Protege 4.0 Alpha update (build 63)

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Protege 4.0 Alpha update (build 63)

Jennifer Vendetti
Administrator
There is a new alpha build available on our Web site:

http://protege.stanford.edu/download/prerelease-alpha/

Changes & Bug Fixes in Protege-OWL
----------------------------------------
- The "Usage" views can now be filtered (see File | Preferences | Usage)
to remove disjoint and simple subclass axioms where the classes on both
sides are named.  This should make the views less cluttered.  Filtering
is off by default.

- All lists of ontologies have been tidied up to render more
consistently (by short name) and are sorted to make finding the correct
ontology easier.

- A refactoring action for converting min cardinality 1 restrictions to
someValuesFrom restrictions is now available.

- Additional rendering preferences allow a combination of an annotation
renderer, but with prefixes. This should help resolve ambiguity in the
interface.

- Bundling an updated version of FaCT++ (the imminent 1.1.12 release) to
solve several bugs, including min cardinality 0 and data facets on
floats.  This version of FaCT++ now also supports 64-bit editions of
Windows.

- Bundling an updated version of the OWL API to solve several parser
errors (particularly those with datatypes and properties).

- Right click menu on the class description view now functions correctly.

- Internationalization on dialog button labels now works.

- Pellet now updating on reclassify when ontology has changed.

- Property (role) chain parser now accepts more than 2 elements.

- Removed bug where axioms were getting crossed out.

- Floating views now show the selection correctly (previously they were
blank).

- Proper screen refresh when closing views.

- Editor in general axioms view now partially implemented.

- Old views for which the "Cannot load" gray button of despair appears
can now be closed.

- Annotations can now be copied when "duplicate selected class" is called.

- Editing the features of properties in the property description view
now works for all sections.

- The search box does not magically disappear for those users lucky
enough to have a tiny little screen.

- Equivalent classes now show in the class hierarchy.

- Ontologies that have been loaded from the Web can now be saved to disk
(rather than the save being ignored).

- The individuals view now has tooltips for the full URI of the individual.

- Carriage returns (generated by Windows) are now correctly ignored in
expression editors (such as DL Query).

- Canceling rename operations is now possible.

- When creating annotations, user are no longer limited to the languages
hard-coded in the dropdown (which is now editable).

- Property trees are now sorted alphabetically for ease of navigation.

- (rdfs)Literal - the top datatype - is now accepted by the expression
editor.

- Fixed a bug that prevented button icons from showing up in the OWLViz tab.


As always, a Web-based version of the release notes is available on our
site [1].

The Protege Team

[1]
http://protege.stanford.edu/download/release_notes/release_notes_alpha.html

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Re: Protege 4.0 Alpha update (build 63)

Michel_Dumontier
Woo hoo!!! :-)

-=Michel=-

-----Original Message-----
From: [hidden email]
[mailto:[hidden email]] On Behalf Of Jennifer
Vendetti
Sent: June 4, 2008 10:06 PM
To: p4-feedback
Subject: [p4-feedback] Protege 4.0 Alpha update (build 63)

There is a new alpha build available on our Web site:

http://protege.stanford.edu/download/prerelease-alpha/

Changes & Bug Fixes in Protege-OWL
----------------------------------------
- The "Usage" views can now be filtered (see File | Preferences | Usage)

to remove disjoint and simple subclass axioms where the classes on both
sides are named.  This should make the views less cluttered.  Filtering
is off by default.

- All lists of ontologies have been tidied up to render more
consistently (by short name) and are sorted to make finding the correct
ontology easier.

- A refactoring action for converting min cardinality 1 restrictions to
someValuesFrom restrictions is now available.

- Additional rendering preferences allow a combination of an annotation
renderer, but with prefixes. This should help resolve ambiguity in the
interface.

- Bundling an updated version of FaCT++ (the imminent 1.1.12 release) to

solve several bugs, including min cardinality 0 and data facets on
floats.  This version of FaCT++ now also supports 64-bit editions of
Windows.

- Bundling an updated version of the OWL API to solve several parser
errors (particularly those with datatypes and properties).

- Right click menu on the class description view now functions
correctly.

- Internationalization on dialog button labels now works.

- Pellet now updating on reclassify when ontology has changed.

- Property (role) chain parser now accepts more than 2 elements.

- Removed bug where axioms were getting crossed out.

