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

Timothy Redmond tredmond at stanford.edu
Fri Nov 12 11:12:11 PST 2010


> 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#"
>
>                 xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
>
>                 
> xmlns:cv_base="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=TrackerItemEdit&tracker_item_id=2815&start=0  <https://bmir-gforge.stanford.edu/gf/project/owleditor/tracker/?action=TrackerItemEdit&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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