State of the Art: Infectious Disease, Viruses, COVID-19, and Ontology

CIDO: The Community-based Infectious Disease Ontology, with Oliver He, Asiyah Lin, Barry Smith, et. al.
(Published in Science Data)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontology has emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented.

The Virus Infectious Disease Ontology (VIDO) and the COVID-19 Infectious Disease Ontology (IDO-COVID-19)
(with Shane Babcock, Lindsay Cowell, Alex Diehl, and Barry Smith)

VIDO is a logical extension of the Infectious Disease Ontology (IDO) with domain that studied by virologists, i.e. viruses, prions, satellites, viroids, as well as virus-related virus and disease surveillance, epidemiology, pathogenesis, treatment, and prevention. VIDO is a reference ontology for further extensions, such as the Coronavirus Infectious Disease Ontology (CIDO) in development by Oliver He and the He Group, and IDO-COVID-19 which builds on both IDO Virus and CIDO, to represent data concerning infection by SARS-CoV-2, the causative virus strain in COVID-19. You can find more information concerning each ontology on Bioportal (here for CIDO; here for VIDO; here for IDO-COVID-19), and follow updates and track development on github through the Infectious Disease Ontology Extensions organization.

The Infectious Disease Ontology in 2020
(with Shane Babcock, Lindsay Cowell, and Barry Smith)

The Infectious Disease Ontology (IDO) 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 within various areas of infectious disease research, 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 the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also 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.

ArgO: An Ontology of Arguments
(with Brian Donohue, Francesco Franda, Jean-Baptiste Guillon, J. Neil Otte, Alan Ruttenberg, and Yonatan Schreiber)

Although the last decade has seen a proliferation of ontologies of arguments, many lack semantic interoperability, are either too wide or too narrow in scope, or employ unprincipled solutions to argument representation. In contrast, we present the Arguments Ontology (ArgO), a modest mid-level ontology of arguments designed to be easily imported and extended by researchers working within an upper-level ontology framework, with logics outside the classical tradition, and with different approaches to argument evaluation. Unlike previous ontologies of arguments, ArgO is designed as an extension of the widely-used Information Artifact Ontology (IAO), itself an extension of the upper-level Basic Formal Ontology (BFO), thus ensuring semantic interoperability with a range of existing ontologies. Moreover, our treatment of arguments as involving premises which provide support for a single conclusion believed to follow from said premises, bridged by cognitive acts of inference, is the appropriate scope for the domain, ruling out, e.g. mere legal principles, while ruling in what intuitively count as arguments. Finally, our proposal is principled, based on rigorous definitions and formal axioms out of which characterizations of arguments naturally fall.

Basic Formal Ontology as an ISO-Standard

The Basic Formal Ontology is currently in the review process for becoming an ISO-Standard. I was fortunate enough to present my work on the first-order axiomatization and the meta-theoretic properties of this top-level ontology at a workshop held by the UB Ontology Research Group. You can find my slides from the talk (as well as slides from Barry Smith's talk and Michael Gruninger's talk) here.

Basic Formal Ontology and Automated Theorem Proving