I need to run semantic similarity searches on human phenotype ontology.

I am aware of packages like GoSim, SemSim etc. These packages works well with GO. I am looking for a package that can take any .obo file and run semantic similarities on top of it. Do you know of any packages that can do it?

Thanks in advance!
This is what dnet package can do. See http://supfam.org/dnet/dDAGtermSim.html. However, in this example you need to replace with human phenotype ontology. More information about how to load different ontologies can be found in http://supfam.org/dnet/docs.html.

If you provide details about your annotation information, then probably I can provide more details.