uPheno 2 review

[matentzn]

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]

@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]

• 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]

• 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]

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

[matentzn]

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