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.

BackgroundEfforts to respond effectively to public health emergencies, such as we are now experiencing with COVID-19, require data sharing across multiple disciplines, and this is hindered by the fact that relevant information is often collected using discipline-specific terminologies and coding systems and stored in heterogenous databases. Ontologies provide a powerful data sharing and integration tool. In practice, however, this method is often undermined by uncoordinated ontology development. Following the principles of the Open Biomedical Ontologies Foundry, the Infectious Disease Ontology (IDO) represents one step towards overcoming such silo problems.ResultsIDO is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we present applications of IDO Core together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including: IDO Virus (VIDO); the Coronavirus Infectious Disease Ontology (CIDO); and an extension of CIDO focusing on COVID-19 (IDO-COVID-19). We discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research.ConclusionsAs we face the continued threat of novel pathogens in the future, 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 already curated data from earlier diseases. IDO’s tightly coordinated suite of ontologies modules provides a powerful method of data integration and sharing that will allow physicians, researchers, and public health organizations to respond rapidly and efficiently both to the current and future public health crises.

The COVID-19 pandemic prompted immense investigation of the SARS-CoV-2 virus. Rapidly, accurately, and easily interpreting generated data is of fundamental concern. Ontologies – structured, controlled, vocabularies – support interoperability, and prevent the development of data silos which undermine interoperability. The Open Biological and Biomedical Ontology Foundry serves to ensure ontologies remain interoperable through adherence by its members to core ontology design principles. For example, the Infectious Disease Ontology (IDO) Core includes terminological content common to investigations of all infectious diseases. Ontologies covering more specific infectious diseases, in turn, extend from IDO Core, such as the Coronavirus Infectious Disease Ontology (CIDO). The growing list of virus specific IDO extensions has motivated construction of a reference ontology covering content common to viral infectious disease investigations: the Virus Infectious Disease Ontology (VIDO). Additionally, the present pandemic has motivated construction of a more specific extension of CIDO, covering terminological content specific to the pandemic: the COVID-19 Infectious Disease Ontology (IDO-COVID-19). We report here the development of VIDO and IDO-COVID-19. More specifically, we examine newly minted terms for each ontology, showcase reuse of terms from existing OBO ontologies, motivate choice-points for ontological decisions based on research from relevant life sciences, apply ontology terms to explicate viral pathogenesis, and discuss the annotating power of virus ontologies for use in machine learning projects.