Protege 5.5.0 Available

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Protege 5.5.0 Available

Matthew Horridge-2
Administrator
Dear Protégé Users,

We are pleased to announce the release of Protégé 5.5.0.  This is a major Protégé release that incorporates various user interface enhancements and fixes many bugs.  You can find detailed release notes below.

You can download Protege 5.5.0 from our downloads page:



We are grateful to the Protégé user community, and in particular our users from the OBO community, for reporting bugs and suggesting features over the beta period.  In particular, we are heavily indebted to the Biomedical Ontology Community for suggestions and feedback on the new features that are contained in this release. We would especially like to thank the participants of the 2017 Berkeley GO Editors Workshop: (in alphabetical order) Kimberly Van Auken, Tanya Berardini, Seth Carbon, Karen Christie, Eric Douglass, Pascale Gaudet, Harold Drabkin, David Hill, Huaiyu Mi, Suzi Lewis, Donghui Li, Chris Mungall, Monica Munoz-Torres, David Osumi-Sutherland, and Nicole Vasilevsky – this work would not have been possible without their input. Special thanks go to Chris Mungall for an invitation to this meeting.

We would also like to thank Ignazio Palmisano, for his tireless work on the OWL API and his speedy response to our OWL API related requests.  Finally, we’d like to acknowledge Yevgeny Kazakov, who has made several significant contributions to the core Protégé code base that made it into this release.

Best regards,

The Protégé Team




Protégé 5.5.0

New Features

  • Added the ability to display relationships other than SubClassOf in the class hierarchy. Please see the documentation for further details. We expect this feature to evolve and we seek feedback from Protégé users.

fig-mixed-hierarchy

  • Added a breadcrumb trail to the top of the Protege window that shows the current path in the current hierarchy. Hovering over a path element in the breadcrumb trail will provide more details about that element. Path elements are also clickable, making it possible to jump up the current hierarchy.

fig-breadcrumb-and-header

  • Added initial Git integration support. When opening ontologies that are contained in a git repository, the current git branch will be displayed in the status bar. It is also possible to use your git user name for automated generation of "created by" annotations in Protege

fig-git-repo-status

fig-git-user-name

  • Improved the various tool tips and search results to display OBO Ids (if present). OBO Ids are now shown in hierarchy tool tips and breadcrumb trail tool tips. Search results now contain a column that displays OBOIds for terms in the search results. It is also possible to search using OBO Id syntax, for example searching for GO:0043231 will return 'intracellular membrane-bounded organelle'. Previously, one had to search using the OBO2OWL IRI syntax to achieve this.

fig-search

  • Entity names in the various hierarchies are now disambiguated if the entity short name or label is not unique. For example in the CL ontology, "cell" is used as the label for two classes. The OBO identifiers are now shown in round brackets next to the occurrences of the "cell" class in the hierarchy. Previously, one had to look at tooltips to disambiguate such occurrences. Thanks go to @nicolevasilevsky for a discussion on GitHub that prompted this.

image

  • Occurrences of single non-unique class names in the class description view are now disambiguated. For example in the CL ontology, "cell" is used as the label for two classes. The OBO identifiers are now shown in round brackets next to the occurrences of the "cell" class in the class description view. In the screenshot below cell CL:0000000 is equivalent to the cell class from the gene ontology GO:0005623.

image

  • Added a popup menu to the entity header that contains useful actions for the selected entity such as being able to copy the display name, IRI or OBO Id.

fig-term-header

  • Added a wizard for deprecating entities. The release included profiles for deprecating entities according to the strategies used by the GO and OBI teams. New profiles can be written as .yaml files and dropped into the configuration directory. Thanks go to the Gene Ontology (GO) editors for ideas and feedback on this.

  • The the log view has been improved so that it is now more scalable and customizable. Preferences can be set on the Log preferences panel. The log window can now be quickly accessed by clicking the log button in the lower right hand corder of the window. Thanks go to @ykazakov for these significant improvements.

image

  • Improved rendering performance for large hierarchies.

