In [2]:

    

from ontobio.ontol_factory import OntologyFactory

# Create ontology object, for mammalian phenotype ontology
# Transparently uses remote SPARQL service.
# (May take a few seconds to run first time, Jupyter will show '*'. BE PATIENT, do
# not re-execute cell)
ofactory = OntologyFactory()
ont = ofactory.create('mp')


    

In [3]:

    

from ontobio.assoc_factory import AssociationSetFactory

MOUSE = 'NCBITaxon:10090'

# Create association set
# Transparently uses remote Monarch service.
# (May take a few seconds to run first time, Jupyter will show '*'. BE PATIENT, do
# not re-execute cell)
afactory = AssociationSetFactory()
aset = afactory.create(ontology=ont,
                       subject_category='gene',
                       object_category='phenotype',
                       taxon=MOUSE)


    

In [9]:

    

[p1] = ont.search("abnormal hippocampus morphology")
[p2] = ont.search("abnormal glucose homeostasis")


    

In [10]:

    

genes = aset.query([p1, p2])


    

In [11]:

    

len(genes)


    

    
Out[11]:





12

In [12]:

    

genes


    

    
Out[12]:





['MGI:88227',
 'MGI:107164',
 'MGI:102548',
 'MGI:1926884',
 'MGI:88145',
 'MGI:97362',
 'MGI:98331',
 'MGI:102709',
 'MGI:109583',
 'MGI:103555',
 'MGI:2145264',
 'MGI:1929213']

In [14]:

    

["{} '{}'".format(g, aset.label(g)) for g in genes]


    

    
Out[14]:





["MGI:88227 'C3'",
 "MGI:107164 'Ppp3ca'",
 "MGI:102548 'Tsc2'",
 "MGI:1926884 'Huwe1'",
 "MGI:88145 'Bdnf'",
 "MGI:97362 'Nos3'",
 "MGI:98331 'Snap25'",
 "MGI:102709 'Cav1'",
 "MGI:109583 'Pten'",
 "MGI:103555 'Clcn3'",
 "MGI:2145264 'Nhlrc1'",
 "MGI:1929213 'Zbtb20'"]

In [28]:

    

z, xlabels, ylabels = aset.similarity_matrix(genes, genes)


    

In [29]:

    

import plotly.plotly as py
import plotly.graph_objs as go
import numpy as np


    

In [35]:

    

trace = go.Heatmap(z=-np.array(z),
                       x=xlabels,
                       y=ylabels)


    

In [36]:

    

py.iplot([trace], filename='labelled-heatmap')


    

    
Out[36]:

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