A python program to compare the semantic similarities of objects annotated to biological ontologies (though it could be used for any ontology presumably). HEre I focused on the Gene Ontology and the Mammalian Phenotype Ontology.
This was created before I had a full realization of the need for orthogonal, modularized code. I would suggest looking at GoSemSim from Bioconductor instead:
http://bioconductor.org/packages/release/bioc/html/GOSemSim.html