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. 2024 Jan 18;19(1):e0285093.
doi: 10.1371/journal.pone.0285093. eCollection 2024.

Coordinating virus research: The Virus Infectious Disease Ontology

John Beverley  1   2 , Shane Babcock  2   3 , Gustavo Carvalho  4 , Lindsay G Cowell  5 , Sebastian Duesing  6 , Yongqun He  7 , Regina Hurley  2   8 , Eric Merrell  1   2 , Richard H Scheuermann  9   10   11 , Barry Smith  1   2
Affiliations

Coordinating virus research: The Virus Infectious Disease Ontology

John Beverley et al. PLoS One. .

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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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Relationships among BFO, GO, OGMS, IDO Core, and OBI.
Fig 2
Fig 2. NCBITaxon imported to IDOBRU, located on Bioportal.
Fig 3
Fig 3. VIDO representation of the Baltimore Classification in Protégé Editor.
Fig 4
Fig 4. Relationships among GO, IDO Core, VIDO, and CIDO.
Fig 5
Fig 5. Relationships among BFO, GO, OGMS, IDO Core, the Cell Ontology (CL), VIDO, the Common Core Ontology (CCO), OBI, IAO, the Uber-Anatomy Ontology (UBERON), CIDO, ChEBI, PRO (Protein Ontology), and PTRANS.
See this image and copyright information in PMC

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