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Re: Problem with classifying the Human Phenotype Ontology

From: Matthias Samwald <matthias.samwald@meduniwien.ac.at>
Date: Mon, 04 Aug 2014 14:03:38 +0200
Message-ID: <53DF769A.5040200@meduniwien.ac.at>
To: public-semweb-lifesci@w3.org
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:

I have not worked with HPO yet, so those are just some general 


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
Received on Monday, 4 August 2014 12:04:09 UTC

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