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