title: Design and evaluation of a bacterial clinical infectious diseases ontology.
abstract: 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.
authors.affiliation: Department 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.
authors.forename: Claire L
authors.initials: CL
authors.lastname: Gordon
authors.affiliation: Division of Infectious Diseases, Department of Medicine, Columbia University, New York.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Pouch
authors.affiliation: Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas.
authors.forename: Lindsay G
authors.initials: LG
authors.lastname: Cowell
authors.affiliation: Department of Biomedical Informatics, Columbia University, New York.
authors.forename: Mary Regina
authors.initials: MR
authors.lastname: Boland
authors.affiliation: Division of Infectious Diseases, Department of Medicine, Columbia University, New York.
authors.forename: Heather L
authors.initials: HL
authors.lastname: Platt
authors.affiliation: Blue Highway Inc., Syracuse, New York.
authors.forename: Albert
authors.initials: A
authors.lastname: Goldfain
authors.affiliation: Department of Biomedical Informatics, Columbia University, New York.
authors.forename: Chunhua
authors.initials: C
authors.lastname: Weng
mesh_terms: D001424:Bacterial Infections / Q000145:classification*; D064229:Biological Ontologies; D020000:Decision Support Systems, Clinical; D006801:Humans; D011381:Programming Languages; D018875:Vocabulary, Controlled