text: user3531: 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
  
  user48: 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. 
  
original_text: 3531: <p>I am testing different <code>Protein-Protein Interaction networks</code> alignment tools. I observed that all alignment tools show some <code>Gene Ontology</code> terms similarity. How can I calculate <code>Functional similarity</code> / <code>average functional similarity</code> for <code>Gene ontology</code>'s terms <code>Biological processes</code>, <code>Cellular components</code>, <code>Molecular functionality</code> of any two proteins networks</p>
   48: <p>You can calculate gene ontology similarity with the <a href="http://bioconductor.org/packages/GOSemSim" rel="nofollow noreferrer">GOSemSim</a> R package (<a href="http://doi.org/10.1093/bioinformatics/btq064" rel="nofollow noreferrer">paper</a>)(disclaimer I'm a contributor to this package). You have several similarity scores implemented, some of them are across the three subontologies.</p>
  
  <p>In python you have the <a href="https://pypi.org/project/goatools/" rel="nofollow noreferrer">GOATOOLS</a> (<a href="https://www.nature.com/articles/s41598-018-28948-z" rel="nofollow noreferrer">paper</a>). I think there was another Python package but now I don't remember its name. </p>
  