Urgent: I need help regarding OWL

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Urgent: I need help regarding OWL

Junaid Shabir
Hi folks,

Hope all of you are doing well. I have got to work on this oncology, and so
far i have tried numerous OWL files; just to get hold of protege,they
weren't relevant with my project, except this file which i want to open and
work on it,  but everytime it says not enough memory, i have made sure every
time i try i got enough memory with me. i.e. 1Gb Ram;while trying to open
this file usually i have more than 500Mb of Ram, yet it gives same error.
file size is not more than 32Mb itself,the source link of this file can be
found on

National Cancer Institute Ontology (NCIO):
http://www.mindswap.org/2003/CancerOntology/
<http://../exchweb/bin/redir.asp?URL=http://www.mindswap.org/2003/CancerOntology/>

" nciOncology.owl<http://www.mindswap.org/2003/CancerOntology/nciOncology.owl>-
This links to an archived, uncompressed version of the ontology that
you
can view in your browser. Warning: This file is ~32MB, and may take a very
long time to download." this is the file that i want to open, or do you
think if there is any other source to get this oncology please do inform me.

  I shall be highly obliged if you may help me by showing me the way.

Regards,

-- Junaid Shabbir
MSc Multimedia Computer System[ in progress]
University of Birmingham
United Kingdom

Tel No:+44 (0) 7790394042

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Re: Urgent: I need help regarding OWL

Tania Tudorache

Hi,

the NCI Thesaurus needs indeed more memory to open than smaller-sized
ontologies. In order to open it, you would have to increase the heap
size allocated for Protege. If you run the Protege executable directly,
you can do that by editing in the Protege.lax file the maxium heap size
(by default it is set to 100MB). The line you need to edit:

#   LAX.NL.JAVA.OPTION.JAVA.HEAP.SIZE.MAX
#   -------------------------------------
#   maximum heap size
lax.nl.java.option.java.heap.size.max=100000000

Or, if you run Protege from the command line, you need to add the
following parameter to set the maximum heap size: -Xmx100M.

I could open the NCI Thesaurus by setting the maximum heap size to 500MB.

Other tips regarding scalability and performance you find here:
http://protege.cim3.net/cgi-bin/wiki.pl?ScalabilityAndTuning

Please ask in future OWL related questions on the OWL mailing list.

Thanks,
Tania


Junaid Shabir wrote:

>Hi folks,
>
>Hope all of you are doing well. I have got to work on this oncology, and so
>far i have tried numerous OWL files; just to get hold of protege,they
>weren't relevant with my project, except this file which i want to open and
>work on it,  but everytime it says not enough memory, i have made sure every
>time i try i got enough memory with me. i.e. 1Gb Ram;while trying to open
>this file usually i have more than 500Mb of Ram, yet it gives same error.
>file size is not more than 32Mb itself,the source link of this file can be
>found on
>
>National Cancer Institute Ontology (NCIO):
>http://www.mindswap.org/2003/CancerOntology/
><http://../exchweb/bin/redir.asp?URL=http://www.mindswap.org/2003/CancerOntology/>
>
>" nciOncology.owl<http://www.mindswap.org/2003/CancerOntology/nciOncology.owl>-
>This links to an archived, uncompressed version of the ontology that
>you
>can view in your browser. Warning: This file is ~32MB, and may take a very
>long time to download." this is the file that i want to open, or do you
>think if there is any other source to get this oncology please do inform me.
>
>  I shall be highly obliged if you may help me by showing me the way.
>
>Regards,
>
>-- Junaid Shabbir
>MSc Multimedia Computer System[ in progress]
>University of Birmingham
>United Kingdom
>
>Tel No:+44 (0) 7790394042
>
>-------------------------------------------------------------------------
>To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>
>
>  
>

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