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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 14:40:22 +0200
Message-ID: <53DF7F36.3080303@meduniwien.ac.at>
To: public-semweb-lifesci@w3.org
 > 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 ;)

It is supposed to classify everything. Maybe you don't have a problem at 
all. ;)

  - Matthias


Am 04.08.2014 14:16, schrieb Andrea Splendiani:
> Hi,
> 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 googling).
>
> best,
> Andrea
>
>
>
> On Mon, Aug 4, 2014 at 2:03 PM, Matthias Samwald 
> <matthias.samwald@meduniwien.ac.at 
> <mailto: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 12:40:52 UTC

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