Open Biomedical Ontologies applied to prostate cancer

Authors:
James A. Overton;Cesare Romagnoli;Rethy Chhem
Affiliations:
(Correspd.) Department of Philosophy, The University of Western Ontario, London, ON, Canada. E-mail: joverto2@uwo.ca;Department of Medical Imaging, London Health Sciences Centre, London, ON, Canada. E-mail: cesare.romagnoli@lhsc.on.ca;Division of Human Health, International Atomic Energy Agency, Vienna, Austria. E-mail: r.chhem@iaea.org
Venue:
Applied Ontology - Biomedical Ontologies
Year:
2011

Citing 2
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Abstract

This paper surveys preliminary results from the Interdisciplinary Prostate Ontology Project (IPOP), in which ontologies from the OBO Foundry have been used to annotate clinical reports about prostate cancer. Our analysis shows that only half of the terms required to annotate these reports are currently included in OBO. However, we discuss methods for filling these gaps, and our reasons for preferring the OBO Foundry approach to annotation using controlled vocabularies such as SNOMED CT, the NCI Thesaurus, RadLex and the UMLS Metathesaurus. We end with a discussion of our ongoing work on image annotation and structured reporting with ontologies.