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esilgard / argos_nlp

main repository for the argos/hidra nlp engine
Apache License 2.0
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Using the NLP Engine for Cytogenetics #41

Open cjamadagni opened 6 years ago

cjamadagni commented 6 years ago

Similar to pathology, are there example disease groups for Cytogenetics? Like how pathology has 'brain' and 'head_neck'.

On inspecting process.py there is a comment saying "disease specific cytogenetics data dictionary (no general algorithms currently)", but when I look at data_dictionary.txt I can't see any disease specific data.

Apologies in advance, I'm new to the area of health and don't understand most medical terms so I may be missing something basic. Could you please provide a sample usage with sample disease groups for Cytogenetics?

esilgard commented 6 years ago

Hi cjamadagni, that's a great question. I should probably state explicitly in the README that there are currently only classifications for hematological malignancies (the 'heme' disease group). That has more to do with which groups I've worked closely with in the past. However cytogenetics data is used much more within hematological malignancies and AML specifically than in diagnosing solid tumors (to my knowledge anyway). Is there a specific disease that you're interested in working with?

the canonical usage for the cytogenetics parsing would be to apply some sort of prognostic risk classification based on a specific abnormality or group of abnormalities. To date I have only done this with acute myeloid leukemia classifications, although there are others.

cjamadagni commented 6 years ago

Thank you so much for telling me how I can execute the code! There is no particular disease as of now. I was trying to understand the code base and just wanted to know how I could run the code for cytogenetics. Thank you.