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.samw...@meduniwien.ac.at<mailto:matthias.samw...@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.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 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 haen...@ohsu.edu<mailto:haen...@ohsu.edu> skype: melissa.haendel 503-407-5970
