Functional similarity of gene products can be estimated by controlled biological vocabularies, such as Gene Ontology (GO). 

Four methods have been presented to determine the semantic similarity of two GO terms based on the annotation statistics of their common ancestor terms (Resnik (Philip, 1999), Jiang (Jiang and Conrath, 1997), Lin (Lin, 1998) and Schlicker (Schlicker et al., 2006)). Wang (Wang et al., 2007) proposed a new method to measure the similarity based on the graph structure of GO. Each of these methods has its own advantages and weaknesses. 

Recently, Yu and colleagues developed a R package named GOSemSim, which can be used to compute semantic similarity among GO terms, sets of GO terms, gene products, and gene clusters,  In addition, GOSemSim provides all five methods mentioned above.