Protégé 5.6.5

This is Protégé 5.6.5, a point release of the Protégé ontology editor.

Changes from Protégé 5.6.4

• Process escape characters when searching for entities (fixes protegeproject/protege#1217).
• Fix saving equivalent objects in OWLCellRenderer (fixes protegeproject/protege#910).
• Improve render string escaping for backslash and double quotes.
• Sort data-/object-propertyAssertions in individual views (partially addresses protegeproject/protege#605).
• Make Show deprecated entities option persistent.
• Use system proxy settings when resolving identifiers.org IDs (fixes protegeproject/protege#1231).

Verifying the release archives

All release archives available below are signed with the maintainer’s personal OpenPGP key:

pub   rsa4096 2014-03-14 [SC] 4FA2 0823 62FE 73AD 03B8 8830 A8DC 7067 E25F BABB

You can find that key at several locations, including:

• Right here on GitHub: https://github.com/gouttegd.gpg
• On the maintainer’s personal site: https://incenp.org/dgouttegattat.asc
• On the keys.openpgp.org key server: https://keys.openpgp.org/search?q=dgouttegattat%40incenp.org
• Using GnuPG’s --locate-keys command, with either the DANE or WKD mechanisms: gpg --auto-key-locate dane,wkd --locate-keys [email protected]

Protégé 5.6.4

This is Protégé 5.6.4, a point release of the Protégé ontology editor.

Changes from Protégé 5.6.3

• The OWLAPI used by Protégé has been updated to version 4.5.29.
• New setting to configure which explanation service(s) to use (protegeproject/protege#1059).
• Fix refreshing of the preferences dialog after preferences are reset (protegeproject/protege#168).
• Fix the Orphanet link extractor (protegeproject/protege#1192).
• Add option to ignore ID range policy files.
• Fix incompatibility between the ”support ID range policy files” and “Remember last ID between Protégé sessions” features (protegeproject/protege#1108).
• Fix Rio Turtle format updating (protegeproject/protege#1023).
• Bundled ELK reasoner plugin updated to version 0.6.0.

Verifying the release archives

All release archives available below are signed with the maintainer’s personal OpenPGP key:

pub   rsa4096 2014-03-14 [SC] 4FA2 0823 62FE 73AD 03B8 8830 A8DC 7067 E25F BABB

You can find that key at several locations, including:

• Right here on GitHub: https://github.com/gouttegd.gpg
• On the maintainer’s personal site: https://incenp.org/dgouttegattat.asc
• On the keys.openpgp.org key server: https://keys.openpgp.org/search?q=dgouttegattat%40incenp.org
• Using GnuPG’s --locate-keys command, with either the DANE or WKD mechanisms: gpg --auto-key-locate dane,wkd --locate-keys [email protected]

Protégé 5.6.3

This is Protégé 5.6.3, a point release of the Protégé ontology editor.

Changes from Protégé 5.6.2

• The OWL API used by Protégé has been updated from version 4.5.25 to version 4.5.26.
• On Windows, opening an ontology file with the Open with ... option in the file explorer contextual menu and selecting Protégé.exe should now work (protegeproject/protege#1162).

Changes from earlier versions

Please see the release notes accompanying the 5.6.2 release.

Verifying the release archives

All release archives available below are signed with the maintainer’s personal OpenPGP key:

pub   rsa4096 2014-03-14 [SC] 4FA2 0823 62FE 73AD 03B8 8830 A8DC 7067 E25F BABB

You can find that key at several locations, including:

• Right here on GitHub: https://github.com/gouttegd.gpg
• On the maintainer’s personal site: https://incenp.org/dgouttegattat.asc
• On the keys.openpgp.org key server: https://keys.openpgp.org/search?q=dgouttegattat%40incenp.org
• Using GnuPG’s --locate-keys command, with either the DANE or WKD mechanisms: gpg --auto-key-locate dane,wkd --locate-keys [email protected]

Protégé 5.6.2

This is Protégé 5.6.2, a bugfix release of the Protégé ontology editor.

Changes from Protégé 5.6.1

• A workaround has been put in place for macOS users who found themselves unable to save files because the file-saving dialog wouldn’t show up on their machines (protegeproject/protege#1106).
• The jvm.conf configuration file now supports using % as a suffix to the value of memory options (for example, max_heap_size=80% is interpreted as requesting that Protégé be allocated 80% of the total available memory on the system).

Changes from earlier versions

Please see the release notes accompanying the 5.6.1 release.

Protégé 5.6.1

This is Protégé 5.6.1, a bugfix release of the Protégé ontology editor.

Changes from Protégé 5.6.0

• The OWL API has been upgraded to version 4.5.25, fixing some issues with the OBO serialiser.
• The macOS version can now run on macOS 10.12 and later, instead of macOS 11.0 and later (protegeproject/protege#1101).
• User-specified file extensions are no longer overridden (protegeproject/protege#1087).

Changes from Protégé 5.5.0

Please see the release notes accompanying the 5.6.0 release

Protégé 5.6.0

The Protégé development team is proud to announce the release of Protégé 5.6.0, the latest major release of your favorite ontology editor.

