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Re: Problem with classifying the Human Phenotype Ontology

From: Melissa Haendel <haendel@ohsu.edu>
Date: Mon, 4 Aug 2014 13:12:40 +0000
To: Matthias Samwald <matthias.samwald@meduniwien.ac.at>
CC: "<public-semweb-lifesci@w3.org>" <public-semweb-lifesci@w3.org>
Message-ID: <7F06436B-C987-4942-A40D-CD105DB5844C@ohsu.edu>
Hi Andrea,
Those of us who work on the HPO (OWL) use ELK for classification, and most other ontologies and it works quite well.
Cheers,
Melissa


On Aug 4, 2014, at 5:40 AM, Matthias Samwald <matthias.samwald@meduniwien.ac.at<mailto: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<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





Dr. Melissa Haendel

Assistant Professor
Ontology Development Group, OHSU Library
www.ohsu.edu/library/ontology<http://www.ohsu.edu/library/ontology>
Department of Medical Informatics and Epidemiology
Oregon Health & Science University
haendel@ohsu.edu<mailto:haendel@ohsu.edu>
skype: melissa.haendel
503-407-5970
Received on Monday, 4 August 2014 13:13:13 UTC

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