The Genetic Interaction Ontology (GIO) incorporating the Genetic Interactions Structured Terminology (GIST)
posterposted on 20.04.2020 by Christian A Grove, Rose Oughtred, Kara Dolinski, Mike Tyers, Paul Sternberg
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Genetic interactions have been studied for more than a century as a means to elucidate gene function. Built on prior work by the authors, a new unified genetic interaction ontology (GIO) incorporating the genetic interactions structured terminology (GIST) is proposed for inclusion into the Human Proteome Organization (HUPO) Protein Standards Initiative (PSI) Molecular Interactions (MI) controlled vocabulary (https://github.com/HUPO-PSI/psi-mi-CV). The updated, proposed ontology includes a restructuring of the upper level of the ontology, clear references to definitions and meanings described in the literature, direct incorporation of genetic interaction terms from the Biological General Repository for Interaction Datasets (BioGRID) database (https://thebiogrid.org/), relabeling of some terms, GIST synonyms for existing terms, obsoletion of outdated terms, and some new proposed terms to incorporate GIST and ensure consistent ontology structure. An important distinction is made between genetic interactions that are reported as modifications of an existing phenotype versus genetic interactions that defy expectation (i.e. deviate significantly from an inherent or mathematically determined expected double genetic perturbation phenotype), as both meanings have been used in the literature and in biological data repositories. The proposed ontology can accommodate many existing use cases for quantitative genetic interactions described in the model organism literature, but is not intended or purported to be exhaustive or comprehensive. Suggestions for edits or new terms from the genetics community are strongly encouraged.