Owl FMA???

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Owl FMA???

Raj M Verma
hi list,

is there any one using FMA with Protege? If so, my question is did you try/succeed in converting FMA(SQL based dump file) to Owl based Ontology? I'm trying to do this but cudn't succeed... I guess Protege is unable to handle such big(108 MB) files!!! is this the reason? I want to use FMA along with an Owl Ontology... any suggestions of how we can integrate them and use!

thanx,
Raj.
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SPARQL and XML results

Luca Cinquini
Hi,
        is there a way to use Protege-Owl to execute a SPARQL query and  
return the results as XML, as opposed to a QueryResults object  
wrapping a Map ?
I'm using the libraries from Protege 3.2beta...

thanks, Luca
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Re: Owl FMA???

Ronnie Valkky
In reply to this post by Raj M Verma
Hi Raj,
 
Tune Protege:
1. find file %ProtegeHome%\Protege.lax
where %ProtegHome% is the folder where you have Proge installed, for example I have it in folder F:\sw\Protege3.2beta
2. change heap size:
#   LAX.NL.JAVA.OPTION.JAVA.HEAP.SIZE.INITIAL
#   -----------------------------------------
#   initial heap size 10000000
#   increased to     100000000 
lax.nl.java.option.java.heap.size.initial=100000000 <---------- just an example, works for me; find your optimum
3. restart Protege
 
Also, read how other guys have tuned Protege for big ontologies
& check your system settings and consurrent applications.
cheers,
Ronnie
 
----- Original Message -----
Sent: Friday, January 27, 2006 5:22 PM
Subject: [protege-owl] Owl FMA???

hi list,

is there any one using FMA with Protege? If so, my question is did you try/succeed in converting FMA(SQL based dump file) to Owl based Ontology? I'm trying to do this but cudn't succeed... I guess Protege is unable to handle such big(108 MB) files!!! is this the reason? I want to use FMA along with an Owl Ontology... any suggestions of how we can integrate them and use!

thanx,
Raj.
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import owl file using API

Daniele De Santis-2
Hi to everybody, 
 
I saw that you have already spoken of import using the protege API. 
 
However I have not succeeded in making to work it. 
 
I have a file "file.owl" in my hard disk and I would like to import this file inside a project OWL without having to use the plugin metadataTab and without the use of the file "ont-policy.rdf" 
 
Can you help me?
 
thank you,
Daniele
 
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Re: Owl FMA???

Jenny ure
In reply to this post by Raj M Verma
I know that Christine Golbreaich and Olivier Dameron (Rennes, Stanford)
did something along those lines using an Owl based version of part of
the FMA as part of a neuro-imaging project - in fact, if anyone has a
copy of the ontology they created.......please let me know!

> hi list,
>
> is there any one using FMA with Protege? If so, my question is did you
> try/succeed in converting FMA(SQL based dump file) to Owl based
> Ontology? I'm trying to do this but cudn't succeed... I guess Protege
> is unable to handle such big(108 MB) files!!! is this the reason? I
> want to use FMA along with an Owl Ontology... any suggestions of how
> we can integrate them and use!
>
> thanx,
> Raj.


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Re: Owl FMA???

Christine Golbreich
(This file includes about 40,000 concepts, i.e. 57% of the 70,000
concepts of the original FMA. Laterality (inessential) distinctions were
ignored, i.e. classes differing from their parents only by laterality.)
We also have other versions (e.g., without N&S).
But, please could you have a look at our paper available at
http://www.med.univ-rennes1.fr/lim/doc_128.pdf
for a discusssion of the current limitations of the OWL versions.
"The Foundational Model of Anatomy in OWL:experience and perspectives"
C. Golbreich, S. Zhang, O. Bodenreider
OWLED, 11-12 nov 2005, Galway, Ireland
For what use do you need it ?

- Our conversion most probably differs from the work that was done
at Stanford by Olivier Dameron et al. (cf. their AMIA 2005 paper) since
we use OWL DL for the whole FMA.
 
regards,

Christine
----- Original Message -----
From: "Jenny ure" <
[hidden email]>
To: <
[hidden email]>
Sent: Sunday, January 29, 2006 7:53 PM
Subject: [protege-owl] Re: Owl FMA???


