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[protege-owl] Newbie question: having trouble with prefix mapping table

John Armstrong johna318 at hotmail.com
Fri Nov 12 11:56:42 PST 2010


You’re right, when I make sure the prefix mapping window is closed and then
load the problematic files the null pointer exceptions don’t happen.  But
the files still don’t load in a fully correct way.  I see the hierarchy, but
when I select classes or properties and mouse-over items in their
descriptions I see “asserted in: (null)” where I would expect to see a URI.

 

This is not an urgent thing for me, I was really just checking out the
resume ontology.  If you want to test yourself at some point, you can fetch
the .rdf files yourself from the two URIs in my original mail.

 

-- John

 

 

 

From: protege-owl-bounces at lists.stanford.edu
[mailto:protege-owl-bounces at lists.stanford.edu] On Behalf Of Timothy Redmond
Sent: Friday, November 12, 2010 2:12 PM
To: protege-owl at lists.stanford.edu
Subject: Re: [protege-owl] Newbie question: having trouble with prefix
mapping table

 





Since you’re already aware of problems in the prefix mapping, should I
assume the null pointer exceptions I got trying to load the resume RDF files
is related and just hack the files a bit to get them working?  BTW I did
some more testing and found that the exception had nothing to do with the
ENTITY defs, and occurs with this gutted version of the resume base.rdf
(http://purl.org/captsolo/resume-rdf/0.2/base#
<http://purl.org/captsolo/resume-rdf/0.2/base> ):


I didn't get to these yet but a casual look at the exception suggests that
the problem will go away if you use a different renderer.




Re your mail, it sounds like you’re saying that the prefix mapper view is
basically a tool that edits the prefixes in the ontology and that the
results of changes are persisted in appropriate from in the written out
ontology file.  This would mean that when you make changes in an ontology
and save it out as RDF/XML you should see the effects in the xmlns attrs at
the top of the file, while if you save it out as say turtle you should see
the effects in the @prefix specifications.  At least I think so.


Yes.

-Timothy




On 11/12/2010 11:01 AM, John Armstrong wrote: 

Thanks for the quick and candid responses to my mails Timothy.  I’m able to
work productively with the version of Protégé-OWL I have, the issues I’ve
reported are not even close to show-stoppers for me.  

 

Since you’re already aware of problems in the prefix mapping, should I
assume the null pointer exceptions I got trying to load the resume RDF files
is related and just hack the files a bit to get them working?  BTW I did
some more testing and found that the exception had nothing to do with the
ENTITY defs, and occurs with this gutted version of the resume base.rdf
(http://purl.org/captsolo/resume-rdf/0.2/base#
<http://purl.org/captsolo/resume-rdf/0.2/base> ):

 

<rdf:RDF xmlns:rdf= <http://www.w3.org/1999/02/22-rdf-syntax-ns>
"http://www.w3.org/1999/02/22-rdf-syntax-ns#" 

                xmlns:rdfs= <http://www.w3.org/2000/01/rdf-schema>
"http://www.w3.org/2000/01/rdf-schema#" 

                xmlns:cv_base=
<http://kaste.lv/~captsolo/semweb/resume/base.rdfs>
"http://kaste.lv/~captsolo/semweb/resume/base.rdfs#">

</rdf:RDF>

 

Re your mail, it sounds like you’re saying that the prefix mapper view is
basically a tool that edits the prefixes in the ontology and that the
results of changes are persisted in appropriate from in the written out
ontology file.  This would mean that when you make changes in an ontology
and save it out as RDF/XML you should see the effects in the xmlns attrs at
the top of the file, while if you save it out as say turtle you should see
the effects in the @prefix specifications.  At least I think so.

 

Again, thanks for your responsiveness.

 

-- John

 

From: protege-owl-bounces at lists.stanford.edu
[mailto:protege-owl-bounces at lists.stanford.edu] On Behalf Of Timothy Redmond
Sent: Friday, November 12, 2010 1:23 PM
To: protege-owl at lists.stanford.edu
Subject: Re: [protege-owl] Newbie question: having trouble with prefix
mapping table

 


The problem is here on our end.  I am not sure what happened but the prefix
mapping code appears to be pretty badly broken.  I have made a GForge for
this [1].  I will try to fix this very soon but I think for now you need to
avoid these two renderers.





