composite-metazoan: review use cases, strategy

CM is incredibly ambitious. It attempts:

• to account for every single ID in every single ontology
• to retain all axioms from those ontologies (as GCIs, if term merged)
• to try and make a single consistent coherent structure despite the fact that the underlying ontologies are massively different in design
• to do the merge in automated way

Note that it is not the fact that we are integrating across species that is the most ambitious aspect (though that is ambitious). It is the fact that the implicit design patterns are massively different, regardless of species differences. Seemingly minor modeling differences (e.g. treatment of X vessel vs X vasculature) can lead to big complications when making a single consistent structure.

we are forced to remove the strict disjointess axioms from uberon but even then there are things that look odd

Additionally a lot of the code is old owltools code and hard for people to mentally reason about

We should review use cases and see if we can explore simpler strategies, perhaps splitting CM into two files, one more minimal and coherent and the other maximal and experimental

• reduce number of species
• exclude intermediate classes, if the main use case is leaf classes

We can also experiment with more pre-empting slurping - if more leafy classes are given uberon IDs and put in the main ontology then they become more visible to normal automation and manual QC workflows