> I know that Christine Golbreaich and Olivier Dameron (Rennes, Stanford)
> did something along those lines using an Owl based version of part of
> the FMA as part of a neuro-imaging project - in fact, if anyone has a
> copy of the ontology they created.......please let me know!
>
> > hi list,
> >
> > is there any one using FMA with Protege? If so, my question is did you
> > try/succeed in converting FMA(SQL based dump file) to Owl based
> > Ontology? I'm trying to do this but cudn't succeed... I guess Protege
> > is unable to handle such big(108 MB) files!!! is this the reason? I
> > want to use FMA along with an Owl Ontology... any suggestions of how
> > we can integrate them and use!
> >
> > thanx,
> > Raj.
>
>
> -------------------------------------------------------------------------
> To unsubscribe go to
http://protege.stanford.edu/community/subscribe.html
>
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Re: Owl FMA???

Jenny ure
Thanks very much for this Christine - obviously a huge amount of work here!

Re the question about use: Was interested in using the FMA as a
reference ontology for a neuro-imaging project involving multiple
partners, The partners are sharing MRI images of the brain for different
purposes, but will need shared reference points in terms of brain
anatomy in the first instance. Will have to develop a purpose specific
ontology of psychosis inthe context of neuro-imaging also. Some related
work on the genetics of psychoses and dementia (part of the focus) has
already been developed, using the FMA and OWL, and others are underway.
Using the FMA in OWl as a common reference point might make it easier to
align with these and other developments in future.

Any comments, advice or suggestions for contacts or further reading
would be very welcome as at the start of this initiative and keen to
learn from other folk's experience!.

Best and thanks again for making so much of this available-it is appreciated
Jenny

> - Concerning our work a partial version of the FMA in OWL is available
> online at
> http://mor.nlm.nih.gov/pubs/supp/2005-owled-cg/FMA-constitutionalPartForNS.owl
> or
> http://www.med.univ-rennes1.fr/~cgolb/Ontologies/FMA/FMA-constitutionalPartForNS.owl 
> <http://www.med.univ-rennes1.fr/%7Ecgolb/Ontologies/FMA/FMA-constitutionalPartForNS.owl>.
> (This file includes about 40,000 concepts, i.e. 57% of the 70,000
> concepts of the original FMA. Laterality (inessential) distinctions were
> ignored, i.e. classes differing from their parents only by laterality.)
> We also have other versions (e.g., without N&S).
> But, please could you have a look at our paper available at
> http://www.med.univ-rennes1.fr/lim/doc_128.pdf
> for a discusssion of the current limitations of the OWL versions.
> "The Foundational Model of Anatomy in OWL:experience and perspectives"
> C. Golbreich, S. Zhang, O. Bodenreider
> OWLED, 11-12 nov 2005, Galway, Ireland
> For what use do you need it ?
>
> - Our conversion most probably differs from the work that was done
> at Stanford by Olivier Dameron et al. (cf. their AMIA 2005 paper) since
> we use OWL DL for the whole FMA.
>  
> regards,
>
> Christine
> ----- Original Message -----
> From: "Jenny ure" <[hidden email] <mailto:[hidden email]>>
> To: <[hidden email] <mailto:[hidden email]>>
> Sent: Sunday, January 29, 2006 7:53 PM
> Subject: [protege-owl] Re: Owl FMA???
>
>
> > I know that Christine Golbreaich and Olivier Dameron (Rennes, Stanford)
> > did something along those lines using an Owl based version of part of
> > the FMA as part of a neuro-imaging project - in fact, if anyone has a
> > copy of the ontology they created.......please let me know!
> >
> > > hi list,
> > >
> > > is there any one using FMA with Protege? If so, my question is did you
> > > try/succeed in converting FMA(SQL based dump file) to Owl based
> > > Ontology? I'm trying to do this but cudn't succeed... I guess Protege
> > > is unable to handle such big(108 MB) files!!! is this the reason? I
> > > want to use FMA along with an Owl Ontology... any suggestions of how
> > > we can integrate them and use!
> > >
> > > thanx,
> > > Raj.
> >
> >
> >
> -------------------------------------------------------------------------
> > To unsubscribe go to
> http://protege.stanford.edu/community/subscribe.html
> >


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[protege-owl] Re: import owl file using API

Matthew Horridge
In reply to this post by Daniele De Santis-2
Hi Daniele,

I saw that you have already spoken of import using the protege API. 
 
However I have not succeeded in making to work it. 
 
I have a file "file.owl" in my hard disk and I would like to import this file inside a project OWL without having to use the plugin metadataTab and without the use of the file "ont-policy.rdf" 

You should first add a LocalFileRepository that contains the file.owl to the project repository.  If you need help with this let me know - apart from looking at the source code, there's not much documentation.

Next, you should use the ImportHelper class, which can be found in the model.util package, which will do the job of importing.

Cheers,

Matthew