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A Python client for Sherlok

Project description

See <http://sherlok.io/>.

pip install --upgrade sherlok

from sherlok import Sherlok

print list(Sherlok().annotate('neuroner', 'layer 4 neuron'))

[(0, 14, 'layer 4 neuron', u'Neuron', {}),
 (8, 14, 'neuron',  u'Neuron', {}),
 (8, 14, 'neuron',  u'NeuronTrigger', {}),
 (0, 7,  'layer 4', u'Layer', {u'ontologyId': u'HBP_LAYER:0000004'})]


 # filtering and finding the text back
s = Sherlok()
txt = 'parvalbumin-positive fast-spiking basket cells, somatostatin-positive regular-spiking bipolar and multipolar cells, and cholecystokinin-positive irregular-spiking bipolar and multipolar cells'
morphology = s.select(s.annotate('neuroner', txt), u'Morphology')
for m in morphology:
    print m

(175, 185, 'multipolar', u'Morphology', {})
(163, 170, 'bipolar', u'Morphology', {})
(98, 108, 'multipolar', u'Morphology', {})
(86, 93, 'bipolar', u'Morphology', {})
(34, 40, 'basket', u'Morphology', {})

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