- Floating views now show the selection correctly (previously they were
blank).

- Proper screen refresh when closing views.

- Editor in general axioms view now partially implemented.

- Old views for which the "Cannot load" gray button of despair appears
can now be closed.

- Annotations can now be copied when "duplicate selected class" is
called.

- Editing the features of properties in the property description view
now works for all sections.

- The search box does not magically disappear for those users lucky
enough to have a tiny little screen.

- Equivalent classes now show in the class hierarchy.

- Ontologies that have been loaded from the Web can now be saved to disk

(rather than the save being ignored).

- The individuals view now has tooltips for the full URI of the
individual.

- Carriage returns (generated by Windows) are now correctly ignored in
expression editors (such as DL Query).

- Canceling rename operations is now possible.

- When creating annotations, user are no longer limited to the languages

hard-coded in the dropdown (which is now editable).

- Property trees are now sorted alphabetically for ease of navigation.

- (rdfs)Literal - the top datatype - is now accepted by the expression
editor.

- Fixed a bug that prevented button icons from showing up in the OWLViz
tab.


As always, a Web-based version of the release notes is available on our
site [1].

The Protege Team

[1]
http://protege.stanford.edu/download/release_notes/release_notes_alpha.h
tml

_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback
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Re: Protege 4.0 Alpha update (build 63)

Nick Drummond
Yeehaa!


On Thu, Jun 5, 2008 at 3:11 AM, Michel_Dumontier <[hidden email]> wrote:
Woo hoo!!! :-)

-=Michel=-

-----Original Message-----
From: [hidden email]
[mailto:[hidden email]] On Behalf Of Jennifer
Vendetti
Sent: June 4, 2008 10:06 PM
To: p4-feedback
Subject: [p4-feedback] Protege 4.0 Alpha update (build 63)

There is a new alpha build available on our Web site:

http://protege.stanford.edu/download/prerelease-alpha/

Changes & Bug Fixes in Protege-OWL
----------------------------------------
- The "Usage" views can now be filtered (see File | Preferences | Usage)

to remove disjoint and simple subclass axioms where the classes on both
sides are named.  This should make the views less cluttered.  Filtering
is off by default.

- All lists of ontologies have been tidied up to render more
consistently (by short name) and are sorted to make finding the correct
ontology easier.

- A refactoring action for converting min cardinality 1 restrictions to
someValuesFrom restrictions is now available.

- Additional rendering preferences allow a combination of an annotation
renderer, but with prefixes. This should help resolve ambiguity in the
interface.

- Bundling an updated version of FaCT++ (the imminent 1.1.12 release) to

solve several bugs, including min cardinality 0 and data facets on
floats.  This version of FaCT++ now also supports 64-bit editions of
Windows.

- Bundling an updated version of the OWL API to solve several parser
errors (particularly those with datatypes and properties).

- Right click menu on the class description view now functions
correctly.

- Internationalization on dialog button labels now works.

- Pellet now updating on reclassify when ontology has changed.

- Property (role) chain parser now accepts more than 2 elements.

- Removed bug where axioms were getting crossed out.

- Floating views now show the selection correctly (previously they were
blank).

- Proper screen refresh when closing views.

- Editor in general axioms view now partially implemented.

- Old views for which the "Cannot load" gray button of despair appears
can now be closed.

- Annotations can now be copied when "duplicate selected class" is
called.

- Editing the features of properties in the property description view
now works for all sections.

- The search box does not magically disappear for those users lucky
enough to have a tiny little screen.

- Equivalent classes now show in the class hierarchy.

- Ontologies that have been loaded from the Web can now be saved to disk

(rather than the save being ignored).

- The individuals view now has tooltips for the full URI of the
individual.

- Carriage returns (generated by Windows) are now correctly ignored in
expression editors (such as DL Query).

- Canceling rename operations is now possible.

- When creating annotations, user are no longer limited to the languages

hard-coded in the dropdown (which is now editable).

- Property trees are now sorted alphabetically for ease of navigation.

- (rdfs)Literal - the top datatype - is now accepted by the expression
editor.

- Fixed a bug that prevented button icons from showing up in the OWLViz
tab.


As always, a Web-based version of the release notes is available on our
site [1].

The Protege Team

[1]
http://protege.stanford.edu/download/release_notes/release_notes_alpha.h
tml


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


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Re: Protege 4.0 Alpha update (build 63)

Nick Drummond
The distribution doesn't appear to have enough memory set to open the gene ontology.

