uPheno 2 review - Githubissues

obophenotype / upheno-dev

Framework for the automated construction of uPheno 2.0

MIT License

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uPheno 2 review #40

Open matentzn opened 1 year ago

matentzn commented 1 year ago

2022-09-16 @rays22, @souzadevinicius, @ar-ibrahim, @matentzn

[ ] Why is there no 'abnormal femur' class in uPheno? - These should be automatically generated?
[ ] 'decreased length femur': why is 'decreased length' under 'decreased size'? see --> PATO:0000122 length
[ ] Try to use NLP or graph ML to predict hierarchies/facilitate categorisation and fill missing gaps?
[ ] Why is 'absent' is not a child of 'abnormal'?

matentzn commented 1 year ago

@rays22 no need to act on this ticket, we will discuss it in the Friday meetings. The important thing is that you and Arwa spend 60-90 minutes each week to just look at uPheno in OLS and figure out "odditities" (classifications that look unintuitive or wrong) and "opportunities" (missing links that should be there).

matentzn commented 1 year ago

rename abnormal phenotype or parts
right now not all intermediate classes (abnormal muscle of abdomen) are created, which seems sometimes a bit random. Maybe create if more than 1 SSPO child?

matentzn commented 1 year ago

remove all logical axioms that don't conform not just EQs - FYPO classes have a lot of subclass of statements that are also broken.

matentzn commented 1 year ago

make QC check to detect normal phenotypes under abnormal ones
make issues for all SSPOs where this violation happens

matentzn commented 1 year ago

Consider removing all axioms other than A sub B from SSPO? Would be a shame for correct partial EQs?