31 found
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  1.  6
    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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  2.  5
    On the Application of Formal Principles to Life Science Data: A Case Study in the Gene Ontology.Jacob Köhler, Anand Kumar & Barry Smith - 2004 - In Proceedings of DILS 2004 (Data Integration in the Life Sciences), (Lecture Notes in Bioinformatics 2994). Berlin: Springer. pp. 79-94.
    Formal principles governing best practices in classification and definition have for too long been neglected in the construction of biomedical ontologies, in ways which have important negative consequences for data integration and ontology alignment. We argue that the use of such principles in ontology construction can serve as a valuable tool in error-detection and also in supporting reliable manual curation. We argue also that such principles are a prerequisite for the successful application of advanced data integration techniques such as ontology-based (...)
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  3. 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 of domain ontologies (...)
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  4.  4
    Revising the UMLS Semantic Network.Steffen Schulze-Kremer, Barry Smith & Anand Kumar - 2004 - In MedInfo.
    The integration of standardized biomedical terminologies into a single, unified knowledge representation system has formed a key area of applied informatics research in recent years. The Unified Medical Language System (UMLS) is the most advanced and most prominent effort in this direction, bringing together within its Metathesaurus a large number of distinct source-terminologies. The UMLS Semantic Network, which is designed to support the integration of these source-terminologies, has proved to be a highly successful combination of formal coherence and broad scope. (...)
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  5.  4
    Controlled Vocabularies in Bioinformatics: A Case Study in the Gene Ontology.Barry Smith & Anand Kumar - 2004 - Drug Discovery Today: Biosilico 2 (6):246-252.
    The automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is rapidly acquiring the (...)
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  6. The Unified Medical Language System and the Gene Ontology: Some Critical Reflections.Anand Kumar & Barry Smith - 2003 - In A. Günter, R. Kruse & B. Neumann (eds.), KI 2003: Advances in Artificial Intelligence. Berlin: Springer. pp. 135-148.
    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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  7.  3
    Towards a Proteomics Meta-Classification.Anand Kumar & Barry Smith - 2004 - In IEEE Fourth Symposium on Bioinformatics and Bioengineering, Taichung, Taiwan. IEEE Press. pp. 419–427.
    that can serve as a foundation for more refined ontologies in the field of proteomics. Standard data sources classify proteins in terms of just one or two specific aspects. Thus SCOP (Structural Classification of Proteins) is described as classifying proteins on the basis of structural features; SWISSPROT annotates proteins on the basis of their structure and of parameters like post-translational modifications. Such data sources are connected to each other by pairwise term-to-term mappings. However, there are obstacles which stand in the (...)
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  8.  2
    Investigating Subsumption in DL-Based Terminologies: A Case Study in SNOMED CT.Olivier Bodenreider, Barry Smith, Anand Kumar & Anita Burgun - 2004 - In Proceedings of the First International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2004). pp. 12-20.
    Formalisms such as description logics (DL) are sometimes expected to help terminologies ensure compliance with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) complies 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 CT classes with respect to these principles. Our major results are: 31% of (...)
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  9.  2
    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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  10.  2
    An Ontology for Carcinoma Classification for Clinical Bioinformatics.Anand Kumar, Yum Lina Yip, Barry Smith, Dirk Marwede & Daniel Novotny - 2005 - Studies in Health Technology and Informatics 116 (1):635-640.
    There are a number of existing classifications and staging schemes for carcinomas, one of the most frequently used being the TNM classification. Such classifications represent classes of entities which exist at various anatomical levels of granularity. We argue that in order to apply such representations to the Electronic Health Records one needs sound ontologies which take into consideration the diversity of the domains which are involved in clinical bioinformatics. Here we outline a formal theory for addressing these issues in a (...)
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  11.  2
    Context-Based Task Ontologies for Clinical Guidelines.Anand Kumar, Paolo Ciccarese, Barry Smith & Matteo Piazza - 2004 - In D. Pisanelli (ed.), Ontologies in Medicine: Proceedings of the Workshop on Medical Ontologies, Rome October 2003 (Studies in Health and Technology Informatics, 102). Amsterdam: IOS Press. pp. 81-94.
    Evidence-based medicine relies on the execution of clinical practice guidelines and protocols. A great deal of of effort has been invested in the development of various tools which automate the representation and execution of the recommendations contained within such guidelines and protocols by creating Computer Interpretable Guideline Models (CIGMs). Context-based task ontologies (CTOs), based on standard terminology systems like UMLS, form one of the core components of such a model. We have created DAML+OIL-based CTOs for the tasks mentioned in the (...)
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  12.  2
    Implementing Clinical Guidelines in an Organizational Setup.Anand Kumar, Barry Smith, Mario Stefanelli, Silvana Quaglini & Matteo Piazza - 2003 - In Proceedings of the Workshop on Model-Based and Qualitative Reasoning in Biomedicine, AIME . pp. 39-44.
    Outcomes research in healthcare has been a topic much addressed in recent years. Efforts in this direction have been supplemented by work in the areas of guidelines for clinical practice and computer-interpretable workflow and careflow models.In what follows we present the outlines of a framework for understanding the relations between organizations, guidelines, individual patients and patient-related functions. The derived framework provides a means to extract the knowledge contained in the guideline text at different granularities, in ways that can help us (...)
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  13.  2
    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.
