Problem with classifying the Human Phenotype Ontology

Hi all,

I have stumbled onto a problem for which I would like to hear from your
experience.

In a project, I am using the Human Phenotype Ontology (
http://www.human-phenotype-ontology.org/).
For the sake of the project, I really only need the is_a structure of the
ontology, but as an OWL version was existing, and as we have anyway an RDF
framework to integrate data, I was thinking of using this version.
The OWL version is not a simple representation of the is_a structure, as it
is including axioms to map phenotypes to, from a quick inspection,
anatomical parts and "qualities".

Now, as with any ontology, I was at first trying to classify it. This is an
ontology (with imports) of around 20k classes (<200k axioms, ~60k logical
axioms). It is big, but not huge.
I simply cannot classify it in any reasonable time.
I have tried a variety of reasoners and, in my longest wait, I have waited
for days but we are under 1%).

Does anybody have experience in classifying it ?

If classification is unfeasible, than which use cases does the OWL
representation cater to?

best,
Andrea Splendiani