Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-10-18T08:48:16.650Z
Answers.Text: 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](https://github.com/tanghaibao/goatools/blob/master/notebooks/semantic_similarity.ipynb) ?
Answers.UserDisplayName: llrs
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-10-18T08:50:45.877Z
Answers.Text: sorry if you feel that way. but did you saw any GO calculated in goatools ?
Answers.UserDisplayName: Mani
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-10-18T08:53:52.957Z
Answers.Text: I linked a notebook explaining how they do it..
Answers.UserDisplayName: llrs
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-10-18T08:46:01.737Z
Answers.Text: thanks @Llopis. i looked into goatools already but i don't think that they are have methods to calculate GO CC, MF or BP
Answers.UserDisplayName: Mani
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Answers.CreationDate: 2018-10-18T08:31:16.950Z
Answers.LastActivityDate: 2018-10-18T08:31:16.950Z
Answers.UserDisplayName: llrs
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-17T19:15:42.387Z
Comments.Text: Welcome.  What tools have you been using?
Comments.UserDisplayName: Bioathlete
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-17T19:16:16.047Z
Comments.Text: hubalign ......
Comments.UserDisplayName: Mani
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-18T07:02:01.513Z
Comments.Text: Do you need it in python? I know one very nice package in R that does that.
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-18T08:24:04.140Z
Comments.Text: @Llopis it would be nice in python but if any R package you know, kindly mention that
Comments.UserDisplayName: Mani
Tags: <phylogenetics><proteins><networks><protein-protein-interaction>
Title: How to calculate Gene Ontology terms in python
ThreadText: # How to calculate Gene Ontology terms in python
  
  (Asked by: username_0 on 2018-10-17)
  
  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
  
  **Tags:** phylogenetics, proteins, networks, protein-protein-interaction
  
  > **Comments:**
  > **username_1**: Welcome.  What tools have you been using?  
  > **username_0**: hubalign ......  
  > **username_2**: Do you need it in python? I know one very nice package in R that does that.  
  > **username_0**: @Llopis it would be nice in python but if any R package you know, kindly mention that  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-10-18. Score: 2
  
  You can calculate gene ontology similarity with the [GOSemSim](http://bioconductor.org/packages/GOSemSim) R package ([paper](http://doi.org/10.1093/bioinformatics/btq064))(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](https://pypi.org/project/goatools/) ([paper](https://www.nature.com/articles/s41598-018-28948-z)). I think there was another Python package but now I don't remember its name.
  
  > **Comments:**
  > **username_0**: thanks @Llopis. i looked into goatools already but i don't think that they are have methods to calculate GO CC, MF or BP  
  > **username_2**: 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](https://github.com/tanghaibao/goatools/blob/master/notebooks/semantic_similarity.ipynb) ?  
  > **username_0**: sorry if you feel that way. but did you saw any GO calculated in goatools ?  
  > **username_2**: I linked a notebook explaining how they do it..  
  
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