I thought this had been set to 500M or so ages ago (which is more than enough for GO).
We will need to up it from the default..

Depending on the system you are using and how you are starting Protege you can do several things.
This is very similar to the Protege3.x instructions [1] but if you start your windows version using the exe you will have to edit the .lax file in a text editor instead of within protege.

Nick




On Thu, Jun 5, 2008 at 10:34 AM, Christine Golbreich <[hidden email]> wrote:
but cannot open obo files :(
and you ?

Christine

2008/6/5 Nick Drummond <[hidden email]>:
> Yeehaa!
>
> On Thu, Jun 5, 2008 at 3:11 AM, Michel_Dumontier
> <[hidden email]> wrote:
>>
>> Woo hoo!!! :-)
>>
>> -=Michel=-
>>
>> -----Original Message-----
>> From: [hidden email]
>> [mailto:[hidden email]] On Behalf Of Jennifer
>> Vendetti
>> Sent: June 4, 2008 10:06 PM
>> To: p4-feedback
>> Subject: [p4-feedback] Protege 4.0 Alpha update (build 63)
>>
>> There is a new alpha build available on our Web site:
>>
>> http://protege.stanford.edu/download/prerelease-alpha/
>>
>> Changes & Bug Fixes in Protege-OWL
>> ----------------------------------------
>> - The "Usage" views can now be filtered (see File | Preferences | Usage)
>>
>> to remove disjoint and simple subclass axioms where the classes on both
>> sides are named.  This should make the views less cluttered.  Filtering
>> is off by default.
>>
>> - All lists of ontologies have been tidied up to render more
>> consistently (by short name) and are sorted to make finding the correct
>> ontology easier.
>>
>> - A refactoring action for converting min cardinality 1 restrictions to
>> someValuesFrom restrictions is now available.
>>
>> - Additional rendering preferences allow a combination of an annotation
>> renderer, but with prefixes. This should help resolve ambiguity in the
>> interface.
>>
>> - Bundling an updated version of FaCT++ (the imminent 1.1.12 release) to
>>
>> solve several bugs, including min cardinality 0 and data facets on
>> floats.  This version of FaCT++ now also supports 64-bit editions of
>> Windows.
>>
>> - Bundling an updated version of the OWL API to solve several parser
>> errors (particularly those with datatypes and properties).
>>
>> - Right click menu on the class description view now functions
>> correctly.
>>
>> - Internationalization on dialog button labels now works.
>>
>> - Pellet now updating on reclassify when ontology has changed.
>>
>> - Property (role) chain parser now accepts more than 2 elements.
>>
>> - Removed bug where axioms were getting crossed out.
>>
>> - Floating views now show the selection correctly (previously they were
>> blank).
>>
>> - Proper screen refresh when closing views.
>>
>> - Editor in general axioms view now partially implemented.
>>
>> - Old views for which the "Cannot load" gray button of despair appears
>> can now be closed.
>>
>> - Annotations can now be copied when "duplicate selected class" is
>> called.
>>
>> - Editing the features of properties in the property description view
>> now works for all sections.
>>
>> - The search box does not magically disappear for those users lucky
>> enough to have a tiny little screen.
>>
>> - Equivalent classes now show in the class hierarchy.
>>
>> - Ontologies that have been loaded from the Web can now be saved to disk
>>
>> (rather than the save being ignored).
>>
>> - The individuals view now has tooltips for the full URI of the
>> individual.
>>
>> - Carriage returns (generated by Windows) are now correctly ignored in
>> expression editors (such as DL Query).
>>
>> - Canceling rename operations is now possible.
>>
>> - When creating annotations, user are no longer limited to the languages
>>
>> hard-coded in the dropdown (which is now editable).
>>
>> - Property trees are now sorted alphabetically for ease of navigation.
>>
>> - (rdfs)Literal - the top datatype - is now accepted by the expression
>> editor.
>>
>> - Fixed a bug that prevented button icons from showing up in the OWLViz
>> tab.
>>
>>
>> As always, a Web-based version of the release notes is available on our
>> site [1].
>>
>> The Protege Team
>>
>> [1]
>> http://protege.stanford.edu/download/release_notes/release_notes_alpha.h
>> tml
>>
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>
>



--
Christine


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