A strategy for improving and integrating biomedical ontologies
In Proceedings of AMIA Symposium. AMIA (2005)
| Abstract | 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 in anatomy, physiology and pathology. | |||||||||
| Keywords | cancer medical ontology realism | |||||||||
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Barry Smith (2005). A Strategy for Improving and Integrating Biomedical Ontologies. In Proceedings of the Annual Symposium of the American Medical Informatics Association. AMIA.
Barry Smith (2007). The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration. Nature Biotechnology 25 (11):1251-1255.
Anand Kumar & Barry Smith (2003). The Unified Medical Language System and the Gene Ontology: Some Critical Reflections. In KI 2003: Advances in Artificial Intelligence.
Barry Smith (2005). Relations in Biomedical Ontologies. Genome Biology 6 (5):R46.
Barry Smith & Cornelius Rosse (2004). The Role of Foundational Relations in the Alignment of Biomedical Ontologies. In Medinfo. IOS Press.
Gary H. Merrill (2010). Ontological Realism: Methodology or Misdirection? Applied Ontology 5 (2):79-108.
Daniel L. Rubin (2012). Finding the Meaning in Images: Annotation and Image Markup. Philosophy, Psychiatry, and Psychology 18 (4).
Janna Hastings, Werner Ceusters, Mark Jensen, Kevin Mulligan & Barry Smith (2012). Representing Mental Functioning: Ontologies for Mental Health and Disease. In Towards an Ontology of Mental Functioning (ICBO Workshop), Proceeedings of the Third International Conference on Biomedical Ontology.
Werner Ceusters (2006). A Realism-Based Approach to the Evolution of Biomedical Ontologies. In Proceedings of the Annual AMIA Symposium. AMIA.
Barry Smith (2010). Ontological Realism: A Methodology for Coordinated Evolution of Scientific Ontologies. Applied Ontology 5:139-188.
Gary H. Merrill (2010). Realism and Reference Ontologies: Considerations, Reflections, and Problems. Applied Ontology 5 (3-4):189-221.
Melissa Haendel, Fabian Neuhaus, David Osumi-Sutherland, Paula M. Mabee, José L. V. Mejino Jr, Chris J. Mungall & Barry Smith (2008). CARO: The Common Anatomy Reference Ontology. In Anatomy Ontologies for Bioinformatics: Principles and Practice. Springer.
Janna Hastings, Nicolas Le Novère, Werner Ceusters, Kevin Mulligan & Barry Smith (2012). Wanting What We Don’T Want to Want: Representing Addiction in Interoperable Bio-Ontologies. In Proceeedings of the Third International Conference on Biomedical Ontology. CEUR.
Janna Hastings, Nicolas Le Novère, Werner Ceusters, Kevin Mulligan & Barry Smith (2012). Wanting What We Don’T Want to Want: Representing Addiction in Interoperable Bio-Ontologies. In Proceeedings of the Third International Conference on Biomedical Ontology. CEUR.
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