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[protege-owl] problem loading galen.owl with protege 3 and protege 4

helen.chen at agfa.com helen.chen at agfa.com
Wed Aug 1 14:06:04 PDT 2007


Mathew

Thanks for checking this out. 

1. "very strange RDF"

 I am trying to use open-Galen in a project.  I believe it is Alan Rector 
(group) or Ian Horrocks at Manchester did the owl version of the Galen 
ontology, the original OWL file is at http://www.co-ode.org/galen/.  I 
link I provided in my previous email is a copy at bioportal (same copy). 
Indeed, it looks strange in the class view in protege.  But I am 
interested in knowing what you meant by your above statement.   I am 
mostly interested in anatomy and pathology terms and relationships, and 
they can be found under "topcategory".

2. proptege 4 version;

4.0_alpha, downloaded this morning.  I used the option of "open OWL 
ontology".   When starting protege program, it has the following warning 
message about 'could not be found for logger'. 



3. not enough memory

After the "parsed: 220000 triples" line, there is no more displaying 
message.  the protege java process went on for about 1-2 minutes, then the 
system went to idle mode. 

I tried to change the memory size to 1G by changing the number in run.bat. 
 But it didn't do the trick for me. 

4. Loading in protege 3. 

yes, after increasing the heap size, I was able to load galen.owl file in 
protege 3. 

Do I need to change other settings in protege 4 in order to load this 
ontology?

Thanks. 

Helen














Matthew Horridge <matthew.horridge at cs.man.ac.uk> 
Sent by: protege-owl-bounces at lists.stanford.edu
08/01/2007 11:45 AM
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Subject
Re: [protege-owl] problem loading galen.owl with protege 3 and  protege 4








On 1 Aug 2007, at 16:23, helen.chen at agfa.com wrote:

>
> Dear list
>
>
> I downloaded protege 4 and trying to open a local copy of galen.owl 
> [1].  The owl file is about 21M..  After loading 220,000 triples 
> (message on console), the system hung forever (I have to kill the 
> process after more than 30 minutes waiting).
>
> This is the same problem with protege 3.2.
>
> Can anyone share his/her experience in loading large ontology in 
> protege?  Is there a place where I can specify a larger memory 
> space for loading large ontology?
>

One more thing.  This seems to be *very* strangely formatted RDF - do 
you know how it was created?

Cheers,

Matthew
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