def test_filter(self):
s = Sherlok('neuroner')
annotations = s.annotate('layer 2/3 nest basket cell').annotations
self.assertEqual(len(annotations), 8)
selected = s.annotate('layer 2/3 nest basket cell',
'Layer').annotations
self.assertEqual(len(selected), 1)
def get_neuroner_annotations(neuron_long_name):
sherlok_instance = Sherlok('neuroner')
r = sherlok_instance.annotate(neuron_long_name)
annot_dict = clean_annotations(r.annotations, neuron_long_name, return_dict = False)
return annot_dict
def test_opennlp_ners(self):
s = Sherlok('opennlp.ners.en')
text = '''Jack Burton (born April 29, 1954 in El Paso), also known as Jake Burton, is an American snowboarder and founder of Burton Snowboards.'''
annotations = s.annotate(text).annotations
self.assertEqual(len(annotations), 3)
for a in annotations:
print a
def test_cleanup(self):
s = Sherlok('neuroner')
an = s.annotate('layer 4 pyramidal long large neuron').annotations
clean = clean_annotations(an)
self.assertEqual(clean, [
'HBP_LAYER:0000004', u'HBP_MORPHOLOGY:0000001', 'Missing:long',
'Size:large', 'NeuronTrigger:neuron'
])
#print('{} ({})'.format(hbp_cell_names[hbp_id][0], hbp_id))
already_printed = []
for nlex_id, score, explain in hits_sorted[:5]:
# only if more than Neocortex
explain_str = ' '.join(flatten(explain))
if nlex_id not in already_printed and explain_str != 'ABA_REGION:315 exact same brain region':
already_printed.append(nlex_id)
#print explain_str
#print '* {} ({}, {})'.format(nlex_cell_names[nlex_id][0], round(score, 2), nlex_id)
outf.write('{}\t{}\t{}\t{}\t{}\t{}\n'.format(hbp_cell_names[hbp_id][0], hbp_id, nlex_cell_names[nlex_id][0], round(score, 2), nlex_id, explain_str))
# In[45]:
cell_= 'Nest Basket Cell' #'nest basket cell'
clean_annotations(neuroner.annotate(cell_).annotations)
# In[47]:
sorted(hbp_hits['HBP_CELL:0000061'], key=get_key, reverse=True)[:5]
# In[ ]:
#print('{} ({})'.format(hbp_cell_names[hbp_id][0], hbp_id))
already_printed = []
for nlex_id, score, explain in hits_sorted[:5]:
# only if more than Neocortex
explain_str = ' '.join(flatten(explain))
if nlex_id not in already_printed and explain_str != 'ABA_REGION:315 exact same brain region':
already_printed.append(nlex_id)
#print explain_str
#print '* {} ({}, {})'.format(nlex_cell_names[nlex_id][0], round(score, 2), nlex_id)
outf.write('{}\t{}\t{}\t{}\t{}\t{}\n'.format(hbp_cell_names[hbp_id][0], hbp_id, nlex_cell_names[nlex_id][0], round(score, 2), nlex_id, explain_str))
# In[45]:
cell_= 'Nest Basket Cell' #'nest basket cell'
_cleanup(neuroner.annotate(cell_).annotations)
# In[47]:
sorted(hbp_hits['HBP_CELL:0000061'], key=get_key, reverse=True)[:5]
# In[ ]:
def test_cleanup(self):
s = Sherlok('neuroner')
an = s.annotate('layer 4 pyramidal long large neuron').annotations
clean = clean_annotations(an)
self.assertEqual(clean, ['HBP_LAYER:0000004', u'HBP_MORPHOLOGY:0000001', 'Missing:long', 'Size:large', 'NeuronTrigger:neuron'])
from sherlok import Sherlok # pip install sherlok pipeline = 'bluima.regions_rules' host = '128.178.97.193' s = Sherlok(pipeline, host=host) text = 'neocortex projects to the nucleus accumbens' res = s.annotate(text) print res.annotations res.refs # in
from sherlok import Sherlok # pip install sherlok pipeline = 'bluima.regions_rules' host = '128.178.97.193' s = Sherlok(pipeline, host=host) text = 'neocortex projects to the nucleus accumbens' res = s.annotate(text) print res.annotations res.refs # in
def test_cleanup(self):
s = Sherlok("neuroner")
an = s.annotate("layer 4 pyramidal long large neuron").annotations
clean = _cleanup(an)
self.assertEqual(clean, ["HBP_LAYER:0000004", u"HBP_MORPHOLOGY:0000001", "Missing:long", "Size:large"])
