Functional Genomics 6 (7/8):379–387.
    Tumors, abscesses, cysts, scars, fractures are familiar types of what we shall call pathological continuant entities. The instances of such types exist always in or on anatomical structures, which thereby become transformed into pathological anatomical structures of corresponding types: a fractured tibia, a blistered thumb, a carcinomatous colon. In previous work on biomedical ontologies we showed how the provision of formal definitions for relations such as is_a, part_of and transformation_of can facilitate the integration of such ontologies in ways which have (...)
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  6. Barry Smith, Jose L. V. Mejino Jr, Stefan Schulz, Anand Kumar & Cornelius Rosse (2005). Anatomical Information Science. In Spatial Information Theory. Springer.
    The Foundational Model of Anatomy (FMA) is a map of the human body. Like maps of other sorts – including the map-like representations we find in familiar anatomical atlases – it is a representation of a certain portion of spatial reality as it exists at a certain (idealized) instant of time. But unlike other maps, the FMA comes in the form of a sophisticated ontology of its objectdomain, comprising some 1.5 million statements of anatomical relations among some 70,000 anatomical kinds. (...)
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  7. Anand Kumar & Barry Smith (2004). Biomedical Informatics and Granularity. Comparative and Functional Genomics 5:501-508.
    An explicit formal-ontological representation of entities existing at multiple levels of granularity is an urgent requirement for biomedical information processing. We discuss some fundamental principles which can form a basis for such a representation. We also comment on some of the implicit treatments of granularity in currently available ontologies and terminologies (GO, FMA, SNOMED CT).
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  8. Anand Kumar & Barry Smith, The Ontology of Blood Pressure: A Case Study in Creating Ontological Partitions in Biomedicine. IFOMIS Reports.
    We provide a methodology for the creation of ontological partitions in biomedicine and we test the methodology via an application to the phenomenon of blood pressure. An ontology of blood pressure must do justice to the complex networks of intersecting pathways in the organism by which blood pressure is regulated. To this end it must deal not only with the anatomical structures and physiological processes involved in such regulation but also with the relations between these at different levels of granularity. (...)
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  9. Anand Kumar & Barry Smith (2003). The Unified Medical Language System and the Gene Ontology: Some Critical Reflections. In KI 2003: Advances in Artificial Intelligence.
    The Unified Medical Language System and the Gene Ontology are among the most widely used terminology resources in the biomedical domain. However, when we evaluate them in the light of simple principles for wellconstructed ontologies we find a number of characteristic inadequacies. Employing the theory of granular partitions, a new approach to the understanding of ontologies and of the relationships ontologies bear to instances in reality, we provide an application of this theory in relation to an example drawn from the (...)
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