I would like to calculate Semantic similarity between pairs of genes in the mammalian phenotype ontology.

Is it possible to use the functions in this package with other ontologies.

Or does anyone know of any other packages which have this functionality.

Thank you!

In principle it should, you should prepare the ontolgoy as described on the vignette with godataand the semantic similarities would work. However, make sure that the ontology follows the same structure than the gene ontology.