Oort simple release missing inferred subclasses when equivalence axioms with cardinality is used

From cmung...@gmail.com on June 08, 2012 11:43:39

If a source ontology contains an equivalence axiom and no additional axioms:

id: UBERON:0009203
name: internasal suture
intersection_of: UBERON:0009199 ! facial suture
intersection_of: connects UBERON:0001681 {cardinality="2"} ! nasal bone

We want the simple file to omit the equivalence axiom, but include the most specific superclass axiom; e.g.

id: UBERON:0009203
name: internasal suture
is_a: UBERON:0009199 ! facial suture

in some cases this may be more specific - e.g UBERON:0011160 ! nasal suture in uberon. The more specific axiom can be found using a DL reasoner. But even in the case of EL reasoners, we should at least be able to infer that it's a subclass of the genus class.

However, the simple file produced by Oort+ELK lacks any logical axioms; e.g. an orphan:

id: UBERON:0009203
name: internasal suture

Presumably this is because the equiv axiom is ignored entirely by Elk. Maybe we need to pre-process and add a subclass?

Original issue: http://code.google.com/p/owltools/issues/detail?id=40

Start with the Oort simple release path and its interaction with the ELK reasoner, using the UBERON:0009203 example in the issue as the reproduction case. Trace how equivalence axioms with cardinality are handled and compare the generated simple output; done means the output includes at least the genus subclass axiom instead of leaving the term orphaned.