Towards the Prokaryotic Regulation Ontology: An Ontological Model to Infer Gene Regulation Physiology from Mechanisms in Bacteria

Citlalli Mejía-Almonte, Julio Collado-Vides


Here we present a formal ontological model that explicitly represents regulatory interactions among the main objects involved in transcriptional regulation in bacteria. These formal relations allow the inference of gene regulation physiology from gene regulation mechanisms. The automatically instantiated classes can be used to assist in the mechanistic interpretation of gene expression experiments done at the physiological level, such as RNA-seq. This is the first step to develop a more comprehensive ontology focused on prokaryotic gene regulation. The ontology is available at


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