Open Science Foundation Preprints (2020)

Regina Hurley
Northwestern University
John Beverley
Northwestern University
Barry Smith
State University of New York, Buffalo
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 Ontologies (OBO) 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 IDOCore, 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 contents 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 choicepoints 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.
Keywords COVID-19  SARS-CoV-2  Infectious Diseases  Open Biomedical Ontologies (OBO)
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Are Viruses Alive? The Replicator Paradigm Sheds Decisive Light on an Old but Misguided Question.Eugene V. Koonin & Petro Starokadomskyy - 2016 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 59:125-134.
Definitions in Ontologies.Selja Seppälä, Alan Ruttenberg, Yonatan Schreiber & Barry Smith - 2016 - Cahiers de Lexicologie 109 (2):175‐207.

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