labels in DL query tab

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labels in DL query tab

David Osumi-Sutherland
Hi there,

I edit various OBO format ontologies for FlyBase and have been recently
trying out Protege 4 using the ontologies I edit. I am particularly
interested in using P4 for DL-querying.

I've managed to load my ontology using the built-in conversion from OBO
(which I believe corresponds to Ian Horrock's mapping (?)). I have
preferences switched to viewing terms by name (label), rather than ID
(using 'Render entities using annotation values' option).  In the
inferred hierarchy, terms with nessary and sufficient definitions in OBO
are correctly integrated into the class heirarchy (so - from this test,
the mapping looks correct).

The DL query tab
The problem I have is that the DL query tab only works when I use names
(labels) which don't contain spaces.  The search box works for these as
long as the name is enclosed in single quotes. Unfortunately, the same
doesn't appear to work for names in the DL query tab.  Is there some
alternative delimiter I can use here - or is this a bug?

Cheers,

David


David Osumi-Sutherland
Curator/Ontologist
FlyBase
Cambridge, UK
+44 1223 333 963

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Re: labels in DL query tab

Matthew Horridge
Hi David,

What build are you using?  This was a problem with the parser in the  
OWL API, but I believe it was fixed a couple of versions ago.

Cheers,

Matthew


On 26 Jun 2008, at 13:43, David Sutherland wrote:

> Hi there,
>
> I edit various OBO format ontologies for FlyBase and have been  
> recently
> trying out Protege 4 using the ontologies I edit. I am particularly
> interested in using P4 for DL-querying.
>
> I've managed to load my ontology using the built-in conversion from  
> OBO
> (which I believe corresponds to Ian Horrock's mapping (?)). I have
> preferences switched to viewing terms by name (label), rather than ID
> (using 'Render entities using annotation values' option).  In the
> inferred hierarchy, terms with nessary and sufficient definitions in  
> OBO
> are correctly integrated into the class heirarchy (so - from this  
> test,
> the mapping looks correct).
>
> The DL query tab
> The problem I have is that the DL query tab only works when I use  
> names
> (labels) which don't contain spaces.  The search box works for these  
> as
> long as the name is enclosed in single quotes. Unfortunately, the same
> doesn't appear to work for names in the DL query tab.  Is there some
> alternative delimiter I can use here - or is this a bug?
>
> Cheers,
>
> David
>
>
> David Osumi-Sutherland
> Curator/Ontologist
> FlyBase
> Cambridge, UK
> +44 1223 333 963
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback

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Re: labels in DL query tab

David Osumi-Sutherland
Hi Matthew,

Build 61. Freshly installed.

Cheers,

David

On Thu, 2008-06-26 at 13:52 +0100, Matthew Horridge wrote:

> Hi David,
>
> What build are you using?  This was a problem with the parser in the  
> OWL API, but I believe it was fixed a couple of versions ago.
>
> Cheers,
>
> Matthew
>
>
> On 26 Jun 2008, at 13:43, David Sutherland wrote:
>
> > Hi there,
> >
> > I edit various OBO format ontologies for FlyBase and have been  
> > recently
> > trying out Protege 4 using the ontologies I edit. I am particularly
> > interested in using P4 for DL-querying.
> >
> > I've managed to load my ontology using the built-in conversion from  
> > OBO
> > (which I believe corresponds to Ian Horrock's mapping (?)). I have
> > preferences switched to viewing terms by name (label), rather than ID
> > (using 'Render entities using annotation values' option).  In the
> > inferred hierarchy, terms with nessary and sufficient definitions in  
> > OBO
> > are correctly integrated into the class heirarchy (so - from this  
> > test,
> > the mapping looks correct).
> >
> > The DL query tab
> > The problem I have is that the DL query tab only works when I use  
> > names
> > (labels) which don't contain spaces.  The search box works for these  
> > as
> > long as the name is enclosed in single quotes. Unfortunately, the same
> > doesn't appear to work for names in the DL query tab.  Is there some
> > alternative delimiter I can use here - or is this a bug?
> >
> > Cheers,
> >
> > David
> >
> >
> > David Osumi-Sutherland
> > Curator/Ontologist
> > FlyBase
> > Cambridge, UK
> > +44 1223 333 963
> >
> > _______________________________________________
> > p4-feedback mailing list
> > [hidden email]
> > https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>

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annotation label renderer - preferred language

Förhécz András
In reply to this post by David Osumi-Sutherland
Hi all,

David wrote:
> I have
> preferences switched to viewing terms by name (label), rather than ID
> (using 'Render entities using annotation values' option).
Doing the same, on the "Annotation Renderer" dialog the column header is
"Languages (comma separated in order of preference)".

