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Beverley J, Babcock S, Carvalho G, Cowell LG, Duesing S, He Y, Hurley R, Merrell E, Scheuermann RH, Smith B. Coordinating virus research: The Virus Infectious Disease Ontology. PLoS One 2024; 19:e0285093. [PMID: 38236918 PMCID: PMC10796065 DOI: 10.1371/journal.pone.0285093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 04/12/2023] [Indexed: 01/22/2024] Open
Abstract
The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies-structured, controlled, vocabularies-are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects.
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Affiliation(s)
- John Beverley
- Department of Philosophy, University at Buffalo, Buffalo, NY, United States of America
- National Center for Ontological Research, Buffalo, NY, United States of America
| | - Shane Babcock
- National Center for Ontological Research, Buffalo, NY, United States of America
- Air Force Research Laboratory, Wright Patterson Air Force Base, Riverside, OH, United States of America
| | - Gustavo Carvalho
- Department of Cognitive Science, Northwestern University, Evanston, IL, United States of America
| | - Lindsay G. Cowell
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Sebastian Duesing
- Department of Philosophy, Loyola University, Chicago, IL, United States of America
| | - Yongqun He
- Computational Medicine and Bioinformatics, University of Michigan Medical School, He Group, Ann Arbor, MI, United States of America
| | - Regina Hurley
- National Center for Ontological Research, Buffalo, NY, United States of America
- Department of Philosophy, Northwestern University, Evanston, IL, United States of America
| | - Eric Merrell
- Department of Philosophy, University at Buffalo, Buffalo, NY, United States of America
- National Center for Ontological Research, Buffalo, NY, United States of America
| | - Richard H. Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States of America
- Department of Pathology, University of California, San Diego, CA, United States of America
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States of America
| | - Barry Smith
- Department of Philosophy, University at Buffalo, Buffalo, NY, United States of America
- National Center for Ontological Research, Buffalo, NY, United States of America
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