DL Query results keyed by display name, not underlying URI?

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DL Query results keyed by display name, not underlying URI?

Joshua TAYLOR
Hi all,

I've got a problem wherein I have similarly named individuals (i.e,
individuals with distinct URIs but which are displayed with the same
name in Protege), e.g.,

http://.../a/ind
http://.../b/ind

I've made the following assertions:

a/ind baz 80
b/ind bar "80"

turned on the FaCT++ reasoner, selected "Individuals" on the right in
the DL Query panel, and executed the query

baz value 80 or bar value "80"

I get two results, as expected, and they're displayed, as expected, as

ind
ind

(see attached screenshot). The problem is that when I click on either
one, I end up in the entity viewer for b/ind . This behavior can be
seen in the attached ontology, twoinds.owl.  I don't mind that both
appear as ind, but that I can only browse one from the DL results is
rather problematic.

The problem I've actually got is even worse, since there are more
'ind's in the ontology, and so more often than not I end up being led
to an individual that wasn't actually part of the DL Query result.
E.g., if I add another individual

http://.../c/ind

and assert that

c/ind bar "90"

and run the same query

baz value 80 or bar value "80"

I still get two results

ind
ind

but when I click on either of them I'm led to the entity view for
c/ind which doesn't have baz value 80 or bar value "80".  This state
of affairs can be seen in the attached ontology, threeinds.owl.

Is this a known problem?  Is there some workaround? This is really
problematic for me at the moment.  I'm processing an ontology wherein
the identifiers have some correspondence with a preexisting hierarchy
(which helps to ensure that individuals have human readable, but
genuinely distinct URIs).  I don't mind the displayed names in Protege
being the same, but I'd hoped that the browsing would be based on
underlying identifiers, not just the display name.

Any and all help much appreciated!
//JT

--
Joshua Taylor, http://www.cs.rpi.edu/~tayloj/

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Re: DL Query results keyed by display name, not underlying URI?

Timothy Redmond

This sounds a lot like GForge #3503.  I have been slightly dreading looking into this because I am wondering how fundamental the issue is.  But it sounds like it would be good to fix.

The one workaround that might be possible is to use the render by qualified name rendering (View->Custom Rendering).  If you have only a limited number of namespaces then it would be possible to use the ontology prefixes view to give different prefixes to these individuals.  In the default state you would see the ontology prefixes in the Active Ontology tab but you can place it anywhere you like with Window->Views->Ontology views->Ontology prefixes.

I don't know if this will work for you.

-Timothy


[1] https://bmir-gforge.stanford.edu/gf/project/owleditor/tracker/?action=TrackerItemEdit&tracker_item_id=3503&start=0

On 09/07/2011 09:59 AM, Joshua TAYLOR wrote:
Hi all,

I've got a problem wherein I have similarly named individuals (i.e,
individuals with distinct URIs but which are displayed with the same
name in Protege), e.g.,

http://.../a/ind
http://.../b/ind

I've made the following assertions:

a/ind baz 80
b/ind bar "80"

turned on the FaCT++ reasoner, selected "Individuals" on the right in
the DL Query panel, and executed the query

baz value 80 or bar value "80"

I get two results, as expected, and they're displayed, as expected, as

ind
ind

(see attached screenshot). The problem is that when I click on either
one, I end up in the entity viewer for b/ind . This behavior can be
seen in the attached ontology, twoinds.owl.  I don't mind that both
appear as ind, but that I can only browse one from the DL results is
rather problematic.

The problem I've actually got is even worse, since there are more
'ind's in the ontology, and so more often than not I end up being led
to an individual that wasn't actually part of the DL Query result.
E.g., if I add another individual

http://.../c/ind

and assert that

c/ind bar "90"

and run the same query

baz value 80 or bar value "80"

I still get two results

ind
ind

but when I click on either of them I'm led to the entity view for
c/ind which doesn't have baz value 80 or bar value "80".  This state
of affairs can be seen in the attached ontology, threeinds.owl.

Is this a known problem?  Is there some workaround? This is really
problematic for me at the moment.  I'm processing an ontology wherein
the identifiers have some correspondence with a preexisting hierarchy
(which helps to ensure that individuals have human readable, but
genuinely distinct URIs).  I don't mind the displayed names in Protege
being the same, but I'd hoped that the browsing would be based on
underlying identifiers, not just the display name.

Any and all help much appreciated!
//JT

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Re: DL Query results keyed by display name, not underlying URI?