At this point not seeing the prefixes is just a minor nuisance, but I’d
still like to understand how the program works and whether I am
doing/assuming something wrong or the prefix mapping table feature is not
working correctly.


The prefixes in the mapping are defined in the ontology.  So in the pizza
ontology for instance there is a section of the ontology that looks like
this:

<rdf:RDF xmlns= <http://www.co-ode.org/ontologies/pizza/pizza.owl>
"http://www.co-ode.org/ontologies/pizza/pizza.owl#"
     xml:base= <http://www.co-ode.org/ontologies/pizza/pizza.owl>
"http://www.co-ode.org/ontologies/pizza/pizza.owl"
     xmlns:owl11= <http://www.w3.org/2006/12/owl11>
"http://www.w3.org/2006/12/owl11#"
     xmlns:pizza= <http://www.co-ode.org/ontologies/pizza/pizza.owl>
"http://www.co-ode.org/ontologies/pizza/pizza.owl#"
     xmlns:owl11xml= <http://www.w3.org/2006/12/owl11-xml>
"http://www.w3.org/2006/12/owl11-xml#"
     xmlns:xsd= <http://www.w3.org/2001/XMLSchema>
"http://www.w3.org/2001/XMLSchema#"
     xmlns:rdfs= <http://www.w3.org/2000/01/rdf-schema>
"http://www.w3.org/2000/01/rdf-schema#"
     xmlns:rdf= <http://www.w3.org/1999/02/22-rdf-syntax-ns>
"http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:owl= <http://www.w3.org/2002/07/owl>
"http://www.w3.org/2002/07/owl#">


This defines prefixes such as pizza: that can be expanded to their full
name, 

http://www.co-ode.org/ontologies/pizza/pizza.owl#
<http://www.co-ode.org/ontologies/pizza/pizza.owl> .


Thus the prefixed name for the concept 

http://www.co-ode.org/ontologies/pizza/pizza.owl#CheeseyPizza


would be pizza:CheeseyPizza.  If the prefix is empty, e.g. just ":", then
instead of writing :CheeseyPizza we usually write CheeseyPizza.  When you
change the prefixes, they will be saved into the ontology when it is saved.

But the reason that you couldn't figure it out is because it currently just
doesn't work.

-Timothy




[1]
https://bmir-gforge.stanford.edu/gf/project/owleditor/tracker/?action=Tracke
rItemEdit
<https://bmir-gforge.stanford.edu/gf/project/owleditor/tracker/?action=Track
erItemEdit&tracker_item_id=2815&start=0> &tracker_item_id=2815&start=0


On 11/11/2010 11:40 AM, John Armstrong wrote: 

I’ve been using the Protégé Owl editor for about a week now and yesterday I
switched my preferences to use qnames for displaying the terms in my
ontologies.

 

I had previously downloaded the FOAF ontology and after changing to qnames I
saw almost all names display with their prefixes, including the base foaf
ones.  (An exception was names from the SKOS ontology, which appeared
without prefixes.)  

 

I didn’t see any change in  the display of my own ontology after changing
the preference, so I went into the prefix mapping table and created an entry
for it, using the option to have the editor grab the base URI for me.

 

After I did this I redisplayed my ontology and still didn’t see the prefix
anywhere.

 

I also noticed that when I exited the program and restarted it my ontology
still did not display with my prefix, and moreover the prefix mapping I had
added previously was not in the table.

 

I had assumed that the table was editable, global (used for all taxonomies),
and persistent, but that didn’t match my actual experience.

 

I read the help page on the prefix mapping table but it didn’t clearly state
how it worked.

 

At this point not seeing the prefixes is just a minor nuisance, but I’d
still like to understand how the program works and whether I am
doing/assuming something wrong or the prefix mapping table feature is not
working correctly.

 

Can anyone advise me?

 

-- John

 

 

 
 
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