Bug Fixes

  • Fixed a bug that could cause some unicode characters to display as boxes on Windows and Linux. (protegeproject/protege#714)
  • Fixed a bug that could cause the incorrect display of the asserted hierarchy in the presence of certain forms of equivalent classes axioms. (protegeproject/protege#847)
  • Entity icons are now aligned with entity names in the various hierarchies when a large font size is selected. (protegeproject/protege#620)
  • Deprecated entity strike out is now aligned better with the vertical position of the font height.
  • Fixed a bug that caused annotations on different individuals axioms to be dropped on save. (protegeproject/protege#747)
  • Fixed a bug that caused Protege to hang when saving OBO files that encoded non-simple axioms in the functional syntax (protegeproject/protege#501)
  • Fixed a bug that could cause Protege to start up off the screen if it had previously been on a secondary screen and that screen is no longer available. (protegeproject/protege#804)
  • Fixed a bug that caused Protege to prompt for missing imports if the imports were loaded via HTTP redirects (protegeproject/protege#839)
  • Fixed a bug that could cause Protege to hang for a long time when loading or saving ontologies from folders with a large number of sub-folders and sub-files. (protegeproject/protege#619)
  • Fixed links to the OWL spec. (protegeproject/protege#792)
  • Fixed a bug where the metrics view would only show the metrics of the first opened ontology (protegeproject/protege#816)
  • Fixed a NullPointerException in search (protegeproject/protege#813)
  • Fixed a problem that prevented some installations from displaying Chinese Characters (protegeproject/protege#824)
  • Fixed a problem that could cause Protégé to hang when loading imported ontologies in some circumstances (in Protégé 5.5.0-beta-7)
  • Fixed a problem that could cause the SPARQL Query Tab to crash when loading
  • Fixed a problem that caused Protege 5.5 to hang while loading OBO Relations Ontology (protegeproject/protege#817)
  • Fixed a bug that could cause Protégé to freeze when entering entity names.
  • Fixed a bug that could cause an error when editing the ontology IRI on some versions of Windows

Other improvements

  • Upgraded the bundled JRE to Java 8 Update 121
  • Upgraded to the OWL API 4.5.8 (protegeproject/protege#835) (Thanks go to @ignazio1977 for all of his work on the OWL API)
  • Made menu items case consistent (protegeproject/protege#843)
  • Made view titles case consistent (protegeproject/protege#842)
  • Renamed view titles for individuals views so that they include "Direct" (protegeproject/protege#829)
  • Entity names are no longer quoted in view headers (protegeproject/protege#841)
  • Tidied the missing imports dialog
  • Cleaned up the ontology catalog manager dialog
  • Tidied up the ontology catalog add entry dialog
  • Removed the "Edit active ontology catalog..." menu item. Superseded by the "Edit ontology catalog..." menu item.
  • Cached mouse positions to improve rendering performance with some JREs. (protegeproject/protege#723). Thanks go to @ykazakov for tracking down the original problem and his help with this.

 

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Re: Protege 5.5.0 Available

Campbell, James R

You have a problem with the 5.5.0 release.  I have used Protege for work with SNOMED CT extensions and workshops for the past many months using the 5.5.0-beta -3  release.  I run on Windows 10 (home and at work) and on both machines I have 24-32GB memory using 64 bit processor with a TB of solid state memory.  To load and classify SNOMED CT , I would change Xmx to 5 GB and Xms to 200 MB in the run.bat files you issued and start protege.  Load of SNOMED CT (OWL) usually took 2-3 minutes and classification with Elk 0.4.3 took 83 seconds.  

When I loaded 5.5.0, I could not get it to run on either machine with Mmx at more than 1GB, although it did then start.  Loading SNOMED CT took 5 minutes and I cancelled classification at an hour and half when it had still not completed.  I strongly suspect that you have memory management issues with your 5.5.0 .  I suspect I may be stressing the software more than most with SNOMED CT development work but I can verify that the beta software was up to the task with the hardware I use.

