Protege 3.4.7 Patch Release

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Protege 3.4.7 Patch Release

Jennifer Vendetti
Administrator
We've posted an update to the 3.4 release (version number 3.4.7, build 620).

Download URL:
http://protege.stanford.edu/download/protege/3.4/installanywhere/Web_Installers/

If you haven't registered to use Protege, please do so before
downloading this patch release.

Registration URL: http://protege.stanford.edu/download/register.html


Core Protege
--------------------
- Fixed a problem that caused a warning dialog to appear each time
Protege started.

- Fixed a bug that caused newly created and renamed instances in OWL
ontologies to be displayed with the original name (only present in
client-server mode).

- Added the serialVersionUID to all serializable classes in
protege-core, owl, and a number of plug-ins (standard-extensions,
protege-pellet-reasoner, rdf-backend, change-management,
change-analysis, protege-collab, chat, prompt, lucene-query,
bioportal-reference-plug). This will improve compatibility between
different versions of Protege servers and clients.

BioPortal Reference Plug-in
---------------------------------------
- Updated the BioPortal Reference Plug-in to work with the latest
release of NCBO BioPortal [1], which now requires a mandatory argument
be appended to all REST calls (read more [2]).

BioPortal Import Plug-in
---------------------------------
- The BioPortal Import Plug-in is now bundled with the default Protege
installation. It is integrated into the OWL Classes tab as an extra
button that allows importation of classes or class sub-tress from
ontologies stored in NCBO BioPortal. The plug-in is highly configurable,
and supports importation of class properties, e.g., labels, synonyms,
definitions, and metadata, e.g., import author, timestamp, source
ontology, etc. (read more [3]). New versions will be downloadable from
the plug-in's wiki page.

BioPortal Java API
---------------------------
- The BioPortal Java API used by both the BioPortal Reference and Import
plug-ins was modified to be less sensitive to NCBO BioPortal service
changes. The API is documented [4] on the Protege wiki.


A web-based version of the release notes is available on the Protege
wiki [5].

Best Regards,
The Protege Team

[1] http://bioportal.bioontology.org/
[2] http://protegewiki.stanford.edu/wiki/BioPortal_Reference_Plugin
[3] http://protegewiki.stanford.edu/wiki/BioPortal_Import_Plugin
[4]
http://protegewiki.stanford.edu/wiki/BioPortal_Reference_Plugin#Developer.27s_Guide
[5] http://protegewiki.stanford.edu/wiki/Protege_3.4.7_Release_Notes

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Protege for Working with Instance data - rdf editing

Bruce Whealton
Hello,
         I was reading a document on the web about using Protégé to edit RDF
data.  It was dealing with Protégé-2000.  Initially, I would have thought
that it would be naïve to try to edit RDF data using an Ontology editor.
Then I thought of a few things about RDF and OWL.  The idea is that there is
no distinction between the schema or ontology, the metadata and the data
itself.  Of course, that may or may not apply to Protégé.  Certainly, it
seems that Protégé is well designed and structured for working as an RDF
editor.  Intuitively, it seems to work as such.  The documentation talks
about the number of frames that can be supported if a file system is used
for storage.  So, I didn't see this issue directly answered in the FAQ for
Protégé, whether or not it now supports RDF creation and editing.
         I wanted to find out about this and what the thoughts are on the
topic.
         I did notice something else in the documentation.  It says in
Section 2 that the OWLViz plug-in is recommended.  Later, I found that this
is included if one installed the full edition of Protégé 4.  I believe I
would have done so.  Is there a way to find out right away?  That plug-in
isn't even listed on the CO-ODE website where it is said to exist in the
documentation.  There is a mention of it in the Protégé 3 Plugin library,
though.
Thanks,
Bruce

++++++++++++++++++++++++++++++++++++++++++++++++++
Bruce Whealton, Owner Future Wave Designs
FOAF: http://whealton.info/BruceWhealtonJr/foaf.rdf
Vcard: http://whealton.info/BruceWhealtonJr/brucewhealtonvcard.html
Web Design and Development http://FutureWaveDesigns.com
http://futurewavedesigns.com/wordpress/
Web Technology wiki: http://futurewavedesigns.com/w/
++++++++++++++++++++++++++++++++++++++++++++++++++


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Re: Protege for Working with Instance data - rdf editing

Tania Tudorache
Hi Bruce,

Please start your own threads, and don't reply to one that is irrelevant
to what you're asking.

You can edit RDF with Protege using either Protege 3 OWL or the Protege
3 RDF backend. You may also edit it in Protege 4, but the output will be
OWL (that RDF libraries should be able to read).

OWLViz is included both with Protege 3 and 4, there is no need to
install anything separately.

