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Biomedical OntologyFormal Ontology
2004

  1. Biomedical Ontology

    • Bertoncini M., Falavigna D., Stefanelli Mario, Beveridge M., Ceusters Werner: "Intelligent Natural Spoken Dialog Systems for Home Monitoring of Chronicle Patients", in: Proceedings of IJM EuroMise 2004, Prague, 2004, 103-109
    • Bittner Thomas, Smith Barry: "Normalizing Medical Ontologies Using Basic Formal Ontology", in: Tagungsband der 49. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (GMDS 2004), 2004
    • Bodenreider Olivier, Smith Barry, Burgun Anita: "The Ontology-Epistemology Divide: A Case Study in Medical Terminology", in: Varzi Achille C., Vieu Laure (eds.): Formal Ontology and Information Systems. Proceedings of the Third International Conference (FOIS 2004), IOS Press, Amsterdam, 2004, 185-195
    • Bodenreider Olivier, Smith Barry, Kumar Anand, Burgun Anita: "Investigating Subsumption in DL-Based Terminologies: A Case Study in SNOMED CT", in: Hahn Udo, Schulz Stefan, Cornet R. (eds.): Proceedings of the First International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2004), 2004, 12-20
    • Ceusters Werner, Smith Barry, Fielding James Matthew: "LinkSuite: Formally Robust Ontology-Based Data and Information Integration", in: Proceedings of DILS 2004 Data Integration in the Life Sciences (Lecture Notes in Computer Science 2994), Springer, Berlin, 2004, 79-94
    • Ceusters Werner, Smith Barry, Kumar Anand, Dhaen Christoffel: "Mistakes in Medical Ontologies: Where Do They Come From and How Can They Be Detected?", in: Pisanelli Domenico M. (ed.): Ontologies in Medicine: Proceedings of the Workshop on Medical Ontologies, Rome, October 2003, IOS Press, Amsterdam, 2004, 145-164
    • Ceusters Werner, Smith Barry, Kumar Anand, Dhaen Christoffel: "Ontology-Based Error Detection in SNOMED-CT", in: Fieschi M. et al. (eds.): Proceedings of MedInfo 2004, IOS Press, Amsterdam, 2004, 482-486
    • Dos Santos Mariana Casella, Dhaen Christoffel, Fielding James Matthew, Ceusters Werner: "Philosophical Scrutiny for Run-Time Support of Application Ontology Development", in: Vieu Laure, Varzi Achille C. (eds.): Formal Ontology and Information Systems. Proceedings of the Third International Conference (FOIS 2004), IOS Press, Amsterdam, 2004, 342-352
    • Fielding James Matthew, Simon Jonathan, Ceusters Werner, Smith Barry: "Ontological Theory for Ontological Engineering: Biomedical Systems Information Integration", in: Proceedings of KR 2004, Ninth International Conference on the Principles of Knowledge Representation and Reasoning, BC, Whistler, 2004, 114-120
    • Grenon Pierre, Smith Barry, Goldberg Louis: "Biodynamic Ontology: Applying BFO in the Biomedical Domain", in: Pisanelli Domenico M. (ed.): Ontologies in Medicine: Proceedings of the Workshop on Medical Ontologies, Rome, October 2003, IOS Press, Amsterdam, 2004, 20-38
    • Kumar Anand: "MetaProt: A Proteomics Meta-Classification", in: Fieschi M. et al. (eds.): Proceedings of MedInfo 2004, IOS Press, Amsterdam, 2004, 1699
    • Kumar Anand, Ciccarese Paolo, Smith Barry, Matteo Piazza: "Context-Based Task Ontologies for Clinical Guidelines", in: Pisanelli Domenico M. (ed.): Ontologies in Medicine: Proceedings of the Workshop on Medical Ontologies, Rome, October 2003, IOS Press, Amsterdam, 2004, 81-94
    • Kumar Anand, Smith Barry: "Towards a Proteomics Meta-Classification", in: Proceedings of Fourth IEEE Symposium on Bioinformatics and Bioengineering, IEEE Press, Taichung, Taiwan, 2004, 419-427
    • Kumar Anand, Smith Barry, Borgelt Christian: "Dependence Relationships between Gene Ontology Terms based on TIGR Gene Product Annotations", in: Ananadiou Sophia, Zweigenbaum Pierre (eds.): Proceedings of CompuTerm 2004: 3rd International Workshop on Computational Terminology, Coling, Geneva, 2004, 31-38
