Ontologies are widely used constructs for encoding and analyzing biomedical data, but the absence of simple and consistent tools has made exploratory and systematic analysis of such data unnecessarily difficult. Here we present three packages which aim to simplify such procedures. The ontologyIndex package enables arbitrary ontologies to be read into R, supports representation of ontological objects by native R types, and provides a parsimonius set of performant functions for querying ontologies. ontologySimilarity and ontologyPlot extend ontologyIndex with functionality for straightforward visualization and semantic similarity calculations, including statistical routines. $\textbf{AVAILABILITY AND IMPLEMENTATION}$: ontologyIndex, ontologyPlot and ontologySimilarity are all available on the Comprehensive R Archive Network website under https://cran.r-project.org/web/packages ; Other ; This work was supported by National Institute for Health Research award RG65966 (D.G. and E.T.) and the Medical Research Council programme grant MC_UP_ 0801/1 (D.G. and S.R.).