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renaud / neuroNER

named entity recognizer for neuronal cells, based on UIMA Ruta rules
GNU Lesser General Public License v3.0
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Issue with identifying protein-triggers #11

Closed stripathy closed 9 years ago

stripathy commented 9 years ago

Why is parvalbumin, calbindin and calretinin not recognized as part of the neuroNER below in the last part of the sentence (see image)? I think it has to do with the updating of the protein-trigger.

screen shot 2015-06-16 at 9 26 05 am

Sentence: In doing so, we find that the vast majority (87%) of parvalbumin-immunoreactive neurons express m1-type muscarinic Acetylcholine receptors. m1 receptors are also expressed by 60% of calbindin-immunoreactive neurons and 40% of calretinin-immunoreactive neurons. m2 AChRs, on the other hand, are expressed by only 31% of parvalbumin neurons, 23% of calbindin neurons, and 25% of calretinin neurons.

stripathy commented 9 years ago

In other words, don't require that the protein trigger be activated before identifying the protein.

Parvalbumin-expressing neurons // works currently parvalbumin neuron // doesn't work currently

neuron expressing parvalbumin // marks, but doesn't get ontology ID currently // [NeuronTrigger] [ProteinTrigger] [ProteinProp]

stripathy commented 9 years ago

In addition to this case listed above: parvalbumin neuron // doesn't work currently //[ProteinProp] [NeuronTrigger]

We also need to support the following case: parvalbumin basket cell //[ProteinProp][NeuronProp][NeuronTrigger]

renaud commented 9 years ago

Should be fixed with 0d72d1f455. Works for the following cases, see the tests