    • Kumar Anand, Smith Barry, Novotny Daniel: "Biomedical Informatics and Granularity", in: Functional and Comparative Genomics, 5 (2004) , 501-508
    • Kumar Anand, Smith Barry, Pisanelli Domenico M., Gangemi Aldo, Stefanelli Mario: "An Ontological Framework for the Implementation of Clinical Guidelines in Health Care Organizations", in: Pisanelli Domenico M. (ed.): Ontologies in Medicine: Proceedings of the Workshop on Medical Ontologies, Rome, October 2003, IOS Press, Amsterdam, 2004, 95-107
    • Kumar Anand, Smith Barry, Schulze-Kremer Steffen: "Revising the UMLS Semantic Network", in: (poster), MedInfo 2004, San Francisco, 2004
    • Kumar Anand, Yip Lina, Jaramek M., Scheib H.: "Ontological Model for Colon Carcinoma: A Case Study for Knowledge Representation in Clinical Bioinformatics", in: Kooperative Versorgung, Vernetzte Forschung, Ubiquitäre Information, Proceedings of GMDS 2004, Videel OHG, Niebüll, 2004, 196-198
    • Mayhew Douglas, Siebert Dirk: "Ontology: The Discipline and the Tool", in: Büchel Gregor, Klein Bertin, Roth-Berghofer Thomas (eds.): Proceedings of the First Workshop on Philosophy and Informatics, Deutsches Forschungszentrum für künstliche Intelligenz, Cologne, 2004, 57-64
    • Simon Jonathan, Fielding James Matthew: "The Ontology of Disease", in: Proceedings of the Third international Interdisciplinary Conference: Making Sense of Health, Illness and Disease., St Catherine's College, Oxford, UK, 2004
    • Simon Jonathan, Fielding James Matthew, Dos Santos Mariana Casella, Smith Barry: "Reference Ontologies for Biomedical Ontology Integration and Natural Language Processing", in: Zvarova Jana et al. (eds.): International Joint Meeting EuroMISE 2004 Proceedings, Prague, 2004, 62
    • Smith Barry: "Ontologie-basierte Qualitätssicherung medizinischer Terminologien", in: Kooperative Versorgung, Vernetzte Forschung, Ubiquitäre Information, Proceedings of GMDS 2004, Videel OHG, Niebüll, 2004, 193-195
    • Smith Barry, Fellbaum Christiane: "Medical WordNet: A New Methodology for the Construction and Validation of Information", in: Proceedings of Coling 2004 - 20th International Conference on Computational Linguistics, Geneva 23-27 August, 2004, 371-382
    • Smith Barry, Ferraris Maurizio, Zaibert Leonardo: "La Costituzione ontologica", in: Il sole 24 Ore, 27 June 2004, 2004
    • Smith Barry, Kumar Anand: "On Controlled Vocabularies in Bioinformatics: A Case Study in the Gene Ontology", in: BIOSILICO: Drug Discovery Today, 2 (2004) , 246-252
    • Smith Barry, Köhler Jacob, Kumar Anand: "On the Application of Formal Principles to Life Science Data: A Case Study in the Gene Ontology", in: Proceedings of DILS 2004 Data Integration in the Life Sciences (Lecture Notes in Computer Science 2994), Springer, Berlin, 2004, 124-139
    • Smith Barry, Munn Katherine, Papakin Igor: "Bodily Systems and the Spatial-Functional Structure of the Human Body", in: Pisanelli Domenico M. (ed.): Ontologies in Medicine: Proceedings of the Workshop on Medical Ontologies, Rome, October 2003, IOS Press, Amsterdam, 2004, 39-63
    • Smith Barry, Rosse Cornelius: "The Role of Foundational Relations in the Alignment of Biomedical Ontologies", in: Fieschi M. et al. (eds.): Proceedings of MedInfo 2004, IOS Press, Amsterdam, 2004, 444-448
    • Smith Barry, Siebert Dirk: "Warum benutzen Ärzte keine Computer", in: Deutsches Ärzteblatt/PraxisComputer, 20 (2004) 1, 18-20
    • Smith Barry, Siebert Dirk, Ceusters Werner: "Was die philosophische Ontologie zur biomedizinischen Informatik beitragen kann", in: Information - Wissenschaft und Praxis, 55 (2004) 3, 143-146
