Re: how does one create a mapping of ontologies to local files for protege 4?

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Re: how does one create a mapping of ontologies to local files for protege 4?

Nick Drummond
Alan,

I've added a bug about the repository coming back with less ontologies than there are files.

The ontology libraries details are saved along with all other settings (the location/method is system dependent) - there is no intention to make this available to the user outside the application.
P4 settings are not saved unless P4 is shut down correctly (ie closed rather than Command-Q on the mac).

Nick

On Sun, Jun 29, 2008 at 6:13 AM, Alan Ruttenberg <[hidden email]> wrote:
Well, not editable in emacs, it appears. On my mac using the ontology library ui updates[*] key

org.protege.editor.owl.ontologylibraries with a java binary serialization

in /Users/alanr/Library/Preferences/com.apple.java.util.prefs.plist

(thank you http://www.fernlightning.com/doku.php?id=software:fseventer:start)

Perhaps consider xstream for serialization of this sort - at least there is a chance of seeing what is going on.
http://www.devx.com/xml/Article/30068 , though it would be better to have an owl representation of the mapping...

Best,
Alan

[*] I don't think it saves ontology library state right after editing in that dialog(as it should?). I've made changes and quit protege to find that they have not been saved when I restart.

btw, when I add the folder (checked out from http://svn.neurocommons.org/svn/trunk/ontologies/neuroscience/neuronbank/tritonia )

It only "sees" one ontology despite there being 4. Presumably because it is confusing xml:base with the ontology name.

grep "owl:Ontology rdf:about=" * | grep -v imports
neuron.owl:    <owl:Ontology rdf:about="http://purl.obofoundry.org/obo/tritonia/neuron.owl"/>
process.owl:  <owl:Ontology rdf:about="http://purl.obofoundry.org/obo/tritonia/process.owl">
synapse.owl:  <owl:Ontology rdf:about="http://purl.obofoundry.org/obo/tritonia/synapse.owl"/>
tritonia.owl:    <owl:Ontology rdf:about="http://purl.obofoundry.org/obo/tritonia.owl">

grep "xml:base" *
neuron.owl:     xml:base="&obo;tritonia/"
process.owl:<rdf:RDF xml:base="http://purl.obofoundry.org/obo/tritonia/"
synapse.owl:<rdf:RDF xml:base="http://purl.obofoundry.org/obo/tritonia/"
tritonia.owl:     xml:base="&obo;tritonia/"







On Jun 28, 2008, at 12:19 AM, Alan Ruttenberg wrote:

Pointer to doc would be fine. Cursory search didn't find it. I don't want to add folders, but rather say exactly where each file is.

Thanks,
Alan




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Re: how does one create a mapping of ontologies to local files for protege 4?

Alan Ruttenberg-2

On Jul 14, 2008, at 11:07 AM, Nick Drummond wrote:
> P4 settings are not saved unless P4 is shut down correctly (ie  
> closed rather than Command-Q on the mac).

Is there any reason not to make command-q on the mac a proper way of  
shutting down protege? Consistency of applications, etc.

Note that my suggestion was simply to save the repository information  
when the dialog is closed, rather than later, which is a small matter  
of moving the save code from one place to another.

-Alan
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Re: how does one create a mapping of ontologies to local files for protege 4?

Nick Drummond
You are right, this should behave the same and I have added a bug to make sure all the tidyup that occurs when shutting down still takes place regardless of how you do this. Command Q is just handled differently internally currently.

Actually, I was wrong again, for some reason the repositories are not actually stored along with the other settings.
I'm going to have a look at the reasons for this and see if it all wants tidyup.
In the meantime the reps are saved when the dialog is OKed (and cancel really cancels now aswell!)

Nick

On Mon, Jul 14, 2008 at 6:47 PM, Alan Ruttenberg <[hidden email]> wrote:

On Jul 14, 2008, at 11:07 AM, Nick Drummond wrote:
P4 settings are not saved unless P4 is shut down correctly (ie closed rather than Command-Q on the mac).

Is there any reason not to make command-q on the mac a proper way of shutting down protege? Consistency of applications, etc.

Note that my suggestion was simply to save the repository information when the dialog is closed, rather than later, which is a small matter of moving the save code from one place to another.

-Alan


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