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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

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    $\begingroup$ Welcome. What tools have you been using? $\endgroup$
    – Bioathlete
    Oct 17, 2018 at 19:15
  • $\begingroup$ hubalign ...... $\endgroup$
    – Mani
    Oct 17, 2018 at 19:16
  • $\begingroup$ Do you need it in python? I know one very nice package in R that does that. $\endgroup$
    – llrs
    Oct 18, 2018 at 7:02
  • $\begingroup$ @Llopis it would be nice in python but if any R package you know, kindly mention that $\endgroup$
    – Mani
    Oct 18, 2018 at 8:24

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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.

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  • $\begingroup$ thanks @Llopis. i looked into goatools already but i don't think that they are have methods to calculate GO CC, MF or BP $\endgroup$
    – Mani
    Oct 18, 2018 at 8:46
  • $\begingroup$ 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 ? $\endgroup$
    – llrs
    Oct 18, 2018 at 8:48
  • $\begingroup$ sorry if you feel that way. but did you saw any GO calculated in goatools ? $\endgroup$
    – Mani
    Oct 18, 2018 at 8:50
  • $\begingroup$ I linked a notebook explaining how they do it.. $\endgroup$
    – llrs
    Oct 18, 2018 at 8:53

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