A fourfold pathogen reference ontology suite.

Journal: Journal of biomedical semantics
Published Date: Jul 9, 2025

Abstract

BACKGROUND: Infectious diseases remain a critical global health challenge, and the integration of standardized ontologies plays a vital role in managing related data. The Infectious Disease Ontology (IDO) and its extensions, such as the Coronavirus Infectious Disease Ontology (CIDO), are essential for organizing and disseminating information related to infectious diseases. The COVID-19 pandemic highlighted the need for updating IDO and its virus-specific extensions. There is an additional need to update IDO extensions specific to bacteria, fungus, and parasite infectious diseases.

Authors

  • John Beverley
    Northwestern University, Evanston, IL, 60208, USA.
  • Shane Babcock
    Department of Philosophy, Niagara University, Lewiston, NY, USA. sbabcock@niagara.edu.
  • Carter Benson
    University at Buffalo, State University of New York, Buffalo, USA.
  • Giacomo De Colle
    National Center for Ontological Research, Buffalo, USA.
  • Sydney Cohen
    National Center for Ontological Research, Buffalo, USA.
  • Alexander D Diehl
    Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, J. Craig Venter Institute, La Jolla, CA 92037, USA, Department of Pathology, University of California, San Diego, CA 92093, USA.
  • Ram A N R Challa
    University at Buffalo, State University of New York, Buffalo, USA.
  • Rachel A Mavrovich
    National Center for Ontological Research, Buffalo, USA.
  • Joshua Billig
    National Center for Ontological Research, Buffalo, USA.
  • Anthony Huffman
    Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States.
  • Yongqun He
    University of Michigan Medical School, Ann Arbor, MI 48109 USA ; Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, and Comprehensive Cancer Center, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Dr., Ann Arbor, MI 48109 USA.

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