In [4]:

    

from ontobio.ontol_factory import OntologyFactory

ofactory = OntologyFactory()
ont = ofactory.create("pato")  ## Connect remotely to PATO over SPARQL
##
## Note: Jupyter may show '*' to indicate kernel busy while this is being
## fetched - should only take a few seconds. Wait before proceeding


    

    




h:pato g:

In [6]:

    

cls = ont.node('PATO:0001374')
cls


    

    
Out[6]:





{'label': 'ploidy'}

In [12]:

    

ancs = ont.descendants('PATO:0001374')
ancs


    

    
Out[12]:





{'PATO:0001375',
 'PATO:0001376',
 'PATO:0001377',
 'PATO:0001378',
 'PATO:0001379',
 'PATO:0001380',
 'PATO:0001381',
 'PATO:0001382',
 'PATO:0001383',
 'PATO:0001384',
 'PATO:0001385',
 'PATO:0001386',
 'PATO:0001387',
 'PATO:0001388',
 'PATO:0001389',
 'PATO:0001390',
 'PATO:0001391',
 'PATO:0001392',
 'PATO:0001393',
 'PATO:0001394',
 'PATO:0001395'}

In [14]:

    

["{} '{}'".format(x, ont.label(x)) for x in ont.descendants('PATO:0001374')]


    

    
Out[14]:





["PATO:0001376 'monoploid'",
 "PATO:0001380 'paleopolyploid'",
 "PATO:0001379 'allopolyploidy'",
 "PATO:0001377 'polyploid'",
 "PATO:0001390 'partial trisomy'",
 "PATO:0001375 'haploid'",
 "PATO:0001392 'endopolyploid'",
 "PATO:0001385 'aneuploid'",
 "PATO:0001395 'haplodiploid'",
 "PATO:0001382 'tetraploid'",
 "PATO:0001378 'autopolyploid'",
 "PATO:0001394 'diploid'",
 "PATO:0001383 'pentaploid'",
 "PATO:0001393 'euploid'",
 "PATO:0001391 'mosaic trisomy'",
 "PATO:0001386 'monosomy'",
 "PATO:0001389 'trisomy'",
 "PATO:0001387 'disomy'",
 "PATO:0001388 'uniparental disomy'",
 "PATO:0001381 'triploid'",
 "PATO:0001384 'hexaploid'"]

In [15]:

    

ont.subsets() ## Issues remote call; Jupyter may show '*' for ~1s


    

    
Out[15]:





['http://purl.obolibrary.org/obo/pato#abnormal_slim',
 'http://purl.obolibrary.org/obo/pato#absent_slim',
 'http://purl.obolibrary.org/obo/pato#attribute_slim',
 'http://purl.obolibrary.org/obo/pato#cell_quality',
 'http://purl.obolibrary.org/obo/pato#disposition_slim',
 'http://purl.obolibrary.org/obo/pato#hpo_slim',
 'http://purl.obolibrary.org/obo/pato#mpath_slim',
 'http://purl.obolibrary.org/obo/pato#relational_slim',
 'http://purl.obolibrary.org/obo/pato#scalar_slim',
 'http://purl.obolibrary.org/obo/pato#value_slim']

In [16]:

    

slim = ont.extract_subset('absent_slim') ## Issues remote call; Jupyter may show '*' for ~1s


    

In [18]:

    

["{} '{}'".format(x, ont.label(x)) for x in slim]


    

    
Out[18]:





["PATO:0000462 'absent'",
 "PATO:0000467 'present'",
 "PATO:0015001 'absence due to degeneration'"]

In [ ]: