Re: protege-user Digest, Vol 3, Issue 36

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Q I
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Re: protege-user Digest, Vol 3, Issue 36

Q I

Hello,

I think it's a safe assumption that even the older mail clients can handle a lot more than 350kb per message. The setting needs to be increased. Most can handle at least 1.5 megs a millennia ago.

-Quincy

On Apr 15, 2014 3:31 PM, <[hidden email]> wrote:
Send protege-user mailing list submissions to
        [hidden email]

To subscribe or unsubscribe via the World Wide Web, visit
        https://mailman.stanford.edu/mailman/listinfo/protege-user
or, via email, send a message with subject or body 'help' to
        [hidden email]

You can reach the person managing the list at
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of protege-user digest..."


Today's Topics:

   1. Re: Trouble installing protege 4.3 on Mac OS (Karen Yook)
   2. Re: Display problem with trees in Protege 4.3 (Csongor Nyulas)


----------------------------------------------------------------------

Message: 1
Date: Tue, 15 Apr 2014 12:13:17 -0700
From: Karen Yook <[hidden email]>
To: User support for WebProtege and Protege Desktop
        <[hidden email]>
Subject: Re: [protege-user] Trouble installing protege 4.3 on Mac OS
Message-ID:
        <CAF4a_bPLXZiZj+FyGVB_G30JHhMG1YsPW0NRj=[hidden email]>
Content-Type: text/plain; charset="utf-8"

Fixed the security settings and got it installed. Thanks everyone!

Also, please forgive my duplicate (triplicate?) posts, I was definitely
clumsy with the
user list signup.

best,
Karen


On Tue, Apr 15, 2014 at 11:31 AM, Matthew Horridge <
[hidden email]> wrote:

> Hi Karen,
>
> Are you running Mac OS X by any chance?  If so, the error message is
> misleading and it?s actually Apple?s security system that?s preventing it
> from running.  To fix this, go to the General tab in your Security &
> Privacy settings in your OS X System Preferences and enable Protege to run
> from there.
>
> Cheers,
>
> Matthew
>
>
>
> On 15 Apr 2014, at 11:07, Karen Yook <[hidden email]> wrote:
>
> Installer installs a damaged protege app.
>
> --
> ~~~~
> Karen Yook
>
> Curator
> WormBase Caltech
> Tel: <a href="tel:626.395.5878" value="+16263955878">626.395.5878
> e-mail: [hidden email]
> e-mail: [hidden email]
> skype name: wbkaren
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user
>
>
>
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user
>
>


--
~~~~
Karen Yook

Curator
WormBase Caltech
Tel: <a href="tel:626.395.5878" value="+16263955878">626.395.5878
e-mail: [hidden email]
e-mail: [hidden email]
skype name: wbkaren
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Message: 2
Date: Tue, 15 Apr 2014 12:30:19 -0700
From: Csongor Nyulas <[hidden email]>
To: [hidden email]
Subject: Re: [protege-user] Display problem with trees in Protege 4.3
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"

This is really strange, indeed. It must be something particular to your
system setup (or the applications installed), because this is the first
time this problem is reported over the many years of providing support
for Protege.
I would be curious to know if changing any preferences (something not
related to Graphviz) once things work normally would also write garbage
in your preferences?

It would be great if you could figure out what is going wrong and report
back, maybe there is something we can fix in the Protege code.
Unfortunately, we can't do too much to help you debug this issue.

Csongor


On 04/15/2014 11:30 AM, Johannes Scharf wrote:
> I've just set the path under Preferences of Protege to Dot.exe and hit
> "OK".
> I did some further research and found out that not GraphViz seems to
> cause the weird rendering of the trees but the preferences dialog
> seems to write a bunch of options into registry after hitting "OK".
> One of the preferences seems to interfer - I removed all of them
> except the OWLViz configuration including GraphViz and suddenly
> Protege 4.0 started rendering the trees again correctly! Moreover
> GraphViz seems to work as well. I hadn't enough time to try this wiht
> Protege 4.3 as well.
> I conclude that the preferences must write some options to the
> registry which seem to interfer with a component of my system? Never
> saw such a strange behaviour before....
> Kind regards,
> Johannes
> *Gesendet:* Dienstag, 15. April 2014 um 19:46 Uhr
> *Von:* "Csongor Nyulas" <[hidden email]>
> *An:* [hidden email]
> *Betreff:* Re: [protege-user] Display problem with trees in Protege 4.3
> How did you configure Graphviz 2.28?
>
> Csongor
>
> On 04/15/2014 05:58 AM, Johannes Scharf wrote:
>
>     Update: I found the cause of the problem: When I configure
>     Graphviz 2.28 the problem occured again in Protege 4.0 and Protege
>     4.3 - any hints?
>     Thanks.
>     *Gesendet:* Dienstag, 15. April 2014 um 11:09 Uhr
>     *Von:* "Tania Tudorache" <[hidden email]>
>     *An:* "User support for WebProtege and Protege Desktop"
>     <[hidden email]>
>     *Betreff:* Re: [protege-user] Display problem with trees in
>     Protege 4.3
>     This is interesting.
>     Is it just the trees that look weird, or also other things? For
>     example, do the menus look OK?
>     I don't have access to a windows machine at this time, but here
>     are a few things you can try:
>     1. File menu -> Preferences -> press on the Reset preferences
>     button at the bottom of the window.
>     Restart Protege, see how it looks. If it doesn't work, then:
>     2. Delete manually the Java preferences for Protege. See here how:
>     http://protegewiki.stanford.edu/wiki/ClearingP4Preferences
>     Hopefully this will do it. If not:
>     3. Try to run Protege using the run.bat file. I assume there is a
>     run.bat in the Protege installation folder. Open a command
>     terminal, cd to the Protege installation folder, and start
>     run.bat. You may need to adjust the java path if "java" is not on
>     your system path.
>     If this still doesn't work (probably it won't), then try the last
>     desperate step:
>     4. Try to install Protege 3.5, and see if the problem also appears
>     there:
>     http://protege.stanford.edu/download/protege/3.5/installanywhere/Web_Installers/
>     Feel free to uninstall it after the test, and please report the
>     result.
>     Tania
>     ------------------------------------------------------------------------
>     *From: *"Johannes Scharf" <[hidden email]>
>     *To: *"User support for WebProtege and Protege Desktop"
>     <[hidden email]>
>     *Sent: *Tuesday, April 15, 2014 12:58:26 AM
>     *Subject: *Re: [protege-user] Display problem with trees in
>     Protege 4.3
>     Hello!
>     I've already tried using the bundled Java that ships with Protege
>     - same results.
>     In the meantime I uninstalled all of my Java version on my machine
>     and installed the latest JDK 1.7.0_51. Unfortunately that hasn't
>     changed anything.
>     However I concluded that this is NOT a problem with Java. As I
>     already mentioned I've observed the same problem running with Java
>     1.6. In fact if you look closely the NoSuchMethodException points
>     at some missing method of a Java class from Protege
>     (e.g. NewAction) itself and NOT Swing.
>     Moreover all my other Java programs run fine on the same
>     machine... What's really strange is that the error appears in
>     Protege 4.0 and 4.3. I've already tried to use another Look and
>     Feel inside Protege - I thought the Plastic LaF could be the
>     problem...
>     Any further ideas?
>     Thanks!
>     Kind regards,
>     Johannes
>     *Gesendet:* Dienstag, 15. April 2014 um 00:12 Uhr
>     *Von:* "Jennifer Vendetti" <[hidden email]>
>     *An:* "User support for WebProtege and Protege Desktop"
>     <[hidden email]>
>     *Betreff:* Re: [protege-user] Display problem with trees in
>     Protege 4.3
>     On 4/14/2014 12:14 PM, Johannes Scharf wrote:
>
>         Of course - I've switched logging to DEBUG level and attached
>         the file.
>
>
>     Thank you for sending the log file.  I noticed a lot of
>     java.lang.NoSuchMethodException error messages for methods from
>     the javax.swing package, e.g.:
>
>     DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is
>     not requesting a menu itemjava.lang.NoSuchMethodException:
>     org.protege.editor.core.ui.action.NewAction.setMenuItem(javax.swing.JMenuItem)
>     org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]
>
>     DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is
>     not requesting its parentjava.lang.NoSuchMethodException:
>     org.protege.editor.core.ui.action.NewAction.setMenuParent(javax.swing.JComponent)
>     org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]
>
>     I'm wondering if there's something wrong with your Java
>     installation.  Could you try installing a version of Protege 4.3
>     with a VM already bundled?  For example, go to the Protege website
>     Products page
>     (http://protege.stanford.edu/products.php#desktop-protege) and
>     click the Download for Windows button.  In the resulting download
>     dialog, choose an installer file marked with the text "(with VM)",
>     e.g., "Protege Desktop for Windows 64bit (with Java VM)", or
>     "Protege Desktop for Windows (with Java VM)".  During the
>     installation process, make sure to choose "Use the Java VM
>     installed with this application":
>
>
>
>     When you run Protege this way, you should see in the console that
>     it uses Java 6:
>
>
>
>     Do you still have the same display issues when you run Protege
>     this way?
>
>     Alternatively, you could try reinstalling Java 7. As I mentioned
>     previously, I can run Protege w/out display issues with the same
>     version of Java 7 that you have installed:
>
>
>         Btw... Protege 4.3 needs to startup about 5 (!) minutes on my
>         i5 quad-core machine.... Protege 4.0 starts up in 2 secs....
>
>
>     There are a number of error messages in the log from Protege's
>     auto-update functionality complaining about connectivity issues:
>
>     java.io.IOException: Server returned HTTP response code: 503 for
>     URL: http://sourceforge.net/p/owllink-owlapi/code/
>         at sun.net.www.protocol.http.HttpURLConnection.getInp
>     <http://www.protocol.http.HttpURLConnection.getInp>utStream(HttpURLConnection.java:1626)
>
>     DEBUG Examining node
>     http://smi-protege/repos/protege/protege4/plugins/org.protege.osgi.jdbc/trunk/etc/update.properties
>     org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
>     DEBUG Cannot open remote plugin file/registry
>     org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
>     java.net.UnknownHostException: smi-protege
>
>     DEBUG Examining node
>     https://raw.githubusercontent.com/protegeproject/dlquery/master/etc/update.properties
>     org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
>     DEBUG Cannot open remote plugin file/registry
>     org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
>     javax.net.ssl.SSLProtocolException: handshake alert: unrecognized_name
>
>     I'm able to hit all of these URLs w/out issue. Try going to File |
>     Preferences... | Plugins, and uncheck the option to "Automatically
>     check for plugins at start up", then restart Protege.  Do you see
>     the same performance issue?
>
>     Jennifer
>
>     _______________________________________________ protege-user
>     mailing list [hidden email]
>     https://mailman.stanford.edu/mailman/listinfo/protege-user
>
>     _______________________________________________
>     protege-user mailing list
>     [hidden email]
>     https://mailman.stanford.edu/mailman/listinfo/protege-user
>     _______________________________________________ protege-user
>     mailing list [hidden email]
>     https://mailman.stanford.edu/mailman/listinfo/protege-user
>
>     _______________________________________________
>     protege-user mailing list
>     [hidden email]
>     https://mailman.stanford.edu/mailman/listinfo/protege-user
>
>
> _______________________________________________ protege-user mailing
> list [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user
>
>
> _______________________________________________
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> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user

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------------------------------

Subject: Digest Footer

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------------------------------

End of protege-user Digest, Vol 3, Issue 36
*******************************************

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Re: protege-user Digest, Vol 3, Issue 36

lesego phoshane

Hi,
Pls remove me from your mail list. I don't use protege anymore.

Thanx

On 15 Apr 2014 15:38, "Q I" <[hidden email]> wrote:

Hello,

I think it's a safe assumption that even the older mail clients can handle a lot more than 350kb per message. The setting needs to be increased. Most can handle at least 1.5 megs a millennia ago.

-Quincy

On Apr 15, 2014 3:31 PM, <[hidden email]> wrote:
Send protege-user mailing list submissions to
        [hidden email]

To subscribe or unsubscribe via the World Wide Web, visit
        https://mailman.stanford.edu/mailman/listinfo/protege-user
or, via email, send a message with subject or body 'help' to
        [hidden email]

You can reach the person managing the list at
        [hidden email]

When replying, please edit your Subject line so it is more specific
than "Re: Contents of protege-user digest..."


Today's Topics:

   1. Re: Trouble installing protege 4.3 on Mac OS (Karen Yook)
   2. Re: Display problem with trees in Protege 4.3 (Csongor Nyulas)


----------------------------------------------------------------------

Message: 1
Date: Tue, 15 Apr 2014 12:13:17 -0700
From: Karen Yook <[hidden email]>
To: User support for WebProtege and Protege Desktop
        <[hidden email]>
Subject: Re: [protege-user] Trouble installing protege 4.3 on Mac OS
Message-ID:
        <CAF4a_bPLXZiZj+FyGVB_G30JHhMG1YsPW0NRj=[hidden email]>
Content-Type: text/plain; charset="utf-8"

Fixed the security settings and got it installed. Thanks everyone!

Also, please forgive my duplicate (triplicate?) posts, I was definitely
clumsy with the
user list signup.

best,
Karen


On Tue, Apr 15, 2014 at 11:31 AM, Matthew Horridge <
[hidden email]> wrote:

> Hi Karen,
>
> Are you running Mac OS X by any chance?  If so, the error message is
> misleading and it?s actually Apple?s security system that?s preventing it
> from running.  To fix this, go to the General tab in your Security &
> Privacy settings in your OS X System Preferences and enable Protege to run
> from there.
>
> Cheers,
>
> Matthew
>
>
>
> On 15 Apr 2014, at 11:07, Karen Yook <[hidden email]> wrote:
>
> Installer installs a damaged protege app.
>
> --
> ~~~~
> Karen Yook
>
> Curator
> WormBase Caltech
> Tel: <a href="tel:626.395.5878" value="+16263955878" target="_blank">626.395.5878
> e-mail: [hidden email]
> e-mail: [hidden email]
> skype name: wbkaren
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user
>
>
>
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user
>
>


--
~~~~
Karen Yook

Curator
WormBase Caltech
Tel: <a href="tel:626.395.5878" value="+16263955878" target="_blank">626.395.5878
e-mail: [hidden email]
e-mail: [hidden email]
skype name: wbkaren
-------------- next part --------------
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------------------------------

Message: 2
Date: Tue, 15 Apr 2014 12:30:19 -0700
From: Csongor Nyulas <[hidden email]>
To: [hidden email]
Subject: Re: [protege-user] Display problem with trees in Protege 4.3
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"

This is really strange, indeed. It must be something particular to your
system setup (or the applications installed), because this is the first
time this problem is reported over the many years of providing support
for Protege.
I would be curious to know if changing any preferences (something not
related to Graphviz) once things work normally would also write garbage
in your preferences?

It would be great if you could figure out what is going wrong and report
back, maybe there is something we can fix in the Protege code.
Unfortunately, we can't do too much to help you debug this issue.

Csongor


On 04/15/2014 11:30 AM, Johannes Scharf wrote:
> I've just set the path under Preferences of Protege to Dot.exe and hit
> "OK".
> I did some further research and found out that not GraphViz seems to
> cause the weird rendering of the trees but the preferences dialog
> seems to write a bunch of options into registry after hitting "OK".
> One of the preferences seems to interfer - I removed all of them
> except the OWLViz configuration including GraphViz and suddenly
> Protege 4.0 started rendering the trees again correctly! Moreover
> GraphViz seems to work as well. I hadn't enough time to try this wiht
> Protege 4.3 as well.
> I conclude that the preferences must write some options to the
> registry which seem to interfer with a component of my system? Never
> saw such a strange behaviour before....
> Kind regards,
> Johannes
> *Gesendet:* Dienstag, 15. April 2014 um 19:46 Uhr
> *Von:* "Csongor Nyulas" <[hidden email]>
> *An:* [hidden email]
> *Betreff:* Re: [protege-user] Display problem with trees in Protege 4.3
> How did you configure Graphviz 2.28?
>
> Csongor
>
> On 04/15/2014 05:58 AM, Johannes Scharf wrote:
>
>     Update: I found the cause of the problem: When I configure
>     Graphviz 2.28 the problem occured again in Protege 4.0 and Protege
>     4.3 - any hints?
>     Thanks.
>     *Gesendet:* Dienstag, 15. April 2014 um 11:09 Uhr
>     *Von:* "Tania Tudorache" <[hidden email]>
>     *An:* "User support for WebProtege and Protege Desktop"
>     <[hidden email]>
>     *Betreff:* Re: [protege-user] Display problem with trees in
>     Protege 4.3
>     This is interesting.
>     Is it just the trees that look weird, or also other things? For
>     example, do the menus look OK?
>     I don't have access to a windows machine at this time, but here
>     are a few things you can try:
>     1. File menu -> Preferences -> press on the Reset preferences
>     button at the bottom of the window.
>     Restart Protege, see how it looks. If it doesn't work, then:
>     2. Delete manually the Java preferences for Protege. See here how:
>     http://protegewiki.stanford.edu/wiki/ClearingP4Preferences
>     Hopefully this will do it. If not:
>     3. Try to run Protege using the run.bat file. I assume there is a
>     run.bat in the Protege installation folder. Open a command
>     terminal, cd to the Protege installation folder, and start
>     run.bat. You may need to adjust the java path if "java" is not on
>     your system path.
>     If this still doesn't work (probably it won't), then try the last
>     desperate step:
>     4. Try to install Protege 3.5, and see if the problem also appears
>     there:
>     http://protege.stanford.edu/download/protege/3.5/installanywhere/Web_Installers/
>     Feel free to uninstall it after the test, and please report the
>     result.
>     Tania
>     ------------------------------------------------------------------------
>     *From: *"Johannes Scharf" <[hidden email]>
>     *To: *"User support for WebProtege and Protege Desktop"
>     <[hidden email]>
>     *Sent: *Tuesday, April 15, 2014 12:58:26 AM
>     *Subject: *Re: [protege-user] Display problem with trees in
>     Protege 4.3
>     Hello!
>     I've already tried using the bundled Java that ships with Protege
>     - same results.
>     In the meantime I uninstalled all of my Java version on my machine
>     and installed the latest JDK 1.7.0_51. Unfortunately that hasn't
>     changed anything.
>     However I concluded that this is NOT a problem with Java. As I
>     already mentioned I've observed the same problem running with Java
>     1.6. In fact if you look closely the NoSuchMethodException points
>     at some missing method of a Java class from Protege
>     (e.g. NewAction) itself and NOT Swing.
>     Moreover all my other Java programs run fine on the same
>     machine... What's really strange is that the error appears in
>     Protege 4.0 and 4.3. I've already tried to use another Look and
>     Feel inside Protege - I thought the Plastic LaF could be the
>     problem...
>     Any further ideas?
>     Thanks!
>     Kind regards,
>     Johannes
>     *Gesendet:* Dienstag, 15. April 2014 um 00:12 Uhr
>     *Von:* "Jennifer Vendetti" <[hidden email]>
>     *An:* "User support for WebProtege and Protege Desktop"
>     <[hidden email]>
>     *Betreff:* Re: [protege-user] Display problem with trees in
>     Protege 4.3
>     On 4/14/2014 12:14 PM, Johannes Scharf wrote:
>
>         Of course - I've switched logging to DEBUG level and attached
>         the file.
>
>
>     Thank you for sending the log file.  I noticed a lot of
>     java.lang.NoSuchMethodException error messages for methods from
>     the javax.swing package, e.g.:
>
>     DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is
>     not requesting a menu itemjava.lang.NoSuchMethodException:
>     org.protege.editor.core.ui.action.NewAction.setMenuItem(javax.swing.JMenuItem)
>     org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]
>
>     DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is
>     not requesting its parentjava.lang.NoSuchMethodException:
>     org.protege.editor.core.ui.action.NewAction.setMenuParent(javax.swing.JComponent)
>     org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]
>
>     I'm wondering if there's something wrong with your Java
>     installation.  Could you try installing a version of Protege 4.3
>     with a VM already bundled?  For example, go to the Protege website
>     Products page
>     (http://protege.stanford.edu/products.php#desktop-protege) and
>     click the Download for Windows button.  In the resulting download
>     dialog, choose an installer file marked with the text "(with VM)",
>     e.g., "Protege Desktop for Windows 64bit (with Java VM)", or
>     "Protege Desktop for Windows (with Java VM)".  During the
>     installation process, make sure to choose "Use the Java VM
>     installed with this application":
>
>
>
>     When you run Protege this way, you should see in the console that
>     it uses Java 6:
>
>
>
>     Do you still have the same display issues when you run Protege
>     this way?
>
>     Alternatively, you could try reinstalling Java 7. As I mentioned
>     previously, I can run Protege w/out display issues with the same
>     version of Java 7 that you have installed:
>
>
>         Btw... Protege 4.3 needs to startup about 5 (!) minutes on my
>         i5 quad-core machine.... Protege 4.0 starts up in 2 secs....
>
>
>     There are a number of error messages in the log from Protege's
>     auto-update functionality complaining about connectivity issues:
>
>     java.io.IOException: Server returned HTTP response code: 503 for
>     URL: http://sourceforge.net/p/owllink-owlapi/code/
>         at sun.net.www.protocol.http.HttpURLConnection.getInp
>     <http://www.protocol.http.HttpURLConnection.getInp>utStream(HttpURLConnection.java:1626)
>
>     DEBUG Examining node
>     http://smi-protege/repos/protege/protege4/plugins/org.protege.osgi.jdbc/trunk/etc/update.properties
>     org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
>     DEBUG Cannot open remote plugin file/registry
>     org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
>     java.net.UnknownHostException: smi-protege
>
>     DEBUG Examining node
>     https://raw.githubusercontent.com/protegeproject/dlquery/master/etc/update.properties
>     org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
>     DEBUG Cannot open remote plugin file/registry
>     org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
>     javax.net.ssl.SSLProtocolException: handshake alert: unrecognized_name
>
>     I'm able to hit all of these URLs w/out issue. Try going to File |
>     Preferences... | Plugins, and uncheck the option to "Automatically
>     check for plugins at start up", then restart Protege.  Do you see
>     the same performance issue?
>
>     Jennifer
>
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