Top level cleanup

[pbuttigieg]

Cleaning up orphaned and oddly imported ; used class at the top-level.

• Many of these were asserted in some axiom, but never imported.
• Some are more puzzling: they seem to be orphaned because their superclasses were asserted in equivalence axioms which were not imported.
• Some, like CHEBI:role, are asserted as equivalent to and a subclass of BFO:role in our PATO import, it seems, which I think gunks things up.

[pbuttigieg]

we're currently here:

But I had to assert stuff in ENVO that I don't think I should have to:

• food material as a subclass of environmental material (has equivalence axiom:
  • environmental material and (has role some food)
  • no subclass axiom
  • CHEBI:food imported
• plant used for... under PO:'whole plant' (already imported)

Other issues are expected.

[pbuttigieg]

Looks better now

The orphan ENVO term will be addressed when we close the remaining PRs from @marieALaporte 's team.

I have no idea what's up with the CHEBI vs BFO role thing that we're apparently coming in from our PATO import.