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AMIA Annu Symp Proc. 2013 Nov 16;2013:502-11. eCollection 2013.

Design and evaluation of a bacterial clinical infectious diseases ontology.

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  • 1Department of Biomedical Informatics, Columbia University, New York ; Division of Infectious Diseases, Department of Medicine, Columbia University, New York ; Department of Medicine, University of Melbourne, Melbourne, Australia.
  • 2Division of Infectious Diseases, Department of Medicine, Columbia University, New York.
  • 3Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas.
  • 4Department of Biomedical Informatics, Columbia University, New York.
  • 5Blue Highway Inc., Syracuse, New York.


With antimicrobial resistance increasing worldwide, there is a great need to use automated antimicrobial decision support systems (ADSSs) to lower antimicrobial resistance rates by promoting appropriate antimicrobial use. However, they are infrequently used mostly because of their poor interoperability with different health information technologies. Ontologies can augment portable ADSSs by providing an explicit knowledge representation for biomedical entities and their relationships, helping to standardize and integrate heterogeneous data resources. We developed a bacterial clinical infectious diseases ontology (BCIDO) using Protégé-OWL. BCIDO defines a controlled terminology for clinical infectious diseases along with domain knowledge commonly used in hospital settings for clinical infectious disease treatment decision-making. BCIDO has 599 classes and 2355 object properties. Terms were imported from or mapped to Systematized Nomenclature of Medicine, Unified Medical Language System, RxNorm and National Center for Bitechnology Information Organismal Classification where possible. Domain expert evaluation using the "laddering" technique, ontology visualization, and clinical notes and scenarios, confirmed the correctness and potential usefulness of BCIDO.

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