> 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.samw...@meduniwien.ac.at
<mailto:matthias.samw...@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