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  14.  84
    The Ontology of Blood Pressure: A Case Study in Creating Ontological Partitions in Biomedicine.Anand Kumar & Barry Smith - 2003 - 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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  15.  53
    The Ontology of Processes and Functions: A Study of the International Classification of Functioning, Disability and Health.Anand Kumar & Barry Smith - 2007 - 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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  16.  59
    On Carcinomas and Other Pathological Entities.Barry Smith, Anand Kumar, Werner Ceusters & Cornelius Rosse - 2005 - 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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  17.  1
    A Framework for Protein Classification.Anand Kumar & Barry Smith - 2003 - In Proceedings of the 2003 German Conference on Bioinformatics, Vol. II. pp. 55-57.
    It is widely understood that protein functions can be exhaustively described in terms of no single parameter, whether this be amino acid sequence or the three-dimensional structure of the underlying protein molecule. This means that a number of different attributes must be used to create an ontology of protein functions. Certainly much of the required information is already stored in databases such as Swiss-Prot, Protein Data Bank, SCOP and MIPS. But the latter have been developed for different purposes and the (...)
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  18.  1
    Clinical Guidelines as Plans: An Ontological Theory.Anand Kumar, Barry Smith, Domenica Pisanelli, Aldo Gangemi & Mario Stefanelli - 2006 - Methods of Information in Medicine 45 (2):204-210.
    Clinical guidelines are special types of plans realized by collective agents. We provide an ontological theory of such plans that is designed to support the construction of a framework in which guideline-based information systems can be employed in the management of workflow in health care organizations. The framework we propose allows us to represent in formal terms how clinical guidelines are realized through the actions of are realized through the actions of individuals organized into teams. We provide various levels of (...)
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  19.  1
    Dependence Relationships Between Gene Ontology Terms Based on TIGR Gene Product Annotations.Anand Kumar, Barry Smith & Christian Borgelt - 2004 - Proceedings of the 3rd International Workshop on Computational Terminology 2004:31-38.
    The Gene Ontology is an important tool for the representation and processing of information about gene products and functions. It provides controlled vocabularies for the designations of cellular components, molecular functions, and biological processes used in the annotation of genes and gene products. These constitute three separate ontologies, of cellular components), molecular functions and biological processes, respectively. The question we address here is: how are the terms in these three separate ontologies related to each other? We use statistical methods and (...)
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  20.  21
    Investigating Subsumption in SNOMED CT: An Exploration Into Large Description Logic-Based Biomedical Terminologies.Olivier Bodenreider, Barry Smith, Anand Kumar & Anita Burgun - 2007 - Artificial Intelligence in Medicine 39 (3):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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  21.  30
    Biomedical Informatics and Granularity.Anand Kumar & Barry Smith - 2004 - Comparative and Functional Genomics 5 (6-7):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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  22.  34
    Anatomical Information Science.Barry Smith, Jose L. V. Mejino Jr, Stefan Schulz, Anand Kumar & Cornelius Rosse - 2005 - In A. G. Cohn & D. M. Mark (eds.), Spatial Information Theory. Springer. pp. 149-164.
    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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  23. Bridging the Gap Between Medical and Bioinformatics: An Ontological Case Study in Colon Carcinoma.Anand Kumar, Yum Lina Yip, Barry Smith & Pierre Grenon - 2006 - Computers in Biology and Medicine 36 (7):694--711.
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  24. Enhancing GO for the Sake of Clinical Bioinformatics.Anand Kumar & Barry Smith - 2004 - Proceedings of the Bio-Ontologies Workshop , Glasgow 133.
    Recent work on the quality assurance of the Gene Ontology (GO, Gene Ontology Consortium 2004) from the perspective of both linguistic and ontological organization has made it clear that GO lacks the kind of formalism needed to support logic-based reasoning. At the same time it is no less clear that GO has proven itself to be an excellent terminological resource that can serve to combine together a variety of biomedical database and information systems. Given the strengths of GO, it is (...)
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  25. Basic Formal Ontology for Bioinformatics.Barry Smith, Anand Kumar & Thomas Bittner - 2005 - IFOMIS Reports.
    Two senses of ‘ontology’ can be distinguished in the current literature. First is the sense favored by information scientists, who view ontologies as software implementations designed to capture in some formal way the consensus conceptualization shared by those working on information systems or databases in a given domain. [Gruber 1993] Second is the sense favored by philosophers, who regard ontologies as theories of different types of entities (objects, processes, relations, functions) [Smith 2003]. Where information systems ontologists seek to maximize reasoning (...)
     
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  26. Oncology Ontology in the NCI Thesaurus.Anand Kumar & Barry Smith - 2005 - Artificial Intelligence in Medicine:213--220.
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  27. Formalizing UMLS Relations Using Semantic Partitions in the Context of Task-Based Clinical Guidelines Model.Anand Kumar, Matteo Piazza, Barry Smith, Silvana Quaglini & Mario Stefanelli - manuscript
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  28. Anatomical Information Science.Barry Smith, Jose Mejino, Stefan Schulz, Anand Kumar & Cornelius Rosse - 2005 - Spatial Information Theory:149--164.
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  29. Basic Formal Ontology for Bioinformatics.Barry Smith, Anand Kumar & Thomas Bittner - 2005 - Ifomis Reports:1--16.
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  30. On the Application of Formal Principles to Life Science Data: A Case Study in the Gene Ontology.Barry Smith, Jacob Köhler & Anand Kumar - 2004 - International Workshop on Data Integration in the Life Sciences.
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  31. On the Proper Treatment of Pathologies in Biomedical Ontologies.Barry Smith & Anand Kumar - 2005 - 8th Annual Bio-Ontologies Meeting 24.
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