Abnormal processes in MP have not all been transformed to use ‘inheres in part of’

[obophenotype-user]

Originally reported on Google Code with ID 90

There are some classes in MP that are abnormal processes but they do not use 'inheres
in part of', instead use 'inheres in'.

Can this be automatically transformed?

Examples
MP_0000119
abnormal tooth eruption
'has part' some (quality and ('has component' some abnormal) and ('inheres in part
of' some 'tooth eruption'))

MP_0020026 abnormal aldehyde oxidase activity
'has part' some (quality and ('inheres in' some 'aldehyde oxidase activity') and ('has
component' some abnormal))

Reported by vasilevs@ohsu.edu on 2015-02-11 23:24:51

[obophenotype-user]

Also, same issue exists in HP

Reported by vasilevs@ohsu.edu on 2015-02-11 23:25:35

[obophenotype-user]

Never mind about tooth eruption above.

Reported by vasilevs@ohsu.edu on 2015-02-11 23:26:24

[obophenotype-user]

Examples in HP:
HP_0000816 Abnormality of Krebs cycle metabolism
HP_0010932 Abnormality of nucleobase metabolism

Reported by vasilevs@ohsu.edu on 2015-04-06 15:41:39

[obophenotype-user]

Reported by vasilevs@ohsu.edu on 2015-04-13 15:16:07

[cindyJax]

Okay, how do you distinguish GO process terms from GO cellular component in a script?

[drseb]

maybe via a DL-query in protege:

for all phenotype classes with biological process execute (with 'subclasses' checked):

'has part' some 
    (quality
     and ('inheres in' some biological_process)
     and ('has modifier' some abnormal))

maybe @cmungall knows a better solution!?

[cindyJax]

That wasn't working for a lot of reasons.... at least I picked up most of the apoptosis terms that I thought I would convert this way (still at 'inheres in')