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. (shrink)

Axiom weakening is a technique that allows for a fine-grained repair of inconsistent ontologies. Its main advantage is that it repairs on- tologies by making axioms less restrictive rather than by deleting them, employing the use of refinement operators. In this paper, we build on pre- viously introduced axiom weakening for ALC, and make it much more irresistible by extending its definitions to deal with SROIQ, the expressive and decidable description logic underlying OWL 2 DL. We extend the definitions of (...) refinement operator to deal with SROIQ constructs, in particular with role hierarchies, cardinality constraints and nominals, and illustrate its application. Finally, we discuss the problem of termi- nation of an iterated weakening procedure. (shrink)