Calculate GO semantic similarity across proteins of different species

Question

[engr.imrannaqvi]

Hi,

I'm new to bio and am working on finding GO semantic similarity between proteins of two (different species) aligned networks (Like in this file where first column is from mouse and second is from worm). I looked into GOSemSim but it calculates GO for one specie only. I also looked into goatools but could not find any useful info out of it. What i exactly want to do is to find GO terms BP, CC & MF average similarity through Relevance Method and input is in the form of attached file. Any help will be greatly appreciated. thanks