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Re: Problem with classifying the Human Phenotype Ontology

From: Andrea Splendiani <andrea.splendiani@iscb.org>
Date: Mon, 4 Aug 2014 14:16:52 +0200
Message-ID: <CAJZps9iDb4XDhZKiYsfApP79DXj7xkOpeqt9xwXwrgfYF6yB=A@mail.gmail.com>
To: Matthias Samwald <matthias.samwald@meduniwien.ac.at>
Cc: public-semweb-lifesci@w3.org
I didn't see the BioHackathon ML message. I have just realised my mail
setup is a bit messed up...
TrOWL I have tried, but I have the impression it doesn't really make a
classification upfront, but rather incrementally on demand. It's just an
impression, but it classified HP in no time ;)

I will give a try to ELK and Konclude.
What I am bit puzzled with is: this is a largely used ontology. The issue
of unfeasible classification should have come up already. Either I am doing
something wrong, or nobody uses the OWL version (or I'm not good at


On Mon, Aug 4, 2014 at 2:03 PM, Matthias Samwald <
matthias.samwald@meduniwien.ac.at> wrote:

> 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
Received on Monday, 4 August 2014 12:17:20 UTC

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