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baileythegreen / PyOntoQuery

Retrieves information from an ontology tree.
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Odd behaviour when disease does not exist in supra_category #4

Open baileythegreen opened 3 years ago

baileythegreen commented 3 years ago

See reported error below:

it works quite well, but i am not sure what it exactly spits out when the term doesn't exist under the selected supra category

for example: interleukin-6 receptor measurement with supracategory disease by anatomical system spits out "nervous system disease" but when you look it up in the EFO browser it comes out under information entity supracategory, it's not in anatomical system

at the same time this is in the log file: interleukin-6 measurement, chronic obstructive pulmonary disease is not a valid entry

does it currently work with partial mapping? in this case my entry traits were exactly the same as the EFO traits, so would be interested in only exact mapping. maybe that's for feature request, partial or exact mapping as an option

baileythegreen commented 3 years ago

Seems resolved, but I am not clear on what caused this to start with (and have not seen the behaviour myself).

Might have been caused by the calls to .lower() and .replace() that were being used for fuzzy matching, though this doesn't really make sense.