    • Trautwein Martin, Grenon Pierre: "Roles: One Dead Armadillo on WordNet's Speedway to Ontology", in: Sojka Petr, Pala Karel, Smrz Pavel, Fellbaum Christiane, Vossen Piek (eds.): Proceedings of GWC 2004 - Second International WordNet Conference, Brno, 2004, 341-346
    • Verschelde Jean-Luc, Dos Santos Mariana Casella, Deray Tom, Smith Barry, Ceusters Werner: "Ontology Assisted Database Integration.", in: Journal of Integrative Bioinformatics (online publication), 2004
    • Vizenor Lowell: "Actions in Health Care Organizations: An Ontological Analysis", in: Fieschi M. et al. (eds.): Proceedings of MedInfo 2004, IOS Press, Amsterdam, 2004, 1403-1408
    • Vizenor Lowell, Smith Barry: "The Ontological Nexus between Speech Acts and Medical Records", in: Zvarova Jana et al. (eds.): International Joint Meeting EuroMISE 2004 Proceedings, Prague, 2004, 61

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  2. Formal Ontology

    • Bittner Thomas: "Axioms for Parthood and Containment Relations in Bio-ontologies", in: Proceedings of the First International Workshop on Knowledge Representation in Medicine (KR-MED 2004), CEUR Workshop Proceedings, 102 (2004) , 4-11
    • Bittner Thomas: "A Mereological Theory of Frames of Reference", in: International Journal on Artificial Intelligence Tools (IJAIT), 13 (2004) 1, 171-198
    • Bittner Thomas, Donnelly Maureen: "The Mereology of Stages and Persistent Entities", in: Mantaras R. L., Saitta L. (eds.): Proceedings of the 16th European Conference of Artificial Intelligence (ECAI04), IOS Press, 2004, 283-287
    • Bittner Thomas, Donnelly Maureen, Smith Barry: "Endurants and Perdurants in Directly Depicting Ontologies", in: AI Communications, IOS Press, Amsterdam, 17 (2004) 4, 247-258
    • Bittner Thomas, Donnelly Maureen, Smith Barry: "Individuals, Universals, Collections: On the Foundational Relations of Ontology", in: Varzi Achille C., Vieu Laure (eds.): Formal Ontology and Information Systems. Proceedings of the Third International Conference (FOIS 2004), IOS Press, Amsterdam, 2004, 37-48
    • Chrudzimski Arkadius, Smith Barry: "Brentano's Ontology", in: Jacquette Dale (ed.): The Cambridge Companion to Brentano, Cambridge University Press, Cambridge, 2004, 175-194
    • Donnelly Maureen: "A Formal Theory for Reasoning about Parthood, Connection, and Location", in: Artificial Intelligence, 160 (2004) , 145-172
    • Donnelly Maureen: "On Parts and Holes: The Spatial Structure of the Human Body", in: Fieschi M. et al. (eds.): Proceedings of MedInfo 2004, IOS Press, Amsterdam, 2004, 351-356
    • Donnelly Maureen: "Relative Places", in: Varzi Achille C., Vieu Laure (eds.): Formal Ontology in Information Systems. Proceedings of the Third International Conference (FOIS 2004), [Winner of IBM Prize for Best Paper at FOIS 2004], IOS Press, Amsterdam, 2004, 249-260
    • Feng C. C., Bittner Thomas, Flewelling D. M.: "Modeling Process with Endurance and Perdurance", in: Egenhofer M. J., Freksa C., Miller H.J. (eds.): Proceedings of GI-Science04, LNCS 3234, Springer Verlag, Berlin, 2004, 67-80
    • Grenon Pierre, Smith Barry: "SNAP and SPAN: Towards Dynamic Spatial Ontology", in: Spatial Cognition and Computation, 4 (2004) 1, 69-104
    • Johansson Ingvar: "On the Transitivity of the Parthood Relation", in: Hocberg H., Mulligan Kevin (eds.): Relations and Predicates, Ontos Verlag, Frankfurt, 2004, 161-181
    • Johansson Ingvar: "Ontological Investigations", in: An Inquiry into the Categories of Nature, Man, and Society, Ontos Verlag, Frankfurt, Lancaster, 2004
