The Autophagy Ontology (AtgO) is an ontology of functions comprising autophagy, a central cellular recycling process implicated in numerous diseases. AtgO is inferred directly from 'omics datasets using the Active Interaction Mapping procedure, combining information from previously published 'omics data with a newly generated genetic interaction map targeted at the autophagy in Saccharomyces cerevisiae. Terms in AtgO represent autophagy subprocesses and components, acting as an automated curation of literature while simultaneously uncovering new autophagy biology.