obophenotype
Clean up owltools expand (if its not being used)
We should clean up uberon.makefile if owltools expand is not needed should check before cleaning up though - not 100% sure if its still being used
Just to clarify the issue before I have the time to actually do it:
The question is not whether owltools is still being used or not – it is absolutely being used. The question is whether it does anything useful.
One of the main uses of owltools in uberon.Makefile is (was?) to expand “macros” like never_in_taxon and the likes, because it used to be that owltools --expand-macros was the only tool we had to perform that operation.
Now it seems that the expansion is done by some SPARQL queries instead, raising the possibility that the macro expansion step performed by owltools --expand-macros might be for nothing. This is what needs to be checked.
Of course, while we’re at it, we can (and will) check whether there are any other uses of owltools that may no longer be needed or where it may be replaced by ROBOT – something we also need to do at the ODK level (INCATools/ontology-development-kit#622).
Just to let you know and to be linked here in this issue, expand-macros is removing the annotation that is being expanded as noted here. It's the only place that expand-macros is relevant in the uberon.Makefile.
owltools expand is already replaced with robot expand however, owltools still needs to remain for composite products (see https://github.com/obophenotype/uberon/issues/2588#issuecomment-1280861427)