A Python client for Sherlok
Sherlok is a flexible and powerful open source, distributed, real-time text-mining engine.
Published as a pip package at https://pypi.python.org/pypi/sherlok/
pip install --upgrade sherlok
from sherlok import Sherlok
s = Sherlok('neuroner')
# returns a list of tuples (begin, end, text, annotation_type, attributes{})
print s.annotate('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
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.annotate(txt, u'Morphology')
for (start, end, text, _type, properties) in morphology:
print text, properties[u'ontologyId']
basket HBP_MORPHOLOGY:0000019
bipolar HBP_MORPHOLOGY:0000006
multipolar HBP_MORPHOLOGY:0000035
bipolar HBP_MORPHOLOGY:0000006
multipolar HBP_MORPHOLOGY:0000035
