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. 2021 Jul 18;12(1):13.
doi: 10.1186/s13326-021-00245-1.

The Infectious Disease Ontology in the age of COVID-19

Shane Babcock  1   2 , John Beverley  3   4 , Lindsay G Cowell  3   5 , Barry Smith  3   6
Affiliations

The Infectious Disease Ontology in the age of COVID-19

Shane Babcock et al. J Biomed Semantics. .

Abstract

Background: Effective response to public health emergencies, such as we are now experiencing with COVID-19, requires data sharing across multiple disciplines and data systems. Ontologies offer a powerful data sharing tool, and this holds especially for those ontologies built on the design principles of the Open Biomedical Ontologies Foundry. These principles are exemplified by the Infectious Disease Ontology (IDO), a suite of interoperable ontology modules aiming to provide coverage of all aspects of the infectious disease domain. At its center is IDO Core, a disease- and pathogen-neutral ontology covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is extended by disease and pathogen-specific ontology modules.

Results: To assist the integration and analysis of COVID-19 data, and viral infectious disease data more generally, we have recently developed three new IDO extensions: IDO Virus (VIDO); the Coronavirus Infectious Disease Ontology (CIDO); and an extension of CIDO focusing on COVID-19 (IDO-COVID-19). Reflecting the fact that viruses lack cellular parts, we have introduced into IDO Core the term acellular structure to cover viruses and other acellular entities studied by virologists. We now distinguish between infectious agents - organisms with an infectious disposition - and infectious structures - acellular structures with an infectious disposition. This in turn has led to various updates and refinements of IDO Core's content. We believe that our work on VIDO, CIDO, and IDO-COVID-19 can serve as a model for yielding greater conformance with ontology building best practices.

Conclusions: IDO provides a simple recipe for building new pathogen-specific ontologies in a way that allows data about novel diseases to be easily compared, along multiple dimensions, with data represented by existing disease ontologies. The IDO strategy, moreover, supports ontology coordination, providing a powerful method of data integration and sharing that allows physicians, researchers, and public health organizations to respond rapidly and efficiently to current and future public health crises.

Keywords: COVID-19; Coronavirus; Data integration; Infectious disease; Infectious disease ontology; Ontology.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Relationships between disease, disorder, and disease courses in IDO Core
Fig. 2
Fig. 2
Some aspects of IDO infectious disposition
Fig. 3
Fig. 3
Infectious Disorder inferred subclass of infection
Fig. 4
Fig. 4
Transitions through epidemic and pandemic
Fig. 5
Fig. 5
A lattice of infectious disease ontologies
Fig. 6
Fig. 6
Protégé representation of Baltimore Classification
Fig. 7
Fig. 7
Links between VIDO, CIDO and IDO-COVID-19
Fig. 8
Fig. 8
DL Query for part_of some virus replication
Fig. 9
Fig. 9
DL Query for preceded_by some SARS-CoV-2 attachment stage
See this image and copyright information in PMC

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