    • Johansson Ingvar: "Truthmaking: A Cognition-Independent Internal Relation with Heterogeneous Relata", in: Experience and Analysis. Papers of the 27th International Wittgensgtein Symposium (Austrian Ludwig Wittgenstein Society, Kirchberg am Wechsel 2004), 2004, 154-156
    • Johansson Ingvar: "Functions, Function Concepts, and Scales", in: The Monist, 87 (2004) , 96-114
    • Johansson Ingvar: "The Ontology of Temperature", in: online Festschrift to Björn Haglund (2004), Göteborg University, Philosphical Communications, Web Series, Göteborg, 32 (2004) , 115-124
    • Jonathan Simon, Fielding James Matthew, Dos Santos Mariana Casella, Smith Barry: "Reference Ontologies for Biomedical Ontology Integration and Natural Language Processing", in: EuroMISE 2004, Prague, 2004
    • Mark David M., Smith Barry: "A Science of Topography: From Qualitative Ontology to Digital Representations", in: Bishop Michael P., Shroder John F. (eds.): Geographic Information Science and Mountain Geomorphology, Springer-Praxis, Chichester, England, 2004, 75-100
    • Mark David M., Smith Barry, Egenhofer M. J., Hirtle S. C.: "2004 Ontological Foundations for Geographic Information Science", in: McMaster R. B., Usery E. L. (eds.): A Research Agenda for Geographic Information Science, CRC Press, Boca Raton, Florida, 2004, 335-350
    • Mayhew Douglas, Siebert Dirk: "Ontologie - Theorie und Praxis", in: Kooperative Versorgung, Vernetzte Forschung, Ubiquitäre Information, Proceedings of GMDS 2004, Videel OHG, Niebüll, 2004, 190-192
    • Menzel Christopher: "Basic Semantic Integration", in: Proceedings of the Dagstuhl Seminar on Semantic Interoperability and Integration, online, 2004
    • Neuhaus Fabian, Grenon Pierre, Smith Barry: "A Formal Theory of Substances, Qualities, and Universals", in: Varzi Achille C., Vieu Laure (eds.): Formal Ontology and Information Systems. Proceedings of the Third International Conference (FOIS 2004), IOS Press, Amsterdam, 2004, 49-58
    • Neuhaus Fabian, Hendricks V., Pedersen S. A., Scheffler U., Wansing H. (eds.): "First-Order Logic Revisited", in: Logos Verlag, Berlin, 2004
    • Simon Jonathan: "Is Lewis a Conventionalist about Mereology?", in: Proceedings of the 27th International Wittgenstein Symposium, 2004, 355-357
    • Simon Jonathan: "How to be a Bicategorialist", in: Vieu L., Varzi Achille C. (eds.): Formal Ontology and Information Systems. Proceedings of the Third International Conference (FOIS 2004), IOS Press, Amsterdam, 2004, 60-69
    • Simon Jonathan, Fielding James Matthew, Smith Barry: "Using Philosophy to Improve the Coherence and Interoperability of Applications Ontologies: A Field Report on the Collaboration of IFOMIS and L&C", in: Büchel Gregor, Klein Bertin, Roth-Berghofer Thomas (eds.): Proceedings of the First Workshop on Philosophy and Informatics. Deutsches Forschungszentrum für Künstliche Intelligenz, Cologne, 2004, 65-72
    • Smith Barry: "Beyond Concepts, or: Ontology as Reality Representation", in: Varzi Achille C., Vieu Laure (eds.): Formal Ontology and Information Systems. Proceedings of the Third International Conference (FOIS 2004), IOS Press, Amsterdam, 2004, 73-84
    • Smith Barry: "Carving Up Reality", in: Gorman Michael, Sanford J. (eds.): Categories: Historical and Systematic Essays, Washington: Catholic University of America Press, 2004, 225-237
    • Smith Barry: "Une théorie unifiée de la vérité et de la référence", in: Monnoyer J.-M. (ed.): La Structure due Monde: Objets, Propriétés, États du choses, Vrin, Paris, 2004, 141-184
    • Smith Barry: "L'ontologia del senso comune", in: Agazzi E. (ed.): Valore e Limiti del Senso Comune, Franco Agneli, Milan, 2004, 261-284
    • Smith Barry, Grenon Pierre: "The Cornucopia of Formal-Ontological Relations", in: Dialectica, 58 (2004) 3, 279-296

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