Jim Campbell


From: protege-user <[hidden email]> on behalf of Matthew Horridge <[hidden email]>
Sent: Friday, March 15, 2019 11:48:58 AM
To: User support for WebProtege and Protege Desktop; [hidden email]
Subject: [protege-user] Protege 5.5.0 Available
 
Non-UNMC email


 
Dear Protégé Users,

We are pleased to announce the release of Protégé 5.5.0.  This is a major Protégé release that incorporates various user interface enhancements and fixes many bugs.  You can find detailed release notes below.

You can download Protege 5.5.0 from our downloads page:



We are grateful to the Protégé user community, and in particular our users from the OBO community, for reporting bugs and suggesting features over the beta period.  In particular, we are heavily indebted to the Biomedical Ontology Community for suggestions and feedback on the new features that are contained in this release. We would especially like to thank the participants of the 2017 Berkeley GO Editors Workshop: (in alphabetical order) Kimberly Van Auken, Tanya Berardini, Seth Carbon, Karen Christie, Eric Douglass, Pascale Gaudet, Harold Drabkin, David Hill, Huaiyu Mi, Suzi Lewis, Donghui Li, Chris Mungall, Monica Munoz-Torres, David Osumi-Sutherland, and Nicole Vasilevsky – this work would not have been possible without their input. Special thanks go to Chris Mungall for an invitation to this meeting.

We would also like to thank Ignazio Palmisano, for his tireless work on the OWL API and his speedy response to our OWL API related requests.  Finally, we’d like to acknowledge Yevgeny Kazakov, who has made several significant contributions to the core Protégé code base that made it into this release.

Best regards,

The Protégé Team




Protégé 5.5.0

New Features

  • Added the ability to display relationships other than SubClassOf in the class hierarchy. Please see the documentation for further details. We expect this feature to evolve and we seek feedback from Protégé users.

fig-mixed-hierarchy

  • Added a breadcrumb trail to the top of the Protege window that shows the current path in the current hierarchy. Hovering over a path element in the breadcrumb trail will provide more details about that element. Path elements are also clickable, making it possible to jump up the current hierarchy.

fig-breadcrumb-and-header

  • Added initial Git integration support. When opening ontologies that are contained in a git repository, the current git branch will be displayed in the status bar. It is also possible to use your git user name for automated generation of "created by" annotations in Protege

fig-git-repo-status

fig-git-user-name

  • Improved the various tool tips and search results to display OBO Ids (if present). OBO Ids are now shown in hierarchy tool tips and breadcrumb trail tool tips. Search results now contain a column that displays OBOIds for terms in the search results. It is also possible to search using OBO Id syntax, for example searching for GO:0043231 will return 'intracellular membrane-bounded organelle'. Previously, one had to search using the OBO2OWL IRI syntax to achieve this.

fig-search

  • Entity names in the various hierarchies are now disambiguated if the entity short name or label is not unique. For example in the CL ontology, "cell" is used as the label for two classes. The OBO identifiers are now shown in round brackets next to the occurrences of the "cell" class in the hierarchy. Previously, one had to look at tooltips to disambiguate such occurrences. Thanks go to @nicolevasilevsky for a discussion on GitHub that prompted this.

image

  • Occurrences of single non-unique class names in the class description view are now disambiguated. For example in the CL ontology, "cell" is used as the label for two classes. The OBO identifiers are now shown in round brackets next to the occurrences of the "cell" class in the class description view. In the screenshot below cell CL:0000000 is equivalent to the cell class from the gene ontology GO:0005623.

image

  • Added a popup menu to the entity header that contains useful actions for the selected entity such as being able to copy the display name, IRI or OBO Id.

fig-term-header

  • Added a wizard for deprecating entities. The release included profiles for deprecating entities according to the strategies used by the GO and OBI teams. New profiles can be written as .yaml files and dropped into the configuration directory. Thanks go to the Gene Ontology (GO) editors for ideas and feedback on this.

