Demonstrates mapping between GO GAF Codes (IEA, ISS, etc) and ECO classes.

See http://purl.obolibrary.org/obo/eco/gaf-eco-mapping.txt



In [1]:

    
## Create an EcoMap object, for mapping to and from ECO classes
from ontobio.ecomap import EcoMap
m = EcoMap()



In [2]:

    
## Create an ontology object for ECO;
## This is optional; we use this in this notebook
## to look up ECO class labels, and parentage
from ontobio.ontol_factory import OntologyFactory
ontol = OntologyFactory().create('eco')



In [3]:

    
## Given a code 'IEA' and no further information, map it
m.coderef_to_ecoclass('IEA')









    Out[3]:





'ECO:0000501'

Including a specific reference, such as GO_REF:000002 Gene Ontology annotation through association of InterPro records with GO terms can increase the specificity of the mapping



In [11]:

    
## Given a combination of a code plus a reference,
## we can map this to a more precise evidence type
cls = m.coderef_to_ecoclass('IEA','GO_REF:0000002')
cls









    Out[11]:





'ECO:0000256'



In [12]:

    
ontol.label(cls)









    Out[12]:





'match to sequence model evidence used in automatic assertion'



In [13]:

    
["{} '{}'".format(c, ontol.label(c)) for c in ontol.ancestors(cls)]









    Out[13]:





["ECO:0000202 'match to sequence model evidence'",
 "ECO:0000501 'evidence used in automatic assertion'",
 "ECO:0000044 'sequence similarity evidence'",
 "ECO:0000000 'evidence'",
 "ECO:0000249 'sequence similarity evidence used in automatic assertion'",
 "ECO:0000203 'automatic assertion'",
 "ECO:0000041 'similarity evidence'",
 "ECO:0000217 'assertion method'",
 "ECO:0000251 'similarity evidence used in automatic assertion'"]



In [14]:

    
m.ecoclass_to_coderef('ECO:0000501')









    Out[14]:





('IEA', None)



In [15]:

    
m.ecoclass_to_coderef('ECO:0000256')









    Out[15]:





('IEA', 'GO_REF:0000002')



In [ ]: