Exporting the Annotations field

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Exporting the Annotations field

Andre Luiz Tietbohl Ramos
Hello,

I'd like to export only the Annotations fields in a relatively large ontology without loosing their classes or properties references. If possible in a ASCII text file for I'll use them in a LaTeX document?  Can it be done?

TIA,

Andre Luiz
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Re: Exporting the Annotations field

Timothy Redmond

It might be possible.

I'd like to export only the Annotations fields in a relatively large ontology

This is possible though it appears that the current mechanisms are a bit awkward.  There is at least one bug report that I need to write against this functionality. The following steps worked for me (I tested with the pizza ontology):
  1. Open the ontology in Protege 4.
  2. Create a new empty ontology (File->New) and say yes to put it in the current window.  (This step is needed to work around a bug in the refactor menus).
  3. Give the new ontology any prefixes that it needs so that the final output is pretty.  By default, the "Ontology Prefixes" view appears in the "Active Ontology" tab (near the bottom).  For the pizza ontology I added one mapping (pizza->http://www.co-ode.org/ontologies/pizza/pizza.owl#).
  4. Switch back to the original open ontology.
  5. Now use the Refactor->Copy/Move/Delete axioms menu to pull up a wizard.  As you work through the wizard you will choose Axioms by type, the AnnotationAssertion axiom type, Copy axioms, "Existing ontology" and finally select the new empty ontology as the place to put the axioms.
  6. Don't panic.  At this point things look very bad.  If you go to the Class hierarchy view for instance, none of your classes will be visible.  But the annotation assertion axioms are there.  They just aren't annotating declared entities that Protege knows how to display.
  7. Save the ontology.  I tried a couple of formats but I am guessing that the best one is the OWL functional syntax format.


When I did the above steps, I saw assertions that looked like this:

AnnotationAssertion(rdfs:label pizza:Caprina "Caprina"@pt)
AnnotationAssertion(rdfs:label pizza:PrinceCarlo "CoberturaPrinceCarlo"@pt)
AnnotationAssertion(rdfs:label pizza:ChickenTopping "CoberturaDeFrango"@pt)
AnnotationAssertion(rdfs:label pizza:SweetPepperTopping "CoberturaDePimentaoDoce"@pt)

When I saved in the LaTeX mode, the result was the empty ontology.  Again, I suspect that this is because LaTeX uses a frame like display of the annotations by entity type and this ontology has no entities, only annotations.

without loosing their classes or properties references.

I am not sure what this means.  If you are referring to the declarations of the entities, then I think it would be good if the steps above included the declarations.  But such is life.


-Timothy



On 12/26/2013 02:35 PM, André Luiz Tietböhl Ramos wrote:
Hello,

I'd like to export only the Annotations fields in a relatively large ontology without loosing their classes or properties references. If possible in a ASCII text file for I'll use them in a LaTeX document?  Can it be done?

TIA,

Andre Luiz

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