New features

• Support for ODK-style -idranges.owl policy files. If such a file is detected alongside the ontology to edit, Protégé will try to use the informations from that file to automatically set the prefix and identifiers range.

Other significant changes

• The OS X package can now run natively on arm64 CPUs, instead of relying on x86_64 emulation. This should drastically improve Protégé’s performances on M1-powered Apple computers.
• Migrated to Java 11.
• Migrated to OWL API 4.5.24. This version includes several changes to some serializers (notably the OBO serializer), which will likely result in huge diffs when ontology files are saved with this version of Protégé for the first time. To minimize the annoyance caused by such diffs, it is advised to:
  • save your ontology with Protégé 5.6.0 without introducing any logical change and commit the resulting file;
  • once the ontology has been saved once with Protégé 5.6.0, avoid editing it again with an older version.
• The GNU/Linux, Windows, and macOS versions now use the same launcher, so that Java memory options can be set for all three versions using the same conf/jvm.conf file.
• The ELK reasoner is now included in the distribution.

Other improvements

• Improve the datatype selection box in the literal value editor (protegeproject/protege#856)
• Make deprecated classes hidden by default (protegeproject/protege#797)
• Trim whitespaces in the class expression editor (protegeproject/protege#770)
• Do not force values as boolean (protegeproject/protege#691)
• Disable expression caching (protegeproject/protege#864, protegeproject/protege#637)
• Use most commonly used entity name if name to entity mapping is ambiguous (protegeproject/protege#869)
• Add a “Jump to selection” in class tree (protegeproject/protege#687)
• Add “No to All” option for Resolve Missing Imports dialog (protegeproject/protege#707)
• Add “Instances (Inferred)” view to the default layout of the Individuals by Class tab (protegeproject/protege#583)
• Render DOI, Wikipedia, OMIM, OMIMPS, ORCID, and Orphanet identifiers as links (protegeproject/protege#1049)

Bug fixes

• Save files using format-specific extensions (protegeproject/protege#1016)
• Avoid freezing the UI when an ontology is inconsistent (protegeproject/protege#877)
• Fix rendering of labels containing an apostrophe (protegeproject/protege#919)

Protégé 5.6.0-beta-2

This is the second beta for the upcoming 5.6.0 version of Protégé.

Changes since the first beta:

• The GNU/Linux, Windows, and macOS versions now use the same launcher, so that Java memory options can be set for all three versions using the same jvm.conf file.
• The ELK reasoner is now included in the distribution.
• The OWL API library has been upgraded from 4.5.22 to 4.5.24, fixing a bug in the OBO serialiser that led to incorrect quoting of IDs in property_value tags.

Protégé 5.6.0-beta-1

Protégé 5.6.0-beta-1

This is beta-1 version of the next major Protégé release, 5.6.0. It is not ready for public use yet – please only use it if you’re willing to help us test the new release and detect any serious problem that would prevent you from working with that release.

New features

• Support for ODK-style -idranges.owl policy files. If such a file is detected alongside the ontology to edit, Protégé will try to use the informations from that file to automatically set the prefix and identifiers range.

Other significant changes

• The OS X package can now run natively on arm64 CPUs, instead of relying on x86_64 emulation. This should improve Protégé’s performances on M1-powered Apple computers.
• Migrated to Java 11.
• Migrated to OWL API 4.5.22.

Bug fixes

• Save files using format-specific extensions (protegeproject/protege#1016)
• Avoid freezing the UI when an ontology is inconsistent (protegeproject/protege#877)
• Fix rendering of labels containing an apostrophe (protegeproject/protege#919)

Other improvements

• Improve the datatype selection box in the literal value editor (protegeproject/protege#856)
• Make deprecated classes hidden by default (protegeproject/protege#797)
• Trim whitespaces in the class expression editor (protegeproject/protege#770)
• Do not force values as boolean (protegeproject/protege#691)
• Disable expression caching (protegeproject/protege#864, protegeproject/protege#637)
• Use most commonly used entity name if name to entity mapping is ambiguous (protegeproject/protege#869)
• Add a “Jump to selection” in class tree (protegeproject/protege#687)
• Add “No to All” option for Resolve Missing Imports dialog (protegeproject/protege#707)
• Add “Instances (Inferred)” view to the default layout of the Individuals by Class tab (protegeproject/protege#583)
• Render DOI, Wikipedia, OMIM, OMIMPS, ORCID, and Orphanet identifiers as links (protegeproject/protege#1049)

(Note: this list of changes may not be complete yet. It will be updated for the final 5.6.0 release.)

Protégé 5.5.0

Protégé 5.5.0

This is a major Protégé release that incorporates various user interface enhancements and fixes many bugs. 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.

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.

• 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.

• 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

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

Protégé 5.5.0-beta-9

Protégé 5.5.0-beta-9

New Features

• 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.

• Single 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.

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)

Other improvements

• Upgraded the bundled JRE to Java 8 Update 121
• Upgraded to the OWL API 4.5.8 (protegeproject/protege#835)
• 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)