  • The the log view has been improved so that it is now more scalable and customizable. Preferences can be set on the Log preferences panel. The log window can now be quickly accessed by clicking the log button in the lower right hand corder of the window. Thanks go to @ykazakov for these significant improvements.

image

  • Improved rendering performance for large hierarchies.

Bug Fixes

  • Fixed a bug that could cause some unicode characters to display as boxes on Windows and Linux. (protegeproject/protege#714)
  • Fixed a bug that could cause the incorrect display of the asserted hierarchy in the presence of certain forms of equivalent classes axioms. (protegeproject/protege#847)
  • Entity icons are now aligned with entity names in the various hierarchies when a large font size is selected. (protegeproject/protege#620)
  • Deprecated entity strike out is now aligned better with the vertical position of the font height.
  • Fixed a bug that caused annotations on different individuals axioms to be dropped on save. (protegeproject/protege#747)
  • Fixed a bug that caused Protege to hang when saving OBO files that encoded non-simple axioms in the functional syntax (protegeproject/protege#501)
  • Fixed a bug that could cause Protege to start up off the screen if it had previously been on a secondary screen and that screen is no longer available. (protegeproject/protege#804)
  • Fixed a bug that caused Protege to prompt for missing imports if the imports were loaded via HTTP redirects (protegeproject/protege#839)
  • Fixed a bug that could cause Protege to hang for a long time when loading or saving ontologies from folders with a large number of sub-folders and sub-files. (protegeproject/protege#619)
  • Fixed links to the OWL spec. (protegeproject/protege#792)
  • Fixed a bug where the metrics view would only show the metrics of the first opened ontology (protegeproject/protege#816)
  • Fixed a NullPointerException in search (protegeproject/protege#813)
  • Fixed a problem that prevented some installations from displaying Chinese Characters (protegeproject/protege#824)
  • Fixed a problem that could cause Protégé to hang when loading imported ontologies in some circumstances (in Protégé 5.5.0-beta-7)
  • Fixed a problem that could cause the SPARQL Query Tab to crash when loading
  • Fixed a problem that caused Protege 5.5 to hang while loading OBO Relations Ontology (protegeproject/protege#817)
  • Fixed a bug that could cause Protégé to freeze when entering entity names.
  • Fixed a bug that could cause an error when editing the ontology IRI on some versions of Windows

Other improvements

  • Upgraded the bundled JRE to Java 8 Update 121
  • Upgraded to the OWL API 4.5.8 (protegeproject/protege#835) (Thanks go to @ignazio1977 for all of his work on the OWL API)
  • Made menu items case consistent (protegeproject/protege#843)
  • Made view titles case consistent (protegeproject/protege#842)
  • Renamed view titles for individuals views so that they include "Direct" (protegeproject/protege#829)
  • Entity names are no longer quoted in view headers (protegeproject/protege#841)
  • Tidied the missing imports dialog
  • Cleaned up the ontology catalog manager dialog
  • Tidied up the ontology catalog add entry dialog
  • Removed the "Edit active ontology catalog..." menu item. Superseded by the "Edit ontology catalog..." menu item.
  • Cached mouse positions to improve rendering performance with some JREs. (protegeproject/protege#723). Thanks go to @ykazakov for tracking down the original problem and his help with this.

 

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.
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Re: Protege 5.5.0 Available

Csongor Nyulas
Administrator
Dear Protégé Users,

We have discovered a problem in the Windows distribution of Protégé 5.5, which prevents allocating more than 2GB of memory to the Java process, and thus working with very large ontologies.

We have fixed this problem.

If you installed Protégé 5.5 for Windows, and you think you will need to work with large ontologies, please download the distribution again, and replace your previous installation with the new one. Here is the direct link to the download:
https://github.com/protegeproject/protege-distribution/releases/download/v5.5.0/Protege-5.5.0-win.zip

Best regards,
The Protégé Team


On 3/17/19 2:22 PM, Campbell, James R wrote:

You have a problem with the 5.5.0 release.  I have used Protege for work with SNOMED CT extensions and workshops for the past many months using the 5.5.0-beta -3  release.  I run on Windows 10 (home and at work) and on both machines I have 24-32GB memory using 64 bit processor with a TB of solid state memory.  To load and classify SNOMED CT , I would change Xmx to 5 GB and Xms to 200 MB in the run.bat files you issued and start protege.  Load of SNOMED CT (OWL) usually took 2-3 minutes and classification with Elk 0.4.3 took 83 seconds.  

