Hi Andrea,
I remember you got the recommendation to try ELK on the Biohackathon
mailing list. Is ELK not working for you?
You might also want to give TrOWL a try if ELK is not working for you
for some reason. Konclude might also be an option as it seems to
outperform most other reasoners, but it does not have a Protege plugin
(don't know if this matters to you). You can also have a look at the
recent results of the OWL reasoner evaluation here:
http://vip.cs.man.ac.uk:8080/live.html
I have not worked with HPO yet, so those are just some general
recommendations.
Best,
Matthias
Am 04.08.2014 13:53, schrieb Andrea Splendiani:
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
