Regina Hurley

'Injury' is a term widely used not only in common speech but also in medical, public health, occupational safety, sports science, as well as in military, legal and police forensic contexts. The definitions of ‘injury’ across these disciplines vary widely, often owing to differences in the priorities in different domains. But these inconsistencies cause problems. They create challenges, for example, in the classification and compilation of pattern data; they contribute to the siloing of data, and they thereby hinder cross-disciplinary research and development. To address these problems, we introduce here the Injury Ontology (INJO), which will provide a unified definition of ‘injury’ while accommodating the specific representational needs across various disciplines.

Curiosity is increasingly recognized as vital to healthy aging, but the potential for leveraging research on curiosity to promote healthy aging is undermined by definitional inconsistencies and ambiguities in the literature—an issue that ontologies are uniquely well positioned to resolve. This paper proposes an ontological framework for modeling curiosity that addresses major shortcomings in existing definitions. Drawing on the Basic Formal Ontology (BFO) and the Emotion Ontology (MFOEM), I define a curiosity-emotion-process in terms of an appraisal of search-worthiness and an exploratory action tendency. I also define a related curiosity disposition. My approach enables clear distinctions among subtypes of both kinds of curiosity. The result is a more flexible, rigorous model of the various phenomena described as “curiosity” that aligns with empirical findings

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. 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 virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects.

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.