Lookup A Gene Ontology Definition With Biopython

Question

[anothergeek]

What is the easiest way to lookup a GO term in Python, given the GO ID?

[Giovanni M Dall'Olio]

currently biopython doesn't have support for GO. What do you want to do, exactly? what do you mean by 'lookup'?

[O.rka]

It's not for Python 3.5 :(

Answer 1

[brentp]

you can also use goatools in python:

it would look like:

>>> from goatools import obo_parser
>>> p = obo_parser.GODag('data/gene_ontology.1_2.obo')
>>> p['GO:0006915'].name
'apoptosis'

you'll just have to download the obo from here.

[Eric Normandeau]

Very interesting to know :)

[Eric Normandeau]

Very interesting to know :) Is there a way in goatools to do statistical testing on a set and a subset of genes to know if the subset contains over-representated functions?

[Simon Cockell]

Didn't know about goatools, will have to investigate further. Thanks :)

Answer 2

[Simon Cockell]

You could use the QuickGO web services. These tools allow you to quickly download relevant information, given a GO ID.

For instance, take the ID GO:0006915.

import urllib
from xml.etree import cElementTree as ElementTree

def get_go_name(go_id):
    #get the GO entry as XML
    xml = urllib.urlopen("http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:"+go_id+"&format=oboxml")
    #open in cElementTree, for fast XML parsing
    for event, element in ElementTree.iterparse(xml):
        #need to make sure we are getting the name contained within the 'term' entry
        if element.tag == 'term':
            for child in element.getchildren():
                #this is the name of the GO ID in the URL above.
                if child.tag == 'name':
                    return child.text

print get_go_name('0006915')

This script should print 'apoptosis'.

Answer 3

[ric]

Is goatools still the most up to date python package?

Any idea how the files in goatools / data / on Github were created?

How would it be possible to use plotgoterm.py (from goatools) to create input files for Cytoscape or VisANT ?

• http://www.cytoscape.org/
• http://visant.bu.edu/