# 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

• Welcome. What tools have you been using? Oct 17 '18 at 19:15
• hubalign ......
– Mani
Oct 17 '18 at 19:16
• Do you need it in python? I know one very nice package in R that does that.
– llrs
Oct 18 '18 at 7:02
• @Llopis it would be nice in python but if any R package you know, kindly mention that
– Mani
Oct 18 '18 at 8:24

## 1 Answer

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.

• thanks @Llopis. i looked into goatools already but i don't think that they are have methods to calculate GO CC, MF or BP
– Mani
Oct 18 '18 at 8:46
• Please, mention in the questions what you have done, because now I feel that I wasted my time trying to answer you when your problem is something else. Did you look at the notebook ?
– llrs
Oct 18 '18 at 8:48
• sorry if you feel that way. but did you saw any GO calculated in goatools ?
– Mani
Oct 18 '18 at 8:50
• I linked a notebook explaining how they do it..
– llrs
Oct 18 '18 at 8:53