How to calculate Gene Ontology terms in python I am testing different Protein-Protein Interaction networks alignment tools. I observed that all alignment tools show some Gene Ontology terms similarity. How can I calculate Functional similarity / average functional similarity for Gene ontology's terms Biological processes, Cellular components, Molecular functionality of any two proteins networks
You can calculate gene ontology similarity with the GOSemSim R package (paper)(disclaimer I'm a contributor to this package). You have several similarity scores implemented, some of them are across the three subontologies.

In python you have the GOATOOLS (paper). I think there was another Python package but now I don't remember its name.