When I loaded 5.5.0, I could not get it to run on either machine with Mmx at more than 1GB, although it did then start.  Loading SNOMED CT took 5 minutes and I cancelled classification at an hour and half when it had still not completed.  I strongly suspect that you have memory management issues with your 5.5.0 .  I suspect I may be stressing the software more than most with SNOMED CT development work but I can verify that the beta software was up to the task with the hardware I use.

Jim Campbell


From: protege-user [hidden email] on behalf of Matthew Horridge [hidden email]
Sent: Friday, March 15, 2019 11:48:58 AM
To: User support for WebProtege and Protege Desktop; [hidden email]
Subject: [protege-user] Protege 5.5.0 Available
 
Non-UNMC email


 
Dear Protégé Users,

We are pleased to announce the release of Protégé 5.5.0.  This is a major Protégé release that incorporates various user interface enhancements and fixes many bugs.  You can find detailed release notes below.

You can download Protege 5.5.0 from our downloads page:



We are grateful to the Protégé user community, and in particular our users from the OBO community, for reporting bugs and suggesting features over the beta period.  In particular, we are heavily indebted to the Biomedical Ontology Community for suggestions and feedback on the new features that are contained in this release. We would especially like to thank the participants of the 2017 Berkeley GO Editors Workshop: (in alphabetical order) Kimberly Van Auken, Tanya Berardini, Seth Carbon, Karen Christie, Eric Douglass, Pascale Gaudet, Harold Drabkin, David Hill, Huaiyu Mi, Suzi Lewis, Donghui Li, Chris Mungall, Monica Munoz-Torres, David Osumi-Sutherland, and Nicole Vasilevsky – this work would not have been possible without their input. Special thanks go to Chris Mungall for an invitation to this meeting.

We would also like to thank Ignazio Palmisano, for his tireless work on the OWL API and his speedy response to our OWL API related requests.  Finally, we’d like to acknowledge Yevgeny Kazakov, who has made several significant contributions to the core Protégé code base that made it into this release.

Best regards,

The Protégé Team




Protégé 5.5.0

New Features

  • Added the ability to display relationships other than SubClassOf in the class hierarchy. Please see the documentation for further details. We expect this feature to evolve and we seek feedback from Protégé users.

fig-mixed-hierarchy

  • Added a breadcrumb trail to the top of the Protege window that shows the current path in the current hierarchy. Hovering over a path element in the breadcrumb trail will provide more details about that element. Path elements are also clickable, making it possible to jump up the current hierarchy.

fig-breadcrumb-and-header

  • Added initial Git integration support. When opening ontologies that are contained in a git repository, the current git branch will be displayed in the status bar. It is also possible to use your git user name for automated generation of "created by" annotations in Protege

fig-git-repo-status

fig-git-user-name

  • Improved the various tool tips and search results to display OBO Ids (if present). OBO Ids are now shown in hierarchy tool tips and breadcrumb trail tool tips. Search results now contain a column that displays OBOIds for terms in the search results. It is also possible to search using OBO Id syntax, for example searching for GO:0043231 will return 'intracellular membrane-bounded organelle'. Previously, one had to search using the OBO2OWL IRI syntax to achieve this.

fig-search

  • Entity names in the various hierarchies are now disambiguated if the entity short name or label is not unique. For example in the CL ontology, "cell" is used as the label for two classes. The OBO identifiers are now shown in round brackets next to the occurrences of the "cell" class in the hierarchy. Previously, one had to look at tooltips to disambiguate such occurrences. Thanks go to @nicolevasilevsky for a discussion on GitHub that prompted this.