Tania


On 07/18/2011 03:01 PM, Bruce Whealton wrote:

> Hello,
>         I was reading a document on the web about using Protégé to
> edit RDF data.  It was dealing with Protégé-2000.  Initially, I would
> have thought that it would be naïve to try to edit RDF data using an
> Ontology editor. Then I thought of a few things about RDF and OWL.  
> The idea is that there is no distinction between the schema or
> ontology, the metadata and the data itself.  Of course, that may or
> may not apply to Protégé.  Certainly, it seems that Protégé is well
> designed and structured for working as an RDF editor.  Intuitively, it
> seems to work as such.  The documentation talks about the number of
> frames that can be supported if a file system is used for storage.  
> So, I didn't see this issue directly answered in the FAQ for Protégé,
> whether or not it now supports RDF creation and editing.
>         I wanted to find out about this and what the thoughts are on
> the topic.
>         I did notice something else in the documentation.  It says in
> Section 2 that the OWLViz plug-in is recommended.  Later, I found that
> this is included if one installed the full edition of Protégé 4.  I
> believe I would have done so.  Is there a way to find out right away?  
> That plug-in isn't even listed on the CO-ODE website where it is said
> to exist in the documentation.  There is a mention of it in the
> Protégé 3 Plugin library, though.
> Thanks,
> Bruce
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++
> Bruce Whealton, Owner Future Wave Designs
> FOAF: http://whealton.info/BruceWhealtonJr/foaf.rdf
> Vcard: http://whealton.info/BruceWhealtonJr/brucewhealtonvcard.html
> Web Design and Development http://FutureWaveDesigns.com
> http://futurewavedesigns.com/wordpress/
> Web Technology wiki: http://futurewavedesigns.com/w/
> ++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
> _______________________________________________
> 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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Re: Protege for Working with Instance data - rdfediting

Bruce Whealton
Hello,
         Wasn't this a separate thread?  I didn't realize it had come
through as part of another irrelevant thread.
Bruce

-----Original Message-----
From: Tania Tudorache
Sent: Tuesday, July 19, 2011 3:50 PM
To: User support for the Protege-OWL editor
Subject: Re: [protege-owl] Protege for Working with Instance data -
rdfediting

Hi Bruce,

Please start your own threads, and don't reply to one that is irrelevant
to what you're asking.

You can edit RDF with Protege using either Protege 3 OWL or the Protege
3 RDF backend. You may also edit it in Protege 4, but the output will be
OWL (that RDF libraries should be able to read).

OWLViz is included both with Protege 3 and 4, there is no need to
install anything separately.

Tania


On 07/18/2011 03:01 PM, Bruce Whealton wrote:

> Hello,
>         I was reading a document on the web about using Protégé to edit
> RDF data.  It was dealing with Protégé-2000.  Initially, I would have
> thought that it would be naïve to try to edit RDF data using an Ontology
> editor. Then I thought of a few things about RDF and OWL.  The idea is
> that there is no distinction between the schema or ontology, the metadata
> and the data itself.  Of course, that may or may not apply to Protégé.
> Certainly, it seems that Protégé is well designed and structured for
> working as an RDF editor.  Intuitively, it seems to work as such.  The
> documentation talks about the number of frames that can be supported if a
> file system is used for storage.  So, I didn't see this issue directly
> answered in the FAQ for Protégé, whether or not it now supports RDF
> creation and editing.
>         I wanted to find out about this and what the thoughts are on the
> topic.
>         I did notice something else in the documentation.  It says in
> Section 2 that the OWLViz plug-in is recommended.  Later, I found that
> this is included if one installed the full edition of Protégé 4.  I
> believe I would have done so.  Is there a way to find out right away?
> That plug-in isn't even listed on the CO-ODE website where it is said to
> exist in the documentation.  There is a mention of it in the Protégé 3
> Plugin library, though.
> Thanks,
> Bruce
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++
> Bruce Whealton, Owner Future Wave Designs
> FOAF: http://whealton.info/BruceWhealtonJr/foaf.rdf
> Vcard: http://whealton.info/BruceWhealtonJr/brucewhealtonvcard.html
> Web Design and Development http://FutureWaveDesigns.com
> http://futurewavedesigns.com/wordpress/
> Web Technology wiki: http://futurewavedesigns.com/w/
> ++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
> _______________________________________________
> 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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Re: Protege for Working with Instance data - rdfediting

Thomas Russ

On Jul 20, 2011, at 7:51 PM, Bruce Whealton wrote:

> Hello,
>        Wasn't this a separate thread?  I didn't realize it had come through as part of another irrelevant thread.
> Bruce

Some mail readers will organize based on the "references" header field in mail messages.  So if you reply to a message and change the subject, those readers will still assign the message to the thread that you reply to.  Other mail interfaces sort just on the subject field and will display differently.  The only fool-proof way to start a new thread is to use a new message to the list rather than replying to a list message.



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