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Re: Problem with classifying the Human Phenotype Ontology

From: Andrea Splendiani <andrea.splendiani@iscb.org>
Date: Mon, 4 Aug 2014 15:24:47 +0200
Message-ID: <CAJZps9h6+bYA2H5qtzGacJ4be3b90copCLUKi6Z1+SVbJ60Qcg@mail.gmail.com>
To: Matthias Samwald <matthias.samwald@meduniwien.ac.at>
Cc: public-semweb-lifesci@w3.org
Yes, I think reasoners that only consider the EL subset are very fast.
>From the site: TrOWL utilises ... a syntactic approximation from OWL2-DL to
OWL2-EL for TBox and ABox reasoning.

best,
Andrea


On Mon, Aug 4, 2014 at 2:40 PM, Matthias Samwald <
matthias.samwald@meduniwien.ac.at> wrote:

>  > 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> 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 13:25:22 UTC

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