<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>

CC BY-SA 4.0
2018-10-18T08:48:16.650Z
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) ?
llrs
CC BY-SA 4.0
2018-10-18T08:50:45.877Z
sorry if you feel that way. but did you saw any GO calculated in goatools ?
Mani
CC BY-SA 4.0
2018-10-18T08:53:52.957Z
I linked a notebook explaining how they do it..
llrs
CC BY-SA 4.0
2018-10-18T08:46:01.737Z
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
CC BY-SA 4.0
2018-10-18T08:31:16.950Z
2018-10-18T08:31:16.950Z
llrs
<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>

CC BY-SA 4.0
2018-10-17T19:15:42.387Z
Welcome.  What tools have you been using?
Bioathlete
CC BY-SA 4.0
2018-10-17T19:16:16.047Z
hubalign ......
Mani
CC BY-SA 4.0
2018-10-18T07:02:01.513Z
Do you need it in python? I know one very nice package in R that does that.
llrs
CC BY-SA 4.0
2018-10-18T08:24:04.140Z
@Llopis it would be nice in python but if any R package you know, kindly mention that
Mani
<phylogenetics><proteins><networks><protein-protein-interaction>
How to calculate Gene Ontology terms in python
# 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  

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## 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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