The primary use of the GO Cellular Component Ontology is for GO annotation, but it has also been used for phenotype annotation, and for the annotation of images. Another ontology with similar scope is the Subcellular Anatomy Ontology (SAO), part of the Neuroscience Information Framework Standard (NIFSTD) suite of ontologies. The SAO also covers cell components, but in the domain of neuroscience.
Recently, the GO Cellular Component Ontology was enriched in content and links to the Biological Process and Molecular Function branches of GO as well as to other ontologies. This was achieved in several ways, one of which was amalgamation of SAO terms with GO Cellular Component ones. As a result, nearly 100 new neuroscience-related terms were added to the GO.
A recent paper describes this effort, along with other recent developments in the GO Cellular Component Ontology.