Can't find T790M mutation in civicmine

[hongiiv]

Hi jakelever,

Thanks for this wonderful project.

When i used the civicmine (http://bionlp.bcgsc.ca/civicmine) i can't find "T790M" in any sentence. It was odd for me because EGFR T790M is very famous biomarker in treatment cancer.

This is a tokenizer problem that Spacy language model (en_core_web_sm) tokenizes the "T790M" as a "T790" and "M". (('T790', 'NOUN'), ('M', 'PROPN'))

I changed the kindred package like this (kindred/Parser.py)

if not model in Parser._models:
      Parser._models[model] = spacy.load(model, disable=['ner'])

      self.nlp = Parser._models[model]
      special_case = [{ORTH: "T790M"}]
      self.nlp.tokenizer.add_special_case("T790M", special_case)

Now "T790M" is ('T790M', 'VERB') fixed.

best, jakelever

[jakelever]

Hi @hongiiv , thanks for looking into this. I'll have a little dig myself and see what other issues there may be.

[stale[bot]]

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