image

  • Occurrences of single non-unique class names in the class description view are now disambiguated. For example in the CL ontology, "cell" is used as the label for two classes. The OBO identifiers are now shown in round brackets next to the occurrences of the "cell" class in the class description view. In the screenshot below cell CL:0000000 is equivalent to the cell class from the gene ontology GO:0005623.

image

  • Added a popup menu to the entity header that contains useful actions for the selected entity such as being able to copy the display name, IRI or OBO Id.

fig-term-header

  • Added a wizard for deprecating entities. The release included profiles for deprecating entities according to the strategies used by the GO and OBI teams. New profiles can be written as .yaml files and dropped into the configuration directory. Thanks go to the Gene Ontology (GO) editors for ideas and feedback on this.

  • The the log view has been improved so that it is now more scalable and customizable. Preferences can be set on the Log preferences panel. The log window can now be quickly accessed by clicking the log button in the lower right hand corder of the window. Thanks go to @ykazakov for these significant improvements.

image

  • Improved rendering performance for large hierarchies.

Bug Fixes

  • Fixed a bug that could cause some unicode characters to display as boxes on Windows and Linux. (protegeproject/protege#714)
  • Fixed a bug that could cause the incorrect display of the asserted hierarchy in the presence of certain forms of equivalent classes axioms. (protegeproject/protege#847)
  • Entity icons are now aligned with entity names in the various hierarchies when a large font size is selected. (protegeproject/protege#620)
  • Deprecated entity strike out is now aligned better with the vertical position of the font height.
  • Fixed a bug that caused annotations on different individuals axioms to be dropped on save. (protegeproject/protege#747)
  • Fixed a bug that caused Protege to hang when saving OBO files that encoded non-simple axioms in the functional syntax (protegeproject/protege#501)
  • Fixed a bug that could cause Protege to start up off the screen if it had previously been on a secondary screen and that screen is no longer available. (protegeproject/protege#804)
  • Fixed a bug that caused Protege to prompt for missing imports if the imports were loaded via HTTP redirects (protegeproject/protege#839)
  • Fixed a bug that could cause Protege to hang for a long time when loading or saving ontologies from folders with a large number of sub-folders and sub-files. (protegeproject/protege#619)
  • Fixed links to the OWL spec. (protegeproject/protege#792)
  • Fixed a bug where the metrics view would only show the metrics of the first opened ontology (protegeproject/protege#816)
  • Fixed a NullPointerException in search (protegeproject/protege#813)
  • Fixed a problem that prevented some installations from displaying Chinese Characters (protegeproject/protege#824)
  • Fixed a problem that could cause Protégé to hang when loading imported ontologies in some circumstances (in Protégé 5.5.0-beta-7)
  • Fixed a problem that could cause the SPARQL Query Tab to crash when loading
  • Fixed a problem that caused Protege 5.5 to hang while loading OBO Relations Ontology (protegeproject/protege#817)
  • Fixed a bug that could cause Protégé to freeze when entering entity names.
  • Fixed a bug that could cause an error when editing the ontology IRI on some versions of Windows

Other improvements

  • Upgraded the bundled JRE to Java 8 Update 121
  • Upgraded to the OWL API 4.5.8 (protegeproject/protege#835) (Thanks go to @ignazio1977 for all of his work on the OWL API)
  • Made menu items case consistent (protegeproject/protege#843)
  • Made view titles case consistent (protegeproject/protege#842)
  • Renamed view titles for individuals views so that they include "Direct" (protegeproject/protege#829)
  • Entity names are no longer quoted in view headers (protegeproject/protege#841)
  • Tidied the missing imports dialog
  • Cleaned up the ontology catalog manager dialog
  • Tidied up the ontology catalog add entry dialog
  • Removed the "Edit active ontology catalog..." menu item. Superseded by the "Edit ontology catalog..." menu item.
  • Cached mouse positions to improve rendering performance with some JREs. (protegeproject/protege#723). Thanks go to @ykazakov for tracking down the original problem and his help with this.

 

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.
_______________________________________________
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