However no matter in which order I specify language codes, my English
and Hungarian labels are displayed randomly.
This may be a bug in the OWL API if the feature is implemented using:
   org.semanticweb.owl.util.AnnotationValueShortFormProvider

Regards,
   András

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Re: labels in DL query tab

Nick Drummond
In reply to this post by David Osumi-Sutherland
David,

This was fixed in build 62. I would recommend updating to the most recent (build 64).

Nick

On Thu, Jun 26, 2008 at 1:57 PM, David Sutherland <[hidden email]> wrote:
Hi Matthew,

Build 61. Freshly installed.

Cheers,

David

On Thu, 2008-06-26 at 13:52 +0100, Matthew Horridge wrote:
> Hi David,
>
> What build are you using?  This was a problem with the parser in the
> OWL API, but I believe it was fixed a couple of versions ago.
>
> Cheers,
>
> Matthew
>
>
> On 26 Jun 2008, at 13:43, David Sutherland wrote:
>
> > Hi there,
> >
> > I edit various OBO format ontologies for FlyBase and have been
> > recently
> > trying out Protege 4 using the ontologies I edit. I am particularly
> > interested in using P4 for DL-querying.
> >
> > I've managed to load my ontology using the built-in conversion from
> > OBO
> > (which I believe corresponds to Ian Horrock's mapping (?)). I have
> > preferences switched to viewing terms by name (label), rather than ID
> > (using 'Render entities using annotation values' option).  In the
> > inferred hierarchy, terms with nessary and sufficient definitions in
> > OBO
> > are correctly integrated into the class heirarchy (so - from this
> > test,
> > the mapping looks correct).
> >
> > The DL query tab
> > The problem I have is that the DL query tab only works when I use
> > names
> > (labels) which don't contain spaces.  The search box works for these
> > as
> > long as the name is enclosed in single quotes. Unfortunately, the same
> > doesn't appear to work for names in the DL query tab.  Is there some
> > alternative delimiter I can use here - or is this a bug?
> >
> > Cheers,
> >
> > David
> >
> >
> > David Osumi-Sutherland
> > Curator/Ontologist
> > FlyBase
> > Cambridge, UK
> > +44 1223 333 963
> >
> > _______________________________________________
> > p4-feedback mailing list
> > [hidden email]
> > https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>

_______________________________________________
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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback


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Re: annotation label renderer - preferred language

Nick Drummond
In reply to this post by Förhécz András
Hi András,

Ah yes. This is a bug.
We do use the OWL API provider.
I'll look into it.

Nick

On Thu, Jun 26, 2008 at 4:10 PM, Förhécz András <[hidden email]> wrote:
Hi all,

David wrote:
> I have
> preferences switched to viewing terms by name (label), rather than ID
> (using 'Render entities using annotation values' option).
Doing the same, on the "Annotation Renderer" dialog the column header is
"Languages (comma separated in order of preference)".

However no matter in which order I specify language codes, my English
and Hungarian labels are displayed randomly.
This may be a bug in the OWL API if the feature is implemented using:
  org.semanticweb.owl.util.AnnotationValueShortFormProvider

Regards,
  András

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p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback


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Re: annotation label renderer - preferred language

Nick Drummond
I've fixed this in the OWL API and will be working in the next build.

Nick

On Fri, Jun 27, 2008 at 10:41 AM, Nick Drummond <[hidden email]> wrote:
Hi András,

Ah yes. This is a bug.
We do use the OWL API provider.
I'll look into it.

Nick


On Thu, Jun 26, 2008 at 4:10 PM, Förhécz András <[hidden email]> wrote:
Hi all,

David wrote:
> I have
> preferences switched to viewing terms by name (label), rather than ID
> (using 'Render entities using annotation values' option).
Doing the same, on the "Annotation Renderer" dialog the column header is
"Languages (comma separated in order of preference)".

However no matter in which order I specify language codes, my English
and Hungarian labels are displayed randomly.
This may be a bug in the OWL API if the feature is implemented using:
  org.semanticweb.owl.util.AnnotationValueShortFormProvider

Regards,
  András

_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback



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[hidden email]
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