Establishing and Harmonizing Ontologies in an Interdisciplinary Health Care and Clinical Research Environment
Studies in Health, Technology and Informatics 134:219-234 (2008)
Abstract
Ontologies are being ever more commonly used in biomedical informatics and we provide a survey of some of these uses, and of the relations between ontologies and other terminology resources. In order for ontologies to become truly useful, two objectives must be met. First, ways must be found for the transparent evaluation of ontologies. Second, existing ontologies need to be harmonised. We argue that one key foundation for both ontology evaluation and harmonisation is the adoption of a realist paradigm in ontology development. For science-based ontologies of the sort which concern us in the eHealth arena, it is reality that provides the common benchmark against which ontologies can be evaluated and aligned within larger frameworks. Given the current multitude of ontologies in the biomedical domain the need for harmonisation is becoming ever more urgent. We describe one example of such harmonisation within the ACGT project, which draws on ontology-based computing as a basis for sharing clinical and laboratory data on cancer research.Author's Profile
My notes
Similar books and articles
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.
Finding the Meaning in Images: Annotation and Image Markup.Daniel L. Rubin - 2011 - Philosophy, Psychiatry, and Psychology 18 (4):311-318.
Adapting Clinical Ontologies in Real-World Environments.Holger Stenzhorn, Stefan Schulz, Martin Boeker & Barry Smith - 2008 - Journal of Universal Computer Science 14 (22):3767-3780.
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.
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.
Reference ontologies — application ontologies: Either/or or both/and?Christopher Menzel - 2004 - In Pierre M. Pierre, Christopher Menzel & Barry Smith (eds.), CEUR Workshop Proceedings, Vol. 94.
Analytics
Added to PP
2013-07-02
Downloads
248 (#49,940)
6 months
19 (#57,251)
2013-07-02
Downloads
248 (#49,940)
6 months
19 (#57,251)
Historical graph of downloads
Author's Profile
Citations of this work
Putting Biomedical Ontologies to Work.Barry Smith & Mathias Brochhausen - 2010 - Methods of Information in Medicine 49 (2):135-40.
Biomedizinische Ontologien für die Praxis.M. Brochhausen & Barry Smith - 2009 - European Journal for Biomedical Informatics 1.
References found in this work
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, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Nigam Shah, Patricia L. Whetzel & Suzanna Lewis - 2007 - Nature Biotechnology 25 (11):1251-1255.
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.
Biodynamic Ontology: Applying BFO in the Biomedical Domain.Barry Smith, Pierre Grenon & Louis Goldberg - 2004 - Studies in Health and Technology Informatics 102:20–38.
Ontology-based error detection in SNOMED-CT.Werner Ceusters, Barry Smith, Anand Kumar & Christoffel Dhaen - 2004 - Proceedings of Medinfo 2004:482-6.
A terminological and ontological analysis of the NCI thesaurus.Werner Ceusters, Barry Smith & Louis Goldberg - 2005 - Methods of Information in Medicine 44 (4):498-507.