Joshua TAYLOR
On Wed, Sep 7, 2011 at 2:55 PM, Timothy Redmond <[hidden email]> wrote:
>
> This sounds a lot like GForge #3503.  I have been slightly dreading looking
> into this because I am wondering how fundamental the issue is.  But it
> sounds like it would be good to fix.

Sorry, I should have searched first.  Yes, my problem seems to be
exactly the same one, just manifesting in individual names rather than
class names.

> The one workaround that might be possible is to use the render by qualified
> name rendering (View->Custom Rendering).  If you have only a limited number
> of namespaces then it would be possible to use the ontology prefixes view to
> give different prefixes to these individuals.  In the default state you
> would see the ontology prefixes in the Active Ontology tab but you can place
> it anywhere you like with Window->Views->Ontology views->Ontology prefixes.

I've actually got only one or two prefixes defined, so this gives
everything rather long display names, but it does let me reliably get
to the right individuals from the DL Query result panes, so it solves
my immediate problem.

As an aside, I noticed that once I started rendering with qnames, I
had to adjust my DL Query too (to use qnames), e.g.,

pref:bar value "80"

That's not unreasonable, but it was a bit surprising (that a rendering
option changed the behavior of input processing).

Actually, I rather like the QName rendering, at least for the naming
scheme used in this ontology.  I probably wouldn't have ever looked
for it otherwise. Many thanks!

//JT
--
Joshua Taylor, http://www.cs.rpi.edu/~tayloj/
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Re: DL Query results keyed by display name, not underlying URI?

Alan Ruttenberg-2
In reply to this post by Timothy Redmond
umm, why not just make reasonable rdfs:labels and render by label??

On Wed, Sep 7, 2011 at 2:55 PM, Timothy Redmond <[hidden email]> wrote:

>
> This sounds a lot like GForge #3503.  I have been slightly dreading looking
> into this because I am wondering how fundamental the issue is.  But it
> sounds like it would be good to fix.
>
> The one workaround that might be possible is to use the render by qualified
> name rendering (View->Custom Rendering).  If you have only a limited number
> of namespaces then it would be possible to use the ontology prefixes view to
> give different prefixes to these individuals.  In the default state you
> would see the ontology prefixes in the Active Ontology tab but you can place
> it anywhere you like with Window->Views->Ontology views->Ontology prefixes.
>
> I don't know if this will work for you.
>
> -Timothy
>
>
> [1]
> https://bmir-gforge.stanford.edu/gf/project/owleditor/tracker/?action=TrackerItemEdit&tracker_item_id=3503&start=0
>
> On 09/07/2011 09:59 AM, Joshua TAYLOR wrote:
>
> Hi all,
>
> I've got a problem wherein I have similarly named individuals (i.e,
> individuals with distinct URIs but which are displayed with the same
> name in Protege), e.g.,
>
> http://.../a/ind
> http://.../b/ind
>
> I've made the following assertions:
>
> a/ind baz 80
> b/ind bar "80"
>
> turned on the FaCT++ reasoner, selected "Individuals" on the right in
> the DL Query panel, and executed the query
>
> baz value 80 or bar value "80"
>
> I get two results, as expected, and they're displayed, as expected, as
>
> ind
> ind
>
> (see attached screenshot). The problem is that when I click on either
> one, I end up in the entity viewer for b/ind . This behavior can be
> seen in the attached ontology, twoinds.owl.  I don't mind that both
> appear as ind, but that I can only browse one from the DL results is
> rather problematic.
>
> The problem I've actually got is even worse, since there are more
> 'ind's in the ontology, and so more often than not I end up being led
> to an individual that wasn't actually part of the DL Query result.
> E.g., if I add another individual
>
> http://.../c/ind
>
> and assert that
>
> c/ind bar "90"
>
> and run the same query
>
> baz value 80 or bar value "80"
>
> I still get two results
>
> ind
> ind
>
> but when I click on either of them I'm led to the entity view for
> c/ind which doesn't have baz value 80 or bar value "80".  This state
> of affairs can be seen in the attached ontology, threeinds.owl.
>
> Is this a known problem?  Is there some workaround? This is really
> problematic for me at the moment.  I'm processing an ontology wherein
> the identifiers have some correspondence with a preexisting hierarchy
> (which helps to ensure that individuals have human readable, but
> genuinely distinct URIs).  I don't mind the displayed names in Protege
> being the same, but I'd hoped that the browsing would be based on
> underlying identifiers, not just the display name.
>
> Any and all help much appreciated!
> //JT
>
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03
>
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03
>
>
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