We have improved the GO annotations available for mouse genes orthologous to the human genes in the SYSCILIA Consortium's Gold Standard set. In addition, ciliary terminology in the GO itself was improved in collaboration with GO ontology developers and the SYSCILIA Consortium. These improvements to the GO terms for the functions and roles of ciliary proteins, along with the increase in annotations of the corresponding genes, enhance the representation of ciliary processes and localizations and improve access to these data during large-scale bioinformatic analyses.